Instance Residue class, used for placed residues and rotamers. More...
#include <Residue.hh>
Public Types | |
| typedef chemical::AtomType | AtomType |
| typedef chemical::ResidueType | ResidueType |
| typedef chemical::ResidueTypeCOP | ResidueTypeCOP |
| typedef chemical::AtomIndices | AtomIndices |
Public Member Functions | |
| Residue (ResidueTypeCOP rsd_type_in, bool const dummy_arg) | |
| constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue. More... | |
| Residue (ResidueType const &rsd_type_in, bool const dummy_arg) | |
| constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue. More... | |
| Residue (ResidueType const &rsd_type_in, Residue const ¤t_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false) | |
| Rotamer-style constructor; orients ideal coords onto backbone of current_rsd. More... | |
| Residue (Residue const &src) | |
| Copy constructor. More... | |
| ~Residue () override | |
| Destructor. More... | |
| ResidueOP | clone () const |
| Copy this residue( allocate actual memory for it ) More... | |
| ResidueOP | clone_flipping_chirality (core::chemical::ResidueTypeSet const &residue_type_set) const |
| Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type. More... | |
| void | show (std::ostream &output=std::cout, bool output_atomic_details=false) const |
| Generate string representation of Residue for debugging purposes. More... | |
| ResidueCOP | get_self_ptr () const |
| self pointers More... | |
| ResidueOP | get_self_ptr () |
| ResidueCAP | get_self_weak_ptr () const |
| ResidueAP | get_self_weak_ptr () |
| AtomType const & | atom_type (Size const atomno) const |
| Returns the AtomType of this residue's atom with index number <atomno> More... | |
| chemical::AtomTypeSet const & | atom_type_set () const |
| Returns the AtomTypeSet of this residue. More... | |
| Size | atom_type_index (Size const atomno) const |
| Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType. More... | |
| Real | atomic_charge (Size const atomno) const |
| Returns the atom charge of this residue's atom with index number <atomno> More... | |
| bool | is_virtual (Size const atomno) const |
| Check if atom is virtual. AMW TODO: somehow SWA spends literally 3.7% of its time calling this function. More... | |
| bool | is_repulsive (Size const atomno) const |
| Check if atom is repulsive. More... | |
| bool | is_virtual_residue () const |
| Check if residue is virtual. More... | |
| Size | atom_index (std::string const &atm) const |
| Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid. More... | |
| Size | natoms () const |
| Returns the number of atoms in this residue. More... | |
| Size | n_hbond_acceptors () const |
| number of hbond_donors More... | |
| Size | n_hbond_donors () const |
| number of hbond_donors More... | |
| Size | nheavyatoms () const |
| Returns the number of heavyatoms in this residue. More... | |
| AtomIndices const & | Hpos_polar () const |
| Returns the AtomIndices of this residue's polar hydrogens. More... | |
| AtomIndices const & | all_bb_atoms () const |
| Returns the AtomIndices of this residue's backbone atoms. More... | |
| AtomIndices const & | Haro_index () const |
| Returns the AtomIndices of this residue's aromatic hydrogens. More... | |
| AtomIndices const & | Hpol_index () const |
| Returns the AtomIndices of this residue's polar hydrogens. More... | |
| AtomIndices const & | Hpos_apolar () const |
| Returns the AtomIndices of this residue's apolar hydrogens. More... | |
| AtomIndices const & | Hpos_polar_sc () const |
| Returns the AtomIndices of this residue's polar sidechain hydrogens. More... | |
| AtomIndices const & | accpt_pos () const |
| Returns the AtomIndices of this residue's h-bond acceptor atoms. More... | |
| AtomIndices const & | accpt_pos_sc () const |
| Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms. More... | |
| void | get_metal_binding_atoms (AtomIndices &metal_binding_indices) const |
| Gets the AtomIndices of the atoms in this residue that can bind to metals. More... | |
| core::Size | n_virtual_atoms () const |
| Returns the number of virtual atoms in this residue. More... | |
| bool | heavyatom_has_polar_hydrogens (Size ind) const |
| Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom) More... | |
| bool | heavyatom_is_an_acceptor (Size ind) const |
| Is a particular atom a heavy atom acceptor? More... | |
| bool | atom_is_polar_hydrogen (Size ind) const |
| Is a particular atom a polar hydrogen? More... | |
| Atoms const & | atoms () const |
| Returns this residue's Atoms (const), a vector1 of Atom objects. More... | |
| Atoms & | atoms () |
| Returns this residue's Atoms (non-const), a vector1 of Atom objects. More... | |
| Atoms::iterator | atom_begin () |
| begin interator, to iterate over atoms More... | |
| Atoms::iterator | atom_end () |
| end interator, to iterate over atoms More... | |
| Atoms::const_iterator | atom_begin () const |
| Atoms::const_iterator | atom_end () const |
| Atoms::const_iterator | sidechainAtoms_begin () const |
| should be safe, given the atom ordering rules? More... | |
| Atoms::const_iterator | heavyAtoms_end () const |
| Atom const & | atom (Size const atm_index) const |
| Returns this residue's Atom with index number <atm_index> (const) More... | |
| Atom & | atom (Size const atm_index) |
| Returns this residue's Atom with index number <atm_index> (non-const) More... | |
| Atom const & | atom (std::string const &atm_name) const |
| Returns this residue's Atom with name <atm_name> (const) More... | |
| Atom & | atom (std::string const &atm_name) |
| Returns this residue's Atom with name <atm_name> (non-const) More... | |
| Vector const & | xyz (Size const atm_index) const |
| Returns the position of this residue's atom with index number <atm_index> More... | |
| Vector const & | xyz (std::string const &atm_name) const |
| Returns the position of this residue's atom with name <atm_name> More... | |
| void | set_xyz (core::Size const atm_index, Vector const &xyz_in) |
| Sets the position of this residue's atom with index number <atm_index> More... | |
| void | set_xyz (std::string const &atm_name, Vector const &xyz_in) |
| Sets the position of this residue's atom with name <atm_name> More... | |
| Size | last_backbone_atom () const |
| Returns the index number of the last backbone heavyatom. More... | |
| Size | first_sidechain_atom () const |
| Returns the index number of the first sidechain heavyatom. More... | |
| Size | first_sidechain_hydrogen () const |
| Returns the index number of the first sidechain hydrogen. More... | |
| Size | attached_H_begin (Size const atom) const |
| Returns the index number of the first hydrogen attached to the atom with index number <atom> More... | |
| Size | attached_H_end (Size const atom) const |
| Returns the index number of the last hydrogen attached to the atom with index number <atom> More... | |
| AtomIndices const & | attached_H_begin () const |
| Returns the AtomIndices of the first hydrogen attached to each heavyatom. More... | |
| AtomIndices const & | attached_H_end () const |
| Returns the AtomIndices of the last hydrogen attached to each heavyatom. More... | |
| bool | has_lower_connect () const |
| Returns true if residue has a valid lower connection. More... | |
| Size | lower_connect_atom () const |
| Returns the index number of this residue's atom which connects to the residue before it in sequence. More... | |
| bool | has_upper_connect () const |
| Returns true if residue has a valid upper connection. More... | |
| Size | upper_connect_atom () const |
| Returns the index number of this residue's atom which connects to the residue after it in sequence. More... | |
| Size | connect_atom (Residue const &other) const |
| Returns the index number of this residue's atom connected to the <other> Residue. More... | |
| core::chemical::AtomIndices | get_adjacent_heavy_atoms (uint const atom_index) const |
| Get a list of heavy atoms connected to a given atom. More... | |
| uint | first_adjacent_heavy_atom (uint const atom_index) const |
| Scan through the list of atoms connected to a given atom and return the 1st heavy atom found. More... | |
| core::chemical::AtomIndices | get_atoms_exocyclic_to_ring_atom (uint const atom_index) const |
| Get a list of exocyclic atoms connected to a given ring atom. More... | |
| core::chemical::AtomIndices | get_substituents_to_ring_atom (uint const atom_index) const |
| Get a list of substituent atoms connected to a given ring atom. More... | |
| core::chemical::AtomIndices | get_hydrogens_bonded_to_ring_atom (uint const atom_index) const |
| Get a list of hydrogen atoms connected to a given ring atom. More... | |
| utility::vector1< int > const & | path_distance (Size atom) const |
| Returns the shortest path distance from <atom> to any other atom in this residue. More... | |
| utility::vector1< utility::vector1< int > > const & | path_distances () const |
| Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2]. More... | |
| int | path_distance (Size at1, Size at2) const |
| Returns the number of bonds separating atom <at1> from <at2> More... | |
| bool | atom_is_backbone (Size const atomno) const |
| Returns true if this residue's atom with index number <atomno> is a backbone atom. More... | |
| bool | atom_is_hydrogen (Size const atomno) const |
| Returns true if this residue's atom with index number <atomno> is a hydrogen. More... | |
| Size | atom_base (Size const atomno) const |
| Returns the atom index of the <atomno> atom's base atom. More... | |
| Size | abase2 (Size const atomno) const |
| Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor) More... | |
| AtomIndices const & | bonded_neighbor (Size const atm) const |
| Returns the AtomIndices for all bonded neighbor atoms of <atm> More... | |
| AtomIndices const & | mainchain_atoms () const |
| Returns the AtomIndices of this residue's mainchain atoms. More... | |
| Size | mainchain_atom (Size const i) const |
| Returns the atom index of the residue's ith mainchain atom. More... | |
| Size | n_mainchain_atoms () const |
| Returns the number of the residue's mainchain atoms. More... | |
| AtomIndices const & | actcoord_atoms () const |
| Returns the AtomIndices of atoms that will be used to define this residue's actcoord. More... | |
| Vector | build_atom_ideal (int const atomno, Conformation const &conformation) const |
| Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms. More... | |
| Size | nbr_atom () const |
| Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids. More... | |
| Real | nbr_radius () const |
| Returns the distance cutoff value used as a radius for neighbor definition. More... | |
| Vector const & | nbr_atom_xyz () const |
| AtomIndices const & | atoms_with_orb_index () const |
| Vector | build_orbital_xyz (Size const orbital_index) const |
| Vector const & | orbital_xyz (Size const orbital_index) const |
| void | set_orbital_xyz (core::Size const orbital_index, Vector const &xyz_in) |
| Size | n_orbitals () const |
| Returns the number of orbitals in this residue. More... | |
| utility::vector1< Size > const & | bonded_orbitals (Size const atm) const |
| std::string const & | orbital_name (Size const orbital_index) const |
| chemical::orbitals::OrbitalType const & | orbital_type (Size const orbital_index) const |
| Size | orbital_type_index (Size const orbital_index) const |
| void | update_orbital_coords () |
| bool | misplaced () const |
| Return whether or not the Residue was incorrectly oriented and placed within the polymer when created. More... | |
| ResidueOP | create_rotamer () const |
| Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out. More... | |
| ResidueOP | create_residue () const |
| Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out. More... | |
| ResidueType const & | type () const |
| Returns this residue's ResidueType. More... | |
| ResidueTypeCOP | type_ptr () const |
| Returns this residue's ResidueType as a COP. More... | |
| chemical::ResidueConnection const & | upper_connect () const |
| Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue. More... | |
| chemical::ResidueConnection const & | lower_connect () const |
| Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue. More... | |
| bool | connections_match (Residue const &other) const |
| Returns true if ??? More... | |
| Size | n_possible_residue_connections () const |
| Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType. More... | |
| Size | n_current_residue_connections () const |
| Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!! More... | |
| Size | n_polymeric_residue_connections () const |
| Returns the number of polymeric ResidueConnections on this residue. More... | |
| Size | n_non_polymeric_residue_connections () const |
| Returns the number of non-polymeric ResidueConnections on this residue. More... | |
| chemical::ResidueConnection const & | residue_connection (Size const resconn_index) const |
| Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue. More... | |
| Size | residue_connect_atom_index (Size const resconn_id) const |
| chemical::ResConnID | connect_map (Size resconn_index) const |
| void | mark_connect_incomplete (Size resconn_index) |
| core::Size | connect_map_size () const |
| Returns the size (number of elements) in the connect_map_ object. More... | |
| void | clear_residue_connections () |
| void | update_connections_to_other_residue (Residue const &other_rsd) |
| Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number). More... | |
| void | copy_residue_connections_from (Residue const &src) |
| bool | has_incomplete_connection () const |
| bool | has_incomplete_connection (core::Size const atomno) const |
| Returns true is <atomno> has complete connectivity? More... | |
| bool | connection_incomplete (Size resconnid) const |
| chemical::ResConnID | actual_residue_connection (Size resconnid) const |
| Get the residue connection. How is this different than residue_connection? More... | |
| id::AtomID | inter_residue_connection_partner (int connid, Conformation const &conformation) const |
| This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More... | |
| Size | connected_residue_at_resconn (Size const resconn_index) const |
| Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More... | |
| Size | connected_residue_at_upper () const |
| Returns the residue number of a residue connected to this residue at this residue's upper_connect. More... | |
| Size | connected_residue_at_lower () const |
| Returns the residue number of a residue connected to this residue at this residue's lower_connect. More... | |
| Size | residue_connection_partner (Size const resconn_index) const |
| Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More... | |
| void | copy_residue_connections (Residue const &src_rsd, bool const suppress_warnings=false) |
| Attempt to take residue connection info from src_rsd. More... | |
| Size | residue_connection_conn_id (Size const resconn_index) const |
| Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index. More... | |
| void | residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid) |
| set a connection to this residue by adding its partner's residue number More... | |
| id::AtomID | resolve_partial_atom_id (id::PartialAtomID const &partial_id) const |
| Resolve a partial atom ID into an AtomID for this residue. More... | |
| Distance | connection_distance (conformation::Conformation const &conf, Size const resconn_index, Vector const &matchpoint) const |
| Distance between a potential residue connection match and the position of the expected atom. More... | |
| bool | is_bonded (Residue const &other) const |
| Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides) More... | |
| bool | is_pseudo_bonded (Residue const &other) const |
| Do I have any pseudobonds to other? More... | |
| bool | is_bonded (Size const other_residue_index) const |
| Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic. More... | |
| bool | is_pseudo_bonded (Size const other_index) const |
| Do I have any pseudobonds to other? More... | |
| bool | is_polymer_bonded (Residue const &other) const |
| Am I polymer bonded to other? More... | |
| bool | is_polymer_bonded (Size const other_index) const |
| Am I polymer-bonded to other? checks lower and upper connections. More... | |
| utility::vector1< Size > const & | connections_to_residue (Residue const &other) const |
| Returns the vector1 of resconn ids that connect this residue to other. More... | |
| utility::vector1< Size > const & | connections_to_residue (Size const other_resid) const |
| Returns the vector1 of resconn ids that connect this residue to other. More... | |
| PseudoBondCollectionCOP | get_pseudobonds_to_residue (Size resid) const |
| std::map< Size, PseudoBondCollectionCOP > const & | pseudobonds () const |
| void | set_pseudobonds_to_residue (Size resid, PseudoBondCollectionCOP pbs) |
| utility::vector1< std::pair< Real, Real > > const & | chi_rotamers (Size const chino) const |
| Returns the chi rotamers available for this residue's chi angle <chino> More... | |
| AtomIndices const & | cut_bond_neighbor (Size const atm) const |
| atom indices for bonded neighbors to which atom-tree connections are disallowed. More... | |
| core::Size | n_bonded_neighbor_all_res (core::Size const atomno, bool virt=false) const |
| Returns the number of atoms bonded to <atomno> in all residues? More... | |
| AtomIndices const & | nbrs (Size const atm) const |
| Convenience synonym for bonded_neighbor. More... | |
| utility::vector1< Real > const & | mainchain_torsions () const |
| Returns the mainchain torsion angles of this residue (const) More... | |
| utility::vector1< Real > & | mainchain_torsions () |
| Returns the mainchain torsion angles of this residue (non-const) More... | |
| void | mainchain_torsions (utility::vector1< Real > const &torsions) |
| Sets the mainchain torsion angles of this residue to <torsions> More... | |
| Real | mainchain_torsion (Size const torsion) const |
| Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid. More... | |
| Size | nchi () const |
| Returns the number of chi angles this residue has. More... | |
| utility::vector1< Real > const & | chi () const |
| Returns the chi torsion angles of this residue (const) More... | |
| utility::vector1< Real > & | chi () |
| Returns the chi torsion angles of this residue (non-const) More... | |
| void | chi (utility::vector1< Real > const &chis) |
| Sets the chi torsion angles of this residue. More... | |
| Real | chi (Size const chino) const |
| get a specific chi torsion angle More... | |
| utility::vector1< AtomIndices > const & | chi_atoms () const |
| Returns the AtomIndices of each set of four atoms defining each chi angle. More... | |
| AtomIndices const & | chi_atoms (Size const chino) const |
| Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle. More... | |
| Size | n_nus () const |
| Return the number of nu (internal ring) angles this residue has. More... | |
| utility::vector1< core::Angle > const & | nus () const |
| Return the nu (internal ring) torsion angles of this residue. More... | |
| utility::vector1< core::Angle > & | nus () |
| Return the nu (internal ring) torsion angles of this residue. (non-const) More... | |
| core::Angle | nu (core::uint const index) const |
| Get a specific nu (internal ring) torsion angle by index. More... | |
| utility::vector1< AtomIndices > const | nu_atoms () const |
| Return the AtomIndices of each set of four atoms defining each nu angle. More... | |
| AtomIndices const | nu_atoms (core::uint const index) const |
| Return the AtomIndices of the four atoms defining the specified nu angle. More... | |
| chemical::rings::RingConformer const & | ring_conformer (core::uint const ring_num, core::Real limit=90.0) const |
| Return the current RingConformer of this residue's nth ring. More... | |
| Size | seqpos () const |
| Returns the sequence position of this residue. More... | |
| void | seqpos (Size const setting) |
| Sets this residue's sequence position to <setting> More... | |
| Size | polymeric_sequence_distance (Residue const &other) const |
| Returns the sequence separation distance between this residue and <other> More... | |
| int | polymeric_oriented_sequence_distance (Residue const &other) const |
| Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence. More... | |
| core::Size | chain () const |
| Returns this residue's chain id. More... | |
| void | chain (core::Size const setting) |
| Sets this residue's chain id. More... | |
| bool | requires_actcoord () const |
| does this residue require an actcoord? More... | |
| void | update_actcoord () |
| Updates actcoord for this residue. More... | |
| Vector const & | actcoord () const |
| Returns the coordinates used for pairE calculations (amino acids only) More... | |
| Vector & | actcoord () |
| Returns the coordinates used for pairE calculations (amino acids only) More... | |
| void | update_sequence_numbering (utility::vector1< Size > const &old2new) |
| Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped. More... | |
| void | update_nus () |
| Calculate the set of nu dihedrals from the xyz coordinates and store them. More... | |
| bool | is_polymer () const |
| Returns true if this residue is a polymer. More... | |
| bool | is_protein () const |
| Returns true if this residue is an amino acid. More... | |
| bool | is_peptoid () const |
| Returns if this residue is a peptoid. More... | |
| bool | is_aramid () const |
| Returns if this residue is an aramid. More... | |
| bool | is_ortho_aramid () const |
| Returns if this residue is an ortho aramid. More... | |
| bool | is_pre_methylene_ortho_aramid () const |
| Returns if this residue is a pre methylene ortho aramid. More... | |
| bool | is_post_methylene_ortho_aramid () const |
| Returns if this residue is a post methylene ortho aramid. More... | |
| bool | is_pre_methylene_post_methylene_ortho_aramid () const |
| Returns if this residue is a post methylene ortho aramid. More... | |
| bool | is_meta_aramid () const |
| Returns if this residue is a meta aramid. More... | |
| bool | is_pre_methylene_meta_aramid () const |
| Returns if this residue is a pre methylene meta aramid. More... | |
| bool | is_post_methylene_meta_aramid () const |
| Returns if this residue is a post methylene meta aramid. More... | |
| bool | is_pre_methylene_post_methylene_meta_aramid () const |
| Returns if this residue is a post methylene meta aramid. More... | |
| bool | is_para_aramid () const |
| Returns if this residue is a para aramid. More... | |
| bool | is_pre_methylene_para_aramid () const |
| Returns if this residue is a pre methylene para aramid. More... | |
| bool | is_post_methylene_para_aramid () const |
| Returns if this residue is a post methylene para aramid. More... | |
| bool | is_pre_methylene_post_methylene_para_aramid () const |
| Returns if this residue is a post methylene para aramid. More... | |
| bool | is_sri () const |
| Is this one of SRI's special heteropolymer building blocks? More... | |
| bool | is_triazolemer () const |
| Returns true if and only if this residue is a triazolemer. More... | |
| bool | is_DNA () const |
| Returns true if this residue is a DNA residue. More... | |
| bool | is_RNA () const |
| Returns true if this residue is a RNA residue. More... | |
| bool | is_TNA () const |
| Returns true if this residue is a TNA residue. More... | |
| bool | is_l_rna () const |
| Returns true if this residue is a L-RNA residue. More... | |
| bool | is_d_rna () const |
| Returns true if this residue is a D-RNA residue. More... | |
| bool | is_NA () const |
| Returns true if this residue is a nucleic acid. More... | |
| bool | is_purine () const |
| Returns true if this residue is a purine. More... | |
| bool | is_pyrimidine () const |
| Returns true if this residue is a pyrimidine. More... | |
| bool | is_carbohydrate () const |
| Returns true if this residue is a carbohydrate. More... | |
| bool | is_water () const |
| Returns true if this residue is water. More... | |
| bool | is_ligand () const |
| Returns true if this residue is a ligand. More... | |
| bool | is_metal () const |
| Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES. More... | |
| bool | is_metalbinding () const |
| Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES. More... | |
| bool | has_sc_orbitals () const |
| Returns true if the residue has side chain orbitals. More... | |
| bool | is_polar () const |
| Returns true if the residue is polar. More... | |
| bool | is_apolar () const |
| bool | is_charged () const |
| Returns true if the residue is charged. More... | |
| bool | is_aromatic () const |
| Returns true if the residue is aromatic. More... | |
| bool | is_coarse () const |
| residue is coarse (used for RNA right now) More... | |
| bool | is_terminus () const |
| Returns true if the residue has a terminus property. More... | |
| bool | is_upper_terminus () const |
| Return true if the residue has an upper terminus property. More... | |
| bool | is_lower_terminus () const |
| Returns true if the residue has a lower terminus property. More... | |
| bool | is_branch_point () const |
| Return true if the residue is a branch point variant. More... | |
| bool | is_similar_rotamer (Residue const &other) const |
| Returns true if the chi angles of another residue all fall within 5 deg. More... | |
| bool | is_similar_aa (Residue const &other) const |
| Returns true if the aa residue types are the same. More... | |
| bool | has_shadow_atoms () const |
| Return true if and only if this residue's type has shadow atoms. More... | |
| bool | has_property (std::string const &property) const |
| Return true if the residue has <property>. More... | |
| bool | has_variant_type (chemical::VariantType const variant_type) const |
| Generic variant access. More... | |
| std::string const & | atom_name (Size const atm) const |
| Returns the name of this residue's atom with index number <atm> More... | |
| std::string const & | mm_atom_name (Size const atom) const |
| Returns the mm_atom_name of this residue's atom with index number <atom> More... | |
| std::string const & | name () const |
| Returns this residue's ResidueType name. More... | |
| std::string const & | name3 () const |
| Returns this residue's 3-letter representation. More... | |
| char | name1 () const |
| Returns this residue's 1-letter representation. More... | |
| std::string | annotated_name (bool const show_all_variants=true) const |
| Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D]. More... | |
| chemical::AA const & | aa () const |
| Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration. More... | |
| chemical::AA const & | backbone_aa () const |
| Returns this residue's backbone_aa type, if any. More... | |
| chemical::AA const & | na_analogue () const |
| Returns the nucleic acid type to be used for fragment sampling. More... | |
| chemical::AtomICoor const & | icoor (Size const atm) const |
| Returns the internal coordinates of this residue's atom with index number <atm> More... | |
| bool | atom_depends_on_lower (core::Size const atom_index) const |
| Does this atom depend on the LOWER_CONNECT? More... | |
| bool | atom_depends_on_upper (core::Size const atom_index) const |
| Does this atom depend on the UPPER_CONNECT? More... | |
| void | set_d (int const chino, Real const setting) |
| bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example More... | |
| void | set_theta (int const chino, Real const setting) |
| bondangle analog to set_chi same idea as set_d More... | |
| void | set_tau (Size const nuno, Real const setting) |
| set_theta for nus More... | |
| void | set_all_nu (utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) |
| void | set_all_ring_nu (Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) |
| void | set_chi (int const chino, Real const setting) |
| Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree. More... | |
| void | set_all_chi (utility::vector1< Real > const &chis) |
| Sets all of this residue's chi angles using the set_chi function (wrapper function) More... | |
| bool | has (std::string const &atm) const |
| Returns true if this residue has an atom named <atm> More... | |
| bool | fill_missing_atoms (utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true) |
| Builds coordinates for atoms missing from this residue assuming ideal internal coordinates. More... | |
| void | select_orient_atoms (Size ¢er, Size &nbr1, Size &nbr2) const |
| Selects three atoms for orienting this residue. More... | |
| void | orient_onto_residue (Residue const &src) |
| Orient our coords onto those of <src>, using the atoms from select_orient_atoms. More... | |
| void | orient_onto_residue (Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) |
| Orient our coords onto those of <src>, using the three atom pairs specified in the input. More... | |
| void | orient_onto_residue_peptoid (Residue const &src, Conformation const &conformation) |
| Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide. More... | |
| void | orient_onto_location (Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) |
| Orients residue object onto atom locations. More... | |
| void | orient_onto_location (Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) |
| Orients residue object onto atom locations. More... | |
| bool | place (Residue const &src, Conformation const &conformation, bool preserve_c_beta=false) |
| Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match. More... | |
| void | apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > R, Vector v) |
| Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space. More... | |
| core::chemical::rna::RNA_Info const & | RNA_info () const |
| Return the RNA_residueType object. This is RNA specific. More... | |
| core::chemical::carbohydrates::CarbohydrateInfoCOP | carbohydrate_info () const |
| Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More... | |
| basic::datacache::BasicDataCacheCOP | data_ptr () const |
| BasicDataCache indexed by enum in residue_datacache.hh. More... | |
| basic::datacache::BasicDataCacheOP | nonconst_data_ptr () |
| BasicDataCache indexed by enum in residue_datacache.hh. More... | |
| basic::datacache::BasicDataCache const & | data () const |
| BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More... | |
| basic::datacache::BasicDataCache & | nonconst_data () |
| BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More... | |
| bool | mirrored_relative_to_type () const |
| Is this residue mirrored relative to its coordinates in the ResidueType? More... | |
| void | set_mirrored_relative_to_type (bool const setting) |
| Set whether this residue is mirrored relative to its coordinates in the ResidueType. More... | |
Private Member Functions | |
| Residue (Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality) | |
| Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve. More... | |
| void | init_residue_from_other (Residue const &src) |
| Function called by both copy constructors, to avoid code duplication. More... | |
| void | update_connections_to_residues () |
| Updates connections_to_residues_ using connect_map_. More... | |
| void | apply_transform_downstream (core::Size const atomno, core::Size const upstream_atomno, numeric::xyzMatrix< Real > const &R, Vector const &v) |
| apply transform of rotation R and translation V for all atoms downstream More... | |
| void | determine_nonstandard_polymer_status () |
| Residue const & | operator= (Residue const &rhs) |
| Assignment operator does not work for class Residue. This function is intentionally unimplemented and private. More... | |
| void | orient_onto_residue (Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2) |
| Orient coords onto those of <src>, using the specified atoms. More... | |
| void | assign_orbitals () |
| Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors. More... | |
Private Attributes | |
| ResidueTypeCOP | rsd_type_ptr_ |
| Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed. More... | |
| ResidueType const & | rsd_type_ |
| our Residue type More... | |
| Atoms | atoms_ |
| our conformation atoms (not kinematic atom pointers) with xyz positions and atom type More... | |
| utility::vector1< orbitals::OrbitalXYZCoordsOP > | orbitals_ |
| Size | seqpos_ |
| the sequence position More... | |
| bool | mirrored_relative_to_type_ |
| Is this residue mirrored relative to its coordinates in the ResidueType? More... | |
| core::Size | chain_ |
| the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. More... | |
| utility::vector1< Real > | chi_ |
| our chi (side chain) torsion angles More... | |
| utility::vector1< Angle > | nus_ |
| our nu (internal ring) torsion angles More... | |
| utility::vector1< Real > | mainchain_torsions_ |
| our (possibly empty) backbone torsion angles More... | |
| Vector | actcoord_ |
| the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair More... | |
| basic::datacache::BasicDataCacheOP | data_cache_ |
| bool | misplaced_ = false |
| Inter-residue connection data. More... | |
| bool | nonstandard_polymer_ |
| true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1 More... | |
| utility::vector1< chemical::ResConnID > | connect_map_ |
| map between connection ids on this residue and the connection points on other residues to which its bonded More... | |
| std::map< Size, utility::vector1< Size > > | connections_to_residues_ |
| lists for each connected residue of the connection points on this residue that connect the pair. More... | |
| std::map< Size, PseudoBondCollectionCOP > | pseudobonds_ |
| other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds) More... | |
Detailed Description
Instance Residue class, used for placed residues and rotamers.
This class is designed to be lightweight. It holds a const-reference ("rsd_type_") to a ResidueType object for access to information common to all instances of a single type, e.g., Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:
- a vector1 of Atoms, which holds the positions (and also the atom-types for fast access during scoring);
- the sequence position and chain number, both integers (See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.)
- the backbone, side-chain, and internal ring (if applicable) torsion angles (of course backbone torsions are not unique to a rotamer, and the chi angles are derivable from the coordinates, but storing them in the residue is convenient for scoring purposes).
- the coordinates of an interaction center or centroid, used e.g., in the knowledge-based full-atom pair term ("actcoord_"). Maybe this will also hold the centroid position for centroid-mode scoring??
Member Typedef Documentation
◆ AtomIndices
◆ AtomType
◆ ResidueType
◆ ResidueTypeCOP
Constructor & Destructor Documentation
◆ Residue() [1/5]
| core::conformation::Residue::Residue | ( | ResidueTypeCOP | rsd_type_in, |
| bool const | dummy_arg | ||
| ) |
constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue.
Constructor from ResidueTypeCOP; sets coords to ideal values create a residue of type residue_type_in.
- Note
- Dummmy arg to prevent secret type conversions from ResidueTypeCOP to Residue
References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().
Referenced by clone_flipping_chirality().
◆ Residue() [2/5]
| core::conformation::Residue::Residue | ( | ResidueType const & | rsd_type_in, |
| bool const | dummy_arg | ||
| ) |
constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue.
Constructor from residue type; sets coords to ideal values create a residue of type residue_type_in.
- Note
- Dummmy arg to prevent secret type conversions from ResidueType to Residue
References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().
◆ Residue() [3/5]
| core::conformation::Residue::Residue | ( | ResidueType const & | rsd_type_in, |
| Residue const & | current_rsd, | ||
| Conformation const & | conformation, | ||
| bool | preserve_c_beta = false, |
||
| bool | allow_alternate_backbone_matching = false |
||
| ) |
Rotamer-style constructor; orients ideal coords onto backbone of current_rsd.
Create a residue/rotamer of type rsd_type_in placed at the position occupied by current_rsd Used primarily in rotamer building. The newly created Residue has the same sequence position, chain id and mainchain torsion angles as current_rsd. It has a ResidueType as defined by rsd_type_in. Its side-chain chi angles are uninitialized as all 0.0 and sidechain atom coords are from ideal coords. Its backbone is aligned with that of current_rsd. Its residue connections and its pseudobonds must be initialized from the original residue.
- Parameters
-
<allow_alternate_backbone_matching> If true, the number of main-chain atoms in the input ResidueType need not match the number in the template Residue. A function will be called that will attempt to align the Residues' connections. If successful, the new Residue will be created; if unsuccessful, an empty Residue will be returned.
References assign_orbitals(), atom(), core::chemical::ResidueType::atom_type_index(), atoms_, chi_, chi_atoms(), core::chemical::ResidueType::chi_atoms(), copy_residue_connections(), core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mainchain_atoms(), mainchain_torsions(), misplaced_, core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::n_nus(), n_nus(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), nus_, place(), pseudobonds_, rsd_type_, core::conformation::TR(), type(), update_nus(), and xyz().
◆ Residue() [4/5]
| core::conformation::Residue::Residue | ( | Residue const & | src | ) |
Copy constructor.
References init_residue_from_other().
◆ ~Residue()
|
overridedefault |
Destructor.
◆ Residue() [5/5]
|
private |
Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve.
References atom(), chi_, chi_atoms(), core::chemical::ResidueType::chi_atoms(), init_residue_from_other(), mirrored_relative_to_type(), nchi(), rsd_type_, set_mirrored_relative_to_type(), type(), and xyz().
Member Function Documentation
◆ aa()
|
inline |
Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration.
References core::chemical::ResidueTypeBase::aa(), and rsd_type_.
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::hybridization::add_non_protein_cst(), protocols::toolbox::sample_around::add_virtual_res(), core::pose::addVirtualResAsRoot(), protocols::denovo_design::components::advance_past_virtual_residues(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::protein_interface_design::Revert::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::idealize::IdealizeMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::nmr::pre::PREMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::simple_moves::VirtualRootMover::apply(), core::pose::rna::RNA_IdealCoord::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::energy_methods::ProQ_Energy::atom13_0(), core::energy_methods::FastDensEnergy::atomistic_energy(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::atoms_with_dof_derivatives(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::idealize::basic_idealize(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::build_rna_rotamers(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), core::energy_methods::MPSpanInsertionEnergy::calc_span_score(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), protocols::simple_moves::SampleSequenceFromProbabilities::calculate_position_diffs(), core::energy_methods::RG_Energy_Fast::calculate_rg_score(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::rna::denovo::check_base_pair(), protocols::denovo_design::components::StructureData::check_pose(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), core::scoring::rna::check_watson_crick_sequence(), protocols::loops::Loop::choose_cutpoint(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), core::scoring::dssp::Dssp::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::sasa_scores::compute_avge_scores(), core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::constraint_generator::compute_hnq_atoms(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), protocols::esm_perplexity::PseudoPerplexityMetric::compute_perplexity(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::relax::AtomCoordinateCstMover::compute_residue_subset(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), protocols::sasa_scores::compute_sasapack_scores(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::simple_moves::SampleSequenceFromProbabilities::construct_modified_sequence(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::energy_methods::ProClosureEnergy::defines_intrares_energy_for_residue(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::energy_methods::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensCenEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensEnergy::defines_residue_pair_energy(), core::energy_methods::FastDensEnergy::defines_residue_pair_energy(), core::energy_methods::PointWaterEnergy::defines_score_for_residue_pair(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::energy_methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::task_operations::RestrictAAsFromProbabilities::disable_AAs(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_proline_design(), core::scoring::constraints::ResidueCouplingConstraint::dist(), core::scoring::constraints::ResidueTypeLinkingConstraint::dist(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FiberDiffractionEnergy::eval_atom_derivative(), core::energy_methods::XtalMLEnergy::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::MgEnergy::eval_intrares_energy(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::energy_methods::CartesianBondedEnergy::eval_singleres_energy(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::rna::denovo::figure_out_base_pair_partner(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), core::energy_methods::MembraneLipo::finalize_total_energy(), core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::dna::find_basepairs(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), protocols::relax::fix_worst_bad_ramas(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_loops(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::pose::motif::get_backbone_reference_frame_atomids(), core::energy_methods::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pack::interaction_graph::SimpleEdge::get_bb_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::pose::get_center_of_mass(), core::energy_methods::HackAroEnergy::get_centroid(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::simple_metrics::per_residue_metrics::CurrentProbabilityMetric::get_current_probabilities(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::data::RNA_DMS_Potential::get_features(), core::pose::motif::get_frame_ala(), core::pose::motif::get_frame_arg(), core::pose::motif::get_frame_asn(), core::pose::motif::get_frame_asp(), core::pose::motif::get_frame_cys(), core::pose::motif::get_frame_gln(), core::pose::motif::get_frame_glu(), core::pose::motif::get_frame_gly(), core::pose::motif::get_frame_his(), core::pose::motif::get_frame_ile(), core::pose::motif::get_frame_leu(), core::pose::motif::get_frame_lys(), core::pose::motif::get_frame_met(), core::pose::motif::get_frame_phe(), core::pose::motif::get_frame_pro(), core::pose::motif::get_frame_ser(), core::pose::motif::get_frame_thr(), core::pose::motif::get_frame_trp(), core::pose::motif::get_frame_tyr(), core::pose::motif::get_frame_val(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hybridization::get_num_residues_nonvirt(), core::pose::rna::get_number_base_pairs(), core::pose::rna::get_number_native_base_pairs(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::sic_dock::get_rg(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pose::motif::get_sidechain_reference_frame(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream(), protocols::electron_density::get_spectrum(), core::import_pose::RNA_BasePairHandler::get_stem_residues(), core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), protocols::hybridization::CartesianSampler::get_transform(), core::scoring::dna::get_z_axis(), core::pose::carbohydrates::glycosylate_pose(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::constel::has_aromatic(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::features::ReportToDB::initialize_pose(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), core::io::serialization::is_pseudoresidue(), is_similar_aa(), is_similar_rotamer(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::simple_filters::ResidueDepthFilter::make_context(), core::pack::make_symmetric_task(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), core::conformation::missing_stubs_build(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::ShearMover::move_with_rama(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::ncbb::ncbb_design_main_loop(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::electron_density::BfactorMultifunc::operator()(), core::conformation::WatsonCrickResidueMatcher::operator()(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::PairEPotential::pair_term_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::ncbb::oop::pep_COM(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), core::scoring::electron_density::pose_has_nonzero_Bs(), core::energy_methods::FastDensEnergy::pose_is_setup_for_density_scoring(), protocols::electron_density::pose_spherical_samples(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::electron_density::remove_occupied_density_from_density(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::CenRotEnvEnergy::residue_energy(), core::energy_methods::EnvEnergy::residue_energy(), core::energy_methods::MembraneCbetaEnergy::residue_energy(), core::energy_methods::MembraneEnvEnergy::residue_energy(), core::energy_methods::MPCbetaEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::energy_methods::P_AA_ss_Energy::residue_energy(), core::energy_methods::RamachandranEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::SequenceDependentRefEnergy::residue_energy(), core::energy_methods::SmoothEnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), core::energy_methods::ElecDensAllAtomCenEnergy::residue_pair_energy(), core::energy_methods::ElecDensAtomwiseEnergy::residue_pair_energy(), core::energy_methods::ElecDensCenEnergy::residue_pair_energy(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), core::energy_methods::FastDensEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::scoring::rna::chemical_shift::ring_current_effect(), core::scoring::rna::chemical_shift::ring_current_effect_individual_ring(), core::scoring::rna::chemical_shift::ring_pos(), core::pack::dunbrack::rotamer_from_chi(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::ResidueTypeLinkingConstraint::score(), core::scoring::MembranePotential::score_normal_center(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::hbnet::HBNet::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), core::pose::setup_dof_mask_from_move_map(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::RG_Energy_Fast::setup_for_derivatives(), core::energy_methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::energy_methods::Abego::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensAtomwiseEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), protocols::scoring::Interface::show(), protocols::hybridization::DDomainParse::split(), core::fragment::SingleResidueFragData::steal(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), protocols::denovo_design::symmetric_fold_tree(), protocols::electron_density::symmetrizeBfactors(), protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(), core::scoring::BB_Pos::take_coordinates_from_pose(), core::scoring::MembranePotential::termini_penalty(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::hybridization::MRMover::trim_target_pose(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(), protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().
◆ abase2()
Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor)
References core::chemical::ResidueType::abase2(), and rsd_type_.
Referenced by core::scoring::hbonds::assign_abase_derivs(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::magnesium::get_cos_theta(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::dna::PDBOutput::output_hbond_info(), and protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().
◆ accpt_pos()
|
inline |
Returns the AtomIndices of this residue's h-bond acceptor atoms.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.accpt_pos() See also: Residue Residue.accpt_pos_sc Residue.atoms Pose
References core::chemical::ResidueType::accpt_pos(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::energy_methods::OccludedHbondSolEnergy::atom_is_acceptor(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_acceptor(), core::pose::rna::atom_is_acceptor(), core::energy_methods::OccludedHbondSolEnergy::atom_is_valid_base(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pose::rna::bases_form_a_hydrogen_bond(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::compute_exact_geosol(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::features::HBondFeatures::report_features(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().
◆ accpt_pos_sc()
|
inline |
Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.accpt_pos_sc() See also: Residue Residue.accpt_pos Residue.atoms Pose
References core::chemical::ResidueType::accpt_pos_sc(), and rsd_type_.
Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().
◆ actcoord() [1/2]
|
inline |
Returns the coordinates used for pairE calculations (amino acids only)
References actcoord_.
◆ actcoord() [2/2]
|
inline |
Returns the coordinates used for pairE calculations (amino acids only)
References actcoord_.
Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows(), core::conformation::orient_residue_for_ideal_bond(), core::scoring::PairEPotential::pair_term_energy(), protocols::features::PairFeatures::report_residue_pairs(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), and update_actcoord().
◆ actcoord_atoms()
|
inline |
Returns the AtomIndices of atoms that will be used to define this residue's actcoord.
References core::chemical::ResidueType::actcoord_atoms(), and rsd_type_.
Referenced by core::energy_methods::PairEnergy::eval_residue_pair_derivatives().
◆ actual_residue_connection()
|
inline |
Get the residue connection. How is this different than residue_connection?
References connect_map_.
Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Conformation::detect_pseudobonds().
◆ all_bb_atoms()
|
inline |
Returns the AtomIndices of this residue's backbone atoms.
- Note
- : heavyatoms and hydrogens, AtomIndices == vector1< Size >
example(s): residue.all_bb_atoms() See also: Residue Residue.atoms Pose
References core::chemical::ResidueType::all_bb_atoms(), and rsd_type_.
Referenced by protocols::indexed_structure_store::apply_residue_entries_to_pose().
◆ annotated_name()
| std::string core::conformation::Residue::annotated_name | ( | bool const | show_all_variants = true | ) | const |
Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D].
References core::chemical::aa_from_oneletter_code(), name(), name1(), core::chemical::name_from_aa(), and core::chemical::oneletter_code_specifies_aa().
Referenced by core::conformation::Conformation::annotated_sequence(), and core::scoring::rna::output_rna_motif().
◆ apply_transform_downstream()
|
private |
apply transform of rotation R and translation V for all atoms downstream
- Note
- note this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.
xyz --> R * xyz + v
this uses information from atom_base array to transform all the downstream atoms along the side chain recursively. it assumes that the atom_base array will not get us into any infinite loops!
- Note
- this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.
References atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), protocols::sic_dock::scores::nbr, nbrs(), core::chemical::ResidueType::root_atom(), rsd_type_, core::conformation::TR(), core::conformation::Atom::xyz(), and xyz().
Referenced by set_all_ring_nu(), set_chi(), set_d(), set_tau(), and set_theta().
◆ apply_transform_Rx_plus_v()
| void core::conformation::Residue::apply_transform_Rx_plus_v | ( | numeric::xyzMatrix< Real > | R, |
| Vector | v | ||
| ) |
Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space.
References core::chemical::ResidueType::natoms(), set_xyz(), type(), and xyz().
◆ assign_orbitals()
|
private |
Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors.
References core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueTypeBase::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, rsd_type_, and type().
Referenced by Residue().
◆ atom() [1/4]
Returns this residue's Atom with index number <atm_index> (non-const)
- Note
- : Atom object is xyz and atom_type
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atoms_.
◆ atom() [2/4]
Returns this residue's Atom with index number <atm_index> (const)
- Note
- : Atom object is xyz and atom_type
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atoms_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::energy_methods::add_to_individual_sol_energies(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::RollMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::contact_map::ContactMap::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), apply_transform_downstream(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::energy_methods::ProQ_Energy::atom_feature(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::atomic_depth::atomic_depth(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), attached_H_begin(), attached_H_end(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), build_orbital_xyz(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), core::conformation::build_residue_tree(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::membrane::calc_helix_axis(), core::select::util::calc_sc_neighbors(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), protocols::pose_sewing::calculate_distance_score_bt_residues(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::energy_methods::ProQ_Energy::calculateZ(), core::select::util::cbeta_vector(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::geometry::center_of_mass(), core::pose::center_of_mass(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::rbsegment_relax::ConfChangeMover::check_gaps(), core::scoring::MembranePotential::check_spanning(), protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::relax::RangeRelaxMover::constrain_to_reference(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::energy_methods::ProQ_Energy::crd(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), protocols::legacy_sewing::create_model_from_pose(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), core::conformation::Conformation::debug_residue_torsions(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::energy_methods::LinearChainbreakEnergy::do_score_dev(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::energy_methods::BranchEnergy::finalize_total_energy(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearBranchEnergy::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::features::strand_assembly::find_sheet(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::electron_density::findLoopFromDensity(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), core::pose::get_center_of_mass(), protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands(), protocols::membrane::get_chain_and_z(), protocols::features::strand_assembly::get_closest_distance_between_strands(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), core::scoring::magnesium::get_cos_theta(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::matdes::get_matching_subunits(), protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::electron_density::get_spectrum(), protocols::hybridization::get_superposition_transformation(), protocols::hybridization::CartesianSampler::get_transform(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), protocols::cryst::getMW(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), core::pose::rna::is_rna_chainbreak(), protocols::features::strand_assembly::is_this_strand_at_edge(), core::pose::rna::is_tna_chainbreak(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), mm_atom_name(), protocols::motifs::Motif::Motif(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::dna::PDBOutput::output_hbond_info(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), path_distance(), protocols::ncbb::oop::pep_COM(), place(), protocols::motifs::Motif::place_atom_(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::motifs::Motif::place_residue_helper(), protocols::electron_density::pose_spherical_samples(), core::scoring::PQR::PQR(), core::energy_methods::FA_GrpElecEnergy::precalc_context(), protocols::viewer::print_node(), core::energy_methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::pose::radius_of_gyration(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::drug_design::replace_residue_type_with_mask(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::SmotifFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::simple_filters::res_res_min_distance(), Residue(), core::conformation::symmetry::residue_center_of_mass(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::energy_methods::FaMPEnvEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::residue_fast_pair_energy_attached_H(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::toolbox::pose_manipulation::rigid_body_move(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), core::select::util::select_coord_for_residue(), set_all_ring_nu(), set_chi(), protocols::hbnet::HBNet::set_constraints(), set_d(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::design_opt::Supercharge::set_surface(), set_tau(), set_theta(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::NeighborList::setup(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_dis_by_terminals(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::hybridization::DDomainParse::split(), protocols::rbsegment_relax::ConfChangeMover::stage2(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), core::util::switch_to_centroid_rot_set(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), core::scoring::MembranePotential::tm_projection_penalty(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), update_nus(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), core::scoring::epr_deer::EPRSpinLabel::weight(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), core::scoring::PoissonBoltzmannPotential::write_pqr(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_starting_loop(), core::chemical::ICoorAtomID::xyz(), and xyz().
◆ atom() [3/4]
|
inline |
Returns this residue's Atom with name <atm_name> (non-const)
- Note
- : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atom_index(), and atoms_.
◆ atom() [4/4]
|
inline |
Returns this residue's Atom with name <atm_name> (const)
- Note
- : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atom_index(), and atoms_.
◆ atom_base()
Returns the atom index of the <atomno> atom's base atom.
References core::chemical::ResidueType::atom_base(), and rsd_type_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), core::energy_methods::add_to_individual_sol_energies(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::hbonds::assign_abase_derivs(), core::energy_methods::assign_rna_atom_type(), core::energy_methods::OccludedHbondSolEnergy::atom_is_valid_base(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pose::rna::bases_form_a_hydrogen_bond(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::energy_methods::compute_exact_geosol(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::pack::interaction_graph::create_hbonds_one_way(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::hbonds::determine_atom_level_edge_info(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), protocols::pockets::PocketGrid::findExemplars(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::magnesium::get_cos_theta(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), protocols::protein_interface_design::hbonded_atom(), core::pose::rna::heavy_atom_is_polar(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::HBondFeatures::insert_site_row(), core::energy_methods::is_base_2(), core::energy_methods::is_phosphate_2(), core::energy_methods::StackElecEnergy::is_rna_base(), core::energy_methods::is_sugar_2(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::dna::PDBOutput::output_hbond_info(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(), protocols::features::HBondFeatures::report_features(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), and protocols::md::Rattle::setup_constraint().
◆ atom_begin() [1/2]
|
inline |
begin interator, to iterate over atoms
References atoms_.
Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::environment::com_calc(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs(), and core::scoring::interface_::DDPscore::residue_pair_energy().
◆ atom_begin() [2/2]
|
inline |
References atoms_.
◆ atom_depends_on_lower()
| bool core::conformation::Residue::atom_depends_on_lower | ( | core::Size const | atom_index | ) | const |
Does this atom depend on the LOWER_CONNECT?
Now based on a simple lookup, based on data initialized during ResidueType::finalize().
References core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(), atom_index(), and rsd_type_.
Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().
◆ atom_depends_on_upper()
| bool core::conformation::Residue::atom_depends_on_upper | ( | core::Size const | atom_index | ) | const |
Does this atom depend on the UPPER_CONNECT?
Now based on a simple lookup, based on data initialized during ResidueType::finalize().
References core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(), atom_index(), and rsd_type_.
Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().
◆ atom_end() [1/2]
|
inline |
end interator, to iterate over atoms
References atoms_.
Referenced by protocols::simple_filters::AtomicContactFilter::compute(), and protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs().
◆ atom_end() [2/2]
|
inline |
References atoms_.
◆ atom_index()
|
inline |
Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid.
example(s): residue.atom_index("CA") See also: Residue AtomType Pose
References core::chemical::ResidueType::atom_index(), and rsd_type_.
Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts_to_rb(), protocols::seeded_abinitio::add_dist_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), core::pose::ncbb::add_generic_hbs_constraint(), protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), protocols::antibody::constraints::add_harmonic_dihedral_cst_general(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::pose::ncbb::add_oop_constraint(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::pose::ncbb::add_triazole_constraint(), protocols::loops::addScoresForLoopParts(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_residue(), core::pose::Pose::append_residue_by_atoms(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::splice::Splice::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_dihedral_bbg(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), protocols::constel::PresenceCommon::are_atoms_pres(), atom(), atom_depends_on_lower(), atom_depends_on_upper(), protocols::hydrate::atom_is_hydratable(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::conformation::build_residue_tree(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), core::select::util::calc_sc_neighbors(), core::energy_methods::GoapEnergy::calculate_dipoles(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::antibody::cdr_backbone_rmsds(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), protocols::loop_grower::LoopGrower::check_coordinates(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), protocols::flxbb::constraints_sheet(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::pose::correctly_add_2prime_connection_variants(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::relax::cyclize_pose(), core::conformation::Conformation::declare_chemical_bond(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), first_adjacent_heavy_atom(), protocols::splice::fix_chain_break_residue(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::form_disulfide(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), get_adjacent_heavy_atoms(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), get_atoms_exocyclic_to_ring_atom(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond(), core::pose::get_constraints_from_link_records(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), get_hydrogens_bonded_to_ring_atom(), protocols::simple_moves::BBConRotMover::get_L_move(), core::scoring::loop_graph::get_loop_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::lDDT_Calculator::get_matching_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), get_substituents_to_ring_atom(), protocols::constel::has_aromatic(), protocols::constel::FilterBySASA::has_low_per_atom_sasa(), protocols::protein_interface_design::hbonded_atom(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::frags::TorsionFragment::insert(), core::pose::Pose::insert_residue_by_atoms(), core::io::pose_from_sfr::is_connected(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::constel::HBondCommon::is_rmoi_hbonded(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), core::pose::make_atom_map(), protocols::simple_moves::BBConRotMover::make_move(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), core::conformation::named_atom_id_to_atom_id(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::tcr::orient_tcr_chain(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::constraint_generator::parse_custom_torsion(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate(), protocols::viewer::print_node(), core::conformation::print_node(), protocols::match::output::print_node(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), core::scoring::constraints::AngleConstraint::read_def(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::features::SaltBridgeFeatures::report_features(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), core::scoring::rna::chemical_shift::ring_pos(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::rbsegment_relax::set_constraints(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::star::setup_constraints(), protocols::simple_moves::DisulfideInsertionMover::setup_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing(), core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::conformation::setup_links(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::loop_grower::LoopGrower::single_grow(), protocols::constel::SingResCnlCrea::strip_atoms(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::grafting::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::docking::ConformerSwitchMover::switch_conformer(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), core::scoring::epr_deer::EPRSpinLabel::weight(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().
◆ atom_is_backbone()
|
inline |
Returns true if this residue's atom with index number <atomno> is a backbone atom.
example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose
References core::chemical::ResidueType::atom_is_backbone(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::hbnet::UnsatSelector::apply(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::HolesFilter::compute(), core::energy_methods::ProQ_Energy::crd(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::energy_methods::ImplicitMembraneElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::dna::get_base_pair_stub_slow(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::is_scatom(), protocols::dna::PDBOutput::output_hbond_info(), protocols::minimization_packing::PertMinMover::pert(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), protocols::pockets::PocketGrid::recenter(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), core::scoring::constraints::remove_nonbb_constraints(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and protocols::constel::SingResCnlCrea::zero_occ_bb_h().
◆ atom_is_hydrogen()
|
inline |
Returns true if this residue's atom with index number <atomno> is a hydrogen.
example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose
References core::chemical::ResidueType::atom_is_hydrogen(), and rsd_type_.
Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::energy_methods::add_to_individual_sol_energies(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::energy_methods::assign_rna_atom_type(), core::scoring::constraints::auto_detect_atoms(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::energy_methods::LK_hack::eval_atom_derivative(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_DomeEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), get_adjacent_heavy_atoms(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), get_hydrogens_bonded_to_ring_atom(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), get_substituents_to_ring_atom(), core::scoring::ResidueNblistData::initialize(), core::energy_methods::is_base_2(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::is_non_peptide_heavy_atom(), core::energy_methods::is_phosphate_2(), core::scoring::is_polymer_heavyatom(), core::energy_methods::StackElecEnergy::is_rna_base(), core::energy_methods::is_sugar_2(), core::scoring::IsHeavyAtomPredicate::operator()(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::NeighborList::setup(), protocols::md::Rattle::setup_constraint(), core::scoring::NeighborList::update_from_wide_nblist(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and protocols::constel::SingResCnlCrea::zero_occ_bb_h().
◆ atom_is_polar_hydrogen()
|
inline |
Is a particular atom a polar hydrogen?
References core::chemical::ResidueType::atom_is_polar_hydrogen(), and rsd_type_.
Referenced by protocols::hbnet::UnsatSelector::apply(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::hbonds::weights_and_derivs_for_hbonds(), and core::scoring::hbonds::weights_for_hbonds().
◆ atom_name()
|
inline |
Returns the name of this residue's atom with index number <atm>
References core::chemical::ResidueType::atom_name(), and rsd_type_.
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), core::util::add_constraints_to_metal(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), protocols::loops::add_single_cutpoint_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_multipole_axes(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::annotated_atom_graph_from_conformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::Conformation::append_residue_by_bond(), core::conformation::Conformation::append_residues(), protocols::ligand_docking::AddHydrogen::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::energy_methods::ProQ_Energy::atom13_0(), core::conformation::atom_graph_from_conformation(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), protocols::hydrate::atom_is_hydratable(), protocols::qsar::scoring_grid::LipidMemGrid::atom_score(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::constraints::auto_detect_atoms(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::rna::movers::bump_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::electron_density::DensityZscores::calc_avg_residue_bfac(), core::scoring::calc_per_atom_sasa_sc(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::import_pose::RNA_JumpMover::check_forward_backward(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::constraints::combine_NMR_atom_string(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), core::energy_methods::compute_exact_geosol(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pose::correctly_add_2prime_connection_variants(), core::energy_methods::ProQ_Energy::crd(), core::pose::create_chemical_edge(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::pose::declare_cutpoint_chemical_bond(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::environment::dof_id_to_string(), core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::SymmetricLigandEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::MgEnergy::eval_residue_pair(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::magnesium::filter_water_ligands(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_helper(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::pockets::PocketGrid::findExemplars(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), IdentifyLigandMotifs::get_atom_trios(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::lDDT_Calculator::get_matching_atom(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::select::get_pymol_selection_for_atoms(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), core::conformation::idealize_hydrogens(), core::conformation::improper_build(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::conformation::is_ideal_position(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_residues_in_contact(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::forge::methods::make_star_foldtree(), core::conformation::missing_stubs_build(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), protocols::dna::PDBOutput::output_hbond_info(), core::pose::rna::output_other_contacts(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), core::chemical::sdf::MolWriter::output_residue(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), place(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::normalmode::NormalMode::prepare_coord(), core::conformation::print_atom(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_info(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::viewer::print_node(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::drug_design::replace_residue_type_with_mask(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::SASAShouldItCount(), protocols::qsar::scoring_grid::LipidMemGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::hbnet::HBNet::set_constraints(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::cyclic_peptide::crosslinker::set_up_lanthionine_constraints(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), core::scoring::ShouldItCount(), show(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), protocols::nmr::pre::PREEnergy::show_additional_info(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::backrub::BackrubSidechainMover::update_segments(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), core::scoring::VdWShouldItCount(), protocols::metal_interface::AddZincSiteConstraints::view_constraints_in_pymol(), and core::scoring::PoissonBoltzmannPotential::write_pqr().
◆ atom_type()
Returns the AtomType of this residue's atom with index number <atomno>
example(s): residue.atom_type(3) See also: Residue Residue.atom_index AtomType Pose
References core::chemical::ResidueType::atom_type(), and rsd_type_.
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::hbnet::UnsatSelector::apply(), core::energy_methods::ProQ_Energy::atom13_0(), core::conformation::atom_graph_from_conformation(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::energy_methods::atom_is_aro(), core::energy_methods::atom_is_aro2(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_single_edge_waters(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::electron_density::DensityZscores::calc_avg_residue_bfac(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::hbnet::HBNet::estimate_saturation(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FiberDiffractionEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::forge::remodel::fast_clash_check(), protocols::pose_metric_calculators::fast_clash_check(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), protocols::magnesium::filter_acceptor_ligands(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_for_complex(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::frac_atoms_within(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), IdentifyLigandMotifs::get_atom_trios(), core::scoring::magnesium::get_cos_theta(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::hbonds::get_hb_acc_chem_type(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::membrane::scoring::ElectricfieldLipidlayer::get_menv_params_for_residue(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::select::get_pymol_selection_for_atoms(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::chemical::rna::get_rna_base_centroid(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::relax::RangeRelaxMover::idealize_pose(), protocols::sic_dock::SICFast::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::GenBornResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_site_row(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::magnesium::is_ligand(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), core::scoring::lkball::LKD_ResidueInfo::LKD_ResidueInfo(), protocols::protein_interface_design::make_hotspot_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::match_by_atomtype(), protocols::motifs::Motif::Motif(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::dna::PDBOutput::output_hbond_info(), core::energy_methods::parcs_ccs(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::viewer::print_node(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::energy_methods::SAXSEnergy::rehash_form_factors(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::energy_methods::WaterAdductIntraEnergy::residue_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), core::conformation::setup_links(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulphur_bond_check(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().
◆ atom_type_index()
Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType.
example(s): residue.atom_type_index(3) See also: Residue Residue.atom_index AtomType Pose
References atoms_.
Referenced by core::energy_methods::add_to_individual_sol_energies(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::energy_methods::compute_exact_geosol(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::chemical::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::electron_density::BfactorMultifunc::operator()(), core::conformation::orient_residue_for_ideal_bond(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::electron_density::pose_spherical_samples(), core::scoring::packing::PoseBalls::PoseBalls(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::electron_density::remove_occupied_density_from_density(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), protocols::legacy_sewing::scoring::LegacyClashScorer::score(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection(), core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc(), and core::scoring::epr_deer::EPRSpinLabel::weight().
◆ atom_type_set()
|
inline |
Returns the AtomTypeSet of this residue.
example(s): residue.atom_type_set() See also: Residue Residue.atom_type_index AtomType Pose
References core::chemical::ResidueTypeBase::atom_type_set(), and rsd_type_.
Referenced by protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::electron_density::pose_spherical_samples(), protocols::electron_density::remove_occupied_density_from_density(), protocols::features::AtomTypesFeatures::report_features(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().
◆ atomic_charge()
Returns the atom charge of this residue's atom with index number <atomno>
example(s): residue.atomic_charge(3) See also: Residue Residue.atom_index Pose
References core::chemical::ResidueType::atom_charge(), and rsd_type_.
Referenced by protocols::qsar::scoring_grid::ChargeGrid::atom_score(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::elec::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::energy_methods::ImplicitMembraneElecEnergy::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::hbnet::HBNet::find_unsats(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::membrane::scoring::ElectricfieldLipidlayer::get_menv_params_for_residue(), core::scoring::GenBornPotential::get_res_res_elecE(), core::chemical::rna::get_rna_base_centroid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::cryst::ReportGradientsMover::normalization(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::qsar::scoring_grid::ChargeGrid::score(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::energy_methods::RNA_FA_ElecEnergy::score_atom_pair(), core::energy_methods::ImplicitMembraneElecEnergy::score_atom_pair(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().
◆ atoms() [1/2]
|
inline |
◆ atoms() [2/2]
|
inline |
Returns this residue's Atoms (const), a vector1 of Atom objects.
example(s): residue.atoms() See also: Residue Pose
References atoms_.
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::pose_sewing::movers::SewAnythingAddMover::align(), core::conformation::atom_id_to_named_atom_id(), protocols::pose_sewing::calculate_motif_score_bt_residues(), core::pose::compare_atom_coordinates(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::loops::loop_rmsd(), orient_onto_location(), orient_onto_residue_peptoid(), place(), protocols::pose_sewing::filters::CoreScorer::report_sm(), core::conformation::setup_corresponding_atoms(), core::util::switch_to_centroid_rot_set(), update_actcoord(), core::io::serialization::write_binary(), and protocols::environment::claims::XYZClaim::yield_elements().
◆ atoms_with_orb_index()
|
inline |
References core::chemical::ResidueType::atoms_with_orb_index(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), update_orbital_coords(), and core::conformation::Conformation::update_orbital_coords().
◆ attached_H_begin() [1/2]
|
inline |
Returns the AtomIndices of the first hydrogen attached to each heavyatom.
example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Residue.nheavyatoms Pose
References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.
◆ attached_H_begin() [2/2]
Returns the index number of the first hydrogen attached to the atom with index number <atom>
example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Pose
References atom(), core::chemical::ResidueType::attached_H_begin(), and rsd_type_.
Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().
◆ attached_H_end() [1/2]
|
inline |
Returns the AtomIndices of the last hydrogen attached to each heavyatom.
example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Residue.nheavyatoms Pose
References core::chemical::ResidueType::attached_H_end(), and rsd_type_.
◆ attached_H_end() [2/2]
Returns the index number of the last hydrogen attached to the atom with index number <atom>
example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Pose
References atom(), core::chemical::ResidueType::attached_H_end(), and rsd_type_.
Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().
◆ backbone_aa()
|
inline |
Returns this residue's backbone_aa type, if any.
This is used for noncanonical alpha-amino acids that are templated on canonicals. For example, 4,5-dihydroxyisoleucine uses the ramachandran and p_aa_pp scoring of isoleucine.
References core::chemical::ResidueTypeBase::backbone_aa(), and rsd_type_.
Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), and core::energy_methods::RamachandranEnergy::residue_energy().
◆ bonded_neighbor()
|
inline |
Returns the AtomIndices for all bonded neighbor atoms of <atm>
References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.
Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::bonded_neighbor_all_res(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), fill_missing_atoms(), get_adjacent_heavy_atoms(), IdentifyLigandMotifs::get_atom_trios(), get_atoms_exocyclic_to_ring_atom(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), n_bonded_neighbor_all_res(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::HbaGrid::score(), and protocols::features::OrbitalsFeatures::set_OrbH_features_data().
◆ bonded_orbitals()
|
inline |
References core::chemical::ResidueType::bonded_orbitals(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), and core::conformation::Conformation::update_orbital_coords().
◆ build_atom_ideal()
|
inline |
Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms.
References core::chemical::AtomICoor::build(), and icoor().
Referenced by protocols::splice::Splice::apply(), protocols::splice::fix_chain_break_residue(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), and protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned().
◆ build_orbital_xyz()
References atom(), core::chemical::orbitals::ICoorOrbitalData::build(), core::chemical::orbitals::ICoorOrbitalData::get_stub1(), core::chemical::orbitals::ICoorOrbitalData::get_stub2(), core::chemical::orbitals::ICoorOrbitalData::get_stub3(), core::chemical::ResidueType::new_orbital_icoor_data(), rsd_type_, and core::conformation::Atom::xyz().
Referenced by assign_orbitals(), update_orbital_coords(), and core::conformation::Conformation::update_orbital_coords().
◆ carbohydrate_info()
| core::chemical::carbohydrates::CarbohydrateInfoCOP core::conformation::Residue::carbohydrate_info | ( | ) | const |
Return the CarbohydrateInfo object containing sugar-specific properties for this residue.
References core::chemical::ResidueType::carbohydrate_info(), core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::io::carbohydrates::residue_range_gws_string(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), and core::pose::carbohydrates::tautomerize_anomer().
◆ chain() [1/2]
|
inline |
Returns this residue's chain id.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_.
Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), core::pose::Pose::chain(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::io::pdb::create_pdb_info_for_single_residue_pose(), core::pose::create_subpose(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::matdes::dup_residue(), core::pose::symmetry::extract_asymmetric_unit(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::forge::methods::fold_tree_from_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), protocols::minimization_packing::ChainGroupDiscriminator::group_id(), protocols::antibody::AntibodyInfo::identify_antibody(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::forge::build::ConnectRight::modify_impl(), orient_onto_residue_peptoid(), core::pose::PDBInfo::PDBInfo(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), core::scoring::PQR::PQR(), protocols::enzdes::enzutil::read_pose_from_file(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::drug_design::replace_residue_type_with_mask(), protocols::antibody::AntibodyFeatures::report_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::energy_methods::RNA_BulgeEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::energy_methods::PoissonBoltzmannEnergy::residue_in_chains(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::conformation::Conformation::sequence_matches(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), core::energy_methods::PoissonBoltzmannEnergy::setup_for_scoring(), protocols::docking::DockingHighResLegacy::setup_packing(), core::conformation::Conformation::update_polymeric_connection(), core::io::serialization::write_binary(), and core::scoring::PoissonBoltzmannPotential::write_pqr().
◆ chain() [2/2]
|
inline |
Sets this residue's chain id.
Don't call directly – In almost all situations, this should be set by the owning Conformation
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_.
◆ chi() [1/4]
|
inline |
Returns the chi torsion angles of this residue (non-const)
References chi_.
◆ chi() [2/4]
|
inline |
Returns the chi torsion angles of this residue (const)
example(s): residue.chi() See also: Residue Residue.nchi Pose Pose.chi
References chi_.
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::Pose::chi(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::legacy_sewing::create_model_from_pose(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::idealize::dihedral_distance(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::dna::DNABase::DNABase(), protocols::metal_interface::dump_chis(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), protocols::indexed_structure_store::extract_residue_entry(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_packed_rotno(), core::chemical::rna::get_residue_base_state(), core::pack::get_residue_current_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::get_rotamer_angle_diffs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::conformation::idealize_position(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), is_similar_rotamer(), protocols::motifs::make_base_pair_mutation(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::pack::optimize_H_and_notify(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::splice::printChi(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), core::energy_methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::pack::dunbrack::rotamer_from_chi(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::ligand_docking::LigandDockProtocol::shear_min_protocol(), protocols::dna::show_dna_geometry(), protocols::dna::show_dna_geometry_extra_details(), protocols::dna::substitute_residue(), core::conformation::Conformation::torsion(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_flexscs(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), and core::conformation::Conformation::update_residue_torsions().
◆ chi() [3/4]
◆ chi() [4/4]
|
inline |
Sets the chi torsion angles of this residue.
CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.
example(s):
See also: Residue Pose Pose.set_chi
References chi_.
◆ chi_atoms() [1/2]
|
inline |
Returns the AtomIndices of each set of four atoms defining each chi angle.
References core::chemical::ResidueType::chi_atoms(), and rsd_type_.
Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::energy_methods::YHHPlanarityEnergy::atoms_with_dof_derivatives(), core::energy_methods::chi2_torsion_atom_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::scoring::dna::get_base_pair_stub_slow(), core::pack::get_residue_current_energy(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::pack::optimize_H_and_notify(), place(), Residue(), set_chi(), core::conformation::set_chi_according_to_coordinates(), set_d(), set_theta(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), core::conformation::setup_corresponding_atoms(), core::conformation::setup_links(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().
◆ chi_atoms() [2/2]
|
inline |
Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle.
References core::chemical::ResidueType::chi_atoms(), and rsd_type_.
◆ chi_rotamers()
|
inline |
Returns the chi rotamers available for this residue's chi angle <chino>
References core::chemical::ResidueType::chi_rotamers(), and rsd_type_.
Referenced by core::pack::rotamer_set::build_rotamers_from_rotamer_bins().
◆ clear_residue_connections()
| void core::conformation::Residue::clear_residue_connections | ( | ) |
References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.
◆ clone()
| ResidueOP core::conformation::Residue::clone | ( | ) | const |
Copy this residue( allocate actual memory for it )
make a copy of this residue( allocate actual memory for it )
Referenced by core::util::add_covalent_linkage_helper(), core::pose::add_variant_type_to_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::seeded_abinitio::combine_two_poses(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), create_residue(), create_rotamer(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::io::pdb::dump_pdb_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::matdes::dup_residue(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::splice::RotLibOut::find_matching_res(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::ligand_docking::get_ligand_torsion_constraints(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::magnesium::MgHydrater::hydrate_magnesium(), core::conformation::idealize_position(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::initialize(), core::conformation::Conformation::insert_conformation_by_jump(), core::conformation::Conformation::insert_residue_by_bond(), protocols::motifs::BuildPosition::keep_rotamer(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::modeler::merge_two_poses(), protocols::hbnet::HBNet::minimize_network(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), core::pose::remove_variant_type_from_residue(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), protocols::denovo_design::components::Segment::set_template_pose(), core::pack::setup_bgres_cops(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::stepwise::modeler::slice(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), protocols::vip::VIP_Mover::try_point_mutants(), and protocols::hydrate::water_specific_hbond_energy().
◆ clone_flipping_chirality()
| ResidueOP core::conformation::Residue::clone_flipping_chirality | ( | core::chemical::ResidueTypeSet const & | residue_type_set | ) | const |
Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.
Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues. The passed ResidueTypeSet is the ResidueTypeSet you want the mirrored type to come from.
- Note
- This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart. It assumes that you've already mirrored all of the coordinates, and just allows you to generate a replacement residue of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms, variant types, etc.).
References core::chemical::ResidueTypeSet::get_mirrored_type(), Residue(), and rsd_type_ptr_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner().
◆ connect_atom()
Returns the index number of this residue's atom connected to the <other> Residue.
Returns the atom-index of my atom which is connected to the other residue.
example(s):
See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Residue.upper_connect_atom Pose
so long as there is only a single connection to other... if there are multiple connections this will fail. If there are no connections this will fail. This is a convenience function that can fail; be careful! Fails if I'm not bonded to the other residue.
- Note
- not well defined if multiple connections to another residue – need more general function
References core::chemical::ResidueConnection::atomno(), connections_to_residues_, is_lower_terminus(), is_polymer(), is_upper_terminus(), lower_connect_atom(), core::chemical::ResidueTypeBase::name(), nonstandard_polymer_, core::chemical::ResidueType::residue_connection(), rsd_type_, seqpos(), seqpos_, core::conformation::TR(), type(), and upper_connect_atom().
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::pose::symmetry::extract_asymmetric_unit(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::form_disulfide(), core::io::pose_from_sfr::is_connected(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), and protocols::viewer::print_interres_bond().
◆ connect_map()
|
inline |
References connect_map_.
Referenced by core::util::add_constraints_to_metal(), core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::chemical::ICoorAtomID::atom_id(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::mm::connection_indices(), copy_residue_connections(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::conformation::disulfide_bonds(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::cyclic_peptide::dump_debug_output(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::get_disulf_partner(), core::pose::Pose::real_to_virtual(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::energy_methods::LK_hack::residue_pair_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().
◆ connect_map_size()
|
inline |
Returns the size (number of elements) in the connect_map_ object.
References connect_map_.
Referenced by core::chemical::ICoorAtomID::atom_id(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::scoring::Ramachandran::is_normally_connected(), core::scoring::methods::lower_upper_connected_across_cutpoint(), and core::pose::show_adjacent_nt_connections().
◆ connected_residue_at_lower()
| Size core::conformation::Residue::connected_residue_at_lower | ( | ) | const |
Returns the residue number of a residue connected to this residue at this residue's lower_connect.
This function returns 0 if this residue lacks a lower_connect or if it's not connected to anything at its lower_connect.
References connected_residue_at_resconn(), has_lower_connect(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_thioether_residues_from_selection(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), orient_onto_residue_peptoid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::pose::set_reasonable_fold_tree(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), protocols::cyclic_peptide::crosslinker::set_up_thioether_variants(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ connected_residue_at_resconn()
|
inline |
Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.
For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6. Exactly the same as residue_connection_partner
References connect_map_.
Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::CrankshaftFlipMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Conformation::atoms_are_bonded(), connected_residue_at_lower(), connected_residue_at_upper(), core::pose::correctly_add_2prime_connection_variants(), core::pose::create_chemical_edge(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::pose::declare_cutpoint_chemical_bond(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::cyclic_peptide::dump_debug_output(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::io::silent::BinarySilentStruct::fill_struct(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::forge::methods::fold_tree_from_pose(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::generate_allowed_partners(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::conformation::get_second_atom_from_connection(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), protocols::cyclic_peptide::CycpepSymmetryFilter::is_cyclic_peptide(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_current_residue_connections(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::pose::Pose::real_to_virtual(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::pose::show_adjacent_nt_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().
◆ connected_residue_at_upper()
| Size core::conformation::Residue::connected_residue_at_upper | ( | ) | const |
Returns the residue number of a residue connected to this residue at this residue's upper_connect.
This function returns 0 if this residue lacks an upper_connect or if it's not connected to anything at its upper_connect.
References connected_residue_at_resconn(), has_upper_connect(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), protocols::backbone_moves::RandomizeBBByRamaPrePro::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::pose::symmetry::extract_asymmetric_unit(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::set_reasonable_fold_tree(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().
◆ connection_distance()
| Distance core::conformation::Residue::connection_distance | ( | conformation::Conformation const & | conf, |
| Size const | resconn_index, | ||
| Vector const & | matchpoint | ||
| ) | const |
Distance between a potential residue connection match and the position of the expected atom.
References core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), name(), core::chemical::ResidueType::residue_connection(), core::conformation::TR(), and type().
Referenced by core::conformation::Conformation::detect_bonds().
◆ connection_incomplete()
| bool core::conformation::Residue::connection_incomplete | ( | Size | resconnid | ) | const |
References connect_map_.
Referenced by protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::detect_bonds(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), has_incomplete_connection(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), core::scoring::Ramachandran::is_normally_connected(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), n_bonded_neighbor_all_res(), core::energy_methods::polymeric_termini_incomplete(), core::scoring::polymeric_termini_incomplete(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), and protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms().
◆ connections_match()
| bool core::conformation::Residue::connections_match | ( | Residue const & | other | ) | const |
Returns true if ???
References connect_map_, and pseudobonds_.
◆ connections_to_residue() [1/2]
|
inline |
Returns the vector1 of resconn ids that connect this residue to other.
References seqpos().
Referenced by core::conformation::Conformation::atoms_are_bonded(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::pose::create_chemical_edge(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::conformation::get_chemical_root_and_anchor_atomnos(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), protocols::simple_moves::CyclizationMover::setup_constraints(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().
◆ connections_to_residue() [2/2]
|
inline |
Returns the vector1 of resconn ids that connect this residue to other.
References connections_to_residues_.
◆ copy_residue_connections()
| void core::conformation::Residue::copy_residue_connections | ( | Residue const & | src_rsd, |
| bool const | suppress_warnings = false |
||
| ) |
Attempt to take residue connection info from src_rsd.
If suppress_warnings is true, we don't warn if residue connections on other residues are invalidated by a change of residue connection numbering in this residue. (Useful if we're calling this function from a context in which we know that we're going to update residue connections after the function call.) Note that warnings are never suppressed if high verbosity is set (TR.Debug.visible() == true).
References atom_index(), atom_name(), core::chemical::ResidueConnection::atomno(), connect_map(), connect_map_, connections_to_residues_, core::chemical::ResConnID::connid(), has(), core::chemical::ResidueType::n_possible_residue_connections(), n_possible_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), pseudobonds_, core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_connection_partner(), core::chemical::ResidueType::residue_connections_for_atom(), seqpos(), core::conformation::TR(), and type().
Referenced by Residue().
◆ copy_residue_connections_from()
| void core::conformation::Residue::copy_residue_connections_from | ( | Residue const & | src | ) |
◆ create_residue()
|
inline |
◆ create_rotamer()
|
inline |
Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out.
References clone().
Referenced by core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), and core::pack::hbonds::hbond_graph_from_partial_rotsets().
◆ cut_bond_neighbor()
|
inline |
atom indices for bonded neighbors to which atom-tree connections are disallowed.
References core::chemical::ResidueType::cut_bond_neighbor(), and rsd_type_.
Referenced by core::conformation::setup_links_simple().
◆ data()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time.
References data_cache_.
Referenced by core::scoring::lkball::LK_BallEnergy::atomistic_pair_energy(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::LK_DomeEnergy::residue_pair_energy(), core::scoring::lkball::retrieve_lkb_resdata(), core::scoring::lkball::retrieve_lkd_resdata(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().
◆ data_ptr()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh.
Return a COP to the data cache
- Note
- Might be a null pointer if the cache has not been initialized
References data_cache_.
Referenced by core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::conformation::Conformation::residue_data(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().
◆ determine_nonstandard_polymer_status()
|
private |
References connect_map_, is_lower_terminus(), is_polymer(), is_upper_terminus(), nonstandard_polymer_, seqpos(), and type().
Referenced by residue_connection_partner(), and update_sequence_numbering().
◆ fill_missing_atoms()
| bool core::conformation::Residue::fill_missing_atoms | ( | utility::vector1< bool > & | missing, |
| Conformation const & | conformation, | ||
| bool | fail = true |
||
| ) |
Builds coordinates for atoms missing from this residue assuming ideal internal coordinates.
If fail is false, will return true if we can fill all the missing atoms, and false if we can't.
missing is passed by non-const ref: it will be updated for the atoms which are filled. (If fail is false, it will end up all false, or you'll get a utility_exit()
this uses ideal internal coords to build any missing atom from its three stub atoms. If any of the stub atoms are missing, build them first. Unable to build a missing atom whose stub atoms are from non-existing polymer connection and its input bogus value will not be changed.
References atom_name(), bonded_neighbor(), core::chemical::AtomICoor::build(), icoor(), core::conformation::improper_build(), core::chemical::INTERNAL, core::conformation::missing_stubs_build(), name(), natoms(), core::chemical::pretty_print_atomicoor(), seqpos(), seqpos_, set_xyz(), core::chemical::ResidueType::show_all_atom_names(), core::chemical::AtomICoor::stub_atom(), core::conformation::TR(), and type().
Referenced by core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), place(), protocols::denovo_design::rebuild_missing_atoms(), and protocols::drug_design::replace_residue_type_with_mask().
◆ first_adjacent_heavy_atom()
Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.
- Returns
- The atom index of the 1st heavy atom next to the given atom (by index) or 0 if no heavy atom is found
This method does not count virtual atoms as heavy atoms.
- Remarks
- This method is crucial for determining atoms defining non-standard torsion angles, such as those found across branch connections or in glycosidic linkages.
References atom_index(), get_adjacent_heavy_atoms(), and core::conformation::TR().
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), and core::conformation::Conformation::branch_connection_torsion_angle_atoms().
◆ first_sidechain_atom()
|
inline |
Returns the index number of the first sidechain heavyatom.
example(s): residue.first_sidechain_atom() See also: Residue Residue.atom Residue.atoms Residue.last_backbone_atom Pose
References core::chemical::ResidueType::first_sidechain_atom(), and rsd_type_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::membrane::AqueousPoreFinder::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::energy_methods::assign_rna_atom_type(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pose::rna::bases_form_a_hydrogen_bond(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::select::util::calc_sc_neighbors(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::relax::derive_sc_sc_restraints(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::pose::rna::figure_out_number_base_contacts(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::cryst::fix_bfactorsMissing(), core::scoring::dna::get_base_pair_stub_slow(), core::energy_methods::HackAroEnergy::get_centroid(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::energy_methods::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::energy_methods::is_sugar_2(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::pose::rna::residue_is_bulge(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::self_scsc(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), protocols::design_opt::Supercharge::set_surface(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), sidechainAtoms_begin(), protocols::hybridization::DDomainParse::split(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::util::switch_to_centroid_rot_set(), and protocols::dna::z_axis_dist().
◆ first_sidechain_hydrogen()
|
inline |
Returns the index number of the first sidechain hydrogen.
example(s): residue.first_sidechain_hydrogen() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose
References core::chemical::ResidueType::first_sidechain_hydrogen(), and rsd_type_.
Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), core::pack::scmin::CartSCMinMinimizerMap::setup(), and core::optimization::CartesianMinimizerMap::setup().
◆ get_adjacent_heavy_atoms()
| utility::vector1< uint > core::conformation::Residue::get_adjacent_heavy_atoms | ( | uint const | atom_index | ) | const |
Get a list of heavy atoms connected to a given atom.
- Returns
- The atom indices of all heavy atoms bonded to the given atom (by index)
This method does not count virtual atoms as heavy atoms.
References atom_index(), atom_is_hydrogen(), bonded_neighbor(), and is_virtual().
Referenced by first_adjacent_heavy_atom(), core::conformation::position_of_atom_on_ring(), and show().
◆ get_atoms_exocyclic_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_atoms_exocyclic_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of exocyclic atoms connected to a given ring atom.
- Returns
- The atom indices of all atoms bonded to the given atom (by index) that are not a part of the ring.
This method does not count virtual atoms as atoms.
References atom_index(), bonded_neighbor(), is_virtual(), and type().
Referenced by get_hydrogens_bonded_to_ring_atom(), and get_substituents_to_ring_atom().
◆ get_hydrogens_bonded_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_hydrogens_bonded_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of hydrogen atoms connected to a given ring atom.
- Returns
- The atom indices of hydrogens bonded to the given ring atom (by index).
This method does not count virtual atoms as atoms.
References atom_index(), atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().
◆ get_metal_binding_atoms()
|
inline |
Gets the AtomIndices of the atoms in this residue that can bind to metals.
- Note
- : AtomIndices == vector1< Size >
References core::chemical::ResidueType::get_metal_binding_atoms(), and rsd_type_.
Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), and core::util::find_metalbinding_atoms_helper().
◆ get_pseudobonds_to_residue()
| PseudoBondCollectionCOP core::conformation::Residue::get_pseudobonds_to_residue | ( | Size | resid | ) | const |
◆ get_self_ptr() [1/2]
|
inline |
◆ get_self_ptr() [2/2]
|
inline |
self pointers
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params(), core::energy_methods::AACompositionEnergy::finalize_total_energy(), core::energy_methods::AARepeatEnergy::finalize_total_energy(), core::energy_methods::MHCEpitopeEnergy::finalize_total_energy(), core::energy_methods::NetChargeEnergy::finalize_total_energy(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::carbohydrates::get_glycosidic_bond_residues(), protocols::ligand_docking::get_ligand_grid_scores(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::pack::guidance_scoreterms::sap::rotamer_sets_from_pose(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), core::energy_methods::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::ligand_docking::Transform::setup_conformers(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_lightning(), and protocols::motifs::IRCollection::try_for_more().
◆ get_self_weak_ptr() [1/2]
|
inline |
◆ get_self_weak_ptr() [2/2]
|
inline |
◆ get_substituents_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_substituents_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of substituent atoms connected to a given ring atom.
- Returns
- The atom indices of all heavy atoms bonded to the given atom (by index) that are not a part of the ring.
This method does not count virtual atoms as atoms.
References atom_index(), atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().
◆ Haro_index()
|
inline |
Returns the AtomIndices of this residue's aromatic hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Haro_index() See also: Residue Residue.atoms Residue.Hpol_index Pose
References core::chemical::ResidueType::Haro_index(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().
◆ has()
|
inline |
Returns true if this residue has an atom named <atm>
References core::chemical::ResidueType::has(), and rsd_type_.
Referenced by core::pose::motif::a(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), core::pose::Pose::append_residue_by_atoms(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::nmr::pre::PREMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::constel::PresenceCommon::are_atoms_pres(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::simple_moves::Ca_coord(), protocols::mpi_refinement::CA_Sscore(), core::energy_methods::GoapEnergy::calculate_dipoles(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), core::select::util::cbeta_vector(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::sic_dock::count_CBs(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pose::declare_cutpoint_chemical_bond(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), protocols::constraint_generator::existing_atoms(), protocols::inverse_folding::extract_coordinates(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::abinitio::abscript::find_disulfide_partner(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::helical_bundle::FitSimpleHelixMultiFunc::FitSimpleHelixMultiFunc(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::sic_dock::get_CB_Vecs_from_pose(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::scoring::loop_graph::get_loop_atom(), core::scoring::lDDT_Calculator::get_matching_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), core::pose::carbohydrates::glycosylate_pose(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::pose::Pose::insert_residue_by_atoms(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_beta_aminoacid(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::constel::HBondCommon::is_rmoi_hbonded(), core::pose::make_atom_map(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::denovo_design::rebuild_missing_atoms(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::SiteGrid::refresh(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::drug_design::replace_residue_type_with_mask(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), protocols::sic_dock::XfoxmScore::score(), core::select::util::select_coord_for_residue(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::ligand_docking::set_repulsive_bb_cores(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::dna::show_dna_geometry_extra_details(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().
◆ has_incomplete_connection() [1/2]
| bool core::conformation::Residue::has_incomplete_connection | ( | ) | const |
References connect_map_, and connection_incomplete().
Referenced by core::pose::append_pose_with_glycan_residues(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::conformation::Conformation::detect_bonds(), protocols::ligand_docking::find_unconnected_residues(), protocols::ligand_docking::has_incomplete_connections(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
◆ has_incomplete_connection() [2/2]
| bool core::conformation::Residue::has_incomplete_connection | ( | core::Size const | atomno | ) | const |
Returns true is <atomno> has complete connectivity?
determine whether an atom is completely connected to all possible bonded partners
References connection_incomplete(), n_possible_residue_connections(), and residue_connect_atom_index().
◆ has_lower_connect()
|
inline |
Returns true if residue has a valid lower connection.
example(s): residue.has_lower_connect()
References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.
Referenced by core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residues(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives(), core::scoring::constraints::auto_detect_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), connected_residue_at_lower(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pose::declare_cutpoint_chemical_bond(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), core::pack::dunbrack::MainchainTorsionReporter::insert_atoms_defining_dof(), core::pack::dunbrack::PeptideTorsionReporter::insert_atoms_defining_dof(), protocols::cyclic_peptide::CycpepSymmetryFilter::is_cyclic_peptide(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), resolve_partial_atom_id(), core::pose::set_reasonable_fold_tree(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().
◆ has_property()
|
inline |
Return true if the residue has <property>.
References core::chemical::ResidueTypeBase::has_property(), and rsd_type_.
Referenced by protocols::ligand_docking::MoveMapBuilder::build(), protocols::membrane::AddMembraneMover::check_pdb_for_mem(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::scoring::P_AA::P_AA_pp_energy(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain(), protocols::kinematic_closure::perturbers::Rama2bPerturber::perturb_subset(), and protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset().
◆ has_sc_orbitals()
|
inline |
Returns true if the residue has side chain orbitals.
References core::chemical::ResidueType::has_sc_orbitals(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().
◆ has_shadow_atoms()
|
inline |
Return true if and only if this residue's type has shadow atoms.
References core::chemical::ResidueType::has_shadow_atoms(), and rsd_type_.
Referenced by core::energy_methods::RingClosureEnergy::eval_residue_derivatives(), and core::energy_methods::RingClosureEnergy::residue_energy().
◆ has_upper_connect()
|
inline |
Returns true if residue has a valid upper connection.
example(s): residue.has_upper_connect()
References core::chemical::ResidueTypeBase::is_polymer(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().
Referenced by core::conformation::Conformation::append_residues(), protocols::cyclic_peptide::CrankshaftFlipMover::apply(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives(), core::scoring::constraints::auto_detect_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), connected_residue_at_upper(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pose::declare_cutpoint_chemical_bond(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), core::pack::dunbrack::MainchainTorsionReporter::insert_atoms_defining_dof(), core::pack::dunbrack::PeptideTorsionReporter::insert_atoms_defining_dof(), protocols::cyclic_peptide::CycpepSymmetryFilter::is_cyclic_peptide(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), resolve_partial_atom_id(), core::pose::set_reasonable_fold_tree(), core::pose::show_adjacent_nt_connections(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().
◆ has_variant_type()
|
inline |
Generic variant access.
References core::chemical::ResidueTypeBase::has_variant_type(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), core::pose::ncbb::add_generic_hbs_constraint(), core::pose::ncbb::add_oop_constraint(), core::pose::ncbb::add_triazole_constraint(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::antibody::H3PerturbCCD::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::fold_from_loops::selectors::CutpointResidueSelector::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pack::dunbrack::DunbrackEnergy::atoms_with_dof_derivatives(), core::energy_methods::P_AA_pp_Energy::atoms_with_dof_derivatives(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::YHHPlanarityEnergy::atoms_with_dof_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::energy_methods::RG_Energy_Fast::calculate_rg_score(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), protocols::stepwise::screener::SugarInstantiator::check_moving_sugar(), core::scoring::rna::check_rna_loop(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), protocols::sasa_scores::compute_avge_scores(), protocols::denovo_design::components::compute_cutpoints(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), protocols::sasa_scores::compute_sasapack_scores(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion(), protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::abinitio::copy_side_chains(), core::pose::correctly_add_2prime_connection_variants(), protocols::relax::cyclize_pose(), core::pose::declare_cutpoint_chemical_bond(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::energy_methods::StackElecEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::conformation::disulfide_bonds(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::anchored_design::dump_cutpoint_info(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::energy_methods::P_AA_pp_Energy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::MgEnergy::eval_intrares_energy(), core::energy_methods::RNA_TorsionEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::energy_methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::energy_methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::energy_methods::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::energy_methods::TNA_SuiteEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer(), core::io::silent::BinarySilentStruct::fill_pose(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::splice::RBInMover::find_disulfide_postions(), protocols::splice::RBOutMover::find_disulfide_postions(), protocols::splice::SpliceInAntibody::find_disulfide_postions(), protocols::splice::SpliceOutAntibody::find_disulfide_postions(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::splice::find_disulfs_in_range(), protocols::rosetta_scripts::find_nearest_disulfide(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_uninstantiated_phosphates(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::splice::Splice::fold_tree(), core::conformation::form_disulfide(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree(), core::pose::rna::get_stub_stub(), core::scoring::SecondaryStructurePotential::identify_ss(), core::pose::ncbb::initialize_hbs(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base(), core::pose::ncbb::initialize_ncbbs(), core::pose::ncbb::initialize_oops(), protocols::recces::sampler::initialize_thermal_sampler(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close(), core::scoring::methods::is_lower_cutpoint(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), core::energy_methods::RNA_BulgeEnergy::is_RNA_bulge(), protocols::stepwise::modeler::rna::sugar::is_sugar_virtual(), core::scoring::methods::is_upper_cutpoint(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::energy_methods::FullatomDisulfideEnergy::old_eval_atom_derivative(), orient_onto_residue_peptoid(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::perform_reaction(), protocols::fold_from_loops::NubInitioMover::post_process(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), protocols::loops::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::FreeDOF_Energy::residue_energy(), core::energy_methods::CenRotEnvEnergy::residue_energy(), core::energy_methods::EnvEnergy::residue_energy(), core::energy_methods::OmegaTetherEnergy::residue_energy(), core::energy_methods::P_AA_pp_Energy::residue_energy(), core::energy_methods::RamachandranEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::ReferenceEnergyNoncanonical::residue_energy(), core::energy_methods::SmoothEnvEnergy::residue_energy(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::energy_methods::YHHPlanarityEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), protocols::scoring::methods::SpecialRotamerEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::energy_methods::RNA_DataBackboneEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::energy_methods::RNA_JR_SuiteEnergy::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::residue_pair_energy(), core::energy_methods::RNA_SuiteEnergy::residue_pair_energy(), core::energy_methods::RNA_TorsionEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResPairDistEnergy::residue_pair_energy(), core::energy_methods::StackElecEnergy::residue_pair_energy(), core::energy_methods::TNA_SuiteEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), core::energy_methods::DisulfideMatchingEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::rbsegment_relax::setup_disconnected(), core::energy_methods::RG_Energy_Fast::setup_for_derivatives(), core::energy_methods::RG_LocalEnergy::setup_for_derivatives(), core::energy_methods::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::conformation::setup_links(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_three_prime_phosphate(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), protocols::splice::Splice::tail_fold_tree(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::conformation::Conformation::update_polymeric_connection(), core::conformation::Conformation::update_residue_torsions(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition(), and core::pose::rna::virtualize_free_rna_moieties().
◆ heavyatom_has_polar_hydrogens()
|
inline |
Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom)
References core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), and rsd_type_.
Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::magnesium::get_closest_non_hoh_contact(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore().
◆ heavyatom_is_an_acceptor()
|
inline |
Is a particular atom a heavy atom acceptor?
References core::chemical::ResidueType::heavyatom_is_an_acceptor(), and rsd_type_.
Referenced by core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::magnesium::get_closest_non_hoh_contact(), core::scoring::magnesium::get_cos_theta(), protocols::magnesium::SampleGrid::get_mg_positions(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().
◆ heavyAtoms_end()
|
inline |
References atoms_, and nheavyatoms().
Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::environment::com_calc(), protocols::simple_filters::AtomicContactFilter::compute(), and core::scoring::interface_::DDPscore::residue_pair_energy().
◆ Hpol_index()
|
inline |
Returns the AtomIndices of this residue's polar hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Hpol_index() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Residue.Hpos_polar Pose
References core::chemical::ResidueType::Hpol_index(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().
◆ Hpos_apolar()
|
inline |
Returns the AtomIndices of this residue's apolar hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Hpos_apolar() See also: Residue Residue.atoms Residue.Hpol_index() Residue.Hpos_polar Pose
References core::chemical::ResidueType::Hpos_apolar(), and rsd_type_.
Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().
◆ Hpos_polar()
|
inline |
Returns the AtomIndices of this residue's polar hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Hpos_polar() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Pose
References core::chemical::ResidueType::Hpos_polar(), and rsd_type_.
Referenced by protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::energy_methods::OccludedHbondSolEnergy::atom_is_donor_h(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_donor_h(), core::pose::rna::atom_is_polar(), core::energy_methods::OccludedHbondSolEnergy::atom_is_valid_base(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pose::rna::bases_form_a_hydrogen_bond(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::compute_exact_geosol(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::pose::rna::heavy_atom_is_polar(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), protocols::features::HBondFeatures::report_features(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), and protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition().
◆ Hpos_polar_sc()
|
inline |
Returns the AtomIndices of this residue's polar sidechain hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Hpos_polar_sc() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_polar Pose
References core::chemical::ResidueType::Hpos_polar_sc(), and rsd_type_.
Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), and protocols::pose_metric_calculators::SaltBridgeCalculator::recompute().
◆ icoor()
|
inline |
Returns the internal coordinates of this residue's atom with index number <atm>
References core::chemical::ResidueType::icoor(), and rsd_type_.
Referenced by build_atom_ideal(), core::select::util::calc_sc_neighbors(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::conformation::idealize_hydrogens(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::conformation::missing_stubs_build(), orient_onto_residue_peptoid(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::md::Rattle::setup_constraint(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ init_residue_from_other()
|
private |
Function called by both copy constructors, to avoid code duplication.
As private member variables are added, add them to this to copy them.
References actcoord_, atoms_, chain_, chi_, connect_map_, connections_to_residues_, data_cache_, mainchain_torsions_, mirrored_relative_to_type_, misplaced_, nonstandard_polymer_, nus_, orbitals_, pseudobonds_, and seqpos_.
Referenced by Residue().
◆ inter_residue_connection_partner()
| id::AtomID core::conformation::Residue::inter_residue_connection_partner | ( | int | connid, |
| Conformation const & | conformation | ||
| ) | const |
This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to.
References core::id::GLOBAL_BOGUS_ATOM_ID, name(), core::chemical::ResidueType::residue_connect_atom_index(), residue_connection_conn_id(), residue_connection_partner(), core::conformation::Conformation::residue_type(), seqpos(), core::conformation::Conformation::size(), and core::conformation::TR().
Referenced by core::chemical::ICoorAtomID::atom_id().
◆ is_apolar()
|
inline |
@briefReturns true if the residue is apolar
- Note
- : apolar is classified as NOT polar, aromatic, or charged
References core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_polar(), and rsd_type_.
Referenced by core::pack::task::operation::ResidueTypeFilter::operator()().
◆ is_aramid()
|
inline |
Returns if this residue is an aramid.
References core::chemical::ResidueType::is_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_aromatic()
|
inline |
Returns true if the residue is aromatic.
References core::chemical::ResidueType::is_aromatic(), and rsd_type_.
Referenced by protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::energy_methods::PairEnergy::defines_score_for_residue_pair(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative(), core::energy_methods::HackAroEnergy::eval_atom_derivative(), core::energy_methods::HackAroEnergy::eval_atom_derivative_aro_aro(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::FA_ElecEnergyAroAll::evaluate_rotamer_background_energies(), core::energy_methods::FA_ElecEnergyAroAro::evaluate_rotamer_background_energies(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energies(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::constel::has_aromatic(), core::pack::task::operation::ResidueTypeFilter::operator()(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy(), core::energy_methods::HackAroEnergy::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::HackAroEnergy::residue_pair_energy_aro_aro(), and core::pose::setup_dof_mask_from_move_map().
◆ is_bonded() [1/2]
|
inline |
Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)
See Also: For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)
first check if it is polymer upper or lower connected to the other residue. then check if it is boned to the other residue through non-polymer connection.
References connections_to_residues_, and seqpos().
Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::pose_sewing::filters::HasDisulfideFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::conformation::Conformation::atoms_are_bonded(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_sidechain_energy(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), protocols::simple_filters::DisulfideEntropyFilter::compute(), protocols::simple_filters::DisulfideEntropyFilter::compute_residual(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::pose::create_chemical_edge(), protocols::cartesian::MolecularDynamics::createBondList(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::toolbox::CovalentResidueNetwork::generate_edges(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::energy_methods::FA_GrpElecEnergy::get_count_pair_function(), core::energy_methods::LK_PolarNonPolarEnergy::get_count_pair_function(), core::energy_methods::StackElecEnergy::get_count_pair_function(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::generalized_kinematic_closure::GeneralizedKIC::has_geometric_connection(), core::scoring::trie::initialize_cpdata_for_atom(), core::io::pose_from_sfr::is_connected(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PeptideBondEnergy::residue_pair_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::energy_methods::RNA_CoarseDistEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pose::set_reasonable_fold_tree(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().
◆ is_bonded() [2/2]
|
inline |
Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic.
See Also: For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)
References connections_to_residues_.
◆ is_branch_point()
|
inline |
Return true if the residue is a branch point variant.
References core::chemical::ResidueType::is_branch_point(), and rsd_type_.
Referenced by core::pose::append_pose_with_glycan_residues(), protocols::analysis::GlycanInfoMover::apply_const(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), protocols::glycan_docking::setup_GlycanDock_movemap(), protocols::simple_moves::ShearMover::setup_list_for_saccharide_residue(), and protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs().
◆ is_carbohydrate()
|
inline |
Returns true if this residue is a carbohydrate.
References core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.
Referenced by protocols::loops::add_single_cutpoint_variant(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::carbohydrates::GlycanTreeModeler::apply(), core::select::residue_selector::GlycanResidueSelector::apply(), core::select::residue_selector::RandomGlycanFoliageSelector::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::electron_density::calculate_rama(), core::pose::carbohydrates::create_glycan_movemap_from_residue_selector(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::energy_methods::LinearChainbreakEnergy::do_score_dev(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), core::io::carbohydrates::dump_gws(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearBranchEnergy::finalize_total_energy(), core::energy_methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::loops::fold_tree_from_loops(), core::pose::get_bb_torsion(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(), core::conformation::carbohydrates::get_distance_to_start(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_glycan_start_points(), protocols::glycan_docking::get_glycolig_subset_with_torsions(), core::conformation::carbohydrates::get_glycosidic_TorsionIDs(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), core::pose::carbohydrates::get_resnums_in_leaf(), core::pose::carbohydrates::get_resnums_in_leaf_on_the_fly(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::pose::carbohydrates::glycosylate_pose(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), core::conformation::idealize_position(), protocols::carbohydrates::GlycanSampler::init_objects(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::is_protein_CA_or_equiv(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), core::energy_methods::SugarBackboneEnergy::residue_energy(), protocols::denovo_design::components::residue_is_compatible(), core::io::carbohydrates::residue_range_gws_string(), core::pose::set_bb_torsion(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::scoring::constraints::SiteConstraint::setup_csts(), core::pose::setup_dof_mask_from_move_map(), protocols::glycan_docking::setup_GlycanDock_movemap(), protocols::simple_moves::ShearMover::setup_list(), protocols::simple_moves::ShearMover::setup_list_for_saccharide_residue(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::carbohydrates::GlycanSampler::setup_movers(), core::pose::carbohydrates::tautomerize_anomer(), and core::conformation::carbohydrates::GlycanNode::update_connectivity_data().
◆ is_charged()
|
inline |
Returns true if the residue is charged.
References core::chemical::ResidueType::is_charged(), and rsd_type_.
Referenced by core::pack::task::operation::ResidueTypeFilter::operator()().
◆ is_coarse()
|
inline |
residue is coarse (used for RNA right now)
References core::chemical::ResidueType::is_coarse(), and rsd_type_.
Referenced by core::import_pose::RNA_JumpMover::check_forward_backward(), core::conformation::Conformation::detect_pseudobonds(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::energy_methods::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::pose::toolbox::AtomLevelDomainMap::set_phosphate_domain(), and core::pose::toolbox::AtomLevelDomainMap::set_sugar_domain().
◆ is_d_rna()
|
inline |
Returns true if this residue is a D-RNA residue.
References core::chemical::ResidueTypeBase::is_d_rna(), and rsd_type_.
Referenced by core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), and core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().
◆ is_DNA()
|
inline |
Returns true if this residue is a DNA residue.
References core::chemical::ResidueTypeBase::is_DNA(), and rsd_type_.
Referenced by core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_torsion_tethers(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::motifs::Motif::apply_check(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::dna::DNAParameters::calculate(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_interres(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_intrares(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), core::scoring::hbonds::create_rotamer_descriptor(), core::energy_methods::DNA_DihedralEnergy::defines_intrares_energy_for_residue(), core::energy_methods::DNA_DihedralEnergy::defines_residue_pair_energy(), core::energy_methods::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::dna::DNABase::DNABase(), protocols::dna::DNABasepair::DNABasepair(), protocols::dna::DNABasestep::DNABasestep(), core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::energy_methods::DNAChiEnergy::eval_dof_derivative(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::energy_methods::FACTSEnergy::eval_intrares_energy(), core::energy_methods::GenBornEnergy::eval_intrares_energy(), core::energy_methods::MultipoleElecEnergy::eval_intrares_energy(), core::energy_methods::VdWTinkerEnergy::eval_intrares_energy(), core::energy_methods::MultipoleElecEnergy::eval_intrares_energy_ext(), core::energy_methods::SASAEnergy::eval_intrares_energy_ext(), core::energy_methods::VdWTinkerEnergy::eval_intrares_energy_ext(), core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy(), core::energy_methods::DirectReadoutEnergy::finalize_total_energy(), protocols::dna::find_basepairs(), core::scoring::dna::get_groove_widths(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::dna::get_z_axis(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::motifs::make_base_pair_mutation(), protocols::relax::make_dna_rigid(), protocols::motifs::Motif::Motif(), core::energy_methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::dna::PDBOutput::output_hbond_info(), protocols::fold_from_loops::NubInitioMover::post_process(), core::energy_methods::DNAChiEnergy::residue_energy(), core::energy_methods::DNA_BaseEnergy::residue_pair_energy(), core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy(), core::energy_methods::FACTSEnergy::residue_pair_energy(), core::energy_methods::GenBornEnergy::residue_pair_energy(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy(), core::energy_methods::SASAEnergy::residue_pair_energy(), core::energy_methods::VdWTinkerEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy_ext(), core::energy_methods::SASAEnergy::residue_pair_energy_ext(), core::energy_methods::VdWTinkerEnergy::residue_pair_energy_ext(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::scoring::dna::seqpos_is_base_step_anchor(), core::conformation::setup_corresponding_atoms(), protocols::dna::show_dna_geometry(), protocols::dna::show_dna_geometry_extra_details(), and core::scoring::dna::DNA_DihedralPotential::skip_torsion().
◆ is_l_rna()
|
inline |
Returns true if this residue is a L-RNA residue.
References core::chemical::ResidueTypeBase::is_l_rna(), and rsd_type_.
Referenced by core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().
◆ is_ligand()
|
inline |
Returns true if this residue is a ligand.
References core::chemical::ResidueType::is_ligand(), and rsd_type_.
Referenced by core::conformation::Conformation::append_residue(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::scoring::Interface::calculate(), protocols::simple_ddg::ddG::calculate(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::energy_methods::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::splice::Splice::fold_tree(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::hbnet::HBNet::get_native_networks(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::sic_dock::make_Cx(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::motifs::Motif::Motif(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::enzdes::enzutil::read_pose_from_file(), protocols::hbnet::HBNet::rec_trav_native(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::features::ResidueConformationFeatures::report_features(), core::io::carbohydrates::residue_gws_string(), protocols::denovo_design::components::residue_is_compatible(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), protocols::ligand_docking::restrict_to_protein_residues(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::denovo_design::components::SegmentCounts::SegmentCounts(), protocols::scoring::Interface::set_pack(), protocols::hbnet::HBNet::traverse_native(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().
◆ is_lower_terminus()
|
inline |
Returns true if the residue has a lower terminus property.
References core::chemical::ResidueType::is_lower_terminus(), and rsd_type_.
Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::loops::add_single_cutpoint_variant(), protocols::denovo_design::components::add_to_pose(), protocols::frags::add_vall_cheating_fragments(), protocols::frags::add_vall_fragments(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue(), core::pose::append_subpose_to_pose(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::chemical::ICoorAtomID::atom_id(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), protocols::idealize::basic_idealize(), core::scoring::GenBornPotential::build_placeholders(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), protocols::sasa_scores::compute_avge_scores(), core::energy_methods::compute_exact_geosol(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), protocols::sasa_scores::compute_sasapack_scores(), connect_atom(), protocols::topology_broker::copy_internal_coords(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms(), protocols::forge::methods::count_cutpoints(), core::pose::create_subpose(), protocols::relax::cyclize_pose(), determine_nonstandard_polymer_status(), protocols::idealize::dihedral_distance(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::pose::symmetry::extract_asymmetric_unit(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::loops::fold_tree_from_loops(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_atomno(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), core::scoring::dna::get_DNA_backbone_bin(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::pack::dunbrack::PeptoidGeneralDOFReporter::get_dof(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), core::scoring::dna::get_groove_widths(), core::scoring::hbonds::get_hb_don_chem_type(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), protocols::forge::methods::grow_left_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::conformation::idealize_position(), protocols::forge::build::SegmentInsert::init(), protocols::forge::build::SegmentSwap::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::pack::dunbrack::PeptoidGeneralDOFReporter::insert_atoms_defining_dof(), core::pack::dunbrack::MainchainTorsionReporter::insert_atoms_defining_dof(), core::pack::dunbrack::PeptideTorsionReporter::insert_atoms_defining_dof(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::Conformation::insert_polymer_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::conformation::is_ideal_position(), core::pose::is_lower_terminus(), core::scoring::Ramachandran::is_normally_connected(), protocols::denovo_design::loop_stop_without_overlap(), protocols::sic_dock::make_Cx(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::denovo_design::components::pose_matches_description(), protocols::normalmode::NormalMode::prepare_coord(), protocols::denovo_design::components::prepend_new_residues(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::rbsegment_relax::setup_disconnected(), protocols::simple_moves::ShearMover::setup_list(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::dna::show_dna_geometry_extra_details(), core::scoring::dna::DNA_DihedralPotential::skip_torsion(), protocols::fldsgn::CircularPermutation::split_chains(), and core::conformation::Conformation::update_polymeric_connection().
◆ is_meta_aramid()
|
inline |
Returns if this residue is a meta aramid.
References core::chemical::ResidueType::is_meta_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_metal()
|
inline |
Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES.
References core::chemical::ResidueType::is_metal(), and rsd_type_.
Referenced by core::util::add_constraints_to_metal(), core::util::add_covalent_linkage_helper(), core::util::add_covalent_linkages_to_metal(), core::util::auto_setup_all_metal_bonds(), core::util::auto_setup_all_metal_constraints(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::simple_moves::SetupMetalsMover::find_metal_resnums(), core::util::find_metalbinding_atoms(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), and core::scoring::GenericBondedPotential::setup_for_scoring().
◆ is_metalbinding()
|
inline |
Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES.
References core::chemical::ResidueType::is_metalbinding(), and rsd_type_.
Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), and core::util::find_metalbinding_atoms_helper().
◆ is_NA()
|
inline |
Returns true if this residue is a nucleic acid.
References core::chemical::ResidueType::is_NA(), and rsd_type_.
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::scoring::Interface::calculate(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::scoring::loop_graph::get_loop_atom(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), core::scoring::rna::RNA_CentroidInfo::initialize_base_centroids_and_stubs(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_base_blob(), and protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_satellite_blob().
◆ is_ortho_aramid()
|
inline |
Returns if this residue is an ortho aramid.
References core::chemical::ResidueType::is_ortho_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_para_aramid()
|
inline |
Returns if this residue is a para aramid.
References core::chemical::ResidueType::is_para_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_peptoid()
|
inline |
Returns if this residue is a peptoid.
References core::chemical::ResidueTypeBase::is_peptoid(), and rsd_type_.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::OmegaTether::eval_omega_score_residue(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::scoring::loop_graph::get_loop_atom(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), place(), and core::energy_methods::OmegaTetherEnergy::residue_energy().
◆ is_polar()
|
inline |
Returns true if the residue is polar.
References core::chemical::ResidueType::is_polar(), and rsd_type_.
Referenced by protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::energy_methods::PairEnergy::defines_score_for_residue_pair(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energies(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::pose::make_atom_map(), core::pack::task::operation::ResidueTypeFilter::operator()(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), and core::energy_methods::PairEnergy::residue_pair_energy().
◆ is_polymer()
|
inline |
Returns true if this residue is a polymer.
References core::chemical::ResidueTypeBase::is_polymer(), and rsd_type_.
Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), core::pose::addVirtualResAsRoot(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), core::conformation::Conformation::append_residue_by_bond(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::hybridization::MRMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::idealize::basic_idealize(), core::select::util::calc_sc_neighbors(), connect_atom(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), determine_nonstandard_polymer_status(), protocols::rna::movers::determine_residues_to_rebuild(), protocols::idealize::dihedral_distance(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::energy_methods::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::loophash::FastGapMover::find_next_gap(), protocols::electron_density::findLoopFromDensity(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::get_anchor_atomno(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::conformation::get_root_atomno(), core::conformation::idealize_position(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::pose::toolbox::AtomID_Mapper::initialize(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_ideal_position(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::pose::is_lower_terminus(), core::scoring::is_polymer_heavyatom(), core::pose::is_upper_terminus(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), protocols::ligand_docking::LigandDockProtocol::random_conformer(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::reorder_with_first_non_mobile_as_root(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis(), core::pose::set_reasonable_fold_tree(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::protein_interface_design::star_fold_tree(), protocols::hybridization::MRMover::trim_target_pose(), and core::conformation::Conformation::update_polymeric_connection().
◆ is_polymer_bonded() [1/2]
|
inline |
Am I polymer bonded to other?
References seqpos().
Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), core::scoring::lkball::LK_BallEnergy::atomistic_pair_energy(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::pose::create_subpose(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), protocols::forge::build::ConnectRight::modify_impl(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::LK_DomeEnergy::residue_pair_energy(), core::scoring::lkball::LK_DomeEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().
◆ is_polymer_bonded() [2/2]
|
inline |
Am I polymer-bonded to other? checks lower and upper connections.
References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), residue_connection_partner(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().
◆ is_post_methylene_meta_aramid()
|
inline |
Returns if this residue is a post methylene meta aramid.
References core::chemical::ResidueType::is_post_methylene_meta_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_post_methylene_ortho_aramid()
|
inline |
Returns if this residue is a post methylene ortho aramid.
References core::chemical::ResidueType::is_post_methylene_ortho_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_post_methylene_para_aramid()
|
inline |
Returns if this residue is a post methylene para aramid.
References core::chemical::ResidueType::is_post_methylene_para_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_meta_aramid()
|
inline |
Returns if this residue is a pre methylene meta aramid.
References core::chemical::ResidueType::is_pre_methylene_meta_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_ortho_aramid()
|
inline |
Returns if this residue is a pre methylene ortho aramid.
References core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_para_aramid()
|
inline |
Returns if this residue is a pre methylene para aramid.
References core::chemical::ResidueType::is_pre_methylene_para_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_post_methylene_meta_aramid()
|
inline |
Returns if this residue is a post methylene meta aramid.
References core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_post_methylene_ortho_aramid()
|
inline |
Returns if this residue is a post methylene ortho aramid.
References core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_pre_methylene_post_methylene_para_aramid()
|
inline |
Returns if this residue is a post methylene para aramid.
References core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), and rsd_type_.
Referenced by core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy().
◆ is_protein()
|
inline |
Returns true if this residue is an amino acid.
References core::chemical::ResidueTypeBase::is_protein(), and rsd_type_.
Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), protocols::hybridization::HybridizeProtocol::add_fragment_csts(), protocols::loop_grower::LoopGrower::add_fragment_csts(), protocols::hybridization::add_non_protein_cst(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::loops::add_single_cutpoint_variant(), core::pose::ncbb::add_triazole_constraint(), protocols::frags::add_vall_cheating_fragments(), protocols::frags::add_vall_fragments(), protocols::loops::addScoresForLoopParts(), core::pose::addVirtualResAsRoot(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::hybridization::TMalign::alignment2AtomMap(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::pose::append_subpose_to_pose(), protocols::simple_moves::WriteSSEMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::electron_density::DensityZscores::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::frags::TorsionFragmentMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::minimization_packing::BoltzmannRotamerMover::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::RBSegmentRelaxImpl::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), core::select::residue_selector::ResidueInMembraneSelector::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::fold_from_loops::selectors::ProteinResidueSelector::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::hybridization::TMalign::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::loops::apply_sequence_mapping(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), protocols::idealize::basic_idealize(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::scoring::GenBornPotential::build_placeholders(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::epr_deer::EPRSpinLabel::calc_sl_for_res(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::simple_ddg::DdGScan::calculate(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::scoring::electron_density::calculate_density_nbr(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< Derived >::calculate_intrares(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::scoring::electron_density::calculate_rama(), protocols::geometry::center_of_mass(), core::pose::center_of_mass(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), core::scoring::dssp::Dssp::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::fldsgn::filters::SecondaryStructureFilter::compute(), protocols::sasa_scores::compute_avge_scores(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), protocols::pockets::PlaidFingerprint::compute_ligand_resnum(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::sasa_scores::compute_sasapack_scores(), protocols::denovo_design::construct_poly_ala_pose(), protocols::abinitio::AbrelaxApplication::copy_structure(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), protocols::hybridization::create_fragment_set(), protocols::hybridization::create_fragment_set_no_ssbias(), core::scoring::hbonds::create_rotamer_descriptor(), core::energy_methods::MPSpanInsertionEnergy::create_updated_span(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::energy_methods::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::energy_methods::PairEnergy::defines_score_for_residue_pair(), core::energy_methods::PointWaterEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), protocols::rna::denovo::delete_non_protein_from_pose(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MPSpanAngleEnergy::eval_atom_derivative(), core::energy_methods::MPSpanInsertionEnergy::eval_atom_derivative(), core::energy_methods::MPHelicalityEnergy::eval_atom_derivative(), core::energy_methods::MPResidueLipophilicityEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::energy_methods::RamachandranEnergy2B::eval_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::RamachandranEnergy2B::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energies(), core::energy_methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::loops::extend_sequence_mapping(), protocols::indexed_structure_store::extract_residue_entries(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::frags::fill_in_gaps(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::protein_interface_design::movers::finalize_stub_set(), core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy(), core::energy_methods::DirectReadoutEnergy::finalize_total_energy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::flxbb::find_ligands(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), protocols::ligand_docking::InterfaceBuilder::find_protein_residues(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::constraint_generator::first_protein_residue(), protocols::simple_moves::RepeatPropagationMover::fix_ligand_residues(), protocols::loops::fold_tree_from_loops(), protocols::comparative_modeling::gather_coords(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::pose::motif::get_backbone_reference_frame(), protocols::match::BfactorMPM::get_ca_bfactors(), protocols::constel::get_chain_terms(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::cryst::get_corresponding_CAs(), core::pose::motif::get_cterminal_peptide_bond_reference_frame(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::toolbox::match_enzdes_util::get_first_protein_residue(), protocols::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::toolbox::match_enzdes_util::get_last_protein_residue(), core::scoring::loop_graph::get_loop_atom(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), protocols::matdes::get_matching_subunits(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::md::CartesianMD::get_native_info(), core::scoring::motif::get_nbrs(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hbnet::get_num_protein_sc_sc_hbonds(), protocols::hybridization::get_num_residues_prot(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), protocols::simple_filters::AbinitioBaseFilter::get_protein_sstype(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), protocols::rna::denovo::get_rnp_docking_fold_tree(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::sic_dock::get_termini_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::hybridization::FragmentBiasAssigner::init(), protocols::simple_moves::RepeatPropagationMover::initial_constrained_residues(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup(), core::pose::toolbox::AtomID_Mapper::initialize(), core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), protocols::fldsgn::topology::SS_Info2::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), protocols::topology_broker::TopologyBroker::initialize_sequence(), protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(), protocols::scoring::methods::TargetClashEnergy::initiate_voxel(), protocols::frags::TorsionFragment::insert(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::pose::is_lower_terminus(), core::scoring::is_non_peptide_heavy_atom(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), core::pose::is_upper_terminus(), protocols::constel::NeighTeller::isneigh(), protocols::constraint_generator::last_protein_residue(), core::pack::dunbrack::load_unboundrot(), protocols::denovo_design::loop_start_without_overlap(), protocols::denovo_design::loop_stop_without_overlap(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::struct_fragment::StructFragmentMover::make_fragment_picker(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::protein_interface_design::MinimizeInterface(), protocols::motifs::Motif::Motif(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::ShearMover::move_with_rama(), core::energy_methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::abinitio::AllResiduesChanged::operator()(), protocols::hybridization::AllResiduesChanged::operator()(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::scoring::PairEPotential::pair_term_energy_exists(), protocols::hybridization::partial_align(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), protocols::fold_from_loops::NubInitioMover::post_process(), core::energy_methods::FA_GrpElecEnergy::precalc_context(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::energy_methods::PoissonBoltzmannEnergy::protein_position_equal_within(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), core::pose::radius_of_gyration(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::pose::read_psipred_ss2_file(), core::util::rebuild_fa_disulfides(), protocols::hbnet::HBNet::rec_trav_native(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::SiteGrid::refresh(), protocols::qsar::scoring_grid::AtrGrid::refresh(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::pose::PDBInfo::replace_res_remap_bfactors(), protocols::simple_ddg::AlaScan::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::features::HelixCapFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_filters::EnergyPerResidueFilter::report_sm(), protocols::fldsgn::filters::SecondaryStructureFilter::report_sm(), protocols::simple_ddg::AlaScan::report_symmetry(), core::conformation::symmetry::residue_center_of_mass(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::MPResidueLipophilicityEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::energy_methods::OmegaTetherEnergy::residue_energy(), core::energy_methods::RamachandranEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), protocols::membrane::scoring::ElectricfieldLipidlayer::residue_energy(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResPairDistEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::features::BetaTurnDetection::residue_range_is_protein(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), protocols::motifs::LigandMotifSearch::run(), protocols::denovo_design::same_pose(), protocols::environment::ClientMover::sandboxed_copy(), protocols::sic_dock::XfoxmScore::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_base_blob(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_satellite_blob(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::simple_filters::SaveResfileToDiskFilter::select_residues(), protocols::ligand_docking::MoveMapBuilder::set_all_bb(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::vip::VIP_Mover::set_excluded_positions(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::abinitio::AllResiduesChanged::set_initial_pose(), protocols::hybridization::AllResiduesChanged::set_initial_pose(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::hbnet::HBNet::setup(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::constraints::SiteConstraint::setup_csts(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::stepwise::modeler::packer::StepWisePacker::setup_pack_task(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::hbnet::HBNet::setup_packer_task_and_starting_residues(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc(), protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(), protocols::abinitio::AllResiduesChanged::show_unmoved(), protocols::hybridization::AllResiduesChanged::show_unmoved(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), protocols::hybridization::DDomainParse::split(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fldsgn::CircularPermutation::split_chains(), core::util::switch_to_residue_type_set(), protocols::protein_interface_design::SymMinimizeInterface(), protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(), core::scoring::BB_Pos::take_coordinates_from_pose(), protocols::hbnet::HBNet::traverse_native(), protocols::hybridization::MRMover::trim_target_pose(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), and core::conformation::Conformation::update_polymeric_connection().
◆ is_pseudo_bonded() [1/2]
|
inline |
Do I have any pseudobonds to other?
References seqpos().
Referenced by core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_sidechain_energy(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::energy_methods::FA_GrpElecEnergy::get_count_pair_function(), core::energy_methods::LK_PolarNonPolarEnergy::get_count_pair_function(), core::energy_methods::StackElecEnergy::get_count_pair_function(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::energy_methods::RNA_CoarseDistEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().
◆ is_pseudo_bonded() [2/2]
|
inline |
Do I have any pseudobonds to other?
References pseudobonds_.
◆ is_purine()
|
inline |
Returns true if this residue is a purine.
References core::chemical::ResidueType::is_purine(), and rsd_type_.
Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), and protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos().
◆ is_pyrimidine()
|
inline |
Returns true if this residue is a pyrimidine.
References core::chemical::ResidueType::is_pyrimidine(), and rsd_type_.
Referenced by protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos().
◆ is_repulsive()
|
inline |
Check if atom is repulsive.
- Note
- A misnomer; this should really be called "is_repulsive_atom()". ~Labonte
References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::is_repulsive(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), and core::energy_methods::StackElecEnergy::residue_pair_energy_one_way().
◆ is_RNA()
|
inline |
Returns true if this residue is a RNA residue.
References core::chemical::ResidueTypeBase::is_RNA(), and rsd_type_.
Referenced by core::energy_methods::FreeDOF_Energy::accumulate_stack_energy(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), core::pose::rna::RNA_IdealCoord::apply(), core::pose::rna::RNA_IdealCoord::apply_coords(), core::pose::rna::RNA_IdealCoord::apply_pucker(), core::pose::rna::RNA_SuiteName::assign(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::scoring::hbonds::calculate_intra_res_hbonds(), protocols::toolbox::sample_around::centroid_dist(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_moved(), core::scoring::rna::check_rna_loop(), protocols::stepwise::screener::TagDefinition::check_screen(), protocols::stepwise::modeler::rna::copy_all_o2prime_torsions(), core::pose::correctly_add_cutpoint_variants(), protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(), core::energy_methods::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::LK_PolarNonPolarEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::energy_methods::RNA_FA_ElecEnergy::evaluate_rotamer_background_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::io::rna::RDAT::fill_header_information(), core::energy_methods::FreeDOF_Energy::finalize_total_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy(), core::scoring::dna::get_base_pair_stub_slow(), core::energy_methods::RNA_FullAtomStackingEnergy::get_count_pair_function(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::pose::rna::get_op2_op1_sign(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::chemical::rna::get_rna_base_centroid(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), protocols::rna::denovo::get_rnp_docking_fold_tree(), core::scoring::dna::get_z_axis(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_green_packer(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::toolbox::rigid_body::initialize_stub(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), core::chemical::rna::is_base_phosphate_atom_pair(), core::scoring::is_protein_CA_or_equiv(), core::energy_methods::RNA_BulgeEnergy::is_RNA_bulge(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), place(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::RNA_DataBackboneEnergy::residue_pair_energy(), core::energy_methods::RNA_FA_ElecEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::energy_methods::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), core::scoring::dna::seqpos_is_base_step_anchor(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::conformation::setup_corresponding_atoms(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), core::energy_methods::RG_Energy_RNA::setup_for_scoring(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::stepwise::modeler::packer::StepWisePacker::setup_pack_task(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants(), protocols::dna::show_dna_geometry(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::use_orientation_dep_rna_ch_o_bonds().
◆ is_similar_aa()
|
inline |
Returns true if the aa residue types are the same.
References aa(), core::chemical::ResidueTypeBase::aa(), and rsd_type_.
◆ is_similar_rotamer()
| bool core::conformation::Residue::is_similar_rotamer | ( | Residue const & | other | ) | const |
Returns true if the chi angles of another residue all fall within 5 deg.
References aa(), core::chemical::ResidueTypeBase::aa(), chi(), chi_, core::chemical::ResidueTypeBase::name3(), name3(), and rsd_type_.
◆ is_sri()
|
inline |
Is this one of SRI's special heteropolymer building blocks?
References core::chemical::ResidueType::is_sri(), and rsd_type_.
◆ is_terminus()
|
inline |
Returns true if the residue has a terminus property.
References core::chemical::ResidueType::is_terminus(), and rsd_type_.
Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::denovo_design::components::StructureData::check_improper_termini(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::RamachandranEnergy2B::eval_dof_derivative(), core::energy_methods::RamachandranEnergy2B::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), protocols::analysis::LoopAnalyzerMover::find_positions(), protocols::mpi_refinement::get_loop_info_full(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), protocols::denovo_design::components::pose_matches_description(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), core::util::switch_to_centroid_rot_set(), and core::scoring::MembranePotential::termini_penalty().
◆ is_TNA()
|
inline |
Returns true if this residue is a TNA residue.
References core::chemical::ResidueType::is_TNA(), and rsd_type_.
Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry_strict(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::TNA_SuitePotential::eval_score(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range(), core::energy_methods::RNA_FullAtomStackingEnergy::get_count_pair_function(), core::scoring::loop_graph::get_loop_atom(), core::pose::rna::is_tna_chainbreak(), and core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way().
◆ is_triazolemer()
|
inline |
Returns true if and only if this residue is a triazolemer.
References core::chemical::ResidueType::is_triazolemer(), and rsd_type_.
◆ is_upper_terminus()
|
inline |
Return true if the residue has an upper terminus property.
References core::chemical::ResidueType::is_upper_terminus(), and rsd_type_.
Referenced by core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::loops::add_single_cutpoint_variant(), protocols::denovo_design::components::add_to_pose(), protocols::frags::add_vall_cheating_fragments(), protocols::frags::add_vall_fragments(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::denovo_design::components::append_new_residues(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::pose::append_pose_with_glycan_residues(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::hybridization::MRMover::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::chemical::ICoorAtomID::atom_id(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), protocols::idealize::basic_idealize(), core::scoring::GenBornPotential::build_placeholders(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), protocols::dna::DNAParameters::calculate(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), protocols::sasa_scores::compute_avge_scores(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), protocols::sasa_scores::compute_sasapack_scores(), connect_atom(), protocols::topology_broker::copy_internal_coords(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms(), protocols::forge::methods::count_cutpoints(), core::pose::create_subpose(), protocols::relax::cyclize_pose(), determine_nonstandard_polymer_status(), protocols::idealize::dihedral_distance(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::pose::symmetry::extract_asymmetric_unit(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::loops::fold_tree_from_loops(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_atomno(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), core::pose::motif::get_cterminal_peptide_bond_reference_frame(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::dna::get_DNA_backbone_bin(), core::pack::dunbrack::PeptoidGeneralDOFReporter::get_dof(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), core::scoring::dna::get_groove_widths(), core::scoring::hbonds::get_hb_acc_chem_type(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), core::pose::carbohydrates::glycosylate_pose(), protocols::forge::methods::grow_right_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::conformation::idealize_position(), protocols::forge::build::SegmentInsert::init(), protocols::forge::build::SegmentSwap::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::frags::TorsionFragment::insert(), core::pack::dunbrack::PeptoidGeneralDOFReporter::insert_atoms_defining_dof(), core::pack::dunbrack::MainchainTorsionReporter::insert_atoms_defining_dof(), core::pack::dunbrack::PeptideTorsionReporter::insert_atoms_defining_dof(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::Conformation::insert_polymer_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::conformation::is_ideal_position(), core::scoring::Ramachandran::is_normally_connected(), core::pose::is_upper_terminus(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::denovo_design::loop_start_without_overlap(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::cryst::MakeLayerMover::place_near_origin(), protocols::denovo_design::components::pose_matches_description(), protocols::normalmode::NormalMode::prepare_coord(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy(), core::io::carbohydrates::residue_range_gws_string(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), core::energy_methods::FA_GrpElecEnergy::set_nres_mono(), core::scoring::elec::FA_ElecEnergy::set_nres_mono(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::rbsegment_relax::setup_disconnected(), protocols::simple_moves::ShearMover::setup_list(), protocols::simple_moves::ShearMover::setup_list_for_saccharide_residue(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::dna::show_dna_geometry_extra_details(), core::scoring::dna::DNA_DihedralPotential::skip_torsion(), and protocols::fldsgn::CircularPermutation::split_chains().
◆ is_virtual()
|
inline |
Check if atom is virtual. AMW TODO: somehow SWA spends literally 3.7% of its time calling this function.
- Note
- A misnomer; this should really be called "is_virtual_atom()". ~Labonte
References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::is_virtual(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), core::util::add_constraints_to_metal(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::scoring::sc::ElectrostaticComplementarityCalculator::AddResidue(), core::scoring::sc::ElectrostaticSimilarityCalculator::AddResidue(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), protocols::stepwise::modeler::packer::check_o2prime_contact(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::conformation::Conformation::fill_missing_atoms(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::energy_methods::StackElecEnergy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), get_adjacent_heavy_atoms(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), get_atoms_exocyclic_to_ring_atom(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), core::scoring::MultipoleElecPotential::get_effective_radii(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::magnesium::SampleGrid::get_mg_positions(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), core::scoring::is_carbohydrate_ring_atom(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::energy_methods::StackElecEnergy::is_rna_base(), protocols::stepwise::modeler::rna::is_virtual_base(), n_bonded_neighbor_all_res(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::scoring::rms_at_corresponding_atoms_no_super(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), core::pose::setup_dof_mask_from_move_map(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), show(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().
◆ is_virtual_residue()
|
inline |
Check if residue is virtual.
References core::chemical::ResidueType::is_virtual_residue(), and rsd_type_.
Referenced by protocols::mpi_refinement::add_init_dev_penalty(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::pose_sewing::movers::SewAnythingAddMover::apply(), core::select::residue_selector::VirtualResidueSelector::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::apply_residue_selectors(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::scoring::Interface::calculate(), protocols::pose_sewing::calculate_blocks(), protocols::pose_sewing::calculate_bw_pose_compat_motifs(), protocols::pose_sewing::calculate_bw_window_motifs(), protocols::pose_creation::MergePDBMover::check_duplicate(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::pose_sewing::movers::SewAnythingAddMover::clashes(), protocols::simple_ddg::ddG::clean_pose(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::scoring::Ramachandran::defines_score_for_residue(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), core::pose::rna::detect_sugar_contacts(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_all(), core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::energy_methods::RingClosureEnergy::eval_residue_derivatives(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), core::scoring::fill_rmsd_coordinates(), protocols::pose_sewing::movers::SewAnythingAddMover::find_mod_terminus(), protocols::evolution::NucleotideMutation::find_neighbors(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), protocols::simple_filters::ResidueDepthFilter::get_n8(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::electron_density::get_spectrum(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::energy_methods::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), protocols::pose_sewing::filters::CoreScorer::report_sm(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::RingClosureEnergy::residue_energy(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::energy_methods::RNA_DataBackboneEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::scoring::rms_at_corresponding_atoms_no_super(), protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions(), core::optimization::CartesianMinimizerMap::setup(), protocols::carbohydrates::GlycanSampler::setup_default_task_factory(), core::energy_methods::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), protocols::rbsegment_relax::ConfChangeMover::sse_contact_strength(), core::pose::rna::virtualize_free_rna_moieties(), and core::scoring::epr_deer::EPRSpinLabel::weight().
◆ is_water()
|
inline |
Returns true if this residue is water.
References core::chemical::ResidueType::is_water(), and rsd_type_.
Referenced by protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::simple_ddg::ddG::calculate(), protocols::simple_ddg::ddG::clean_pose(), protocols::simple_ddg::ddG::do_minimize(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::simple_moves::ExplicitWaterMover::find_closest(), core::select::util::find_interface_pointing_residues_from_neighbs(), protocols::scoring::Interface::protein_calculate(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::setup_for_scoring(), and protocols::simple_ddg::ddG::setup_solvated_task().
◆ last_backbone_atom()
|
inline |
Returns the index number of the last backbone heavyatom.
- Note
- The heavyatoms come first in atom ordering, first backbone then sidechain, hydrogens follow the order of their attached heavyatom.
example(s): residue.last_backbone_atom() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose
References core::chemical::ResidueType::last_backbone_atom(), and rsd_type_.
Referenced by core::scoring::constraints::add_coordinate_constraints(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::relax::loop::LoopRelaxMover::apply(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::relax::generate_bb_coordinate_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), core::scoring::inline_residue_atom_pair_energy_backbone_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::pack::task::residue_selector::is_sc_bb_clash(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), and core::energy_methods::FastSAXSEnergy::setup_for_scoring().
◆ lower_connect()
|
inline |
Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue.
References core::chemical::ResidueType::lower_connect(), and rsd_type_.
Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::loops::loop_closure::ccd::get_deviation(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), resolve_partial_atom_id(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ lower_connect_atom()
|
inline |
Returns the index number of this residue's atom which connects to the residue before it in sequence.
- Note
- : polymers only, example: for an amino acid, residue.lower_connect_atom() = atom_index("N")
example(s): residue.lower_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.upper_connect_atom Pose
References core::chemical::ResidueType::lower_connect_atom(), and rsd_type_.
Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::loops::add_single_cutpoint_variant(), core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residue_by_bond(), core::conformation::Conformation::append_residues(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::scoring::constraints::auto_detect_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), connect_atom(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::loophash::FastGapMover::find_next_gap(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), and protocols::loops::set_loop_cutpoint_in_pose_fold_tree().
◆ mainchain_atom()
Returns the atom index of the residue's ith mainchain atom.
References core::chemical::ResidueType::mainchain_atom(), and rsd_type_.
Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::get_anchor_atomno(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::conformation::get_root_atomno(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::Conformation::set_torsion(), and core::kinematics::jacobian::ModuleType1::update_screw_vectors().
◆ mainchain_atoms()
|
inline |
Returns the AtomIndices of this residue's mainchain atoms.
References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.
Referenced by protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics(), protocols::backrub::connected_mainchain_atomids(), core::conformation::Conformation::debug_residue_torsions(), core::energy_methods::LinearChainbreakEnergy::do_score_dev(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::get_anchor_atomno(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::loops::loop_closure::ccd::get_deviation(), core::conformation::get_root_atomno(), core::pose::rna::get_stub_stub(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_torsion_axis(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), resolve_partial_atom_id(), core::conformation::Conformation::set_torsion(), core::conformation::setup_corresponding_atoms(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), core::conformation::setup_links(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf().
◆ mainchain_torsion()
Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid.
example(s): residue.mainchain_torsion(2) See also: Residue Pose Pose.omega Pose.phi Pose.psi
References mainchain_torsions_.
Referenced by core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), core::pose::rna::RNA_SuiteName::assign(), protocols::pose_metric_calculators::RotamerRecovery::bb_bins_from_pose(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::rna::RNA_SuiteName::closest_by_dist4(), core::pose::rna::RNA_SuiteName::closest_suite(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::copy_CCD_torsions_general(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::idealize::dihedral_distance(), protocols::dna::DNABase::DNABase(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), protocols::indexed_structure_store::extract_residue_entry(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::scoring::dna::get_DNA_backbone_bin(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::pack::dunbrack::PeptoidGeneralDOFReporter::get_dof(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), core::scoring::P_AA::get_Paa_pp_deriv(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::chemical::rna::get_residue_pucker_state(), core::scoring::dna::get_sugar_torsions(), core::conformation::idealize_position(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), core::pose::Pose::mu(), core::pose::Pose::omega(), core::scoring::P_AA::P_AA_pp_energy(), core::pose::Pose::phi(), protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::Pose::psi(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), core::energy_methods::OmegaTetherEnergy::residue_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::stepwise::sampler::screener::RNA_TorsionScreener::screen(), protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native(), protocols::dna::show_dna_geometry(), protocols::dna::show_dna_geometry_extra_details(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::pose::Pose::theta(), core::conformation::Conformation::torsion(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf().
◆ mainchain_torsions() [1/3]
|
inline |
Returns the mainchain torsion angles of this residue (non-const)
References mainchain_torsions_.
◆ mainchain_torsions() [2/3]
|
inline |
Returns the mainchain torsion angles of this residue (const)
example(s): residue.mainchain_torsions() See also: Residue Pose Pose.omega Pose.phi Pose.psi
References mainchain_torsions_.
Referenced by protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::simple_moves::bin_transitions::InitializeByBins::apply(), protocols::simple_moves::bin_transitions::PerturbByBins::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::minimization_packing::GreenPacker::compare_input_pose_geometry_to_reference(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap(), core::io::silent::RNA_SilentStruct::fill_struct(), core::scoring::bin_transitions::BinTransitionCalculator::find_data_and_bin(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix(), core::scoring::bin_transitions::BinTransitionData::in_bin_i(), core::scoring::bin_transitions::BinTransitionData::in_bin_iplus1(), protocols::motifs::load_build_position_data(), protocols::cyclic_peptide::CycpepSymmetryFilter::mainchain_torsions_differ(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1(), core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bins(), Residue(), core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::conformation::Conformation::set_torsion(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::setup_torsions(), protocols::minimization_packing::GreenPacker::store_reference_pose_geometry(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::conformation::Conformation::update_residue_torsions(), and protocols::comparative_modeling::features::TorsionFeature::values_from_pose().
◆ mainchain_torsions() [3/3]
|
inline |
Sets the mainchain torsion angles of this residue to <torsions>
example(s): residue.mainchain_torsions() See also: Residue Pose Pose.set_omega Pose.set_phi Pose.set_psi
References mainchain_torsions_.
◆ mark_connect_incomplete()
| void core::conformation::Residue::mark_connect_incomplete | ( | Size | resconn_index | ) |
References connect_map_, and connections_to_residues_.
Referenced by core::conformation::Conformation::sever_chemical_bond().
◆ mirrored_relative_to_type()
|
inline |
Is this residue mirrored relative to its coordinates in the ResidueType?
Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.
References mirrored_relative_to_type_.
Referenced by Residue(), core::energy_methods::RamachandranEnergy::residue_energy(), and show().
◆ misplaced()
|
inline |
Return whether or not the Residue was incorrectly oriented and placed within the polymer when created.
References misplaced_.
◆ mm_atom_name()
|
inline |
Returns the mm_atom_name of this residue's atom with index number <atom>
References atom(), core::chemical::ResidueType::mm_name(), and rsd_type_.
◆ n_bonded_neighbor_all_res()
| Size core::conformation::Residue::n_bonded_neighbor_all_res | ( | core::Size const | atomno, |
| bool | virt = false |
||
| ) | const |
Returns the number of atoms bonded to <atomno> in all residues?
determine how many atoms n the residue and adjacent residues are bonded to the given atom (by default, intraresidue virtual atoms are excluded)
References bonded_neighbor(), connection_incomplete(), is_virtual(), n_possible_residue_connections(), and residue_connect_atom_index().
Referenced by protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), and protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check().
◆ n_current_residue_connections()
| core::Size core::conformation::Residue::n_current_residue_connections | ( | ) | const |
Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!!
References connected_residue_at_resconn(), and n_possible_residue_connections().
Referenced by core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::pose::carbohydrates::get_resnums_in_leaf(), and core::pose::carbohydrates::get_resnums_in_leaf_on_the_fly().
◆ n_hbond_acceptors()
|
inline |
number of hbond_donors
References core::chemical::ResidueType::n_hbond_acceptors(), and rsd_type_.
Referenced by core::pose::num_hbond_acceptors().
◆ n_hbond_donors()
|
inline |
number of hbond_donors
References core::chemical::ResidueType::n_hbond_donors(), and rsd_type_.
Referenced by core::pose::num_hbond_donors().
◆ n_mainchain_atoms()
|
inline |
Returns the number of the residue's mainchain atoms.
References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.
Referenced by protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::idealize::dihedral_distance(), protocols::topology_broker::fix_mainchain_connect(), protocols::helical_bundle::generate_atom_positions(), core::conformation::get_anchor_atomno(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::conformation::get_root_atomno(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), and core::pose::carbohydrates::is_glycosidic_torsion().
◆ n_non_polymeric_residue_connections()
|
inline |
Returns the number of non-polymeric ResidueConnections on this residue.
References core::chemical::ResidueType::n_non_polymeric_residue_connections(), and rsd_type_.
Referenced by core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().
◆ n_nus()
|
inline |
Return the number of nu (internal ring) angles this residue has.
Example: residue.n_nus()
See also:
Residue
Residue.nu
Residue.nus
Pose.set_ring_conformation
Pose
Pose.nu
References core::chemical::ResidueType::n_nus(), and rsd_type_.
Referenced by Residue(), ring_conformer(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), update_nus(), core::conformation::Conformation::update_residue_torsions(), and protocols::environment::claims::TorsionClaim::yield_elements().
◆ n_orbitals()
|
inline |
Returns the number of orbitals in this residue.
References core::chemical::ResidueTypeBase::n_orbitals(), and rsd_type_.
◆ n_polymeric_residue_connections()
|
inline |
Returns the number of polymeric ResidueConnections on this residue.
References core::chemical::ResidueType::n_polymeric_residue_connections(), and rsd_type_.
Referenced by core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::energy_methods::polymeric_termini_incomplete(), core::scoring::polymeric_termini_incomplete(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::io::pose_from_sfr::show_residue_connections(), and core::conformation::Conformation::show_residue_connections().
◆ n_possible_residue_connections()
|
inline |
Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType.
References core::chemical::ResidueType::n_possible_residue_connections(), and rsd_type_.
Referenced by core::util::add_constraints_to_metal(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), core::pose::Pose::append_residue_by_atoms(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::scoring::mm::connection_indices(), copy_residue_connections(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::declare_chemical_bond(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), protocols::forge::methods::fold_tree_from_pose(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::generate_allowed_partners(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), has_incomplete_connection(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::pose::Pose::insert_residue_by_atoms(), core::scoring::PolymerBondedEnergyContainer::is_valid(), n_bonded_neighbor_all_res(), n_current_residue_connections(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::io::carbohydrates::residue_range_gws_string(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::conformation::setup_corresponding_atoms(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), update_connections_to_residues(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), and core::conformation::ConformationKinWriter::write_coords().
◆ n_virtual_atoms()
|
inline |
Returns the number of virtual atoms in this residue.
This calls the function with the same name in ResidueType, which counts virts on the fly (memory-efficient, performance-poor). This being the case, don't call this function repeatedly! Call it once, and store the return value!
References core::chemical::ResidueType::n_virtual_atoms(), and rsd_type_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), and IdentifyLigandMotifs::process_for_motifs().
◆ na_analogue()
|
inline |
Returns the nucleic acid type to be used for fragment sampling.
References core::chemical::ResidueTypeBase::na_analogue(), and rsd_type_.
Referenced by core::scoring::rna::check_watson_crick_sequence(), and core::scoring::rna::get_rna_motifs().
◆ name()
|
inline |
Returns this residue's ResidueType name.
- Note
- : for proteins, this will be the amino acid type and variant type
References core::chemical::ResidueTypeBase::name(), and rsd_type_.
Referenced by core::pose::motif::a(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::pose::ncbb::add_generic_hbs_constraint(), core::pose::ncbb::add_oop_constraint(), core::pose::ncbb::add_triazole_constraint(), protocols::relax::add_virtual_residue_to_cterm(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_multipole_axes(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), annotated_name(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::Conformation::append_residue(), protocols::simple_moves::RingConformationMover::apply(), protocols::drug_design::DrugDesignMover::apply(), protocols::drug_design::DrugPolishMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::simple_filters::ResidueDepthFilter::apply(), core::select::residue_selector::ResidueNameSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::vip::are_seqs_different(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::chemical::ICoorAtomID::atom_id(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::match::downstream::ClassicMatchAlgorithm::build(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_single_edge_waters(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate(), protocols::simple_ddg::ddG::calculate(), protocols::glycopeptide_docking::calculate_additional_glycosylation_metrics(), protocols::glycopeptide_docking::calculate_sampled_distance(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::simple_filters::ResidueCountFilter::compute(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector(), protocols::vip::VIP_Mover::compute_number_cavities(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::constraint_generator::compute_ref_atom(), protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), connection_distance(), protocols::relax::coordinate_constrain_selection(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pose::correctly_add_2prime_connection_variants(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::count_res(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::scoring::trie::create_trie(), protocols::md::CartesianMD::cst_on_pose_dynamic(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::conformation::Conformation::declare_chemical_bond(), protocols::simple_moves::ExplicitWaterMover::delete_waters(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), protocols::hydrate::enforce_all_waters(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), core::energy_methods::PointWaterEnergy::eval_intrares_energy(), core::energy_methods::Fa_MbsolvEnergy::eval_intrares_energy(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::eval_nrchi_score(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::energy_methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv(), core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::facts::FACTSPotential::evaluate_polar_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::scoring::rna::get_bin(), protocols::vip::VIP_Mover::get_cavity_positions(), core::select::residue_selector::get_cyclic_pose_residue_mappings_from_selectors(), protocols::vip::VIP_Report::get_GOE_packstat_report(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), core::scoring::hbonds::get_hb_acc_chem_type(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::hydrate::get_ready_for_sew_packing(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::get_residue_at_origin_with_matching_type(), core::chemical::rna::get_rna_base_centroid(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::ligand_docking::has_incomplete_connections(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::initialize_residues_for_type(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::ResidueFeatures::insert_residue_rows(), inter_residue_connection_partner(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::metal_check(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::pack::optimize_H_and_notify(), orient_onto_residue(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::simple_moves::CopyDofMover::pose_string(), core::conformation::print_atom(), protocols::hydrate::print_residues_near_water(), IdentifyLigandMotifs::process_for_motifs(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), protocols::glycopeptide_docking::record_pose_metrics(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::hydrate::remove_all_anchors_and_ENF(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), protocols::drug_design::replace_residue_type_with_mask(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report(), protocols::drug_design::SAScoreFilter::report(), core::energy_methods::AromaticBackboneRestraintEnergy::residue_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::WaterSpecificEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), protocols::hydrate::residue_near_water(), core::scoring::hbonds::residue_near_water(), core::energy_methods::Fa_MbsolvEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::conformation::Conformation::residues_insert(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::denovo_design::same_pose(), protocols::hydrate::set_dew_waters_not_to_be_included(), protocols::match::set_ligpose_rotamer(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), protocols::hydrate::set_water_info_and_add_de_novo_water(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), core::pose::show_adjacent_nt_connections(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), protocols::hydrate::show_water_hb_network(), protocols::vip::VIP_Mover::sort_fill_energies(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), core::pose::carbohydrates::tautomerize_anomer(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), update_connections_to_other_residue(), core::pose::rna::update_map(), protocols::simple_moves::ExplicitWaterMover::update_packer_task(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::hydrate::water_specific_hbond_energy(), core::conformation::ResidueKinWriter::write_rsd_coords(), and protocols::match::output::ResidueKinemageWriter::write_rsd_coords().
◆ name1()
|
inline |
Returns this residue's 1-letter representation.
- Note
- : for proteins, this will be the 1-letter amino acid code
References core::chemical::ResidueTypeBase::name1(), and rsd_type_.
Referenced by core::pack::task::residue_selector::add_clashes_to_shell(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::loop_grower::LoopGrower::add_fragment_csts(), annotated_name(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::protein_mpnn::ProteinMPNNMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::simple_moves::ShortBackrubMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_filters::StemFinder::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::splice::Splice::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::loops::apply_sequence_mapping(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::idealize::basic_idealize(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::pose_sewing::calculate_motif_score_bt_residues(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::rna::denovo::check_base_pair(), protocols::antibody::clusters::check_if_pose_renumbered_for_clusters(), core::import_pose::libraries::RNA_ChunkLibrary::check_res_map(), protocols::splice::SpliceManager::check_sequence_profile(), core::pose::rna::classify_base_pairs(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), protocols::denovo_design::filters::PreProlineFilter::compute_spline(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody_legacy::Antibody::detect_regular_CDR_H3_stem_type(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::loops::extend_sequence_mapping(), protocols::indexed_structure_store::extract_residue_entry(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::io::rna::RDAT::fill_header_information(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), protocols::splice::RotLibOut::find_matching_res(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::hbnet::HBNet::find_unsats(), core::scoring::gdtha(), core::scoring::gdtsc(), core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa(), protocols::splice::Splice::generate_sequence_profile(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::get_bin(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::hbnet::HBNet::get_num_native_seq(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::energy_methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), core::scoring::dna::DNA_DihedralPotential::get_sugar_torsion_mean_and_sdev(), protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::hbnet::his_tyr_connectivity(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), protocols::antibody::kink_dihedral(), protocols::tcr::match_template_and_target_sequence(), protocols::design_opt::PointMutationCalculator::mutate_and_relax(), protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), core::pack::pack_rotamers_loop(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::design_opt::Supercharge::print_netcharge_and_mutations(), protocols::read_in_mutations(), protocols::pmut_scan::PointMutScanDriver::read_mutants_list_file(), protocols::hbnet::HBNet::rec_trav_native(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::sasa::rel_per_res_sc_sasa(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::pose_sewing::filters::CoreScorer::report_sm(), core::energy_methods::ProQ_Energy::res6(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), protocols::hbnet::HBNet::select_best_networks(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::sequence_recovery(), protocols::design_opt::Supercharge::set_resfile(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_sequence(), core::conformation::setup_corresponding_atoms(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_base_step_params(), protocols::dna::show_dna_geometry(), protocols::dna::show_dna_geometry_extra_details(), core::scoring::dna::show_new_base_step_params(), core::scoring::motif::MotifHits::stat_motifs(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::hbnet::HBNet::traverse_native(), core::pose::rna::update_edge_hbond_numbers(), protocols::antibody_legacy::Antibody::update_sequence(), and protocols::simple_filters::SaveResfileToDiskFilter::write_resfile().
◆ name3()
|
inline |
Returns this residue's 3-letter representation.
- Note
- : for proteins, this will be the 3-letter amino acid code
References core::chemical::ResidueTypeBase::name3(), and rsd_type_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::environment::add_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::electron_density::DensityZscores::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::magnesium::MgHydrater::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::pose_sewing::movers::SewAnythingAddMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::protein_interface_design::Revert::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), core::select::residue_selector::BFactorSelector::apply(), core::select::residue_selector::ResidueNameSelector::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::apply(), protocols::simple_filters::NeighborTypeFilter::apply(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::splice::Splice::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::motifs::Motif::apply_check(), protocols::analysis::GlycanInfoMover::apply_const(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::energy_methods::ProQ_Energy::atom13_0(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), core::scoring::constraints::auto_detect_atoms(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::motifs::Motif::backward_check(), protocols::LoopRebuild::barcode_extend_stems(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), core::conformation::break_disulfide(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::motifs::MotifSearch::BuildPosition_from_Size(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_per_res_hydrophobic_sasa(), core::select::util::calc_sc_neighbors(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::simple_ddg::DdGScan::calculate(), core::scoring::electron_density::calculate_density_nbr(), protocols::antibody::CDR_H3_cter_filter(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::membrane::AddMembraneMover::check_pdb_for_mem(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), protocols::cryst::ReportGradientsMover::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::simple_filters::ResidueCountFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_modified_ddg(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::membrane::concave_shell(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::count_diff(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::toolbox::ResidueNetwork::create_from_pose(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), core::scoring::bin_transitions::BinTransitionData::criteria_match_i(), core::scoring::bin_transitions::BinTransitionData::criteria_match_iplus1(), protocols::simple_ddg::DdGScan::ddG_for_single_residue(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::antibody_legacy::AntibodyModeler::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::magnesium::MgScanner::distance_to_closest_magnesium(), protocols::environment::dof_id_to_string(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::design_opt::Supercharge::energy_comparison(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::energy_methods::SymmetricLigandEnergy::eval_atom_derivative(), core::energy_methods::MgEnergy::eval_intrares_energy(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::contact_map::ContactMap::fill_contacts(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::fill_coords(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::magnesium::filter_water_ligands(), protocols::dna::find_basepairs(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::flxbb::find_ligands(), protocols::seeded_abinitio::find_nearest_residue(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), core::conformation::form_disulfide(), protocols::motifs::Motif::forward_check(), protocols::docking::membrane::MPFindInterfaceMover::fractions_small_residues(), protocols::kinematic_closure::ClosureProblem::frame(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy(), protocols::magnesium::get_closest_non_hoh_contact(), protocols::enzdes::ResidueConformerFilter::get_current_conformer(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::magnesium::get_hoh_xyz(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), protocols::design_opt::Supercharge::get_net_charge(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::magnesium::get_res_with_name(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::chemical::rna::get_rna_base_coordinate_system(), core::pack::get_rotamer_angle_diffs(), protocols::magnesium::MgScanner::get_score(), protocols::magnesium::MgScanner::get_unique_mg_res(), core::pose::carbohydrates::glycosylate_pose(), core::pose::carbohydrates::glycosylate_pose_by_file(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), protocols::motifs::MotifSearch::identify_motif_BuildPositions(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::motifs::MotifSearch::initialize(), protocols::topology_broker::TopologyBroker::initialize_cuts(), core::pack::palette::PackerPalette::initialize_residue_level_task(), protocols::scoring::methods::TargetClashEnergy::initiate_voxel(), protocols::features::ResidueFeatures::insert_residue_rows(), core::pose::symmetry::intracomponent_contact(), protocols::pockets::GenPharmacophore::is_buried_ring(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), is_similar_rotamer(), protocols::antibody::kink_Trp_Hbond(), IdentifyLigandMotifs::ligand_to_residue_analysis(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::motifs::make_dna_mutations(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::environment::ProtectedConformation::match_variants(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::motifs::Motif::Motif(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::design_opt::PointMutationCalculator::mutate_and_relax(), protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), core::conformation::ExactResidueMatcher::operator()(), protocols::dna::PDBOutput::output_hbond_info(), core::io::sequence_comparation::DesignContrast::output_sqc_file(), protocols::antibody::paratope_charge(), protocols::antibody::paratope_sasa(), core::pose::parse_selection_block(), protocols::enzymatic_movers::DNAMethyltransferaseMover::perform_reaction(), protocols::motifs::Motif::place_atoms(), protocols::motifs::Motif::place_residue(), protocols::antibody::pose_charge(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::design_opt::Supercharge::print_netcharge_and_mutations(), protocols::splice::printChi(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::membrane::MPLipidAccessibility::protein_in_membrane(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_previous(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::magnesium::remove_mg_bound_waters(), protocols::magnesium::remove_waters_except_mg_bound(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::report(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::report(), protocols::enzdes::LigInterfaceEnergyFilter::report(), protocols::simple_ddg::AlaScan::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_filters::NeighborTypeFilter::report(), protocols::simple_filters::ResidueBurialFilter::report(), protocols::simple_filters::TotalSasaFilter::report(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::simple_ddg::AlaScan::report_symmetry(), core::energy_methods::ReferenceEnergyNoncanonical::residue_energy(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), protocols::membrane::scoring::ElectricfieldLipidlayer::residue_energy(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::energy_methods::GoapEnergy::residue_pair_energy(), core::energy_methods::MgEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::environment::rm_variant(), protocols::loop_grower::LoopGrower::RMStonative(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::pack::annealer::SequenceSymmetricAnnealer::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::magnesium::MgScanner::scan_magnesiums(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(), protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions(), protocols::design_opt::Supercharge::set_resfile_AvNAPSA(), protocols::design_opt::Supercharge::set_surface(), protocols::magnesium::set_water_numbers_to_zero(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::backrub::BackrubSidechainMover::setup_histograms(), core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation(), core::scoring::packstat::MultiProbePoseAccumulator::show(), protocols::protein_interface_design::filters::FilterScanFilter::single_substitution(), protocols::magnesium::strip_out_magnesiums(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), core::pose::carbohydrates::tautomerize_anomer(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), protocols::splice::SpliceOut::write_database_to_file(), protocols::splice::SpliceOutTail::write_database_to_file(), core::scoring::PoissonBoltzmannPotential::write_pqr(), and protocols::simple_ddg::DdGScan::write_to_pdb().
◆ natoms()
|
inline |
Returns the number of atoms in this residue.
example(s): residue.natoms() See also: Residue Pose
References core::chemical::ResidueType::natoms(), and rsd_type_.
Referenced by core::util::add_constraints_to_metal(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::energy_methods::add_to_individual_sol_energies(), core::scoring::sc::ElectrostaticComplementarityCalculator::AddResidue(), core::scoring::sc::ElectrostaticSimilarityCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_multipole_axes(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::align_pose(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::drug_design::align_residues(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), core::conformation::all_atom_center(), core::pose::all_atom_center(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::conformation::annotated_atom_graph_from_conformation(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(), protocols::cyclic_peptide::FlipChiralityMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::membrane::MPLipidAccessibility::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::RollMover::apply(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), protocols::hbnet::UnsatSelector::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::nmr::pcs::PCSLigandTransformMover::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::conformation::Conformation::apply_transform_Rx_plus_v(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::conformation::atom_graph_from_conformation(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), core::scoring::constraints::auto_detect_atoms(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::conformation::build_residue_tree(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::chemical::ICoorAtomID::buildable(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::MultipoleElecPotential::calculate_fixed_fields_for_polarization(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::MultipoleElecPotential::calculate_induced_fields_for_polarization(), core::pack::guidance_scoreterms::sap::calculate_per_res_sap(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), core::pose::Pose::center(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::MultipoleElecPotential::clear_induced_fields(), protocols::constel::cnl_com(), protocols::environment::collect_dofs(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::cryst::ReportGradientsMover::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::star::copy_residues(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::pack::create_scmin_minimizer_map(), core::scoring::trie::create_trie(), protocols::cartesian::MolecularDynamics::createCartesianArray(), protocols::cartesian::MolecularDynamics::createCartesianDerivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::relax::derive_sc_sc_restraints(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::dist(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_residue_kinemage(), protocols::membrane::scoring::ElectricfieldLipidlayer::eval_atom_derivative(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::energy_methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_DomeEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::energy_methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::FACTSEnergy::evaluate_rotamer_pair_energies(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), protocols::match::fill_grid_with_residue_spheres(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::energy_methods::RNA_CoarseDistEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::enzdes::PredesignPerturbMover::find_rotation_center(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::electron_density::findLoopFromDensity(), protocols::loops::fix_with_coord_cst(), protocols::splice::Splice::fold_tree(), core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::toolbox::rigid_body::get_atom_coordinates(), IdentifyLigandMotifs::get_atom_trios(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::magnesium::get_closest_orbital_axis(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::MultipoleElecPotential::get_effective_radii(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), core::scoring::get_pairwise_atom_energies(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::pack::get_residue_current_energy(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::get_second_atom_from_connection(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chains(), core::scoring::get_single_atom_energies(), core::scoring::facts::FACTSPotential::get_single_rotamer_born_radii(), core::scoring::GenBornPotential::get_single_rotamer_born_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::scoring::facts::FACTSPotential::get_template_born_radii(), core::scoring::GenBornPotential::get_template_born_radii(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), protocols::cryst::getMW(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pose::Pose::has_dof(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::conformation::idealize_hydrogens(), protocols::relax::RangeRelaxMover::idealize_pose(), core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::ResidueNblistData::initialize(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), core::scoring::VdWTinkerResidueInfo::initialize(), core::scoring::facts::FACTSResidueInfo::initialize(), core::pose::initialize_dof_id_map(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::facts::FACTSPoseInfo::is_changed(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::conformation::is_ideal_position(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_residues_in_contact(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), IdentifyLigandMotifs::ligand_to_residue_analysis(), core::pose::make_atom_map(), core::pose::symmetry::make_symmetric_movemap(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::pose::MiniPose::MiniPose(), core::conformation::missing_stubs_build(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms(), core::energy_methods::MPHelicalityEnergy::neighboring_atoms(), core::energy_methods::MPResidueLipophilicityEnergy::neighboring_atoms(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), protocols::cryst::ReportGradientsMover::normalization(), core::pose::num_atoms(), core::pose::PDBInfo::on_identity_change(), core::pose::PDBInfo::on_length_change(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::qsar::scoring_grid::AllAtomNormalization::operator()(), core::conformation::orient_residue_for_ideal_bond(), core::chemical::sdf::MolWriter::output_residue(), IdentifyLigandMotifs::output_single_motif_to_pdb(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::minimization_packing::PertMinMover::pert(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), place(), protocols::drug_design::place_new_restype_rotamer_align(), protocols::motifs::Motif::place_residue_(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::scoring::PQR::PQR(), protocols::normalmode::NormalMode::prepare_coord(), core::scoring::NeighborList::prepare_for_scoring(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_sho_energies(), core::energy_methods::PoissonBoltzmannEnergy::protein_position_equal_within(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), protocols::simple_moves::PeriodicBoxMover::recenter_pose(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::energy_methods::SAXSEnergy::rehash_form_factors(), core::scoring::MultipoleElecPotential::relax_induced_dipoles(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::drug_design::replace_residue_type_with_mask(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ResidueGridScoresFeatures::report_features(), core::scoring::facts::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), protocols::simple_filters::res_res_min_distance(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::optimization::CartesianMinimizerMap::reset(), core::optimization::MinimizerMap::reset(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), core::energy_methods::RingClosureEnergy::residue_energy(), core::energy_methods::WaterAdductIntraEnergy::residue_energy(), protocols::membrane::scoring::ElectricfieldLipidlayer::residue_energy(), core::energy_methods::GoapEnergy::residue_pair_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::MgEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), protocols::toolbox::pose_manipulation::rigid_body_move(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::toolbox::sample_around::rotate_into_phosphate_frame(), protocols::rotamer_recovery::RRProtocolRelax::run(), protocols::qsar::scoring_grid::ChargeGrid::score(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::LipidMemGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::qsar::scoring_grid::SingleGrid::score(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::serialize_residue_xyz_coords(), protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), core::scoring::NeighborList::setup(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), core::conformation::setup_corresponding_atoms(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::rbsegment_relax::setup_disconnected(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::energy_methods::GoapEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation(), core::conformation::setup_links(), core::conformation::setup_links_simple(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), show(), core::scoring::MultipoleElecPotential::store_induced_dipoles(), core::scoring::facts::FACTSResidueInfo::store_xyz(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::superimpose_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), core::scoring::sym_rmsd_with_super_subset(), protocols::electron_density::symmetrizeBfactors(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::cartesian::MolecularDynamics::testCartesianDerivatives(), protocols::protein_interface_design::PatchdockReader::transform_pose(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), protocols::environment::update_pdb_info(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_coordinates(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), protocols::kinmatch::xform_rsd_gl2(), protocols::constel::SingResCnlCrea::zero_occ_bb_h(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().
◆ nbr_atom()
|
inline |
Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids.
References core::chemical::ResidueType::nbr_atom(), and rsd_type_.
Referenced by protocols::abinitio::DomainAssembly::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::task_operations::DesignAroundOperation::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::select::util::calc_sc_neighbors(), core::energy_methods::MPHelicalityEnergy::centroid_neighbors(), core::energy_methods::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), protocols::kinematic_closure::ClosureSolution::check_overlap(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::LigBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::RG_Energy_Fast::eval_atom_derivative(), core::energy_methods::RG_LocalEnergy::eval_atom_derivative(), core::energy_methods::FA_GrpElecEnergy::eval_context_derivatives(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::select::filter_neighbors_by_distance(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::ddg::ddGMover::find_nbrs(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), core::scoring::is_nbr_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::scoring::Interface::ligand_calculate(), core::pose::make_atom_map(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::MinimizeInterface(), protocols::sic_dock::neighbor_count(), protocols::ddg::ddGMover::neighborhood_of_mutations(), core::energy_methods::MPHelicalityEnergy::neighboring_atoms(), core::energy_methods::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::energy_methods::FA_GrpElecEnergy::precalc_context(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::conformation::residue_point_graph_from_conformation(), core::scoring::methods::residues_interact(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::restrain_ligand_nbr_atom(), core::select::util::select_coord_for_residue(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), core::util::switch_to_centroid_rot_set(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), and core::conformation::ResidueKinWriter::write_kin_header().
◆ nbr_atom_xyz()
|
inline |
References atoms_, core::chemical::ResidueType::nbr_atom(), and rsd_type_.
Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::electron_density::DensityZscores::apply(), core::scoring::ScoreFunction::are_they_neighbors(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::energy_methods::ContactOrderEnergy::calculate_contact_order(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), core::energy_methods::RG_Energy_Fast::calculate_rg_score(), protocols::scoring::Interface::center(), protocols::geometry::center_of_mass(), core::pose::center_of_mass(), protocols::toolbox::sample_around::centroid_dist(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), core::pose::rna::classify_base_pairs(), protocols::dna::close_to_dna(), protocols::fold_from_loops::utils::Nub::closest_binder(), protocols::scoring::Interface::closest_interface_residue(), protocols::denovo_design::filters::CavityVolumeFilter::compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), core::energy_methods::MPSpanInsertionEnergy::create_updated_span(), core::pose::rna::detect_base_contacts(), core::scoring::lDDT_Calculator::determine_alt_states(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), protocols::magnesium::SampleGrid::figure_out_scan_res(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::ligand_docking::find_attach_pt(), protocols::evolution::NucleotideMutation::find_neighbors(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::matdes::get_intra_contacts(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), protocols::sic_dock::get_rg(), core::scoring::lDDT_Calculator::get_stats_for_state(), protocols::mpi_refinement::get_touched_res(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::hbnet::HBNetStapleInterface::interhelical_contact(), IdentifyLigandMotifs::ligand_to_residue_analysis(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::magnesium::pdbslice(), protocols::simple_moves::point_graph_dme(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), core::pose::radius_of_gyration(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::replace_ligand(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::nv::NVscore::residue_energy(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::restrain_ligand_nbr_atom(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::energy_methods::RG_Energy_Fast::setup_for_derivatives(), core::energy_methods::RG_LocalEnergy::setup_for_derivatives(), protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore(), core::energy_methods::Burial_v2Energy::using_atom_distance(), protocols::hbnet::HBNet::water_clashes(), and protocols::dna::z_axis_dist().
◆ nbr_radius()
|
inline |
Returns the distance cutoff value used as a radius for neighbor definition.
References core::chemical::ResidueType::nbr_radius(), and rsd_type_.
Referenced by core::select::residue_selector::CloseContactResidueSelector::apply(), core::scoring::ScoreFunction::are_they_neighbors(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::kinematic_closure::ClosureSolution::check_overlap(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::scoring::lDDT_Calculator::determine_alt_states(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_pair_energies(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::evolution::NucleotideMutation::find_neighbors(), core::pack::find_residue_max_radii(), protocols::relax::LocalRelax::get_neighbor_graph(), core::scoring::lDDT_Calculator::get_stats_for_state(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::scoring::Interface::ligand_calculate(), IdentifyLigandMotifs::ligand_to_residue_analysis(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::pose::pose_max_nbr_radius(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::methods::residues_interact(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), and core::scoring::NeighborList::setup().
◆ nbrs()
|
inline |
Convenience synonym for bonded_neighbor.
References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.
Referenced by apply_transform_downstream(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::viewer::dump_residue_kinemage(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::conformation::setup_links_simple(), core::conformation::ResidueKinWriter::write_rsd_coords(), and protocols::match::output::ResidueKinemageWriter::write_rsd_coords().
◆ nchi()
|
inline |
Returns the number of chi angles this residue has.
example(s): residue.nchi() See also: Residue Pose Pose.chi Pose.set_chi
References core::chemical::ResidueType::nchi(), and rsd_type_.
Referenced by core::pose::add_variant_type_to_residue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::pose_creation::MakePolyXMover::apply(), protocols::simple_moves::sidechain_moves::SetChiMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_chi_for_interpolated_rotamer(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::Conformation::debug_residue_torsions(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::idealize::dihedral_distance(), protocols::metal_interface::dump_chis(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), protocols::indexed_structure_store::extract_residue_entry(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), core::conformation::idealize_position(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), core::pose::num_chi_angles(), protocols::qsar::scoring_grid::ChiAngleNormalization::operator()(), core::pack::optimize_H_and_notify(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::perturb(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::pose::remove_variant_type_from_residue(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), Residue(), core::energy_methods::FreeDOF_Energy::residue_energy(), protocols::loop_grower::ResTorsions::ResTorsions(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), set_all_chi(), core::conformation::set_chi_according_to_coordinates(), protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), protocols::ligand_docking::LigandDockProtocol::shear_min_protocol(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::SimpleEntropy(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_torsions(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().
◆ nheavyatoms()
|
inline |
Returns the number of heavyatoms in this residue.
example(s): residue.nheavyatoms() See also: Residue Pose
References core::chemical::ResidueType::nheavyatoms(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::constraints::add_coordinate_constraints(), protocols::hybridization::add_non_protein_cst(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::advanced_select_points(), core::energy_methods::LK_hack::allocate_appropriate_memory(), core::scoring::Membrane_FAEmbed::allocate_appropriate_memory(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), core::energy_methods::ProQ_Energy::atom_feature(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), core::energy_methods::FastDensEnergy::atomistic_energy(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::scoring::automorphic_rmsd(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::lkball::LKB_ResidueInfo::build_waters(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::scoring::calc_per_res_hydrophobic_sasa(), core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::scoring::packstat::cavity_distance_constraint(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::check_voxel_distance_to_receptor(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), core::energy_methods::ProQ_Energy::crd(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::cryst::crystRMS(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_atom_derivative(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::energy_methods::MgEnergy::eval_residue_pair(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::Membrane_FAPotential::fa_projection(), core::pose::rna::figure_out_number_base_contacts(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::forge::methods::fill_non_loop_cst_set(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), core::scoring::cryst::fix_bfactorsH(), core::scoring::cryst::fix_bfactorsMissing(), protocols::ligand_docking::frac_atoms_within(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::dna::get_base_pair_stub_slow(), core::pose::get_center_of_mass(), core::energy_methods::HackAroEnergy::get_centroid(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::magnesium::get_closest_non_hoh_contact(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::magnesium::get_mg_ligands(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), protocols::ligand_docking::get_radius_of_gyration(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::chemical::rna::get_rna_base_centroid(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), protocols::electron_density::get_spectrum(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), core::energy_methods::RNA_DataBackboneEnergy::get_sugar_env_score(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), protocols::constel::FilterBySASA::has_low_per_atom_sasa(), heavyAtoms_end(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::conformation::idealize_hydrogens(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), core::energy_methods::FaMPEnvEnergy::init(), core::energy_methods::FaMPSolvEnergy::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::is_base_blob(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::energy_methods::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::scoring::Interface::ligand_calculate(), core::scoring::lkball::LKD_ResidueInfo::LKD_ResidueInfo(), core::pose::make_atom_map(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::match_by_atomtype(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_natoms(), core::pose::num_heavy_atoms(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::qsar::scoring_grid::HeavyAtomNormalization::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), core::pose::rna::output_ligands(), core::pose::rna::output_other_contacts(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::ncbb::oop::pep_COM(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::electron_density::pose_spherical_samples(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::stepwise::modeler::rna::print_heavy_atoms(), IdentifyLigandMotifs::process_for_motifs(), protocols::pockets::PocketGrid::recenter(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::SiteGrid::refresh(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::electron_density::remove_occupied_density_from_density(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::energy_methods::FaMPEnvEnergy::residue_energy(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::pose::rna::residue_is_bulge(), protocols::sic_dock::residue_is_floppy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::pockets::PlaidFingerprint::rmsd(), core::pack::dunbrack::RotamerConstraint::RotamerConstraint(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_base_blob(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_satellite_blob(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), protocols::design_opt::Supercharge::set_surface(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::FaMPEnvEnergy::setup_for_fullatom(), core::energy_methods::FaMPSolvEnergy::setup_for_fullatom(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), core::import_pose::setup_jumps(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::hybridization::DDomainParse::split(), core::util::switch_to_centroid_rot_set(), protocols::hybridization::MRMover::trim_target_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().
◆ nonconst_data()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time.
References data_cache_.
◆ nonconst_data_ptr()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh.
Return an OP to the datacache
- Note
- Will create new one if not already initialized
References data_cache_, and core::conformation::residue_datacache::n_cacheable_types.
Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), and core::conformation::Conformation::residue_data().
◆ nu()
|
inline |
Get a specific nu (internal ring) torsion angle by index.
Example: residue.nu(1)
See also:
Residue
Residue.nus
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu
- Note
- It is intentional that there is no set_nu() function; nu angles should only be modified together. Use Pose.set_ring_conformation() instead.
References nus_.
Referenced by core::conformation::Conformation::torsion().
◆ nu_atoms() [1/2]
|
inline |
Return the AtomIndices of each set of four atoms defining each nu angle.
References core::chemical::ResidueType::nu_atoms(), and rsd_type_.
Referenced by core::conformation::Conformation::get_torsion_angle_atom_ids(), set_all_ring_nu(), set_tau(), and update_nus().
◆ nu_atoms() [2/2]
|
inline |
Return the AtomIndices of the four atoms defining the specified nu angle.
References core::chemical::ResidueType::nu_atoms(), and rsd_type_.
◆ nus() [1/2]
|
inline |
Return the nu (internal ring) torsion angles of this residue. (non-const)
References nus_.
◆ nus() [2/2]
|
inline |
Return the nu (internal ring) torsion angles of this residue.
Example: residue.nus()
See also:
Residue
Residue.nu
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu
References nus_.
Referenced by ring_conformer(), set_all_nu(), set_all_ring_nu(), and core::conformation::Conformation::update_residue_torsions().
◆ operator=()
Assignment operator does not work for class Residue. This function is intentionally unimplemented and private.
◆ orbital_name()
| std::string const & core::conformation::Residue::orbital_name | ( | Size const | orbital_index | ) | const |
◆ orbital_type()
|
inline |
References core::chemical::ResidueTypeBase::orbital_type(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), and protocols::features::OrbitalsFeatures::set_OrbOrb_features_data().
◆ orbital_type_index()
References orbitals_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), and core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy().
◆ orbital_xyz()
References orbitals_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().
◆ orient_onto_location() [1/2]
| void core::conformation::Residue::orient_onto_location | ( | Size | center, |
| Size | nbr1, | ||
| Size | nbr2, | ||
| Vector | center_locaton, | ||
| Vector | nbr1_locaton, | ||
| Vector | nbr2_locaton | ||
| ) |
Orients residue object onto atom locations.
- Note
- Orients onto the atom numbers center, nbr1, nbr2.
References atom(), atoms(), core::conformation::membrane::center, core::chemical::ResidueType::natoms(), protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), rsd_type_, and xyz().
Referenced by protocols::indexed_structure_store::apply_residue_entries_to_pose(), orient_onto_location(), and orient_onto_residue().
◆ orient_onto_location() [2/2]
| void core::conformation::Residue::orient_onto_location | ( | Vector | center_locaton, |
| Vector | nbr1_locaton, | ||
| Vector | nbr2_locaton | ||
| ) |
Orients residue object onto atom locations.
- Note
- Orients using default orient atoms taken from select_orient_atoms
References core::conformation::membrane::center, protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), orient_onto_location(), and select_orient_atoms().
◆ orient_onto_residue() [1/3]
| void core::conformation::Residue::orient_onto_residue | ( | Residue const & | src | ) |
Orient our coords onto those of <src>, using the atoms from select_orient_atoms.
Helper function: selects atoms to orient on and transforms all of my atoms to orient onto another residue. Used by place(). Need to think a bit more about the restrictions on src...
References atom_index(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::conformation::membrane::center, core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name(), name(), protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), rsd_type_, select_orient_atoms(), core::conformation::TR(), and type().
Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::hbnet::hbnet_symm_one_body_energies(), orient_onto_residue(), place(), and core::conformation::Conformation::replace_residue().
◆ orient_onto_residue() [2/3]
|
private |
Orient coords onto those of <src>, using the specified atoms.
References atom(), core::conformation::membrane::center, protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), orient_onto_location(), and core::conformation::Atom::xyz().
◆ orient_onto_residue() [3/3]
| void core::conformation::Residue::orient_onto_residue | ( | Residue const & | src, |
| utility::vector1< std::pair< std::string, std::string > > const & | atom_pairs | ||
| ) |
Orient our coords onto those of <src>, using the three atom pairs specified in the input.
- Parameters
-
atom_pairs
References atom_index(), and orient_onto_residue().
◆ orient_onto_residue_peptoid()
| void core::conformation::Residue::orient_onto_residue_peptoid | ( | Residue const & | src, |
| Conformation const & | conformation | ||
| ) |
Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide.
oritent onto residue for peptoids Not too proud of this as I think there is probably a more general way but at the moment it is alluding me To align a peptoid the N is the center and the nbrs are the lower connect and the CA. The lower connect is not stored in the atom index so we need to get the xyz coord a different way.
References core::chemical::ACETYLATED_NTERMINUS_VARIANT, atom(), atom_index(), atoms(), chain(), core::conformation::Conformation::chain_end(), connected_residue_at_lower(), core::chemical::AtomICoor::d(), has_variant_type(), icoor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::natoms(), core::conformation::Conformation::num_chains(), core::chemical::AtomICoor::phi(), core::conformation::Conformation::residue(), rsd_type_, core::conformation::Conformation::size(), core::chemical::AtomICoor::theta(), type(), core::conformation::Atom::xyz(), and xyz().
Referenced by place().
◆ path_distance() [1/2]
Returns the number of bonds separating atom <at1> from <at2>
example(s):
See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose
References core::chemical::ResidueType::path_distance(), and rsd_type_.
◆ path_distance() [2/2]
|
inline |
Returns the shortest path distance from <atom> to any other atom in this residue.
example(s):
See also: Residue Residue.atom Residue.atoms Pose
References atom(), core::chemical::ResidueType::path_distance(), and rsd_type_.
Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::conformation::Conformation::detect_pseudobonds(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::trie::initialize_cpdata_for_atom(), core::chemical::rna::is_base_phosphate_atom_pair(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK().
◆ path_distances()
|
inline |
Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2].
example(s):
See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose
References core::chemical::ResidueType::path_distances(), and rsd_type_.
◆ place()
| bool core::conformation::Residue::place | ( | Residue const & | src, |
| Conformation const & | conformation, | ||
| bool | preserve_c_beta = false |
||
| ) |
Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match.
Place/orient "this" Residue onto "src" Residue by backbone superimposition. This function is mainly used to place a rotamer onto the backbone of "src" residue. Meanwhile, it can also be used to add sidechains to one pose/conformation from another pose/conformation.
Current logic:
- Find backbone atom with bonded neighbors in sidechain, and which is the base_atom of those neighbors.
- Take that backbone atom and find two neighboring backbone heavyatoms.
- The three atoms to be superimposed with are
- the center/base atom,
- the backbone neighbor 1,
- and the mid-point of backbone neighbor 1 and 2. This way, we can avoid large perturbation on backbone neighbor 2 after superimpostion if the two sets of backbone atoms are not perfectly superimposable, (e.g., with slightly different backbone geometry).
- After all atoms in "this" Residue are oriented, copy any corresponding backbone atom coords from "src", and if there are any backbone atoms missing from "src", (for example, src is a proline with HN missing), build them using ideal internal coords. (That is why "conformation" is needed as an input argument).
- For residues without any backbone atoms, (e.g., some ligands,) center on nbr_atom instead and two of its bonded neighbors, (preferring heavy atoms to hydrogens if possible.)
- Returns
- true on success; false on failure
References atom(), atom_depends_on_lower(), atom_depends_on_upper(), atom_index(), core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_is_hydrogen(), atom_name(), core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), atoms(), chi_atoms(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), core::kinematics::tree::distance_squared(), fill_missing_atoms(), core::chemical::ResidueType::first_sidechain_atom(), has(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_peptoid(), is_peptoid(), core::chemical::ResidueTypeBase::is_polymer(), is_RNA(), natoms(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), orient_onto_residue(), orient_onto_residue_peptoid(), rsd_type_, core::chemical::AtomICoor::stub_atom1(), type(), core::conformation::Atom::xyz(), and xyz().
Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), and Residue().
◆ polymeric_oriented_sequence_distance()
|
inline |
Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence.
References chain(), chain_, is_polymer(), protocols::mean_field::max(), and seqpos_.
Referenced by core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), and core::scoring::hbonds::hbond_evaluation_type().
◆ polymeric_sequence_distance()
Returns the sequence separation distance between this residue and <other>
- Note
- : magnitude of distance only
References chain(), chain_, is_polymer(), and seqpos_.
Referenced by protocols::stepwise::screener::PartitionContactScreener::check_screen(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::lDDT_Calculator::determine_alt_states(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::lDDT_Calculator::get_stats_for_state(), core::scoring::PairEPotential::pair_term_energy(), protocols::features::PairFeatures::report_residue_pairs(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), and core::energy_methods::GaussianOverlapEnergy::residue_pair_energy().
◆ pseudobonds()
|
inline |
References pseudobonds_.
Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamer().
◆ requires_actcoord()
|
inline |
does this residue require an actcoord?
References core::chemical::ResidueType::requires_actcoord(), and rsd_type_.
◆ residue_connect_atom_index()
References core::chemical::ResidueType::residue_connect_atom_index(), and rsd_type_.
Referenced by core::pose::Pose::append_residue_by_atoms(), protocols::ligand_docking::AddHydrogen::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::conformation::Conformation::atoms_are_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::conformation::get_second_atom_from_connection(), has_incomplete_connection(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::trie::initialize_cpdata_for_atom(), core::pose::Pose::insert_residue_by_atoms(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_bonded_neighbor_all_res(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::show_adjacent_nt_connections(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), and core::conformation::ConformationKinWriter::write_coords().
◆ residue_connection()
|
inline |
Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue.
References core::chemical::ResidueType::residue_connection(), and rsd_type_.
Referenced by core::util::add_constraints_to_metal(), core::conformation::Conformation::append_residue_by_bond(), protocols::ligand_docking::AddHydrogen::apply(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::mm::connection_indices(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::pose::create_chemical_edge(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::io::silent::BinarySilentStruct::fill_struct(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::Conformation::insert_residue_by_bond(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), resolve_partial_atom_id(), and protocols::simple_moves::CyclizationMover::setup_constraints().
◆ residue_connection_conn_id()
|
inline |
Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index.
For example, if this were a normally-connected alpha amino acid, residue_connection_conn_id(1) would return 2, since the first connection in this residue is attached to the second connection in the previous residue.
References connect_map_.
Referenced by protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::conformation::Conformation::atoms_are_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::pose::correctly_add_2prime_connection_variants(), core::pose::create_chemical_edge(), core::pose::declare_cutpoint_chemical_bond(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::methods::find_relevant_connections(), core::scoring::methods::find_relevant_connections_onersd(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::conformation::get_second_atom_from_connection(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), inter_residue_connection_partner(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::pose::show_adjacent_nt_connections(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().
◆ residue_connection_partner() [1/2]
|
inline |
Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.
For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6.
References connect_map_.
Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), copy_residue_connections(), core::conformation::Conformation::declare_chemical_bond(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_pseudobonds(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::scoring::methods::determine_lo_and_hi_residues(), protocols::viewer::dump_residue_kinemage(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), inter_residue_connection_partner(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::Ramachandran::is_normally_connected(), is_polymer_bonded(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::io::carbohydrates::residue_range_gws_string(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and update_connections_to_other_residue().
◆ residue_connection_partner() [2/2]
| void core::conformation::Residue::residue_connection_partner | ( | Size const | resconn_index, |
| Size const | otherres, | ||
| Size const | other_connid | ||
| ) |
set a connection to this residue by adding its partner's residue number
set a connection to this residue by adding its partner's residue number
References connect_map_, determine_nonstandard_polymer_status(), and update_connections_to_residues().
◆ resolve_partial_atom_id()
| id::AtomID core::conformation::Residue::resolve_partial_atom_id | ( | id::PartialAtomID const & | partial_id | ) | const |
Resolve a partial atom ID into an AtomID for this residue.
References core::chemical::ResidueType::atom_base(), core::chemical::ResidueConnection::atomno(), core::id::PartialAtomID::atomno(), core::id::AtomID::BOGUS_ATOM_ID(), core::id::PartialAtomID::bonds_from_resconn(), core::id::PartialAtomID::complete(), has_lower_connect(), has_upper_connect(), lower_connect(), mainchain_atoms(), core::id::PartialAtomID::resconnid(), residue_connection(), core::id::PartialAtomID::rsd(), seqpos(), type(), upper_connect(), and core::id::PartialAtomID::valid().
Referenced by core::conformation::Conformation::resolve_partial_atom_id().
◆ ring_conformer()
| chemical::rings::RingConformer const & core::conformation::Residue::ring_conformer | ( | core::uint const | ring_num, |
| core::Real | limit = 90.0 |
||
| ) | const |
Return the current RingConformer of this residue's nth ring.
References core::chemical::rings::AROMATIC, core::chemical::ResidueType::is_cyclic(), n_nus(), core::chemical::ResidueType::n_rings(), nus(), nus_, core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), core::chemical::ResidueType::ring_saturation_type(), and rsd_type_.
Referenced by core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), and show().
◆ RNA_info()
|
inline |
Return the RNA_residueType object. This is RNA specific.
References core::chemical::ResidueType::RNA_info(), and rsd_type_.
Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::chemical::rna::get_rna_base_centroid(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), and core::chemical::rna::is_base_phosphate_atom_pair().
◆ select_orient_atoms()
| void core::conformation::Residue::select_orient_atoms | ( | Size & | center, |
| Size & | nbr1, | ||
| Size & | nbr2 | ||
| ) | const |
Selects three atoms for orienting this residue.
References core::conformation::membrane::center, protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), rsd_type_, and core::chemical::ResidueType::select_orient_atoms().
Referenced by core::conformation::get_stub_from_residue(), orient_onto_location(), and orient_onto_residue().
◆ seqpos() [1/2]
|
inline |
Returns the sequence position of this residue.
References seqpos_.
Referenced by protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::environment::add_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_multipole_axes(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), core::select::residue_selector::ResidueInMembraneSelector::apply(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::chemical::ICoorAtomID::atom_id(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), core::energy_methods::FastDensEnergy::atomistic_energy(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::lkball::LK_BallEnergy::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), core::scoring::methods::atoms_interact(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::YHHPlanarityEnergy::atoms_with_dof_derivatives(), core::scoring::automorphic_rmsd(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::dna::DNA_BasePotential::base_step_score(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::build_bbdep_rotamers(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::conformation::build_residue_tree(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::energy_methods::MPHelicalityEnergy::calc_energy(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), core::energy_methods::MembraneEnvSmoothEnergy::calc_energy(), core::energy_methods::FaMPEnvSmoothEnergy::calc_energy(), core::energy_methods::MPSpanInsertionEnergy::calc_span_score(), core::energy_methods::GoapEnergy::calculate_dipoles(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), core::energy_methods::MPHelicalityEnergy::centroid_neighbors(), core::energy_methods::MPResidueLipophilicityEnergy::centroid_neighbors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::constraint_generator::compute_ref_atom(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), connect_atom(), protocols::backrub::connected_mainchain_atomids(), core::scoring::mm::connection_indices(), connections_to_residue(), core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::pack::interaction_graph::create_hbonds_one_way(), core::io::pdb::create_pdb_info_for_single_residue_pose(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), protocols::cartesian::MolecularDynamics::createDihedral(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::energy_methods::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::defines_score_for_residue_pair(), core::energy_methods::LK_PolarNonPolarEnergy::defines_score_for_residue_pair(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::energy_methods::StackElecEnergy::defines_score_for_residue_pair(), core::energy_methods::RNA_CoarseDistEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), core::pack::hbonds::determine_atom_level_edge_info(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), determine_nonstandard_polymer_status(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::matdes::dup_residue(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::ImplicitMembraneElecEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(), protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues(), core::energy_methods::FA_GrpElecEnergy::eval_context_derivatives(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::energy_methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::FA_GrpElecEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::Fa_MbsolvEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::energy_methods::FA_GrpElecEnergy::eval_intrares_energy(), core::energy_methods::DNATorsionEnergy::eval_intrares_energy(), core::energy_methods::FACTSEnergy::eval_intrares_energy(), core::energy_methods::GenBornEnergy::eval_intrares_energy(), core::energy_methods::MultipoleElecEnergy::eval_intrares_energy(), core::energy_methods::VdWTinkerEnergy::eval_intrares_energy(), core::scoring::constraints::ConstraintSet::eval_intrares_energy(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::eval_nrchi_score(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::FA_GrpElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::energy_methods::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::energy_methods::TNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::RNA_CoarseDistEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::facts::FACTSPotential::evaluate_polar_energy(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::energy_methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::energy_methods::MembraneLipo::finalize_total_energy(), core::pack::hbonds::find_hbonds_in_residue_pair(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::pockets::PocketGrid::findExemplars(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::dna::get_base_step_params(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(), core::energy_methods::RNA_FullAtomStackingEnergy::get_count_pair_function(), core::scoring::vdwaals::VDW_Energy::get_count_pair_function_trie(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function_trie(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::loop_graph::get_loop_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::membrane::scoring::ElectricfieldLipidlayer::get_menv_params_for_residue(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::conformation::get_residue_connections(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::conformation::get_root_residue_root_atomno(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), core::conformation::get_second_atom_from_connection(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::hbonds::get_ssdep_weight(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::pack::palette::PackerPalette::initialize_residue_level_task(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), core::conformation::Conformation::insert_residue_by_bond(), core::conformation::Conformation::insert_residue_by_jump(), core::conformation::insert_residue_into_atom_tree(), inter_residue_connection_partner(), core::chemical::rna::is_base_phosphate_atom_pair(), is_bonded(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::scoring::Interface::is_interface(), protocols::scoring::InterfaceInfo::is_interface(), core::scoring::Ramachandran::is_normally_connected(), protocols::scoring::Interface::is_pair(), is_polymer_bonded(), is_pseudo_bonded(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::environment::ProtectedConformation::match_variants(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), core::energy_methods::MPHelicalityEnergy::neighboring_atoms(), core::energy_methods::MPResidueLipophilicityEnergy::neighboring_atoms(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1(), core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::KinFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::kinmatch::KinFunGroupTK::place_h(), protocols::normalmode::NormalMode::prepare_coord(), core::conformation::print_atom(), protocols::viewer::print_interres_bond(), protocols::viewer::print_node(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), core::pack::reinitialize_mingraph_neighborhood_for_residue(), core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), protocols::environment::Environment::remove_chainbreak_variants(), core::conformation::replace_residue_in_atom_tree(), protocols::drug_design::replace_residue_type_with_mask(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::rotamer_recovery::RRReporterSQLite::report_predicted_features(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), protocols::rotamer_recovery::PerNativeRRReporterHuman::report_rotamer_recovery(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::facts::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), core::scoring::func::ResidueXYZ::residue(), core::scoring::func::ResiduePairXYZ::residue(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::FreeDOF_Energy::residue_energy(), core::energy_methods::RNA_BulgeEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::CovalentLabelingEnergy::residue_energy(), core::energy_methods::CovalentLabelingFAEnergy::residue_energy(), core::energy_methods::DEPC_MS_Energy::residue_energy(), core::energy_methods::EnvEnergy::residue_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::energy_methods::FaMPEnvEnergy::residue_energy(), core::energy_methods::HRF_MSLabelingEnergy::residue_energy(), core::energy_methods::HRFDynamicsEnergy::residue_energy(), core::energy_methods::MembraneCbetaEnergy::residue_energy(), core::energy_methods::MembraneEnvEnergy::residue_energy(), core::energy_methods::MPCbetaEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::energy_methods::P_AA_ss_Energy::residue_energy(), core::energy_methods::SequenceDependentRefEnergy::residue_energy(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::methods::NMerRefEnergy::residue_energy(), core::scoring::methods::NMerSVMEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::GoapEnergy::residue_pair_energy(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::OccludedHbondSolEnergy::residue_pair_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy(), core::energy_methods::CustomAtomPairEnergy::residue_pair_energy(), core::energy_methods::DNA_BaseEnergy::residue_pair_energy(), core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy(), core::energy_methods::FA_GrpElecEnergy::residue_pair_energy(), core::energy_methods::Fa_MbsolvEnergy::residue_pair_energy(), core::energy_methods::FACTSEnergy::residue_pair_energy(), core::energy_methods::GenBornEnergy::residue_pair_energy(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::energy_methods::PeptideBondEnergy::residue_pair_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::energy_methods::RNA_DataBackboneEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::energy_methods::RNA_JR_SuiteEnergy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::VdWTinkerEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), core::energy_methods::DisulfideMatchingEnergy::residue_pair_energy(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), core::energy_methods::FastDensEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::energy_methods::PoissonBoltzmannEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::energy_methods::RNA_StubCoordinateEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::energy_methods::DEEREnergy::residue_pair_energy(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(), protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::energy_methods::FA_GrpElecEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy_ext(), core::energy_methods::VdWTinkerEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_CoarseDistEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), resolve_partial_atom_id(), protocols::environment::rm_variant(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::same_polarization_group(), core::scoring::SASAShouldItCount(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), core::energy_methods::RNA_CoarseDistEnergy::score_atom_pair(), core::scoring::MembranePotential::score_normal_center(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue(), core::energy_methods::VdWTinkerEnergy::setup_for_minimizing_for_residue(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue(), core::energy_methods::FA_GrpElecEnergy::setup_for_minimizing_for_residue_pair(), core::energy_methods::RNA_FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::energy_methods::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(), protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair(), core::energy_methods::RNA_CoarseDistEnergy::setup_for_minimizing_for_residue_pair(), core::energy_methods::GoapEnergy::setup_for_scoring(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::ShouldItCount(), protocols::scoring::Interface::show(), core::pose::show_adjacent_nt_connections(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_residue_type_set(), core::scoring::MembranePotential::termini_penalty(), core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanTree::update_on_length_change(), core::scoring::VdWShouldItCount(), protocols::symmetry::SymmetrySlider::very_far_away(), core::conformation::ConformationKinWriter::write_coords(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::conformation::ResidueKinWriter::write_rsd_coords(), and protocols::match::output::ResidueKinemageWriter::write_rsd_coords().
◆ seqpos() [2/2]
|
inline |
Sets this residue's sequence position to <setting>
References seqpos_.
◆ set_all_chi()
| void core::conformation::Residue::set_all_chi | ( | utility::vector1< Real > const & | chis | ) |
Sets all of this residue's chi angles using the set_chi function (wrapper function)
References nchi(), and set_chi().
Referenced by protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), and protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept().
◆ set_all_nu()
| void core::conformation::Residue::set_all_nu | ( | utility::vector1< Real > const & | nus, |
| utility::vector1< Real > const & | taus | ||
| ) |
References nus(), nus_, and set_all_ring_nu().
◆ set_all_ring_nu()
| void core::conformation::Residue::set_all_ring_nu | ( | Size | start, |
| Size | end, | ||
| utility::vector1< Real > const & | nus, | ||
| utility::vector1< Real > const & | taus | ||
| ) |
References apply_transform_downstream(), atom(), nu_atoms(), core::chemical::ResidueType::nu_atoms(), nus(), nus_, rsd_type_, set_tau(), update_actcoord(), and xyz().
Referenced by set_all_nu().
◆ set_chi()
| void core::conformation::Residue::set_chi | ( | int const | chino, |
| Real const | setting | ||
| ) |
Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree.
this assumes that change propagates according to the information from atom_base array, not from atom tree. So be sure not to get into an endless loop.
References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), chi_, chi_atoms(), core::chemical::ResidueType::chi_atoms(), rsd_type_, update_actcoord(), and xyz().
Referenced by protocols::minimization_packing::RotamerizeMover::apply(), protocols::constraint_movers::assert_that_all_atoms_are_moved_by_chi_angle(), core::scoring::atomic_depth::AtomicDepth::AtomicDepth(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::rotamer_recovery::RRProtocolRelax::run(), and set_all_chi().
◆ set_d()
| void core::conformation::Residue::set_d | ( | int const | chino, |
| Real const | setting | ||
| ) |
bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example
References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), chi_atoms(), core::chemical::ResidueType::chi_atoms(), rsd_type_, update_actcoord(), and xyz().
◆ set_mirrored_relative_to_type()
|
inline |
Set whether this residue is mirrored relative to its coordinates in the ResidueType.
Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.
References mirrored_relative_to_type_.
Referenced by Residue().
◆ set_orbital_xyz()
| void core::conformation::Residue::set_orbital_xyz | ( | core::Size const | orbital_index, |
| Vector const & | xyz_in | ||
| ) |
◆ set_pseudobonds_to_residue()
| void core::conformation::Residue::set_pseudobonds_to_residue | ( | Size | resid, |
| PseudoBondCollectionCOP | pbs | ||
| ) |
References pseudobonds_.
◆ set_tau()
set_theta for nus
References apply_transform_downstream(), atom(), nu_atoms(), core::chemical::ResidueType::nu_atoms(), nus_, rsd_type_, update_actcoord(), and xyz().
Referenced by set_all_ring_nu().
◆ set_theta()
| void core::conformation::Residue::set_theta | ( | int const | chino, |
| Real const | setting | ||
| ) |
bondangle analog to set_chi same idea as set_d
References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), chi_atoms(), core::chemical::ResidueType::chi_atoms(), rsd_type_, update_actcoord(), and xyz().
◆ set_xyz() [1/2]
| void core::conformation::Residue::set_xyz | ( | core::Size const | atm_index, |
| Vector const & | xyz_in | ||
| ) |
Sets the position of this residue's atom with index number <atm_index>
example(s):
See also: Residue Residue.atom Residue.atoms Residue.xyz Pose
References atoms_.
Referenced by protocols::drug_design::align_residues(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), protocols::splice::Splice::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), apply_transform_Rx_plus_v(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), fill_missing_atoms(), protocols::splice::fix_chain_break_residue(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::idealize_hydrogens(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::conformation::orient_residue_for_ideal_bond(), IdentifyLigandMotifs::output_single_motif_to_pdb(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_coordinates(), and protocols::kinmatch::xform_rsd_gl2().
◆ set_xyz() [2/2]
| void core::conformation::Residue::set_xyz | ( | std::string const & | atm_name, |
| Vector const & | xyz_in | ||
| ) |
Sets the position of this residue's atom with name <atm_name>
example(s):
See also: Residue Residue.atom Residue.atoms Residue.xyz Pose
References atom(), and core::conformation::Atom::xyz().
◆ show()
| void core::conformation::Residue::show | ( | std::ostream & | output = std::cout, |
| bool | output_atomic_details = false |
||
| ) | const |
Generate string representation of Residue for debugging purposes.
References atom_name(), atoms_, core::chemical::rings::AXIAL, core::chemical::rings::EQUATORIAL, get_adjacent_heavy_atoms(), core::conformation::is_atom_axial_or_equatorial_to_ring(), core::chemical::ResidueType::is_cyclic(), is_virtual(), mirrored_relative_to_type(), core::chemical::ResidueType::n_rings(), natoms(), core::chemical::rings::NEITHER, core::chemical::ResidueType::ring_atoms(), ring_conformer(), rsd_type_, seqpos_, core::conformation::Atom::show(), and core::chemical::ResidueType::show().
Referenced by core::conformation::operator<<().
◆ sidechainAtoms_begin()
|
inline |
should be safe, given the atom ordering rules?
References atoms_, and first_sidechain_atom().
Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), and protocols::simple_filters::AtomicContactFilter::compute().
◆ type()
|
inline |
Returns this residue's ResidueType.
example(s): residue.type() See also: Residue Residue.type_ptr Residue.atom_type
References rsd_type_.
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), core::pose::add_custom_variant_type_to_pose_residue(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::motifs::add_motif_bb_constraints(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::conformation::add_variant_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), core::select::util::any_atoms_within_cutoff(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::pose::append_pose_with_glycan_residues(), core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residue_by_bond(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::conformation::Conformation::append_residues(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::cyclic_peptide::FlipChiralityMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::simple_moves::RingConformationMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cyclic_peptide::CrankshaftFlipMover::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::DumpSingleResidueRotamers::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::pose_sewing::filters::HasDisulfideFilter::apply(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::nmr::pre::PREMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_dihedral_bbg(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::loops::apply_sequence_mapping(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), apply_transform_Rx_plus_v(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), assign_orbitals(), core::chemical::ICoorAtomID::atom_id(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::scoring::atomic_depth::atomic_depth(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::conformation::Conformation::atoms_are_bonded(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), core::pack::dunbrack::DunbrackEnergy::atoms_with_dof_derivatives(), core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::atoms_with_dof_derivatives(), core::scoring::automorphic_rmsd(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pack::dunbrack::PeptideTorsionReporter::bb_torsion_index_for_rsd(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamerLibrary::best_rotamer_energy(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::conformation::break_disulfide(), protocols::match::downstream::ClassicMatchAlgorithm::build(), protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::pack::rotamer_set::build_single_edge_waters(), core::scoring::lkball::LKB_ResidueInfo::build_waters(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::drug_design::RDKitMetric::calculate(), protocols::antibody::AntibodyFeatures::calculate_cdr_aromatic_nres(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), core::io::carbohydrates::chain_gws_string(), core::conformation::check_good_cutpoint_neighbour(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::drug_design::AtomExistsFilter::compute(), protocols::drug_design::HeteroHeteroBondFilter::compute(), protocols::drug_design::NChiFilter::compute(), protocols::drug_design::RDKitMetricFilter::compute(), protocols::drug_design::SAScoreFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::ResidueChiralityFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), connect_atom(), connection_distance(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), protocols::legacy_sewing::create_model_from_pose(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::ArgCationPiEnergy::defines_score_for_residue_pair(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::energy_methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count(), determine_nonstandard_polymer_status(), core::scoring::constraints::NonResidueTypeConstraint::dist(), core::scoring::constraints::ResidueTypeConstraint::dist(), core::scoring::constraints::SequenceProfileConstraint::dist(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), core::io::carbohydrates::dump_gws(), protocols::viewer::dump_residue_kinemage(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::GenericBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::energy_methods::RingClosureEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::constraint_generator::existing_atoms(), protocols::protein_grid::ProteinGrid::export_protein_matrix_to_pose(), protocols::rna::denovo::figure_out_base_pair_partner(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector_bbdep(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::pose::rna::fix_sugar_coords(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), protocols::ligand_docking::frac_atoms_within(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_and_root_atoms(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::scoring::custom_pair_distance::PairFuncMap::get_atom_pair_func_list(), get_atoms_exocyclic_to_ring_atom(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::scoring::dna::get_base_stub(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::rna::get_bin(), protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pose::get_constraints_from_link_records(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), core::scoring::lDDT_Calculator::get_matching_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::pose::rna::get_number_base_pairs(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::P_AA::get_Paa_pp_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_packed_rotno(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::energy_methods::ArgCationPiEnergy::get_ring(), core::energy_methods::ArgCationPiEnergy::get_ring_params(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::conformation::get_root_atomno(), core::conformation::get_root_residue_root_atomno(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static_voronoi(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), core::conformation::get_second_atom_from_connection(), core::pose::rna::get_sugar_centroid(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::pack::palette::PackerPalette::get_types_on_residue(), core::scoring::lkball::LKB_ResidueInfo::get_water_builder(), core::scoring::dna::get_y_axis(), protocols::cryst::getMW(), core::pose::carbohydrates::glycosylate_pose(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::conformation::idealize_position(), core::conformation::improper_build(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::scoring::facts::FACTSPoseInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::initialize_residues_for_type(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::toolbox::rigid_body::initialize_stub(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::Conformation::insert_polymer_residue(), core::conformation::Conformation::insert_residue_by_bond(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), core::conformation::is_atom_axial_or_equatorial(), core::scoring::is_carbohydrate_ring_atom(), core::conformation::is_ideal_position(), core::scoring::sasa::SasaMethod::is_polar_atom(), core::energy_methods::StackElecEnergy::is_rna_base(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_tna_chainbreak(), core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(), core::pack::dunbrack::load_unboundrot(), core::energy_methods::IdealParametersDatabase::lookup_angle_legacy(), core::energy_methods::IdealParametersDatabase::lookup_length_legacy(), protocols::motifs::make_base_pair_mutation(), core::pose::mass(), protocols::environment::ProtectedConformation::match_variants(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), core::conformation::missing_stubs_build(), protocols::denovo_design::DisulfidizeMover::mixed_disulfide(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::ShearMover::move_with_rama(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::legacy_sewing::Assembly::native_positions(), protocols::cryst::ReportGradientsMover::normalization(), core::scoring::OmegaTether::omega_index(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::qsar::scoring_grid::MolecularWeightNormalization::operator()(), core::pack::optimize_H_and_notify(), orient_onto_residue(), orient_onto_residue_peptoid(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::chemical::sdf::MolWriter::output_residue(), core::scoring::OmegaTether::phi_index(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), place(), protocols::normalmode::NormalMode::prepare_coord(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), core::conformation::print_node(), protocols::match::output::print_node(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::OmegaTether::psi_index(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), protocols::denovo_design::rebuild_missing_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), core::conformation::remove_variant_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), protocols::environment::ProtectedConformation::replace_residue_sandbox(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::HBondFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), Residue(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::GenericBondedPotential::residue_derivatives(), core::energy_methods::SplitUnfoldedTwoBodyEnergy::residue_energy(), core::energy_methods::CovalentLabelingFAEnergy::residue_energy(), core::energy_methods::DEPC_MS_Energy::residue_energy(), core::energy_methods::HRFDynamicsEnergy::residue_energy(), core::energy_methods::OmegaTetherEnergy::residue_energy(), core::energy_methods::pHEnergy::residue_energy(), core::energy_methods::RamachandranEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::ReferenceEnergyNoncanonical::residue_energy(), core::energy_methods::RingClosureEnergy::residue_energy(), core::energy_methods::UnfoldedStateEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy(), core::energy_methods::CustomAtomPairEnergy::residue_pair_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::PeptideBondEnergy::residue_pair_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResPairDistEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), core::energy_methods::DisulfideMatchingEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::energy_methods::PoissonBoltzmannEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::energy_methods::ArgCationPiEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), resolve_partial_atom_id(), protocols::multistate_design::restrict_to_canonical_aas(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_deriv_bbdep(), core::pack::dunbrack::RotamerLibrary::rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv(), core::pack::dunbrack::rotamer_from_chi(), core::scoring::ResidueExclParams::same_rsdpairs(), protocols::qsar::scoring_grid::LigandPropertyScore::score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::scoring::constraints::NonResidueTypeConstraint::score(), core::scoring::constraints::ResidueCouplingConstraint::score(), core::scoring::constraints::ResidueTypeConstraint::score(), core::scoring::ProQPotential::score(), core::pack::dunbrack::RotamerConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), core::select::util::select_coord_for_residue(), protocols::loops::select_loop_residues(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::Conformation::sequence_matches(), core::conformation::Conformation::set_polymeric_connection(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pose::Pose::set_ring_conformation(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), core::pose::setup_dof_mask_from_move_map(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::GoapEnergy::setup_for_scoring(), core::energy_methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::GenericBondedPotential::setup_for_scoring(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::RingConformationMover::setup_residue_list(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::SimpleEntropy(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), core::scoring::PoissonBoltzmannPotential::solve_pb(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords(), core::scoring::orbitals::surrogate_atom_for_orbital(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), core::pose::carbohydrates::tautomerize_anomer(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), protocols::cyclic_peptide::CrankshaftFlipMover::try_peptide_flip(), protocols::cyclic_peptide::CrankshaftFlipMover::try_peptoid_flip(), protocols::cyclic_peptide::CrankshaftFlipMover::try_pre_gly_flip(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), update_connections_to_other_residue(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), core::pose::rna::update_map(), core::scoring::facts::FACTSPotential::update_residue_for_packing(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::io::serialization::write_binary(), and core::chemical::ICoorAtomID::xyz().
◆ type_ptr()
|
inline |
Returns this residue's ResidueType as a COP.
example(s): residue.typei_ptr() See also: Residue Residue.type Residue.atom_type
References rsd_type_ptr_.
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::scoring::RamaPrePro::atoms_w_dof_derivatives(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer(), core::scoring::trie::create_trie(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_chem_comp_type(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf().
◆ update_actcoord()
| void core::conformation::Residue::update_actcoord | ( | ) |
Updates actcoord for this residue.
loop over all actcoord atoms for this ResidueType, average their actual positions in this residue.
References actcoord(), core::chemical::ResidueType::actcoord_atoms(), atoms(), and rsd_type_.
Referenced by set_all_ring_nu(), set_chi(), set_d(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_tau(), set_theta(), and core::conformation::Conformation::update_residue_coordinates().
◆ update_connections_to_other_residue()
| void core::conformation::Residue::update_connections_to_other_residue | ( | Residue const & | other_rsd | ) |
Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number).
Throws an error if this residue doesn't have a connection id indicated by the other residue. Overwrites connection ids otherwise, with no consideration of whether the original connection was to other_rsd.
References connect_map(), connect_map_, connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::n_possible_residue_connections(), name(), residue_connection_partner(), seqpos(), core::conformation::TR(), and type().
◆ update_connections_to_residues()
|
private |
Updates connections_to_residues_ using connect_map_.
Private function to keep the connections_to_residues_ array up to date
- Note
- This could be made faster – connections_to_residues_ is a std::map< > so operator[] calls are slow
References connect_map_, connections_to_residues_, and n_possible_residue_connections().
Referenced by residue_connection_partner(), and update_sequence_numbering().
◆ update_nus()
| void core::conformation::Residue::update_nus | ( | ) |
Calculate the set of nu dihedrals from the xyz coordinates and store them.
References atom(), core::chemical::ResidueType::n_nus(), n_nus(), nu_atoms(), core::chemical::ResidueType::nu_atoms(), nus_, rsd_type_, and xyz().
Referenced by Residue().
◆ update_orbital_coords()
|
inline |
◆ update_sequence_numbering()
| void core::conformation::Residue::update_sequence_numbering | ( | utility::vector1< Size > const & | old2new | ) |
Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped.
update sequence numbers for this residue and the numbers stored about its connections. called by our owning conformation when the sequence numbers are remapped
References connect_map_, determine_nonstandard_polymer_status(), pseudobonds_, seqpos_, and update_connections_to_residues().
◆ upper_connect()
|
inline |
Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue.
References rsd_type_, and core::chemical::ResidueType::upper_connect().
Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), protocols::loops::loop_closure::ccd::get_deviation(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::energy_methods::ProClosureEnergy::measure_chi4(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), resolve_partial_atom_id(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ upper_connect_atom()
|
inline |
Returns the index number of this residue's atom which connects to the residue after it in sequence.
- Note
- : polymers only, example: for an amino acid, residue.upper_connect_atom() = atom_index("C")
example(s): residue.upper_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Pose
References rsd_type_, and core::chemical::ResidueType::upper_connect_atom().
Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::loops::add_single_cutpoint_variant(), core::conformation::Conformation::append_residue_by_bond(), core::conformation::Conformation::append_residues(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::scoring::constraints::auto_detect_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), connect_atom(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::loophash::FastGapMover::find_next_gap(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), and core::pose::show_adjacent_nt_connections().
◆ xyz() [1/2]
Returns the position of this residue's atom with index number <atm_index>
- Note
- : position is a Vector
example(s): residue.xyz(3) See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose
References atoms_.
Referenced by core::pose::motif::a(), protocols::LoopRebuild::acceptable_rmsd_change(), protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), core::scoring::lkball::LK_DomeEnergy::accumulate_single_atom_contributions(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::hybridization::add_constraints(), protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints(), core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::relax::add_coordinate_constraints_to_pose(), core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(), protocols::seeded_abinitio::add_dist_constraints(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::add_macrocycle_constraints(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::advanced_select_points(), protocols::pose_sewing::movers::SewAnythingAddMover::align(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::align_pose(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::drug_design::align_residues(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis(), core::conformation::all_atom_center(), core::pose::all_atom_center(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), core::conformation::annotated_atom_graph_from_conformation(), core::scoring::APBSConfig::APBSConfig(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::magnesium::MgMinimizer::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_moves::ReportXYZ::apply(), protocols::simple_moves::ShortBackrubMover::apply(), protocols::simple_moves::SixDoFGridDockMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::antibody::CloseOneCDRLoop::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::task_operations::DesignAroundOperation::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::nmr::pcs::PCSLigandTransformMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::splice::Splice::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_rmsd_selector(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), apply_transform_downstream(), apply_transform_Rx_plus_v(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::constraint_movers::assert_that_all_atoms_are_moved_by_chi_angle(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), protocols::match::upstream::ProteinUpstreamBuilder::atom_coordinate_unacceptable(), protocols::splice::atom_dist_with_zero(), protocols::simple_filters::atom_distance(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), core::conformation::atom_graph_from_conformation(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), protocols::hydrate::atom_is_hydratable(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::LipidMemGrid::atom_score(), protocols::qsar::scoring_grid::ShapeGrid::atom_score(), protocols::qsar::scoring_grid::SingleGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), protocols::motifs::atom_specific_rms(), protocols::stepwise::modeler::rna::atom_square_deviation(), core::conformation::Conformation::atom_tree_torsion(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::methods::atoms_interact(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::backbone_sidechain_energy(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::pose::rna::bases_form_a_hydrogen_bond(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::features::BetaTurnDetection::beta_turn_present(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::lkball::WaterBuilder::build(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::match::downstream::RigidLigandBuilder::build(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::match::downstream::ClassicMatchAlgorithm::build_from_three_coords(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::build_rotated_water_rotamers(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::rna::movers::bump_check(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::fold_from_loops::movers::Ca_coord(), protocols::simple_moves::Ca_coord(), protocols::protein_interface_design::filters::Ca_coords(), protocols::simple_moves::Ca_coords(), protocols::splice::Ca_coords(), protocols::mpi_refinement::CA_Sscore(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::scoring::epr_deer::EPRSpinLabel::calc_sl_for_res(), protocols::fldsgn::topology::calc_strand_helix_angle(), protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::calculate(), protocols::glycopeptide_docking::calculate_additional_glycosylation_metrics(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), core::energy_methods::GoapEnergy::calculate_dipoles(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters_helper(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), protocols::splice::calculate_rmsd(), protocols::glycopeptide_docking::calculate_sampled_distance(), core::scoring::packstat::cavity_distance_constraint(), protocols::antibody::cdr_CN_anchor_distance(), protocols::antibody::CDR_H3_cter_filter(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), core::energy_methods::MPHelicalityEnergy::centroid_neighbors(), core::energy_methods::MPResidueLipophilicityEnergy::centroid_neighbors(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::chainbreak_check(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry_strict(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), protocols::pose_creation::MergePDBMover::check_duplicate(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor(), core::pose::rna::check_phosphate_contacts_donor(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::check_voxel_distance_to_receptor(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::pose_sewing::movers::SewAnythingAddMover::clashes(), protocols::pose_creation::MergePDBatOverlapMover::closest_non_overlap_residue(), protocols::pose_creation::MergePDBMover::closest_non_overlap_residue(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::constel::cnl_com(), protocols::rna::movers::com_of_true_residues(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_bounding_box(), protocols::forge::remodel::compute_center_of_mass(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), core::energy_methods::SAXSEnergy::compute_distance_histogram(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::simple_filters::InterfaceHbondsFilter::compute_salt_bridges(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::flxbb::constraints_sheet(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), protocols::simple_filters::coords(), protocols::splice::coords(), core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::constraint_generator::CoordinateConstraintGenerator::create_coordinate_constraint(), core::pack::interaction_graph::create_hbonds_one_way(), core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::cryst::crystRMSfast(), protocols::antibody_legacy::CDRH3Modeler::cutpoint_separation(), protocols::antibody::cutpoint_separation(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::energy_methods::RNA_CoarseDistEnergy::deriv_atom_pair(), core::scoring::lkball::WaterBuilder::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::relax::derive_sc_sc_restraints(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), core::pose::rna::detect_base_contacts(), core::conformation::Conformation::detect_bonds(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::cryst::MakeLayerMover::detect_connecting_subunits(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), core::pose::rna::detect_sugar_contacts(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::protein_interface_design::filters::RmsdSimpleFilter::dist_bb(), protocols::magnesium::MgScanner::distance_to_closest_magnesium(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), core::energy_methods::eval(), protocols::membrane::scoring::ElectricfieldLipidlayer::eval_atom_derivative(), protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_atom_derivative(), protocols::rna::AlignmentEnergy::eval_atom_derivative(), core::energy_methods::ImplicitMembraneElecEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::facts::FACTSPotential::eval_atom_nonpolar_derivative(), core::scoring::facts::FACTSPotential::eval_atom_polar_derivative(), core::energy_methods::FA_GrpElecEnergy::eval_context_derivatives(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::energy_methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_DomeEnergy::eval_residue_pair_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::RNA_CoarseDistEnergy::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::kinematic_closure::ClosureProblem::extract_cartesian_coordinates(), protocols::inverse_folding::extract_coordinates(), protocols::indexed_structure_store::extract_residue_entry(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd(), core::scoring::Membrane_FAPotential::fa_projection(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), protocols::rna::denovo::figure_out_base_pair_partner(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), core::pose::rna::figure_out_number_base_contacts(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::fill_chainTORS_info(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::conformation::Conformation::fill_missing_atoms(), protocols::forge::methods::fill_non_loop_cst_set(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::io::silent::RNA_SilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::Lanthionine_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), protocols::stepwise::monte_carlo::mover::filter_for_proximity(), core::select::filter_neighbors_by_distance(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::dna::find_basepairs(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::splice::find_disulfs_in_range(), protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), protocols::environment::find_implied_cut(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::recces::scratch::find_likely_first_chain_ending(), core::util::find_metalbinding_atoms_helper(), protocols::ddg::ddGMover::find_nbrs(), protocols::rna::movers::find_nearby_res(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::find_nearest_residue(), protocols::seeded_abinitio::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::pose::carbohydrates::find_neighbor(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_phosphate_contacts_other_partition(), protocols::enzdes::PredesignPerturbMover::find_rotation_center(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::pockets::PocketGrid::findExemplars(), protocols::splice::fix_chain_break_residue(), protocols::loops::fix_with_coord_cst(), protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs(), protocols::splice::Splice::fold_tree(), protocols::ligand_docking::frac_atoms_within(), protocols::motif_grafting::movers::MotifGraftMover::fragments_permutation_test_by_CA_distances(), protocols::features::LoopAnchorFeatures::frame_for_residue(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::comparative_modeling::gather_coords(), protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::relax::generate_bb_coordinate_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::energy_methods::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::scoring::dna::get_base_stub(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation_wTipsExtraInfo(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_distance(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::vip::VIP_Mover::get_cav_approx(), protocols::sic_dock::get_CB_Vecs_from_map(), protocols::sic_dock::get_CB_Vecs_from_pose(), core::energy_methods::HackAroEnergy::get_centroid(), protocols::rna::movers::RNA_LoopCloser::get_chainbreak_xyz(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::magnesium::get_closest_non_hoh_contact(), core::scoring::magnesium::get_closest_orbital_axis(), protocols::simple_filters::get_contact_features(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::cryst::get_corresponding_CAs(), core::scoring::magnesium::get_cos_theta(), core::io::raw_data::DecoyStruct::get_debug_rmsd(), core::io::silent::BinarySilentStruct::get_debug_rmsd(), core::io::silent::ProteinSilentStruct_Template< T >::get_debug_rmsd(), core::io::silent::RNA_SilentStruct::get_debug_rmsd(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::splice::RBOutMover::get_disulf_jump(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::MultipoleElecPotential::get_effective_radii(), protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::rna::movers::RNA_LoopCloser::get_gap_distance(), core::scoring::dna::get_groove_widths(), core::scoring::elec::GroupElec::get_grpdis2(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms(), protocols::magnesium::get_hoh_xyz(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::sic_dock::get_leap_lower_stub(), protocols::sic_dock::get_leap_upper_stub(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::scoring::loop_graph::get_loop_atom(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loop_rmsd(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::magnesium::SampleGrid::get_mg_positions(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::scoring::motif::get_nbrs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::vip::VIP_Mover::get_neighbors(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), core::pose::rna::get_op2_op1_sign(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), protocols::ligand_docking::get_radius_of_gyration(), protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue(), protocols::hydrate::get_ready_for_sew_packing(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), protocols::membrane::MPMutateRelaxMover::get_repack_residues(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::pack::get_residue_current_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::energy_methods::ArgCationPiEnergy::get_ring(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::energy_methods::ArgCationPiEnergy::get_ring_params(), protocols::normalmode::NormalModeRelaxMover::get_RMSD(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), protocols::magnesium::MgScanner::get_score(), protocols::simple_filters::ResidueDepthFilter::get_SDE_score(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::energy_methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), core::conformation::get_stub_from_residue(), core::pose::rna::get_stub_stub(), core::pose::rna::get_sugar_centroid(), core::energy_methods::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::dna::get_sugar_pucker(), core::scoring::dna::get_sugar_pucker_distr(), core::scoring::dna::get_sugar_torsions(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pose::symmetry::get_symm_axis(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_torsion_axis(), protocols::mpi_refinement::get_touched_res(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_xyz(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::getaxis(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::getcenter(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(), protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(), protocols::sic_dock::getxform(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::constel::has_prox_termini(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), protocols::relax::RangeRelaxMover::idealize_pose(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), core::energy_methods::FaMPEnvEnergy::init(), core::energy_methods::FaMPSolvEnergy::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), core::scoring::ResidueNblistData::initialize(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::magnesium::instantiate_water_at_octahedral_vertex(), core::pose::symmetry::intracomponent_contact(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), core::conformation::is_atom_axial_or_equatorial_to_ring(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::is_buried(), core::scoring::facts::FACTSPoseInfo::is_changed(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::hydrate::is_inside(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_residues_in_contact(), protocols::constel::FilterByProxTerm::is_satisfied(), protocols::constel::FilterByIndoleCOO::is_satisfied(), protocols::constel::FilterByTryptamine::is_satisfied(), protocols::constel::FilterByAmphetamine::is_satisfied(), protocols::constel::FilterByHistamine::is_satisfied(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), protocols::antibody::kink_dihedral(), protocols::antibody::kink_Trp_Hbond(), protocols::scoring::Interface::ligand_calculate(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), IdentifyLigandMotifs::ligand_to_residue_analysis(), protocols::indexed_structure_store::FragmentLookup::lookup_closest_pose_fragments(), protocols::indexed_structure_store::FragmentLookup::lookup_pose_fragments(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::fragment::make_pose_from_frags(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::match_by_atomtype(), core::energy_methods::ProClosureEnergy::measure_chi4(), core::conformation::membrane::MembraneInfo::membrane_center(), core::conformation::membrane::MembraneInfo::membrane_normal(), core::pack::min_pack_optimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), protocols::electron_density::DockPDBIntoDensityMover::minimize_poseOP_into_density(), protocols::protein_interface_design::MinimizeInterface(), core::pose::MiniPose::MiniPose(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::sic_dock::neighbor_count(), protocols::ddg::ddGMover::neighborhood_of_mutations(), core::energy_methods::MPHelicalityEnergy::neighboring_atoms(), core::energy_methods::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::splice::neighbors_in_vector(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), core::conformation::membrane::MembraneGeometry::normal_vector(), protocols::cryst::ReportGradientsMover::normalization(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), orient_onto_location(), orient_onto_residue_peptoid(), core::conformation::orient_residue_for_ideal_bond(), core::pose::rna::output_ligands(), core::pose::rna::output_other_contacts(), core::chemical::sdf::MolWriter::output_residue(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), IdentifyLigandMotifs::output_single_motif_to_pdb(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::energy_methods::parcs_ccs(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), protocols::loops::pick_loops_chainbreak(), place(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::cryst::MakeLayerMover::place_near_origin(), protocols::drug_design::place_new_restype_rotamer_align(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::motifs::Motif::place_residue_(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::magnesium::MgOrbitalFrameFinder::point_orbitals_to_closest_ligands(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same(), protocols::membrane::pose_tm_com(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate(), protocols::normalmode::NormalMode::prepare_coord(), core::scoring::NeighborList::prepare_for_scoring(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::pose::rna::prepare_scratch_residue(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::simple_moves::DEEROptimizeCoordsMover::print_coords(), core::conformation::print_node(), protocols::match::output::print_node(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::membrane::MPLipidAccessibility::protein_in_membrane(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::hybridization::TMalign::read_pose(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::recenter(), protocols::pockets::PocketGrid::recenter(), protocols::simple_moves::PeriodicBoxMover::recenter_pose(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::SiteGrid::refresh(), protocols::hydrate::remove_non_buried_wat(), protocols::electron_density::remove_occupied_density_from_density(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::replace_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::facts::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), Residue(), core::energy_methods::CovalentLabelingEnergy::residue_energy(), core::energy_methods::CovalentLabelingFAEnergy::residue_energy(), core::energy_methods::DEPC_MS_Energy::residue_energy(), core::energy_methods::HRF_MSLabelingEnergy::residue_energy(), core::energy_methods::HRFDynamicsEnergy::residue_energy(), core::energy_methods::RingClosureEnergy::residue_energy(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), core::energy_methods::WaterSpecificEnergy::residue_energy(), core::pose::rna::residue_is_bulge(), protocols::sic_dock::residue_is_floppy(), protocols::hydrate::residue_near_water(), core::scoring::hbonds::residue_near_water(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::energy_methods::GoapEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::CustomAtomPairEnergy::residue_pair_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::PairEnergy::residue_pair_energy(), core::energy_methods::PeptideBondEnergy::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::energy_methods::ImplicitMembraneElecEnergy::residue_pair_energy(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::energy_methods::ArgCationPiEnergy::residue_pair_energy(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::lDDT_Calculator::residue_pair_stats(), core::conformation::residue_point_graph_from_conformation(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::scoring::methods::residues_interact(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position(), core::energy_methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::scoring::rna::chemical_shift::ring_pos(), protocols::protein_interface_design::filters::RmsdSimpleFilter::rmsd_bb(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::toolbox::sample_around::rotate_into_phosphate_frame(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::RTMin::rtmin(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), protocols::qsar::scoring_grid::ChargeGrid::score(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::LipidMemGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::qsar::scoring_grid::SingleGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::sic_dock::XfoxmScore::score(), core::scoring::constraints::NamedAngleConstraint::score(), core::scoring::constraints::NamedDihedralConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::energy_methods::RNA_CoarseDistEnergy::score_atom_pair(), core::energy_methods::RNA_FA_ElecEnergy::score_atom_pair(), core::energy_methods::ImplicitMembraneElecEnergy::score_atom_pair(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_base_blob(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::score_satellite_blob(), core::select::util::select_coord_for_residue(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points(), protocols::features::serialize_residue_xyz_coords(), set_all_ring_nu(), set_chi(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::match::downstream::TargetRotamerCoords::set_coordinates_for_rotamer(), set_d(), core::scoring::nmr::NMRGridSearch::set_grid_search_center(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), protocols::hydrate::set_task_and_movemap(), set_tau(), protocols::denovo_design::components::Segment::set_template_pose(), set_theta(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), core::scoring::NeighborList::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::facts::FACTSPotential::setup_for_derivatives(), core::energy_methods::DEEREnergy::setup_for_derivatives(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), core::import_pose::setup_jumps(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain(), protocols::dna::show_dna_geometry_extra_details(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), core::energy_methods::RNA_CoarseDistEnergy::sidechain_sidechain_energy(), protocols::loops::split_by_ca_ca_dist(), core::pack::scmin::CartSCMinMinimizerMap::starting_dofs(), protocols::minimization_packing::GreenPacker::store_reference_pose_geometry(), core::scoring::facts::FACTSResidueInfo::store_xyz(), core::scoring::dna::strand_orientation_vector(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), core::scoring::superimpose_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::scoring::sym_rmsd_with_super_subset(), protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(), core::scoring::BB_Pos::take_coordinates_from_pose(), protocols::protein_interface_design::movers::test_res_res_aln(), core::conformation::membrane::MembraneGeometry::thickness_vector(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), protocols::hybridization::MRMover::trim_target_pose(), protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), update_nus(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::energy_methods::Burial_v2Energy::using_atom_distance(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), protocols::symmetry::SymmetrySlider::very_far_away(), protocols::antibody::vl_vh_orientation_coords(), protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::scoring::PoissonBoltzmannPotential::write_config(), core::conformation::ResidueKinWriter::write_kin_header(), protocols::kinmatch::xform_rsd_gl2(), and protocols::dna::z_axis_dist().
◆ xyz() [2/2]
|
inline |
Returns the position of this residue's atom with name <atm_name>
- Note
- : position is a Vector
example(s): residue.xyz("CA") See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose
References atom(), and core::conformation::Atom::xyz().
Member Data Documentation
◆ actcoord_
|
private |
the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair
Referenced by actcoord(), and init_residue_from_other().
◆ atoms_
|
private |
our conformation atoms (not kinematic atom pointers) with xyz positions and atom type
Referenced by atom(), atom_begin(), atom_end(), atom_type_index(), atoms(), heavyAtoms_end(), init_residue_from_other(), nbr_atom_xyz(), Residue(), set_xyz(), show(), sidechainAtoms_begin(), and xyz().
◆ chain_
|
private |
the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
Referenced by chain(), init_residue_from_other(), polymeric_oriented_sequence_distance(), and polymeric_sequence_distance().
◆ chi_
|
private |
our chi (side chain) torsion angles
Referenced by chi(), init_residue_from_other(), is_similar_rotamer(), Residue(), and set_chi().
◆ connect_map_
|
private |
map between connection ids on this residue and the connection points on other residues to which its bonded
Referenced by actual_residue_connection(), clear_residue_connections(), connect_map(), connect_map_size(), connected_residue_at_resconn(), connection_incomplete(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), determine_nonstandard_polymer_status(), has_incomplete_connection(), init_residue_from_other(), mark_connect_incomplete(), residue_connection_conn_id(), residue_connection_partner(), update_connections_to_other_residue(), update_connections_to_residues(), and update_sequence_numbering().
◆ connections_to_residues_
|
private |
lists for each connected residue of the connection points on this residue that connect the pair.
Referenced by clear_residue_connections(), connect_atom(), connections_to_residue(), copy_residue_connections(), copy_residue_connections_from(), init_residue_from_other(), is_bonded(), mark_connect_incomplete(), and update_connections_to_residues().
◆ data_cache_
|
private |
Referenced by data(), data_ptr(), init_residue_from_other(), nonconst_data(), and nonconst_data_ptr().
◆ mainchain_torsions_
|
private |
our (possibly empty) backbone torsion angles
Referenced by init_residue_from_other(), mainchain_torsion(), and mainchain_torsions().
◆ mirrored_relative_to_type_
|
private |
Is this residue mirrored relative to its coordinates in the ResidueType?
Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures. False by default.
Referenced by init_residue_from_other(), mirrored_relative_to_type(), and set_mirrored_relative_to_type().
◆ misplaced_
|
private |
Inter-residue connection data.
Was the Residue incorrectly oriented and placed within the polymer when created?
Referenced by init_residue_from_other(), misplaced(), and Residue().
◆ nonstandard_polymer_
|
private |
true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1
Referenced by clear_residue_connections(), connect_atom(), copy_residue_connections_from(), determine_nonstandard_polymer_status(), and init_residue_from_other().
◆ nus_
|
private |
our nu (internal ring) torsion angles
Referenced by init_residue_from_other(), nu(), nus(), Residue(), ring_conformer(), set_all_nu(), set_all_ring_nu(), set_tau(), and update_nus().
◆ orbitals_
|
private |
Referenced by assign_orbitals(), init_residue_from_other(), orbital_type_index(), orbital_xyz(), and set_orbital_xyz().
◆ pseudobonds_
|
private |
other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds)
Referenced by clear_residue_connections(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), get_pseudobonds_to_residue(), init_residue_from_other(), is_pseudo_bonded(), pseudobonds(), Residue(), set_pseudobonds_to_residue(), and update_sequence_numbering().
◆ rsd_type_
|
private |
our Residue type
Referenced by aa(), abase2(), accpt_pos(), accpt_pos_sc(), actcoord_atoms(), all_bb_atoms(), apply_transform_downstream(), assign_orbitals(), atom_base(), atom_depends_on_lower(), atom_depends_on_upper(), atom_index(), atom_is_backbone(), atom_is_hydrogen(), atom_is_polar_hydrogen(), atom_name(), atom_type(), atom_type_set(), atomic_charge(), atoms_with_orb_index(), attached_H_begin(), attached_H_end(), backbone_aa(), bonded_neighbor(), bonded_orbitals(), build_orbital_xyz(), carbohydrate_info(), chi_atoms(), chi_rotamers(), connect_atom(), connected_residue_at_lower(), connected_residue_at_upper(), cut_bond_neighbor(), first_sidechain_atom(), first_sidechain_hydrogen(), get_metal_binding_atoms(), Haro_index(), has(), has_lower_connect(), has_property(), has_sc_orbitals(), has_shadow_atoms(), has_upper_connect(), has_variant_type(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), Hpol_index(), Hpos_apolar(), Hpos_polar(), Hpos_polar_sc(), icoor(), is_apolar(), is_aramid(), is_aromatic(), is_branch_point(), is_carbohydrate(), is_charged(), is_coarse(), is_d_rna(), is_DNA(), is_l_rna(), is_ligand(), is_lower_terminus(), is_meta_aramid(), is_metal(), is_metalbinding(), is_NA(), is_ortho_aramid(), is_para_aramid(), is_peptoid(), is_polar(), is_polymer(), is_polymer_bonded(), is_post_methylene_meta_aramid(), is_post_methylene_ortho_aramid(), is_post_methylene_para_aramid(), is_pre_methylene_meta_aramid(), is_pre_methylene_ortho_aramid(), is_pre_methylene_para_aramid(), is_pre_methylene_post_methylene_meta_aramid(), is_pre_methylene_post_methylene_ortho_aramid(), is_pre_methylene_post_methylene_para_aramid(), is_protein(), is_purine(), is_pyrimidine(), is_repulsive(), is_RNA(), is_similar_aa(), is_similar_rotamer(), is_sri(), is_terminus(), is_TNA(), is_triazolemer(), is_upper_terminus(), is_virtual(), is_virtual_residue(), is_water(), last_backbone_atom(), lower_connect(), lower_connect_atom(), mainchain_atom(), mainchain_atoms(), mm_atom_name(), n_hbond_acceptors(), n_hbond_donors(), n_mainchain_atoms(), n_non_polymeric_residue_connections(), n_nus(), n_orbitals(), n_polymeric_residue_connections(), n_possible_residue_connections(), n_virtual_atoms(), na_analogue(), name(), name1(), name3(), natoms(), nbr_atom(), nbr_atom_xyz(), nbr_radius(), nbrs(), nchi(), nheavyatoms(), nu_atoms(), orbital_name(), orbital_type(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), path_distance(), path_distances(), place(), requires_actcoord(), Residue(), residue_connect_atom_index(), residue_connection(), ring_conformer(), RNA_info(), select_orient_atoms(), set_all_ring_nu(), set_chi(), set_d(), set_orbital_xyz(), set_tau(), set_theta(), show(), type(), update_actcoord(), update_nus(), update_orbital_coords(), upper_connect(), and upper_connect_atom().
◆ rsd_type_ptr_
|
private |
Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed.
Referenced by clone_flipping_chirality(), and type_ptr().
◆ seqpos_
|
private |
the sequence position
Referenced by connect_atom(), fill_missing_atoms(), init_residue_from_other(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), seqpos(), show(), and update_sequence_numbering().
The documentation for this class was generated from the following files:
- src/core/conformation/Residue.hh
- src/core/conformation/Residue.cc
