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Rosetta 3.5
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Rosetta 3.5
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silly demo class – what would the most familiar residue look like? More...
#include <ResidueType.hh>
Public Member Functions | |
| virtual | ~ResidueType () |
| destructor More... | |
| ResidueType (AtomTypeSetCAP atom_types, ElementSetCAP element_types, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types) | |
| constructor More... | |
| ResidueTypeOP | clone () const |
| make a copy More... | |
| AtomTypeSet const & | atom_type_set () const |
| access by reference the atomset for which this residue is constructed More... | |
| ElementSet const & | element_set () const |
| access by reference the atomset for which this residue is constructed More... | |
| AtomTypeSetCAP | atom_type_set_ptr () const |
| access by const pointer the atomset for which this residue is constructed More... | |
| Atom & | atom (Size const atom_index) |
| Atom const & | atom (Size const atom_index) const |
| Atom & | atom (std::string const &atom_name) |
| Atom const & | atom (std::string const &atom_name) const |
| Orbital const & | orbital (Size const orbital_index) const |
| Orbital const & | orbital (std::string const &orbital_name) const |
| AtomType const & | atom_type (Size const atomno) const |
| Get the chemical atom_type for this atom by it index number in this residue. More... | |
| Size | natoms () const |
| Get the chemical atom_type index number for this atom by its index number in this residue. More... | |
| Size | nheavyatoms () const |
| number of heavy atoms More... | |
| Size | n_hbond_acceptors () const |
| number of hbond_acceptors More... | |
| Size | n_hbond_donors () const |
| number of hbond_donors More... | |
| Size | lower_connect_atom () const |
| index number of the atom which connects to the lower connection More... | |
| int | path_distance (Size at1, Size at2) const |
| path distance (number of bonds separated) between a pair of atoms More... | |
| utility::vector1< int > const & | path_distance (Size atom) const |
| shortest path distance for an atom to all other residue atoms More... | |
| utility::vector1 < utility::vector1< int > > const & | path_distances () const |
| accessor of path_distance_ data for this residue, which is a 2D array More... | |
| Size | attached_H_begin (Size const atom) const |
| index number of the first attached Hydrogen on an atom More... | |
| Size | attached_H_end (Size const atom) const |
| index number of the last attached Hydrogen on an atom More... | |
| AtomIndices const & | attached_H_begin () const |
| for all heavy atoms, index numbers of their first attached Hydrogen More... | |
| AtomIndices const & | attached_H_end () const |
| for all heavy atoms, index numbers of their last attached Hydrogen More... | |
| Size | number_bonded_hydrogens (Size const atomno) const |
| indicates how many proton bonded neighbors an atom has More... | |
| Size | number_bonded_heavyatoms (Size const atomno) const |
| indicates how many heavyatom bonded neighbors an atom has More... | |
| AtomIndices const & | bonded_neighbor (Size const atomno) const |
| indices of the bonded neighbors for an atom More... | |
| utility::vector1< BondName > const & | bonded_neighbor_types (Size const atomno) const |
| AtomIndices const & | cut_bond_neighbor (Size const atomno) const |
| indices of the bonded neighbors for an atom More... | |
| AtomIndices const & | nbrs (Size const atomno) const |
| indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno) More... | |
| AtomIndices const & | chi_atoms (Size const chino) const |
| indices of the atoms which are used to define a given chi angle (chino) More... | |
| utility::vector1< AtomIndices > const & | chi_atoms () const |
| indices of the atoms which are used to define all the chi angles More... | |
| AtomIndices const & | all_bb_atoms () const |
| Indices of all backbone atoms, hydrogens and heavyatoms. More... | |
| AtomIndices const & | all_sc_atoms () const |
| Indices of all sidechain atoms, hydrogens and heavyatoms. More... | |
| AtomIndices const & | Haro_index () const |
| return indices of aromatic Hydrogens More... | |
| AtomIndices const & | Hpol_index () const |
| return indices of polar Hydrogens More... | |
| AtomIndices const & | Hpos_polar () const |
| indices of polar hydrogens as Hbond donors More... | |
| AtomIndices const & | Hpos_apolar () const |
| indices of non-polar hydrogens as potential carbon Hbond donors More... | |
| AtomIndices const & | Hpos_polar_sc () const |
| AtomIndices const & | accpt_pos () const |
| indices of atoms as Hbond acceptors More... | |
| AtomIndices const & | accpt_pos_sc () const |
| indices of atoms as Hbond acceptors More... | |
| bool | heavyatom_has_polar_hydrogens (Size ind) const |
| bool | heavyatom_is_an_acceptor (Size ind) const |
| bool | atom_is_polar_hydrogen (Size ind) const |
| AtomIndices const & | mainchain_atoms () const |
| indices of all mainchain atoms More... | |
| Size | mainchain_atom (Size const atm) const |
| index of mainchain atom More... | |
| void | set_mainchain_atoms (AtomIndices const &mainchain) |
| set indices of all mainchain atoms More... | |
| bool | has (std::string const &atom_name) const |
| is this atom present in this residue? More... | |
| Size | atom_base (Size const atomno) const |
| get index of an atom's base atom More... | |
| Size | abase2 (Size const atomno) const |
| get index of an atom's second base atom More... | |
| std::string const & | atom_name (Size const index) const |
| get atom name by index More... | |
| bool | has_atom_name (std::string const &name) const |
| Check if residue type has an atom by a given atomname. More... | |
| Size | atom_index (std::string const &name) const |
| get atom index by name More... | |
| void | show_all_atom_names (std::ostream &out) const |
| Size | last_backbone_atom () const |
| index of the last backbone heavy atom More... | |
| Size | first_sidechain_atom () const |
| index of the first sidechain atom (heavy or hydrogen) More... | |
| Size | first_sidechain_hydrogen () const |
| index of the first sidehchain hydrogen More... | |
| bool | atom_is_backbone (Size const atomno) const |
| is a backbone atom (heavy or hydorgen)? More... | |
| bool | atom_is_hydrogen (Size const atomno) const |
| quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last. More... | |
| utility::vector1< Size > const & | last_controlling_chi () const |
| Read access to the last_controlling_chi_ array. More... | |
| Size | last_controlling_chi (Size atomno) const |
| The last_controlling_chi for an atom. 0 if an atom is controlled by no chi. More... | |
| utility::vector1< AtomIndices > const & | atoms_last_controlled_by_chi () const |
| Read access to the atoms_last_controlled_by_chi_ array. More... | |
| AtomIndices const & | atoms_last_controlled_by_chi (Size chi) const |
| Read access to the Atoms last controlled by a particular chi. More... | |
| AtomIndices const & | actcoord_atoms () const |
| get indices for atoms used to define actcoord More... | |
| MMAtomType const & | mm_atom_type (Size const atomno) const |
| Get the MM atom_type for this atom by its index number in this residue. More... | |
| chemical::orbitals::OrbitalType const & | orbital_type (int const orbital_index) const |
| Get the MM atom_type index number for this atom by its index number in this residue. More... | |
| Size | n_orbitals () const |
| number of orbitals More... | |
| utility::vector1< core::Size > const & | bonded_orbitals (Size const atomno) const |
| indices of the orbitals bonded to an atom More... | |
| bool | has_orbital (std::string const &orbital_name) const |
| is this orbital present in this residue? More... | |
| AtomIndices const & | atoms_with_orb_index () const |
| core::Size | orbital_index (std::string const &name) const |
| orbital name by index More... | |
| ResidueTypeSet const & | residue_type_set () const |
| void | residue_type_set (ResidueTypeSetCAP set_in) |
| set the residue type set of origin. More... | |
| Size | nchi () const |
| number of chi angles More... | |
| Size | n_proton_chi () const |
| number of proton chis More... | |
| bool | is_proton_chi (Size const chino) const |
| number of proton chis More... | |
| Size | proton_chi_2_chi (Size proton_chi_id) const |
| translate proton_chi to global chi More... | |
| Size | chi_2_proton_chi (Size chi_index) const |
| utility::vector1< Real > const & | proton_chi_samples (Size proton_chi) const |
| utility::vector1< Real > const & | proton_chi_extra_samples (Size proton_chi) const |
| void | set_lower_connect_atom (std::string const &atm_name) |
| set the atom which connects to the lower connection More... | |
| ResidueConnection const & | upper_connect () const |
| ResidueConnection const & | lower_connect () const |
| Size | upper_connect_id () const |
| Size | lower_connect_id () const |
| Size | upper_connect_atom () const |
| index number of the atom which connects to the upper connection More... | |
| void | set_upper_connect_atom (std::string const &atm_name) |
| set the atom which connects to the upper connection More... | |
| utility::vector1< std::pair < Real, Real > > const & | chi_rotamers (Size const chino) const |
| all rotamers bins (mean, std) for a given chi angle More... | |
| Size | n_residue_connections () const |
| number of ResidueConnections, counting polymeric residue connections More... | |
| Size | n_polymeric_residue_connections () const |
| Size | n_non_polymeric_residue_connections () const |
| ResidueConnection const & | residue_connection (Size const i) const |
| get a ResidueConection More... | |
| ResidueConnection & | residue_connection (Size const i) |
| bool | atom_forms_residue_connection (Size const atomid) |
| Does an atom form any inter-residue chemical bonds? More... | |
| Size | n_residue_connections_for_atom (Size const atomid) const |
| How many inter-residue chemical bonds does a particular atom form? More... | |
| Size | residue_connection_id_for_atom (Size const atomid) const |
| Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom. More... | |
| utility::vector1< Size > const & | residue_connections_for_atom (Size const atomid) const |
| bool | residue_connection_is_polymeric (Size const resconn_id) const |
| Size | residue_connect_atom_index (Size const resconn_id) const |
| bool | requires_actcoord () const |
| require actcoord? More... | |
| void | update_actcoord (conformation::Residue &rot) const |
| update actcoord More... | |
| void | add_atom (std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge) |
| add an atom into this residue More... | |
| void | delete_atom (std::string const &name) |
| flag an atom for deletion by adding its index to the delete_atom_ list More... | |
| void | set_atom_type (std::string const &atom_name, std::string const &atom_type_name) |
| set atom type More... | |
| void | set_mm_atom_type (std::string const &atom_name, std::string const &mm_atom_type_name) |
| set mm atom type More... | |
| void | add_bond (std::string const &atom_name1, std::string const &atom_name2) |
| add a bond between atom1 and atom2, if bond type is not specified, default to SingleBond More... | |
| void | add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel) |
| void | add_cut_bond (std::string const &atom_name1, std::string const &atom_name2) |
| add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond More... | |
| void | nbr_atom (std::string const &atom_name) |
| set nbr_atom used to define residue-level neighbors More... | |
| Size | nbr_atom () const |
| get nbr_atom used to define residue-level neighbors More... | |
| void | nbr_radius (Real const radius) |
| set nbr_radius_ used to define residue-level neighbors More... | |
| Real | nbr_radius () const |
| get nbr_radius_ used to define residue-level neighbors More... | |
| core::Real const & | molecular_mass () const |
| get the molecular weight of this residue More... | |
| core::Real const & | molar_mass () const |
| get the molecular weight of this residue More... | |
| void | set_atom_base (std::string const &atom_name1, std::string const &atom_name2) |
| sets atom_base[ atom1 ] = atom2 More... | |
| void | set_backbone_heavyatom (std::string const &name) |
| set an atom as backbone heavy atom More... | |
| void | debug_dump_icoor () |
| Dump out atomnames and icoor values. More... | |
| AtomICoor const & | icoor (Size const atm) const |
| AtomICoord of an atom. More... | |
| void | set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false) |
| set AtomICoor for an atom More... | |
| void | set_icoor (Size const &index, std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false) |
| set AtomICoor for an atom More... | |
| void | assign_neighbor_atom () |
| void | assign_internal_coordinates () |
| void | calculate_icoor (std::string const &child, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3) |
| calculate AtomICoor for an atom and set it More... | |
| void | set_ideal_xyz (std::string const &atm, Vector const &xyz_in) |
| void | set_ideal_xyz (Size index, Vector const &xyz_in) |
| void | add_orbital (std::string &orbital_name, std::string &orbital_type_name) |
| add an orbital onto a residue based upon atom More... | |
| void | add_orbital_bond (std::string const &atom_name1, std::string const &orbital_name) |
| add an orbital bond between an atom and an orbital. More... | |
| orbitals::ICoorOrbitalData const & | orbital_icoor_data (Size const orbital_index) const |
| orbitals::ICoorOrbitalData const & | new_orbital_icoor_data (Size const orbital_index) const |
| void | set_orbital_icoor_id (std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3) |
| set OrbitalICoor for an orbital More... | |
| void | add_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) |
| add a chi angle defined by four atoms More... | |
| void | redefine_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4) |
| redefine a chi angle based on four atoms More... | |
| void | set_proton_chi (Size chino, utility::vector1< Real > dihedral_samples, utility::vector1< Real > extra_samples) |
| void | add_chi_rotamer (Size const chino, Real const mean, Real const sdev) |
| add a rotamer bin for a given chi More... | |
| void | finalize () |
| recalculate derived data, potentially reordering atom-indices More... | |
| void | require_final () const |
| an assertion funtion to ensure an ResidueType has been finalized More... | |
| Size | add_residue_connection (std::string const &atom_name) |
| add a ResidueConnection Doesnt set the ideal geometry – maybe it should? More... | |
| utility::vector1< std::string > const & | properties () const |
| acess specified properties More... | |
| void | add_property (std::string const &property) |
| add properties More... | |
| void | delete_property (std::string const &property) |
| delete properties More... | |
| void | add_actcoord_atom (std::string const &atom) |
| add an atom to the list for calculating actcoord center More... | |
| bool | is_polymer () const |
| is polymer? More... | |
| bool | is_protein () const |
| is protein? More... | |
| bool | is_DNA () const |
| is DNA? More... | |
| bool | is_RNA () const |
| is RNA? More... | |
| bool | is_coarse () const |
| is coarse? More... | |
| bool | is_NA () const |
| is Nucleic Acid? More... | |
| bool | is_carbohydrate () const |
| is carbohydrate? More... | |
| bool | is_ligand () const |
| bool | is_surface () const |
| is surface? (e.g. enamel) More... | |
| bool | has_sc_orbitals () const |
| does this residue have sidechain orbitals? More... | |
| bool | is_polar () const |
| is polar? More... | |
| bool | is_charged () const |
| is charged? More... | |
| bool | is_aromatic () const |
| is aromatic? More... | |
| bool | is_terminus () const |
| is terminus? More... | |
| bool | is_lower_terminus () const |
| is lower terminus? More... | |
| bool | is_upper_terminus () const |
| is upper terminus? More... | |
| bool | is_acetylated_nterminus () const |
| is acetylated n terminus More... | |
| bool | is_methylated_cterminus () const |
| is methylated c terminus More... | |
| bool | is_branch_point () const |
| is branch point for a branched polymer? More... | |
| bool | is_virtual (Size const &atomno) const |
| Check if atom is virtual. More... | |
| bool | is_virtual_residue () const |
| Check if residue is 'VIRTUAL_RESIDUE'. More... | |
| bool | is_adduct () const |
| is an adduct-modified residue? More... | |
| void | set_adduct_flag (bool adduct_in) |
| bool | has_property (std::string const &property) const |
| Generic property access – SLOW!!!!! More... | |
| bool | has_variant_type (VariantType const &variant_type) const |
| Generic variant access – SLOW!!!!! More... | |
| utility::vector1< VariantType > const & | variant_types () const |
| get all the variant types for this ResidueType More... | |
| bool | variants_match (ResidueType const &other) const |
| Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property. More... | |
| bool | nonadduct_variants_match (ResidueType const &other) const |
| similar to variants_match(), but allows different adduct-modified states More... | |
| void | add_variant_type (VariantType const &variant_type) |
| add one more variant type to this ResidueType More... | |
| void | aa (std::string const &type) |
| set our aa-type (could be "UNK") More... | |
| void | rotamer_aa (std::string const &type) |
| AA to use for rotamer library. More... | |
| std::string const & | name () const |
| get our (unique) residue name More... | |
| void | name (std::string const &name_in) |
| set our (unique) residue name More... | |
| std::string const & | name3 () const |
| get our 3letter code More... | |
| void | name3 (std::string const &name_in) |
| set our 3letter code More... | |
| char | name1 () const |
| get our 1letter code More... | |
| void | name1 (char const code) |
| set our 1letter code More... | |
| void | set_mol_data (sdf::MolData const &mol_data) |
| set the MolData object More... | |
| sdf::MolData | get_mol_data () const |
| AA const & | aa () const |
| our traditional residue type, if any More... | |
| AA const & | rotamer_aa () const |
| void | set_RotamerLibraryName (std::string const &filename) |
| std::string | get_RotamerLibraryName () const |
| A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use. More... | |
| dihedral_atom_set const & | dihedral (Size const dihe) const |
| dihedral methods More... | |
| utility::vector1< Size > const & | dihedrals_for_atom (Size atomno) const |
| Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom. More... | |
| Size | ndihe () const |
| Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms. More... | |
| void | print_dihedrals () const |
| bondangle_atom_set const & | bondangle (Size const bondang) const |
| Return the indices for the set of atoms that define a particular intraresidue angle. More... | |
| utility::vector1< Size > const & | bondangles_for_atom (Size atomno) const |
| Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More... | |
| Size | num_bondangles () const |
| get number of intraresidue bond angles More... | |
| void | print_bondangles () const |
| print intraresidue bond angles to standard out More... | |
| void | print_pretty_path_distances () const |
| print chemical-bond path distances to standard out More... | |
| void | set_ncaa_rotlib_path (std::string const &path) |
| Sets the path for the NCAA rotlib for the ResidueType. More... | |
| std::string const & | get_ncaa_rotlib_path () const |
| Returns the path to the NCAA rotlib for the residue type. More... | |
| void | set_use_ncaa_rotlib (bool flag) |
| Sets whether we are using a NCAA rotlib for the residue type. More... | |
| bool | get_use_ncaa_rotlib () const |
| Returns whether we are using a NCAA rotlib for the residue type. More... | |
| void | set_ncaa_rotlib_n_rotameric_bins (Size n_rots) |
| Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More... | |
| Size | set_ncaa_rotlib_n_rotameric_bins () const |
| Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More... | |
| void | set_ncaa_rotlib_n_bin_per_rot (utility::vector1< Size > n_bins_per_rot) |
| Sets the number of rotamers for each rotatable bond described by the NCAA rotlib. More... | |
| Size | get_ncaa_rotlib_n_bin_per_rot (Size n_rot) |
| Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond. More... | |
| utility::vector1< Size > const & | get_ncaa_rotlib_n_bin_per_rot () const |
| Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds. More... | |
| utility::vector1< two_atom_set > const & | atoms_within_one_bond_of_a_residue_connection (Size resconn) const |
| Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1< std::pair < Size, Size > > const & | within1bonds_sets_for_atom (Size atomid) const |
| Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More... | |
| utility::vector1 < three_atom_set > const & | atoms_within_two_bonds_of_a_residue_connection (Size resconn) const |
| Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn. More... | |
| utility::vector1< std::pair < Size, Size > > | within2bonds_sets_for_atom (Size atomid) const |
| Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More... | |
| core::chemical::rna::RNA_ResidueType const & | RNA_type () const |
| core::chemical::carbohydrates::CarbohydrateInfoCOP | carbohydrate_info () const |
| Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More... | |
| void | force_nbr_atom_orient (bool force_orient) |
| Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More... | |
| bool | force_nbr_atom_orient () const |
| Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More... | |
| void | select_orient_atoms (Size ¢er, Size &nbr1, Size &nbr2) const |
| Selects three atoms for orienting this residue type. More... | |
| utility::vector1< Adduct > const & | defined_adducts () const |
| get the adducts defined for this residue More... | |
| void | add_adduct (Adduct &adduct_in) |
| void | report_adducts () |
| void | nondefault (bool in) |
| void | base_restype_name (std::string const &in) |
| std::string | base_restype_name () const |
Public Attributes | |
| bool | serialized_ |
Private Member Functions | |
| void | setup_atom_ordering (AtomIndices &old2new) |
| set up atom ordering map old2new, called by finalize() More... | |
| void | reorder_primary_data (AtomIndices const &old2new) |
| reorder primary data in ResidueType given the old2new map, called by finalize() More... | |
| void | update_derived_data () |
| update derived data in ResidueType, called by finalize() More... | |
| void | update_residue_connection_mapping () |
| void | update_last_controlling_chi () |
| compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom. More... | |
| void | note_chi_controls_atom (Size chi, Size atomno) |
| Recursive subroutine invoked by update_last_controlling_chi(). More... | |
| void | assign_internal_coordinates (std::string const ¤t_atom) |
| @ recursive function to assign internal coordinates More... | |
Private Attributes | |
| AtomTypeSetCAP | atom_types_ |
| AtomTypeSet Object. More... | |
| ElementSetCAP | elements_ |
| MMAtomTypeSetCAP | mm_atom_types_ |
| MMAtomTypeSet. More... | |
| orbitals::OrbitalTypeSetCAP | orbital_types_ |
| Orbital types. More... | |
| ResidueTypeSetCAP | residue_type_set_ |
| utility::vector1< Atom > | atoms_ |
| vector of atoms: More... | |
| utility::vector1< Orbital > | orbitals_ |
| Size | natoms_ |
| number of atoms More... | |
| Size | nheavyatoms_ |
| number of heavy atoms More... | |
| Size | n_hbond_acceptors_ |
| number of hbond_acceptors More... | |
| Size | n_hbond_donors_ |
| number of hbond_donors More... | |
| Size | n_orbitals_ |
| number of orbitals More... | |
| Size | n_backbone_heavyatoms_ |
| number of backbone heavy atoms More... | |
| Size | first_sidechain_hydrogen_ |
| the index of first sidechain hydrogen atom More... | |
| Size | ndihe_ |
| number of dihedral angle atom sets More... | |
| utility::vector1 < utility::vector1< core::Size > > | orbital_bonded_neighbor_ |
| indices of the atoms psuedo bonded atoms. Used in orbital code More... | |
| utility::vector1< AtomIndices > | bonded_neighbor_ |
| indices of each atom's bonded neighbors More... | |
| utility::vector1 < utility::vector1< BondName > > | bonded_neighbor_type_ |
| indices of each atom's bonded neighbor type (uses the same indexing scheme and order as bonded_neighbor_ More... | |
| utility::vector1< AtomIndices > | cut_bond_neighbor_ |
| indices of each atom's bonded neighbors More... | |
| utility::vector1< Size > | atom_base_ |
| indices of each atom's base atom More... | |
| utility::vector1< Size > | abase2_ |
| indices of each atom's second base atom, for acceptors atom only More... | |
| utility::vector1< Size > | attached_H_begin_ |
| indices of each heavyatom's first attached hydrogen More... | |
| utility::vector1< Size > | attached_H_end_ |
| indices of each heavyatom's last attached hydrogen More... | |
| utility::vector1< Size > | parents_ |
| atom parents More... | |
| utility::vector1 < dihedral_atom_set > | dihedral_atom_sets_ |
| vector of sets of atoms that make up dihedral angles in the residue More... | |
| utility::vector1 < utility::vector1< Size > > | dihedrals_for_atom_ |
| all intra-residue dihedral angles that each atom "participates" in. More... | |
| utility::vector1 < bondangle_atom_set > | bondangle_atom_sets_ |
| vector of sets of atoms that make up bond angles in the residue More... | |
| utility::vector1 < utility::vector1< Size > > | bondangles_for_atom_ |
| all intra-residue bond angles that each atom "participates" in. More... | |
| utility::vector1< Size > | last_controlling_chi_ |
| utility::vector1< AtomIndices > | atoms_last_controlled_by_chi_ |
| AtomIndices | atoms_with_orb_index_ |
| indices of Hbond acceptor positions More... | |
| AtomIndices | Haro_index_ |
| AtomIndices | Hpol_index_ |
| AtomIndices | accpt_pos_ |
| AtomIndices | Hpos_polar_ |
| indices of polar Hydrogens for Hbond donors More... | |
| AtomIndices | Hpos_apolar_ |
| indices of apolar hydrogens More... | |
| AtomIndices | accpt_pos_sc_ |
| AtomIndices | Hpos_polar_sc_ |
| AtomIndices | all_bb_atoms_ |
| Indices of all backbone atoms, hydrogens and heavyatoms. More... | |
| AtomIndices | all_sc_atoms_ |
| Indices of all sidechain atoms, hydrogens and heavyatoms. More... | |
| utility::vector1< int > | heavyatom_has_polar_hydrogens_ |
| utility::vector1< int > | heavyatom_is_an_acceptor_ |
| utility::vector1< int > | atom_is_polar_hydrogen_ |
| AtomIndices | mainchain_atoms_ |
| indices of all mainchain atoms More... | |
| AtomIndices | actcoord_atoms_ |
| indices of action coordinate centers More... | |
| utility::vector1< AtomIndices > | chi_atoms_ |
| indices of four atoms to build each chi angle More... | |
| utility::vector1< bool > | is_proton_chi_ |
| utility::vector1< Size > | proton_chis_ |
| utility::vector1< Size > | chi_2_proton_chi_ |
| utility::vector1 < utility::vector1< Real > > | proton_chi_samples_ |
| utility::vector1 < utility::vector1< Real > > | proton_chi_extra_samples_ |
| utility::vector1 < utility::vector1< int > > | path_distance_ |
| number of bonds separated between any pair of atoms in this residue More... | |
| std::map< std::string, int > | atom_index_ |
| atom index lookup by atom name string More... | |
| std::map< std::string, int > | orbitals_index_ |
| atom index lookup by atom name string More... | |
| utility::vector1 < utility::vector1< std::pair < Real, Real > > > | chi_rotamers_ |
| Additional non-dunbrack rotamer bins. More... | |
| std::string | rotamer_library_name_ |
| bool | use_ncaa_rotlib_ |
| std::string | ncaa_rotlib_path_ |
| path to the NCAA rotlib More... | |
| Size | ncaa_rotlib_n_rots_ |
| the number of non-hydrogen chi angles in the NCAA rotlib More... | |
| utility::vector1< Size > | ncaa_rotlib_n_bins_per_rot_ |
| the number of rotamer bins for each chi angle in the NCAA rotlib More... | |
| utility::vector1< std::string > | properties_ |
| residue properties as defined in the residue param files More... | |
| bool | is_polymer_ |
| bool | is_protein_ |
| bool | is_charged_ |
| bool | is_polar_ |
| bool | has_sc_orbitals_ |
| bool | is_aromatic_ |
| bool | is_DNA_ |
| bool | is_RNA_ |
| bool | is_NA_ |
| bool | is_carbohydrate_ |
| bool | is_ligand_ |
| bool | is_surface_ |
| bool | is_terminus_ |
| bool | is_lower_terminus_ |
| bool | is_upper_terminus_ |
| bool | is_phosphonate_ |
| bool | is_phosphonate_upper_ |
| bool | is_acetylated_nterminus_ |
| bool | is_methylated_cterminus_ |
| bool | is_coarse_ |
| bool | is_adduct_ |
| utility::vector1< VariantType > | variant_types_ |
| here we store the patch operations/variant types that describe this residue More... | |
| AA | aa_ |
| standard rosetta aa-type for knowledge-based potentials, may be aa_unk More... | |
| AA | rotamer_aa_ |
| std::string | name_ |
| unique residue id More... | |
| std::string | name3_ |
| pdb-file id, need not be unique More... | |
| char | name1_ |
| one-letter code, also not necessarily unique More... | |
| Size | nbr_atom_ |
| atom used for calculating residue-level neighbors More... | |
| Real | nbr_radius_ |
| radius cutoff to define neighors More... | |
| bool | force_nbr_atom_orient_ |
| Real | molecular_mass_ |
| Real | molar_mass_ |
| Size | n_actcoord_atoms_ |
| number of actcoord atoms More... | |
| sdf::MolData | mol_data_ |
| the unprocessed metadata More... | |
| utility::vector1 < ResidueConnection > | residue_connections_ |
| Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections. More... | |
| utility::vector1 < utility::vector1< Size > > | atom_2_residue_connection_map_ |
| utility::vector1 < utility::vector1 < two_atom_set > > | atoms_within_one_bond_of_a_residue_connection_ |
| For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1 < utility::vector1< std::pair < Size, Size > > > | within1bonds_sets_for_atom_ |
| For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. More... | |
| utility::vector1 < utility::vector1 < three_atom_set > > | atoms_within_two_bonds_of_a_residue_connection_ |
| For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1 < utility::vector1< std::pair < Size, Size > > > | within2bonds_sets_for_atom_ |
| For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. More... | |
| Size | lower_connect_id_ |
| Polymer lower connections. More... | |
| Size | upper_connect_id_ |
| Polymer upper connections. More... | |
| Size | n_non_polymeric_residue_connections_ |
| Size | n_polymeric_residue_connections_ |
| utility::vector1< std::string > | branch_point_atoms_ |
| AtomIndices | delete_atoms_ |
| a list of atom indices to be deleted More... | |
| AtomIndices | force_bb_ |
| atom indices forced to be considered backbone More... | |
| core::chemical::rna::RNA_ResidueType | rna_residuetype_ |
| core::chemical::carbohydrates::CarbohydrateInfoOP | carbohydrate_info_ |
| bool | finalized_ |
| status More... | |
| utility::vector1< Adduct > | defined_adducts_ |
| bool | nondefault_ |
| std::string | base_restype_name_ |
silly demo class – what would the most familiar residue look like?
Basically a slice of aaproperties pack!
This is an exercise to define the properties of an alternative Residue object, arising from frustration with the conformation::Residue hierarchy.
Properties:
Questions:
Definition at line 160 of file ResidueType.hh.
|
virtual |
| core::chemical::ResidueType::ResidueType | ( | AtomTypeSetCAP | atom_types, |
| ElementSetCAP | element_types, | ||
| MMAtomTypeSetCAP | mm_atom_types, | ||
| orbitals::OrbitalTypeSetCAP | orbital_types | ||
| ) |
constructor
We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc.
Definition at line 114 of file ResidueType.cc.
Referenced by clone().
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inline |
set our aa-type (could be "UNK")
Definition at line 1346 of file ResidueType.hh.
References aa_, and core::chemical::aa_from_name().
Referenced by protocols::simple_moves::MinimalRotamer::aa(), core::conformation::Residue::aa(), protocols::loops::add_loop(), protocols::motifs::add_motif_bb_constraints(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), protocols::motifs::backbone_stub_match(), core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::get_parallel_h_for_arg(), core::scoring::dna::get_y_axis_atoms(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::constraints::is_aromatic(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), protocols::multistate_design::limit_rotamer_set(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::constraints::requires_CB_mapping(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy(), core::scoring::methods::residue_type_has_waters(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().
|
inline |
our traditional residue type, if any
Used for knowledge-based scores, dunbrack, etc. could be "aa_unk"
Not clear what AA is – maybe an int, maybe an enum, maybe a "key"
Definition at line 1434 of file ResidueType.hh.
References aa_.
get index of an atom's second base atom
Definition at line 388 of file ResidueType.cc.
References abase2_.
Referenced by core::conformation::Residue::abase2().
|
inline |
indices of atoms as Hbond acceptors
Definition at line 417 of file ResidueType.hh.
References accpt_pos_.
Referenced by core::conformation::Residue::accpt_pos().
|
inline |
indices of atoms as Hbond acceptors
Definition at line 424 of file ResidueType.hh.
References accpt_pos_sc_.
Referenced by core::conformation::Residue::accpt_pos_sc().
|
inline |
get indices for atoms used to define actcoord
Definition at line 574 of file ResidueType.hh.
References actcoord_atoms_.
Referenced by core::conformation::Residue::actcoord_atoms(), and core::chemical::write_topology_file().
| void core::chemical::ResidueType::add_actcoord_atom | ( | std::string const & | atom) |
add an atom to the list for calculating actcoord center
Definition at line 1016 of file ResidueType.cc.
References actcoord_atoms_, atom_index(), finalized_, is_protein(), n_actcoord_atoms_, name_, and core::chemical::tr().
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inline |
Definition at line 1692 of file ResidueType.hh.
References defined_adducts_.
| void core::chemical::ResidueType::add_atom | ( | std::string const & | atom_name, |
| std::string const & | atom_type_name, | ||
| std::string const & | mm_atom_type_name, | ||
| Real const | charge | ||
| ) |
add an atom into this residue
Definition at line 397 of file ResidueType.cc.
References atom_2_residue_connection_map_, atom_base_, atom_index_, atom_name(), atom_types_, atoms_, bonded_neighbor_, bonded_neighbor_type_, cut_bond_neighbor_, elements_, finalized_, mm_atom_types_, molar_mass_, molecular_mass_, n_hbond_acceptors_, n_hbond_donors_, natoms_, orbital_bonded_neighbor_, parents_, core::chemical::strip_whitespace(), and core::chemical::tr().
Referenced by core::chemical::AddAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_atom().
| void core::chemical::ResidueType::add_bond | ( | std::string const & | atom_name1, |
| std::string const & | atom_name2 | ||
| ) |
add a bond between atom1 and atom2, if bond type is not specified, default to SingleBond
add a bond between atom1 and atom2 and add a BondType object referencing the bond (default bond type of SingleBond) update bonded_neighbor_ and resize it as necessary
Definition at line 554 of file ResidueType.cc.
References atom_index_, bonded_neighbor_, bonded_neighbor_type_, finalized_, has(), and core::chemical::SingleBond.
Referenced by core::chemical::AddBond::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_bond().
| void core::chemical::ResidueType::add_bond | ( | std::string const & | atom_name1, |
| std::string const & | atom_name2, | ||
| BondName | bondLabel | ||
| ) |
add a bond between atom1 and atom2 and add a BondType object referencing the bond using the specified bondName
Definition at line 591 of file ResidueType.cc.
References atom_index_, bonded_neighbor_, bonded_neighbor_type_, finalized_, and has().
| void core::chemical::ResidueType::add_chi | ( | Size const | chino, |
| std::string const & | atom_name1, | ||
| std::string const & | atom_name2, | ||
| std::string const & | atom_name3, | ||
| std::string const & | atom_name4 | ||
| ) |
add a chi angle defined by four atoms
Definition at line 708 of file ResidueType.cc.
References atom_index_, chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, has(), and is_proton_chi_.
Referenced by core::chemical::AddChi::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi().
| void core::chemical::ResidueType::add_chi_rotamer | ( | Size const | chino, |
| Real const | mean, | ||
| Real const | sdev | ||
| ) |
add a rotamer bin for a given chi
add a rotamer bin for a given chi a rotamer bin has the mean and standard deviation
Definition at line 766 of file ResidueType.cc.
References chi_rotamers_.
Referenced by core::chemical::AddChiRotamer::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer().
| void core::chemical::ResidueType::add_cut_bond | ( | std::string const & | atom_name1, |
| std::string const & | atom_name2 | ||
| ) |
add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond
add a cut_bond between atom1 and atom2, which disallows an atom-tree connection, though the atoms are really bonded. update cut_bond_ and resize it as necessary
Definition at line 671 of file ResidueType.cc.
References atom_index_, cut_bond_neighbor_, finalized_, and has().
Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond().
| void core::chemical::ResidueType::add_orbital | ( | std::string & | orbital_name, |
| std::string & | orbital_type_name | ||
| ) |
add an orbital onto a residue based upon atom
Definition at line 506 of file ResidueType.cc.
References finalized_, n_orbitals_, orbital_types_, orbitals_, orbitals_index_, and core::chemical::strip_whitespace().
| void core::chemical::ResidueType::add_orbital_bond | ( | std::string const & | atom_name1, |
| std::string const & | orbital_name | ||
| ) |
add an orbital bond between an atom and an orbital.
Definition at line 628 of file ResidueType.cc.
References atom_index_, finalized_, has(), has_orbital(), orbital_bonded_neighbor_, and orbitals_index_.
| void core::chemical::ResidueType::add_property | ( | std::string const & | property) |
add properties
add a property to this residue update boolean property member data accordingly
Definition at line 831 of file ResidueType.cc.
References finalized_, has_sc_orbitals_, is_acetylated_nterminus_, is_aromatic_, is_carbohydrate_, is_charged_, is_coarse_, is_DNA_, is_ligand_, is_lower_terminus_, is_methylated_cterminus_, is_NA_, is_phosphonate_, is_phosphonate_upper_, is_polar_, is_polymer_, is_protein_, is_RNA_, is_surface_, is_terminus_, is_upper_terminus_, properties_, and core::chemical::tr().
Referenced by core::chemical::AddProperty::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_properties().
| Size core::chemical::ResidueType::add_residue_connection | ( | std::string const & | atom_name) |
add a ResidueConnection Doesnt set the ideal geometry – maybe it should?
Definition at line 1821 of file ResidueType.cc.
References atom_index(), finalized_, n_non_polymeric_residue_connections_, residue_connections_, and update_residue_connection_mapping().
Referenced by core::chemical::AddConnect::apply().
|
inline |
add one more variant type to this ResidueType
Definition at line 1337 of file ResidueType.hh.
References has_variant_type(), and variant_types_.
Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_variant().
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inline |
Indices of all backbone atoms, hydrogens and heavyatoms.
Definition at line 369 of file ResidueType.hh.
References all_bb_atoms_.
Referenced by core::conformation::Residue::all_bb_atoms(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), and core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy().
|
inline |
Indices of all sidechain atoms, hydrogens and heavyatoms.
Definition at line 375 of file ResidueType.hh.
References all_sc_atoms_.
Referenced by core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), and core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy().
| void core::chemical::ResidueType::assign_internal_coordinates | ( | ) |
Definition at line 2024 of file ResidueType.cc.
References atom_name(), core::chemical::ICoorAtomID::atomno(), icoor(), nbr_atom_, set_icoor(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), and core::chemical::AtomICoor::stub_atom3().
Referenced by assign_internal_coordinates().
|
private |
@ recursive function to assign internal coordinates
Definition at line 2033 of file ResidueType.cc.
References assign_internal_coordinates(), atom_index(), atom_name(), core::chemical::ICoorAtomID::atomno(), bonded_neighbor_, calculate_icoor(), icoor(), nbr_atom_, parents_, core::io::serialization::size(), and core::chemical::AtomICoor::stub_atom2().
| void core::chemical::ResidueType::assign_neighbor_atom | ( | ) |
Definition at line 1996 of file ResidueType.cc.
References atom_is_hydrogen(), atoms_, core::kinematics::distance(), protocols::ddg::min_index(), name(), and nbr_atom().
Definition at line 213 of file ResidueType.cc.
References atom_index(), and atoms_.
Referenced by core::chemical::SetAtomicCharge::apply(), core::conformation::Residue::atomic_charge(), attached_H_begin(), attached_H_end(), protocols::match::bump_grid_to_enclose_pose(), calculate_icoor(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), debug_dump_icoor(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::mm_atom_name(), path_distance(), core::scoring::PQR::PQR(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::conformation::Residue::Residue(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::pack::task::operation::util::select_coord_for_residue(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
Definition at line 216 of file ResidueType.cc.
References atom_index(), and atoms_.
| Atom & core::chemical::ResidueType::atom | ( | std::string const & | atom_name) |
Definition at line 219 of file ResidueType.cc.
References atom_index(), and atoms_.
| Atom const & core::chemical::ResidueType::atom | ( | std::string const & | atom_name) | const |
Definition at line 222 of file ResidueType.cc.
References atom_index(), and atoms_.
get index of an atom's base atom
Definition at line 380 of file ResidueType.cc.
References atom_base_.
Referenced by core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::atom_base(), core::scoring::hbonds::create_rotamer_descriptor(), select_orient_atoms(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), and core::conformation::Residue::set_theta().
Does an atom form any inter-residue chemical bonds?
Definition at line 777 of file ResidueType.hh.
References atom_2_residue_connection_map_.
| Size core::chemical::ResidueType::atom_index | ( | std::string const & | name) | const |
get atom index by name
Definition at line 1763 of file ResidueType.cc.
References atom_index_, is_protein(), name3(), show_all_atom_names(), and core::chemical::tr().
Referenced by add_actcoord_atom(), core::coarse::Translator::add_atom(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::hybridization::add_non_protein_cst(), add_residue_connection(), protocols::hybridization::TMalign::alignment2AtomMap(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::antibody::GraftOneMover::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(), assign_internal_coordinates(), atom(), core::conformation::Residue::atom_index(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::io::pdb::build_pose_as_is1(), calculate_icoor(), protocols::fldsgn::MatchResidues::compute_comb(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), protocols::match::Matcher::create_ds_builder(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_atom(), protocols::topology_broker::fix_mainchain_connect(), protocols::loops::fix_with_coord_cst(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::forge::constraints::NtoC_RCG::generate_remodel_constraints(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::ICoorAtomID::ICoorAtomID(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), core::pose::named_atom_id_to_atom_id(), nbr_atom(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), core::scoring::constraints::parse_NMR_name_old(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), protocols::constraints_additional::BindingSiteConstraint::read_def(), core::scoring::constraints::BigBinConstraint::read_def(), protocols::evaluation::PCA::read_structure(), core::scoring::constraints::requires_CB_mapping(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), core::pack::task::operation::util::select_coord_for_residue(), select_orient_atoms(), set_atom_type(), set_backbone_heavyatom(), set_ideal_xyz(), set_lower_connect_atom(), set_mm_atom_type(), set_upper_connect_atom(), protocols::rna::setup_base_pair_constraints(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and protocols::fldsgn::MatchResidues::superimpose_comb().
is a backbone atom (heavy or hydorgen)?
Definition at line 530 of file ResidueType.hh.
References finalized_, first_sidechain_hydrogen_, n_backbone_heavyatoms_, natoms_, and nheavyatoms_.
Referenced by core::conformation::Residue::atom_is_backbone(), core::scoring::hbonds::create_rotamer_descriptor(), core::conformation::Residue::place(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::constraints::requires_CB_mapping(), select_orient_atoms(), and core::scoring::methods::setup_water_builders_for_residue_type().
quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.
Definition at line 541 of file ResidueType.hh.
References finalized_, natoms_, and nheavyatoms_.
Referenced by assign_neighbor_atom(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), and core::scoring::is_protein_sidechain_heavyatom().
Definition at line 442 of file ResidueType.hh.
References atom_is_polar_hydrogen_, and finalized_.
Referenced by core::conformation::Residue::atom_is_polar_hydrogen().
| std::string const & core::chemical::ResidueType::atom_name | ( | Size const | index) | const |
get atom name by index
Get the atom name by index.
Definition at line 372 of file ResidueType.cc.
References atoms_.
Referenced by core::coarse::Translator::add_atom(), add_atom(), assign_internal_coordinates(), core::conformation::Residue::atom_name(), protocols::swa::rna::atom_square_deviation(), protocols::swa::rna::base_atoms_square_deviation(), core::io::pdb::build_pose_as_is1(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::swa::RigidBodySampler::check_num_hbonds(), protocols::swa::StepWiseScreener::copy_coords(), protocols::swa::protein::StepWiseProteinScreener::copy_coords(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), protocols::toolbox::AllowInsert::initialize(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_atom(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::MiniPose::MiniPose(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), protocols::swa::rna::print_atom_info(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::swa::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::swa::rna::Print_torsion_info(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::methods::setup_water_builders_for_residue_type(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), and core::chemical::write_topology_file().
Get the chemical atom_type for this atom by it index number in this residue.
If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below
Definition at line 364 of file ResidueType.cc.
References atom_types_, and atoms_.
Referenced by core::conformation::Residue::atom_type(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::conformation::Residue::is_virtual(), is_virtual(), print_bondangles(), print_dihedrals(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), setup_atom_ordering(), core::scoring::methods::setup_water_builders_for_residue_type(), and core::chemical::write_topology_file().
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access by reference the atomset for which this residue is constructed
Definition at line 197 of file ResidueType.hh.
References atom_types_.
Referenced by core::conformation::Residue::atom_type_set(), and protocols::features::AtomAtomPairFeatures::report_atom_pairs().
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access by const pointer the atomset for which this residue is constructed
Definition at line 211 of file ResidueType.hh.
References atom_types_.
Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_scoring(), core::scoring::etable::CoarseEtableEnergy::setup_for_scoring_(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), and core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_().
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Read access to the atoms_last_controlled_by_chi_ array.
Definition at line 562 of file ResidueType.hh.
References atoms_last_controlled_by_chi_.
Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().
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Read access to the Atoms last controlled by a particular chi.
Definition at line 568 of file ResidueType.hh.
References atoms_last_controlled_by_chi_.
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Definition at line 633 of file ResidueType.hh.
References atoms_with_orb_index_.
Referenced by core::conformation::Residue::atoms_with_orb_index(), core::conformation::Residue::Residue(), and core::conformation::Residue::update_orbital_coords().
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Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.
Definition at line 1608 of file ResidueType.hh.
References atoms_within_one_bond_of_a_residue_connection_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().
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Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn.
Definition at line 1630 of file ResidueType.hh.
References atoms_within_two_bonds_of_a_residue_connection_.
Referenced by core::scoring::methods::MMTorsionEnergy::residue_pair_energy().
index number of the first attached Hydrogen on an atom
Definition at line 285 of file ResidueType.hh.
References atom(), and attached_H_begin_.
Referenced by core::coarse::Translator::add_atom(), core::conformation::Residue::attached_H_begin(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), and protocols::simple_moves::MinimalRotamer::record_internal_geometry().
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for all heavy atoms, index numbers of their first attached Hydrogen
Definition at line 299 of file ResidueType.hh.
References attached_H_begin_.
index number of the last attached Hydrogen on an atom
Definition at line 292 of file ResidueType.hh.
References atom(), and attached_H_end_.
Referenced by core::coarse::Translator::add_atom(), core::conformation::Residue::attached_H_end(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), and protocols::simple_moves::MinimalRotamer::record_internal_geometry().
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for all heavy atoms, index numbers of their last attached Hydrogen
Definition at line 306 of file ResidueType.hh.
References attached_H_end_.
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Definition at line 2106 of file ResidueType.hh.
References base_restype_name_.
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Definition at line 2107 of file ResidueType.hh.
References base_restype_name_.
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Return the indices for the set of atoms that define a particular intraresidue angle.
Definition at line 1515 of file ResidueType.hh.
References bondangle_atom_sets_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_angles().
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Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.
Definition at line 1524 of file ResidueType.hh.
References bondangles_for_atom_.
Referenced by core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().
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indices of the bonded neighbors for an atom
Definition at line 328 of file ResidueType.hh.
References bonded_neighbor_.
Referenced by core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::bonded_neighbor(), core::chemical::get_residue_path_distances(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::Residue::nbrs(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), and select_orient_atoms().
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Definition at line 333 of file ResidueType.hh.
References bonded_neighbor_type_.
Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_bond().
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indices of the orbitals bonded to an atom
Definition at line 618 of file ResidueType.hh.
References orbital_bonded_neighbor_.
Referenced by core::conformation::Residue::bonded_orbitals(), core::conformation::Residue::Residue(), and core::conformation::Residue::update_orbital_coords().
| void core::chemical::ResidueType::calculate_icoor | ( | std::string const & | child, |
| std::string const & | stub_atom1, | ||
| std::string const & | stub_atom2, | ||
| std::string const & | stub_atom3 | ||
| ) |
calculate AtomICoor for an atom and set it
Definition at line 2090 of file ResidueType.cc.
References atom(), atom_index(), core::kinematics::distance(), core::chemical::Atom::ideal_xyz(), protocols::swa::phi(), set_icoor(), and core::chemical::tr().
Referenced by assign_internal_coordinates().
| core::chemical::carbohydrates::CarbohydrateInfoCOP core::chemical::ResidueType::carbohydrate_info | ( | ) | const |
Return the CarbohydrateInfo object containing sugar-specific properties for this residue.
Definition at line 2149 of file ResidueType.cc.
References carbohydrate_info_.
Referenced by core::conformation::Residue::carbohydrate_info(), core::pose::carbohydrates::carbohydrate_phi_offset_from_BB(), core::pose::Pose::omega(), core::pose::Pose::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().
Definition at line 696 of file ResidueType.hh.
References chi_2_proton_chi_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), and protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery().
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indices of the atoms which are used to define a given chi angle (chino)
Definition at line 354 of file ResidueType.hh.
References chi_atoms_.
Referenced by protocols::simple_moves::MinimalRotamer::atom_is_ideal(), core::conformation::Residue::chi_atoms(), protocols::simple_moves::MinimalRotamer::chi_matches_coords(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::conformation::Residue::Residue(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), protocols::ligand_docking::torsion_constraints_from_mean_sd(), and core::chemical::write_topology_file().
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indices of the atoms which are used to define all the chi angles
Definition at line 361 of file ResidueType.hh.
References chi_atoms_.
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all rotamers bins (mean, std) for a given chi angle
Definition at line 748 of file ResidueType.hh.
References chi_rotamers_.
Referenced by core::conformation::Residue::chi_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), and protocols::ligand_docking::torsion_constraints_from_chi_rotamers().
| ResidueTypeOP core::chemical::ResidueType::clone | ( | ) | const |
make a copy
Definition at line 200 of file ResidueType.cc.
References ResidueType().
Referenced by protocols::ligand_docking::AddHydrogen::apply(), and core::chemical::PatchCase::apply().
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indices of the bonded neighbors for an atom
Definition at line 340 of file ResidueType.hh.
References cut_bond_neighbor_.
Referenced by core::conformation::Residue::cut_bond_neighbor(), and core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond().
| void core::chemical::ResidueType::debug_dump_icoor | ( | ) |
Dump out atomnames and icoor values.
Definition at line 2525 of file ResidueType.cc.
References atom(), atom_name(), core::chemical::Atom::ideal_xyz(), name3(), natoms(), and core::chemical::tr().
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get the adducts defined for this residue
Definition at line 1686 of file ResidueType.hh.
References defined_adducts_.
Referenced by core::chemical::apply_adducts_to_residue(), core::chemical::ResidueTypeSet::create_adduct_combinations(), core::chemical::error_check_requested_adducts(), and core::chemical::ResidueTypeSet::place_adducts().
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flag an atom for deletion by adding its index to the delete_atom_ list
Definition at line 850 of file ResidueType.hh.
References atom_index(), delete_atoms_, finalized_, and has().
Referenced by core::chemical::DeleteAtom::apply().
| void core::chemical::ResidueType::delete_property | ( | std::string const & | property) |
delete properties
delete a property to this residue update boolean property member data accordingly
Definition at line 918 of file ResidueType.cc.
References finalized_, has_sc_orbitals_, is_acetylated_nterminus_, is_aromatic_, is_carbohydrate_, is_charged_, is_coarse_, is_DNA_, is_ligand_, is_lower_terminus_, is_methylated_cterminus_, is_phosphonate_, is_phosphonate_upper_, is_polar_, is_polymer_, is_protein_, is_RNA_, is_surface_, is_terminus_, is_upper_terminus_, properties_, and core::chemical::tr().
Referenced by core::chemical::DeleteProperty::apply().
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dihedral methods
Return the indices for the set of atoms that define a particular intraresidue dihedral
Definition at line 1485 of file ResidueType.hh.
References dihedral_atom_sets_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions().
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Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.
Definition at line 1494 of file ResidueType.hh.
References dihedrals_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().
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access by reference the atomset for which this residue is constructed
Definition at line 204 of file ResidueType.hh.
References elements_.
| void core::chemical::ResidueType::finalize | ( | ) |
recalculate derived data, potentially reordering atom-indices
This routine updates all the derived data.
Atom order will probably change after this call, so if you add a new property that depends on atom-indices that will have to be updated below.
Definition at line 1669 of file ResidueType.cc.
References delete_atoms_, finalized_, force_bb_, reorder_primary_data(), setup_atom_ordering(), and update_derived_data().
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index of the first sidechain atom (heavy or hydrogen)
Definition at line 513 of file ResidueType.hh.
References n_backbone_heavyatoms_, natoms_, and nheavyatoms_.
Referenced by core::coarse::Translator::add_remaining_sidechain(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::conformation::Residue::first_sidechain_atom(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), and select_orient_atoms().
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index of the first sidehchain hydrogen
Definition at line 521 of file ResidueType.hh.
References finalized_, and first_sidechain_hydrogen_.
Referenced by core::conformation::Residue::first_sidechain_hydrogen().
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Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.
Definition at line 1659 of file ResidueType.hh.
References force_nbr_atom_orient_.
Referenced by core::chemical::SetOrientAtom::apply(), and core::chemical::write_topology_file().
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Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.
Definition at line 1665 of file ResidueType.hh.
References force_nbr_atom_orient_.
Referenced by select_orient_atoms().
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Definition at line 1420 of file ResidueType.hh.
References mol_data_.
Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond.
Definition at line 1592 of file ResidueType.hh.
References ncaa_rotlib_n_bins_per_rot_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary().
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Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds.
Definition at line 1599 of file ResidueType.hh.
References ncaa_rotlib_n_bins_per_rot_.
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Returns the path to the NCAA rotlib for the residue type.
Definition at line 1553 of file ResidueType.hh.
References ncaa_rotlib_path_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary().
| std::string core::chemical::ResidueType::get_RotamerLibraryName | ( | ) | const |
A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use.
Definition at line 1990 of file ResidueType.cc.
References rotamer_library_name_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library(), and core::chemical::ResidueDatabaseIO::report_residue_type().
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Returns whether we are using a NCAA rotlib for the residue type.
Definition at line 1567 of file ResidueType.hh.
References use_ncaa_rotlib_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library().
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return indices of aromatic Hydrogens
Definition at line 382 of file ResidueType.hh.
References Haro_index_.
Referenced by core::conformation::Residue::Haro_index().
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is this atom present in this residue?
Definition at line 472 of file ResidueType.hh.
References atom_index_.
Referenced by core::coarse::Translator::add_atom(), add_bond(), add_chi(), add_cut_bond(), protocols::hybridization::add_non_protein_cst(), add_orbital_bond(), core::pack::task::operation::util::any_atoms_within_cutoff(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddConnect::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), core::io::pdb::build_pose_as_is1(), protocols::hybridization::InsertChunkMover::check_overlap(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_atom(), protocols::swa::protein::do_set_xyz(), core::conformation::Residue::has(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::place(), redefine_chi(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::pack::task::operation::util::select_coord_for_residue(), set_atom_base(), set_icoor(), protocols::rna::setup_coarse_chainbreak_constraints(), and core::coarse::Translator::Translator().
| bool core::chemical::ResidueType::has_atom_name | ( | std::string const & | name) | const |
Check if residue type has an atom by a given atomname.
Definition at line 1752 of file ResidueType.cc.
References atom_index_.
Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), and core::scoring::setup_matching_atoms_with_given_names().
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is this orbital present in this residue?
Definition at line 626 of file ResidueType.hh.
References orbitals_index_.
Referenced by add_orbital_bond().
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Generic property access – SLOW!!!!!
Definition at line 1303 of file ResidueType.hh.
References properties_.
Referenced by protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), core::conformation::Residue::has_property(), core::pack::task::operation::ResidueHasProperty::operator()(), and core::chemical::Selector_PROPERTY::operator[]().
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does this residue have sidechain orbitals?
Definition at line 1208 of file ResidueType.hh.
References has_sc_orbitals_.
Referenced by core::conformation::Residue::has_sc_orbitals().
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Generic variant access – SLOW!!!!!
Definition at line 1310 of file ResidueType.hh.
References variant_types_.
Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), add_variant_type(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants(), core::io::pdb::build_pose_as_is1(), protocols::swa::InputStreamWithResidueInfo::cleanup_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::swa::Figure_out_moving_residues(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::Residue::has_variant_type(), core::scoring::rna::is_cutpoint_open(), is_virtual_residue(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_sequence(), nonadduct_variants_match(), core::chemical::Selector_VARIANT_TYPE::operator[](), core::chemical::Selector_MATCH_VARIANTS::operator[](), protocols::swa::protein::StepWiseProteinPoseMinimizer::pose_has_chainbreak(), protocols::swa::rna::remove_all_variant_types(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::swa::rna::Remove_virtual_O2Star_hydrogen(), core::scoring::methods::pHEnergy::residue_energy(), core::pose::residue_types_from_sequence(), protocols::swa::StepWisePoseSetup::setup_disulfides(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), and variants_match().
Definition at line 430 of file ResidueType.hh.
References finalized_, and heavyatom_has_polar_hydrogens_.
Referenced by core::conformation::Residue::heavyatom_has_polar_hydrogens().
Definition at line 436 of file ResidueType.hh.
References finalized_, and heavyatom_is_an_acceptor_.
Referenced by core::conformation::Residue::heavyatom_is_an_acceptor().
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return indices of polar Hydrogens
Definition at line 389 of file ResidueType.hh.
References Hpol_index_.
Referenced by core::conformation::Residue::Hpol_index().
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indices of non-polar hydrogens as potential carbon Hbond donors
Definition at line 404 of file ResidueType.hh.
References Hpos_apolar_.
Referenced by core::conformation::Residue::Hpos_apolar().
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indices of polar hydrogens as Hbond donors
Definition at line 397 of file ResidueType.hh.
References Hpos_polar_.
Referenced by core::conformation::Residue::Hpos_polar().
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Definition at line 410 of file ResidueType.hh.
References Hpos_polar_sc_.
Referenced by core::conformation::Residue::Hpos_polar_sc().
AtomICoord of an atom.
Definition at line 1815 of file ResidueType.cc.
References atoms_.
Referenced by assign_internal_coordinates(), protocols::simple_moves::MinimalRotamer::atom_is_ideal(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Residue::icoor(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), reorder_primary_data(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), set_orbital_icoor_id(), and core::chemical::write_topology_file().
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is acetylated n terminus
Definition at line 1257 of file ResidueType.hh.
References is_acetylated_nterminus_.
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is an adduct-modified residue?
Definition at line 1289 of file ResidueType.hh.
References is_adduct_.
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is aromatic?
Definition at line 1229 of file ResidueType.hh.
References is_aromatic_.
Referenced by core::conformation::Residue::is_apolar(), core::conformation::Residue::is_aromatic(), core::scoring::methods::residue_type_has_waters(), and core::chemical::write_topology_file().
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is branch point for a branched polymer?
Definition at line 1271 of file ResidueType.hh.
References branch_point_atoms_.
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is carbohydrate?
Definition at line 1188 of file ResidueType.hh.
References is_carbohydrate_.
Referenced by core::io::pdb::build_pose_as_is1(), core::conformation::Residue::carbohydrate_info(), and core::conformation::Residue::is_carbohydrate().
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is charged?
Definition at line 1222 of file ResidueType.hh.
References is_charged_.
Referenced by core::conformation::Residue::is_apolar(), core::conformation::Residue::is_charged(), core::scoring::methods::residue_type_has_waters(), and core::chemical::write_topology_file().
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is coarse?
Definition at line 1174 of file ResidueType.hh.
References is_coarse_.
Referenced by core::conformation::Residue::is_coarse(), and protocols::toolbox::AllowInsert::renumber_after_variant_changes().
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is DNA?
Definition at line 1160 of file ResidueType.hh.
References is_DNA_.
Referenced by protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::dna::design_residues_list(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), core::conformation::Residue::is_DNA(), protocols::motifs::MotifSearch::position_vector_setup(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::dna::DnaInterfacePacker::protein_scan(), and core::chemical::write_topology_file().
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Definition at line 1194 of file ResidueType.hh.
References is_ligand_.
Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::EnzdesBaseProtocol::catalytic_res(), protocols::enzdes::enzutil::catalytic_res(), protocols::enzdes::LigDSasaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::ligand_docking::get_ligand_seqpos(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::is_ligand(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::toolbox::match_enzdes_util::EnzdesCstCache::ordered_constrained_positions(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), and core::chemical::write_topology_file().
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is lower terminus?
Definition at line 1243 of file ResidueType.hh.
References is_lower_terminus_.
Referenced by protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::io::pdb::build_pose_as_is1(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), protocols::swa::Figure_out_moving_residues(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), core::conformation::Residue::is_lower_terminus(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::dna::set_base_segment_chainbreak_constraints(), and core::chemical::write_topology_file().
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is methylated c terminus
Definition at line 1264 of file ResidueType.hh.
References is_methylated_cterminus_.
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is Nucleic Acid?
Definition at line 1181 of file ResidueType.hh.
References is_NA_.
Referenced by protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), and core::conformation::Residue::is_NA().
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is polar?
Definition at line 1215 of file ResidueType.hh.
References is_polar_.
Referenced by core::conformation::Residue::is_apolar(), core::conformation::Residue::is_polar(), core::scoring::methods::residue_type_has_waters(), and core::chemical::write_topology_file().
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is polymer?
Definition at line 1146 of file ResidueType.hh.
References is_polymer_.
Referenced by protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), core::io::pdb::build_pose_as_is1(), protocols::ligand_docking::constrain_ligand_torsions(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::loops::find_non_protein_chunks(), protocols::loophash::get_rt_over_leap_fast(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_polymer_bonded(), core::io::serialization::read_binary(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::pose::residue_types_from_sequence(), and core::chemical::write_topology_file().
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is protein?
Definition at line 1153 of file ResidueType.hh.
References is_protein_.
Referenced by add_actcoord_atom(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), atom_index(), protocols::toolbox::CA_superimpose(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::simple_moves::ConsensusDesignMover::create_sequence_profile_constraints(), core::scoring::methods::dfire::DFIRE_Energy::defines_residue_pair_energy(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::loops::extract_secondary_structure_chunks(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), protocols::loops::find_non_protein_chunks(), protocols::match::BfactorMPM::get_ca_bfactors(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::fldsgn::topology::SS_Info2::initialize(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::ResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), protocols::match::AddAllPositionsMPM::modified_match_positions(), protocols::match::RemoveNorCTermMPM::modified_match_positions(), protocols::loops::native_loop_core_CA_rmsd(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::motifs::MotifSearch::position_vector_setup(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::hybridization::TMalign::read_pose(), protocols::toolbox::pose_metric_calculators::HPatchCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ChargeCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PackstatCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::pose::set_ss_from_phipsi(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::swa::protein::setup_protein_backbone_atom_id_map(), protocols::swa::protein::setup_protein_CA_atom_id_map(), core::pose::transfer_phi_psi(), and core::chemical::write_topology_file().
number of proton chis
Definition at line 684 of file ResidueType.hh.
References proton_chis_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), and core::chemical::write_topology_file().
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is RNA?
Definition at line 1167 of file ResidueType.hh.
References is_RNA_.
Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::conformation::Residue::is_RNA(), protocols::swa::pdbslice(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), protocols::rna::RNA_FragmentMover::RNA_FragmentMover(), protocols::rna::setup_coarse_chainbreak_constraints(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::rna::RNA_FragmentMover::update_insert_map(), and core::chemical::write_topology_file().
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is surface? (e.g. enamel)
Definition at line 1201 of file ResidueType.hh.
References is_surface_.
Referenced by core::conformation::Residue::is_surface(), and core::chemical::write_topology_file().
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is terminus?
Definition at line 1236 of file ResidueType.hh.
References is_terminus_.
Referenced by protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::conformation::Residue::is_terminus(), and core::chemical::write_topology_file().
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is upper terminus?
Definition at line 1250 of file ResidueType.hh.
References is_upper_terminus_.
Referenced by core::io::pdb::build_pose_as_is1(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), protocols::loops::find_non_protein_chunks(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), core::conformation::Residue::is_upper_terminus(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::dna::set_base_segment_chainbreak_constraints(), and core::chemical::write_topology_file().
Check if atom is virtual.
Definition at line 2557 of file ResidueType.cc.
References atom_type().
Referenced by protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res().
| bool core::chemical::ResidueType::is_virtual_residue | ( | ) | const |
Check if residue is 'VIRTUAL_RESIDUE'.
Definition at line 2564 of file ResidueType.cc.
References has_variant_type().
Referenced by core::conformation::Residue::is_virtual_residue().
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index of the last backbone heavy atom
Definition at line 506 of file ResidueType.hh.
References n_backbone_heavyatoms_.
Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias(), core::conformation::Residue::last_backbone_atom(), and protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned().
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Read access to the last_controlling_chi_ array.
Definition at line 550 of file ResidueType.hh.
References last_controlling_chi_.
Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type().
The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.
Definition at line 556 of file ResidueType.hh.
References last_controlling_chi_.
| ResidueConnection const & core::chemical::ResidueType::lower_connect | ( | ) | const |
Definition at line 306 of file ResidueType.cc.
References is_polymer_, lower_connect_id_, and residue_connections_.
Referenced by core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::lower_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
| Size core::chemical::ResidueType::lower_connect_atom | ( | ) | const |
index number of the atom which connects to the lower connection
Definition at line 315 of file ResidueType.cc.
References is_polymer_, lower_connect_id_, and residue_connections_.
Referenced by core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::chemical::ICoorAtomID::xyz().
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Definition at line 732 of file ResidueType.hh.
References lower_connect_id_.
Referenced by core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), and core::conformation::Residue::is_polymer_bonded().
index of mainchain atom
Definition at line 457 of file ResidueType.hh.
References mainchain_atoms_.
Referenced by core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), and core::conformation::Residue::mainchain_atom().
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indices of all mainchain atoms
Definition at line 449 of file ResidueType.hh.
References mainchain_atoms_.
Referenced by core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), and core::conformation::Residue::Residue().
| MMAtomType const & core::chemical::ResidueType::mm_atom_type | ( | Size const | atomno) | const |
Get the MM atom_type for this atom by its index number in this residue.
Definition at line 485 of file ResidueType.cc.
References atoms_, and mm_atom_types_.
Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init(), print_bondangles(), print_dihedrals(), and core::chemical::write_topology_file().
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get the molecular weight of this residue
Definition at line 930 of file ResidueType.hh.
References molar_mass_.
Referenced by core::pose::molar_mass().
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get the molecular weight of this residue
Definition at line 923 of file ResidueType.hh.
References molecular_mass_.
Referenced by core::pose::molecular_mass().
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number of hbond_acceptors
Definition at line 249 of file ResidueType.hh.
References n_hbond_acceptors_.
Referenced by core::conformation::Residue::n_hbond_acceptors().
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number of hbond_donors
Definition at line 256 of file ResidueType.hh.
References n_hbond_donors_.
Referenced by core::conformation::Residue::n_hbond_donors().
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Definition at line 765 of file ResidueType.hh.
References n_non_polymeric_residue_connections_.
Referenced by core::conformation::Residue::n_non_polymeric_residue_connections().
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number of orbitals
Definition at line 611 of file ResidueType.hh.
References n_orbitals_.
Referenced by core::conformation::Residue::n_orbitals().
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Definition at line 760 of file ResidueType.hh.
References n_polymeric_residue_connections_.
Referenced by core::conformation::Residue::n_polymeric_residue_connections().
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number of proton chis
Definition at line 677 of file ResidueType.hh.
References proton_chis_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), and core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().
| Size core::chemical::ResidueType::n_residue_connections | ( | ) | const |
number of ResidueConnections, counting polymeric residue connections
Definition at line 332 of file ResidueType.cc.
References residue_connections_.
Referenced by core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::viewer::dump_residue_kinemage(), core::chemical::expand_icoor_atom_name(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::chemical::ICoorAtomID::ICoorAtomID(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::is_disulfide_bond(), core::conformation::Residue::n_residue_connections(), core::conformation::Residue::Residue(), and core::import_pose::set_reasonable_fold_tree().
How many inter-residue chemical bonds does a particular atom form?
Definition at line 783 of file ResidueType.hh.
References atom_2_residue_connection_map_.
Referenced by core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().
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get our (unique) residue name
Definition at line 1370 of file ResidueType.hh.
References name_.
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::chemical::Patch::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::apply_adducts_to_residue(), assign_neighbor_atom(), core::io::pdb::build_pose_as_is1(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::relax::delete_virtual_residues(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::conformation::Residue::fill_missing_atoms(), core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::loops::get_tenA_neighbor_residues(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::methods::LKB_ResidueInfo::initialize_residue_type(), protocols::features::HBondFeatures::insert_site_row(), core::pack::dunbrack::load_unboundrot(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::conformation::Residue::name(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::coarse::CoarseEtable::print_residue_info(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::pose::remove_virtual_residues(), reorder_primary_data(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::loops::select_loop_residues(), select_orient_atoms(), core::import_pose::set_reasonable_fold_tree(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), core::scoring::methods::setup_water_builders_for_residue_type(), core::util::switch_to_residue_type_set(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), core::io::serialization::write_binary(), core::chemical::ResidueDatabaseIO::write_residuetype_to_database(), and core::chemical::write_topology_file().
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get our 1letter code
Definition at line 1400 of file ResidueType.hh.
References name1_.
Referenced by core::chemical::SetIO_String::apply(), protocols::contact_map::ContactMap::fill_contacts(), core::conformation::is_disulfide_bond(), core::conformation::Residue::name1(), core::chemical::Selector_NAME1::operator[](), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::hybridization::TMalign::read_pose(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::chemical::write_topology_file().
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get our 3letter code
Definition at line 1385 of file ResidueType.hh.
References name3_.
Referenced by protocols::loops::add_loop(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), core::pack::task::operation::OptCysHG::apply(), protocols::match::MatcherMover::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::chemical::SetIO_String::apply(), atom_index(), core::scoring::automorphic_rmsd(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::ligand_docking::MoveMapBuilder::build(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), debug_dump_icoor(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::frac_atoms_within(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::get_restag(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), core::conformation::Residue::is_similar_rotamer(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::conformation::Residue::name3(), core::pack::task::operation::ResidueName3Is::operator()(), core::chemical::Selector_NAME3::operator[](), orbital_index(), core::scoring::constraints::parse_NMR_name_old(), protocols::dna::DnaChains::print(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::viewer::print_node(), protocols::dna::DnaInterfacePacker::protein_scan(), core::chemical::ResidueDatabaseIO::read_residue_type(), report_adducts(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::conformation::setup_corresponding_atoms(), core::scoring::hbonds::HBond::show(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_residue_type_set(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().
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Get the chemical atom_type index number for this atom by its index number in this residue.
number of atoms
Definition at line 235 of file ResidueType.hh.
References natoms_.
Referenced by core::conformation::annotated_atom_graph_from_conformation(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::PlaceFragments::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::apply_transform_Rx_plus_v(), protocols::hybridization::apply_transformation(), core::conformation::atom_graph_from_conformation(), core::scoring::automorphic_rmsd(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::io::pdb::build_pose_as_is1(), protocols::toolbox::CA_superimpose(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::toolbox::AllowInsert::calculate_atom_id_domain_map(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::swa::StepWiseScreener::copy_coords(), protocols::swa::protein::StepWiseProteinScreener::copy_coords(), core::pose::copy_dofs(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::io::silent::BinaryRNASilentStruct::fill_pose(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::ligand_docking::frac_atoms_within(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::get_residue_path_distances(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::toolbox::AllowInsert::initialize(), core::pose::initialize_atomid_map(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::natoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), core::conformation::symmetry::recenter(), protocols::toolbox::AllowInsert::renumber_after_variant_changes(), protocols::fibril::reorient_extended_fibril(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::conformation::Residue::Residue(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), protocols::swa::rotate(), select_orient_atoms(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), core::scoring::methods::setup_water_builders_for_residue_type(), core::scoring::superimpose_pose(), protocols::swa::translate(), core::chemical::write_topology_file(), protocols::sic_dock::xform_pose(), core::fragment::xform_pose(), and protocols::sic_dock::xform_pose_rev().
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set nbr_atom used to define residue-level neighbors
Definition at line 895 of file ResidueType.hh.
References atom_index(), and nbr_atom_.
Referenced by core::chemical::SetNbrAtom::apply(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::chemical::write_topology_file().
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get nbr_atom used to define residue-level neighbors
Definition at line 902 of file ResidueType.hh.
References nbr_atom_.
Referenced by assign_neighbor_atom(), and select_orient_atoms().
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set nbr_radius_ used to define residue-level neighbors
Definition at line 909 of file ResidueType.hh.
References nbr_radius_.
Referenced by core::chemical::SetNbrRadius::apply(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), core::scoring::Energies::update_neighbor_links(), and core::chemical::write_topology_file().
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get nbr_radius_ used to define residue-level neighbors
Definition at line 916 of file ResidueType.hh.
References nbr_radius_.
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indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)
Definition at line 347 of file ResidueType.hh.
References bonded_neighbor_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), note_chi_controls_atom(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), select_orient_atoms(), setup_atom_ordering(), and core::chemical::write_topology_file().
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number of chi angles
Definition at line 670 of file ResidueType.hh.
References chi_atoms_.
Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::MinimalRotamer::atom_is_ideal(), protocols::comparative_modeling::chis_from_pose(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::conformation::Residue::nchi(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::simple_moves::MinimalRotamer::record_chi(), protocols::swa::protein::StepWiseProteinPacker::reinstate_side_chain_angles(), protocols::swa::protein::StepWiseProteinResidueSampler::reinstate_side_chain_angles(), protocols::swa::protein::reinstate_side_chain_angles(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::conformation::Residue::Residue(), update_last_controlling_chi(), and core::chemical::write_topology_file().
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Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms.
Definition at line 1503 of file ResidueType.hh.
References ndihe_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions().
| orbitals::ICoorOrbitalData const & core::chemical::ResidueType::new_orbital_icoor_data | ( | Size const | orbital_index) | const |
Definition at line 662 of file ResidueType.cc.
References orbital_index(), and orbitals_.
Referenced by core::conformation::Residue::build_orbital_xyz().
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number of heavy atoms
Definition at line 242 of file ResidueType.hh.
References nheavyatoms_.
Referenced by core::coarse::Translator::add_all_remaining(), core::coarse::Translator::add_remaining_sidechain(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::swa::RigidBodySampler::check_o2star_needs_optimization(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Residue::nheavyatoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::conformation::Residue::place(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), select_orient_atoms(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), and protocols::swa::RigidBodySampler::setup_heavy_atoms().
| bool core::chemical::ResidueType::nonadduct_variants_match | ( | ResidueType const & | other) | const |
similar to variants_match(), but allows different adduct-modified states
Definition at line 1728 of file ResidueType.cc.
References core::chemical::ADDUCT, has_variant_type(), and variant_types_.
Referenced by core::pack::task::ResidueLevelTask_::ResidueLevelTask_().
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Definition at line 2105 of file ResidueType.hh.
References nondefault_.
Recursive subroutine invoked by update_last_controlling_chi().
O(N) recursive algorithm for determining the last chi for each atom. Each atom is visited at most twice.
Definition at line 2420 of file ResidueType.cc.
References atom_base_, bonded_neighbor_, last_controlling_chi_, and nbrs().
Referenced by update_last_controlling_chi().
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get number of intraresidue bond angles
Definition at line 1531 of file ResidueType.hh.
References bondangle_atom_sets_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_angles().
indicates how many heavyatom bonded neighbors an atom has
Definition at line 321 of file ResidueType.hh.
References bonded_neighbor_, and number_bonded_hydrogens().
indicates how many proton bonded neighbors an atom has
Definition at line 313 of file ResidueType.hh.
References attached_H_begin_, and attached_H_end_.
Referenced by number_bonded_heavyatoms(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), and protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute().
Definition at line 225 of file ResidueType.cc.
References orbital_index(), and orbitals_.
Referenced by core::conformation::Residue::orbital_name(), core::conformation::Residue::Residue(), and core::conformation::Residue::set_orbital_xyz().
| Orbital const & core::chemical::ResidueType::orbital | ( | std::string const & | orbital_name) | const |
Definition at line 228 of file ResidueType.cc.
References orbital_index(), and orbitals_.
| orbitals::ICoorOrbitalData const & core::chemical::ResidueType::orbital_icoor_data | ( | Size const | orbital_index) | const |
Definition at line 656 of file ResidueType.cc.
References orbital_index(), and orbitals_.
| core::Size core::chemical::ResidueType::orbital_index | ( | std::string const & | name) | const |
orbital name by index
get orbital index by name
Definition at line 1786 of file ResidueType.cc.
References name3(), and orbitals_index_.
Referenced by new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), reorder_primary_data(), and set_orbital_icoor_id().
| orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type | ( | int const | orbital_index) | const |
Get the MM atom_type index number for this atom by its index number in this residue.
Definition at line 491 of file ResidueType.cc.
References orbital_index(), orbital_types_, and orbitals_.
Referenced by core::conformation::Residue::orbital_type().
path distance (number of bonds separated) between a pair of atoms
Definition at line 267 of file ResidueType.hh.
References path_distance_.
Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Residue::path_distance().
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shortest path distance for an atom to all other residue atoms
Definition at line 271 of file ResidueType.hh.
References atom(), and path_distance_.
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accessor of path_distance_ data for this residue, which is a 2D array
Definition at line 278 of file ResidueType.hh.
References path_distance_.
Referenced by core::conformation::Residue::path_distances(), and update_derived_data().
| void core::chemical::ResidueType::print_bondangles | ( | ) | const |
print intraresidue bond angles to standard out
Definition at line 2283 of file ResidueType.cc.
References atom_type(), atoms_, bondangle_atom_sets_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), and core::chemical::tr().
| void core::chemical::ResidueType::print_dihedrals | ( | ) | const |
as non-member so it has not to show up in the header
this might return 0, so please check for that
Definition at line 2241 of file ResidueType.cc.
References atom_type(), atoms_, dihedral_atom_sets_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), ndihe_, and core::chemical::tr().
| void core::chemical::ResidueType::print_pretty_path_distances | ( | ) | const |
print chemical-bond path distances to standard out
Definition at line 2319 of file ResidueType.cc.
References atoms_, natoms_, path_distance_, and core::chemical::tr().
| utility::vector1< std::string > const & core::chemical::ResidueType::properties | ( | ) | const |
acess specified properties
get all specified properties for this residue type
Definition at line 821 of file ResidueType.cc.
References properties_.
Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_properties().
translate proton_chi to global chi
Definition at line 691 of file ResidueType.hh.
References proton_chis_.
Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().
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Definition at line 708 of file ResidueType.hh.
References proton_chi_extra_samples_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().
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Definition at line 702 of file ResidueType.hh.
References proton_chi_samples_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().
| void core::chemical::ResidueType::redefine_chi | ( | Size const | chino, |
| std::string const & | atom_name1, | ||
| std::string const & | atom_name2, | ||
| std::string const & | atom_name3, | ||
| std::string const & | atom_name4 | ||
| ) |
redefine a chi angle based on four atoms
Definition at line 978 of file ResidueType.cc.
References atom_index_, chi_2_proton_chi_, chi_atoms_, finalized_, has(), and is_proton_chi_.
Referenced by core::chemical::RedefineChi::apply().
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reorder primary data in ResidueType given the old2new map, called by finalize()
update the rest private data in ResidueType object after old2new map is set up by calling setup_atom_ordering (some data have been updated there also)
Definition at line 1144 of file ResidueType.cc.
References actcoord_atoms_, atom_2_residue_connection_map_, atom_base_, atom_index_, core::chemical::ICoorAtomID::atomno(), atoms_, bonded_neighbor_, bonded_neighbor_type_, chi_atoms_, cut_bond_neighbor_, icoor(), core::chemical::ICoorAtomID::INTERNAL, mainchain_atoms_, n_actcoord_atoms_, name(), natoms_, nbr_atom_, orbital_bonded_neighbor_, orbital_index(), orbitals_, parents_, residue_connections_, core::io::serialization::size(), core::chemical::strip_whitespace(), core::chemical::AtomICoor::stub_atom(), core::chemical::ICoorAtomID::type(), and update_residue_connection_mapping().
Referenced by finalize().
| void core::chemical::ResidueType::report_adducts | ( | ) |
Definition at line 2513 of file ResidueType.cc.
References core::chemical::Adduct::adduct_name(), core::chemical::Adduct::atom_name(), defined_adducts_, name3(), and core::chemical::tr().
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an assertion funtion to ensure an ResidueType has been finalized
Definition at line 1102 of file ResidueType.hh.
References finalized_.
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require actcoord?
Definition at line 815 of file ResidueType.hh.
References is_aromatic_, is_polar_, is_protein_, and n_actcoord_atoms_.
Referenced by core::conformation::Residue::requires_actcoord().
Definition at line 338 of file ResidueType.cc.
References residue_connections_.
Referenced by core::conformation::Residue::residue_connect_atom_index(), and core::chemical::ICoorAtomID::xyz().
| ResidueConnection const & core::chemical::ResidueType::residue_connection | ( | Size const | i) | const |
get a ResidueConection
Definition at line 345 of file ResidueType.cc.
References residue_connections_.
Referenced by core::conformation::Residue::connect_atom(), core::conformation::Residue::connection_distance(), core::conformation::Residue::copy_residue_connections(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::is_disulfide_bond(), core::conformation::Residue::residue_connection(), core::conformation::setup_corresponding_atoms(), and core::chemical::ICoorAtomID::xyz().
| ResidueConnection & core::chemical::ResidueType::residue_connection | ( | Size const | i) |
Definition at line 351 of file ResidueType.cc.
References residue_connections_.
Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom.
Definition at line 791 of file ResidueType.hh.
References atom_2_residue_connection_map_, and core::io::serialization::size().
Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), core::conformation::Residue::copy_residue_connections(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), and core::conformation::Conformation::fix_disulfides().
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Definition at line 804 of file ResidueType.hh.
References lower_connect_id_, and upper_connect_id_.
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Definition at line 798 of file ResidueType.hh.
References atom_2_residue_connection_map_.
Referenced by core::conformation::Residue::copy_residue_connections(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().
| ResidueTypeSet const & core::chemical::ResidueType::residue_type_set | ( | ) | const |
Definition at line 187 of file ResidueType.cc.
References residue_type_set_.
Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), protocols::comparative_modeling::ThreadingMover::apply(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_residue_typeset(), protocols::comparative_modeling::rebuild_loops_until_closed(), core::conformation::Residue::residue_type_set(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), and core::io::serialization::write_binary().
| void core::chemical::ResidueType::residue_type_set | ( | ResidueTypeSetCAP | set_in) |
set the residue type set of origin.
Definition at line 208 of file ResidueType.cc.
References residue_type_set_.
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Definition at line 1648 of file ResidueType.hh.
References rna_residuetype_.
Referenced by core::conformation::Residue::RNA_type().
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AA to use for rotamer library.
Definition at line 1352 of file ResidueType.hh.
References core::chemical::aa_from_name(), and rotamer_aa_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library(), and core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded().
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Definition at line 1440 of file ResidueType.hh.
References aa_, core::chemical::aa_unk, and rotamer_aa_.
| void core::chemical::ResidueType::select_orient_atoms | ( | Size & | center, |
| Size & | nbr1, | ||
| Size & | nbr2 | ||
| ) | const |
Selects three atoms for orienting this residue type.
Definition at line 2444 of file ResidueType.cc.
References atom_base(), atom_index(), atom_is_backbone(), bonded_neighbor(), first_sidechain_atom(), force_nbr_atom_orient(), name(), natoms(), nbr_atom(), nbrs(), nheavyatoms(), and core::io::serialization::size().
Referenced by core::conformation::Residue::select_orient_atoms().
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Definition at line 1295 of file ResidueType.hh.
References is_adduct_.
| void core::chemical::ResidueType::set_atom_base | ( | std::string const & | atom_name1, |
| std::string const & | atom_name2 | ||
| ) |
sets atom_base[ atom1 ] = atom2
sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary
Definition at line 782 of file ResidueType.cc.
References atom_base_, atom_index_, bonded_neighbor_, cut_bond_neighbor_, finalized_, has(), and natoms_.
Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), and set_icoor().
| void core::chemical::ResidueType::set_atom_type | ( | std::string const & | atom_name, |
| std::string const & | atom_type_name | ||
| ) |
set atom type
Definition at line 464 of file ResidueType.cc.
References atom_index(), atom_types_, and atoms_.
Referenced by core::chemical::SetAtomType::apply().
| void core::chemical::ResidueType::set_backbone_heavyatom | ( | std::string const & | name) |
set an atom as backbone heavy atom
backbone stuff is a little tricky if we want to allow newly added atoms, eg in patching, to be backbone atoms. We move any exsiting backbone heavy atoms back into force_bb_ list and add the new one. Afterwards, the new backbone heavy atom list will be generated in finalize() using info from force_bb_.
Definition at line 1800 of file ResidueType.cc.
References atom_index(), finalized_, force_bb_, and n_backbone_heavyatoms_.
Referenced by core::chemical::SetBackboneHeavyatom::apply().
| void core::chemical::ResidueType::set_icoor | ( | std::string const & | atm, |
| Real const | phi, | ||
| Real const | theta, | ||
| Real const | d, | ||
| std::string const & | stub_atom1, | ||
| std::string const & | stub_atom2, | ||
| std::string const & | stub_atom3, | ||
| bool const | update_xyz = false |
||
| ) |
set AtomICoor for an atom
Definition at line 1903 of file ResidueType.cc.
References atom_base_, atoms_, core::chemical::AtomICoor::build(), core::chemical::ICoorAtomID::CONNECT, has(), core::chemical::ICoorAtomID::INTERNAL, lower_connect_id_, core::chemical::ICoorAtomID::POLYMER_LOWER, core::chemical::ICoorAtomID::POLYMER_UPPER, residue_connections_, set_atom_base(), set_ideal_xyz(), and upper_connect_id_.
Referenced by core::chemical::AddConnect::apply(), core::chemical::SetICoor::apply(), assign_internal_coordinates(), calculate_icoor(), and core::chemical::ResidueDatabaseIO::read_residue_type_icoor().
| void core::chemical::ResidueType::set_icoor | ( | Size const & | index, |
| std::string const & | atm, | ||
| Real const | phi, | ||
| Real const | theta, | ||
| Real const | d, | ||
| std::string const & | stub_atom1, | ||
| std::string const & | stub_atom2, | ||
| std::string const & | stub_atom3, | ||
| bool const | update_xyz = false |
||
| ) |
set AtomICoor for an atom
set AtomICoor for an atom
will update the xyz coords as well if desired, useful inside a patching operation where new atoms are being added.
Definition at line 1853 of file ResidueType.cc.
References atom_base_, atoms_, core::chemical::AtomICoor::build(), core::chemical::ICoorAtomID::CONNECT, has(), core::chemical::ICoorAtomID::INTERNAL, lower_connect_id_, core::chemical::ICoorAtomID::POLYMER_LOWER, core::chemical::ICoorAtomID::POLYMER_UPPER, residue_connections_, set_atom_base(), set_ideal_xyz(), and upper_connect_id_.
| void core::chemical::ResidueType::set_ideal_xyz | ( | std::string const & | atm, |
| Vector const & | xyz_in | ||
| ) |
Definition at line 2128 of file ResidueType.cc.
References atom_index().
Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), and set_icoor().
Definition at line 2138 of file ResidueType.cc.
References atoms_.
| void core::chemical::ResidueType::set_lower_connect_atom | ( | std::string const & | atm_name) |
set the atom which connects to the lower connection
Definition at line 236 of file ResidueType.cc.
References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, residue_connections_, core::chemical::tr(), update_residue_connection_mapping(), and upper_connect_id_.
Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().
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set indices of all mainchain atoms
Definition at line 465 of file ResidueType.hh.
References mainchain_atoms_.
Referenced by core::chemical::PrependMainchainAtom::apply(), and core::chemical::AppendMainchainAtom::apply().
| void core::chemical::ResidueType::set_mm_atom_type | ( | std::string const & | atom_name, |
| std::string const & | mm_atom_type_name | ||
| ) |
set mm atom type
Definition at line 475 of file ResidueType.cc.
References atom_index(), atoms_, and mm_atom_types_.
Referenced by core::chemical::SetMMAtomType::apply().
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| void core::chemical::ResidueType::set_ncaa_rotlib_n_bin_per_rot | ( | utility::vector1< Size > | n_bins_per_rot) |
Sets the number of rotamers for each rotatable bond described by the NCAA rotlib.
Definition at line 2546 of file ResidueType.cc.
References ncaa_rotlib_n_bins_per_rot_, and ncaa_rotlib_n_rots_.
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Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)
Definition at line 1574 of file ResidueType.hh.
References ncaa_rotlib_n_rots_.
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Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)
Definition at line 1581 of file ResidueType.hh.
References ncaa_rotlib_n_rots_.
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Sets the path for the NCAA rotlib for the ResidueType.
Definition at line 1546 of file ResidueType.hh.
References ncaa_rotlib_path_.
Referenced by core::chemical::NCAARotLibPath::apply().
| void core::chemical::ResidueType::set_orbital_icoor_id | ( | std::string const & | orbital, |
| Real const | phi, | ||
| Real const | theta, | ||
| Real const | d, | ||
| std::string const & | stub_atom1, | ||
| std::string const & | stub_atom2, | ||
| std::string const & | stub_atom3 | ||
| ) |
set OrbitalICoor for an orbital
Definition at line 1953 of file ResidueType.cc.
References atom_index_, icoor(), orbital_index(), and orbitals_.
| void core::chemical::ResidueType::set_proton_chi | ( | Size | chino, |
| utility::vector1< Real > | dihedral_samples, | ||
| utility::vector1< Real > | extra_samples | ||
| ) |
Describe proton behavior for residue type; where should rotamer samples be considered, and if expanded rotamers are desired, what deviations from the original rotamer samples should be included. E.g. dihedral_samples of 60, -60, and 180 could have an extra_sample of 20 which would produce rotamers at 40 60 & 80, -40 -60 & -80, and -160, 180 & 160. Extra_samples at 10 and 20 would produce 15 different rotamer samples.
Definition at line 748 of file ResidueType.cc.
References chi_2_proton_chi_, is_proton_chi_, proton_chi_extra_samples_, proton_chi_samples_, and proton_chis_.
Referenced by core::chemical::AddProtonChi::apply().
| void core::chemical::ResidueType::set_RotamerLibraryName | ( | std::string const & | filename) |
Definition at line 1982 of file ResidueType.cc.
References protocols::abinitio::filename(), and rotamer_library_name_.
Referenced by core::chemical::ResidueDatabaseIO::read_residue_type().
| void core::chemical::ResidueType::set_upper_connect_atom | ( | std::string const & | atm_name) |
set the atom which connects to the upper connection
Definition at line 267 of file ResidueType.cc.
References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, residue_connections_, core::chemical::tr(), update_residue_connection_mapping(), and upper_connect_id_.
Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().
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Sets whether we are using a NCAA rotlib for the residue type.
Definition at line 1560 of file ResidueType.hh.
References use_ncaa_rotlib_.
Referenced by core::chemical::NCAARotLibPath::apply().
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set up atom ordering map old2new, called by finalize()
set up atom ordering map old2new, called by finalize() because some new heavy atoms are added by patching, some are flagged to be deleted in delete_atoms_ and some are forced to be backbon atoms as in force_bb_
old2new[old_atom_index] = new_atom_index
sets natoms_, nheavyatoms_, and n_backbone_heavyatoms_
also fills attached_H_begin, attached_H_end
Definition at line 1043 of file ResidueType.cc.
References atom_type(), atom_types_, atoms_, attached_H_begin_, attached_H_end_, bonded_neighbor_, delete_atoms_, force_bb_, core::scoring::is_heavyatom(), n_backbone_heavyatoms_, natoms_, nbrs(), nheavyatoms_, and core::chemical::tr().
Referenced by finalize().
| void core::chemical::ResidueType::show_all_atom_names | ( | std::ostream & | out) | const |
Definition at line 2537 of file ResidueType.cc.
References atoms_, and core::sequence::end.
Referenced by atom_index().
| void core::chemical::ResidueType::update_actcoord | ( | conformation::Residue & | rot) | const |
update actcoord
update actcoord average geometrical center of the set of actcoord_atoms_
Definition at line 1834 of file ResidueType.cc.
References core::conformation::Residue::actcoord(), actcoord_atoms_, core::conformation::Residue::atoms(), and n_actcoord_atoms_.
Referenced by core::conformation::Residue::update_actcoord().
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update derived data in ResidueType, called by finalize()
update derived data in ResidueType, called by finalize() after primary data have been reordered, update derived data acoordingly, including
, Hbond donor and acceptors, path_distance etc.
Definition at line 1329 of file ResidueType.cc.
References abase2_, accpt_pos_, accpt_pos_sc_, all_bb_atoms_, all_sc_atoms_, atom_base_, core::chemical::AtomType::atom_has_orbital(), atom_is_polar_hydrogen_, atom_types_, atoms_, atoms_last_controlled_by_chi_, atoms_with_orb_index_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, attached_H_begin_, attached_H_end_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor_, carbohydrate_info_, dihedral_atom_sets_, dihedrals_for_atom_, first_sidechain_hydrogen_, core::chemical::get_residue_path_distances(), Haro_index_, heavyatom_has_polar_hydrogens_, heavyatom_is_an_acceptor_, Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, core::chemical::AtomType::is_acceptor(), is_carbohydrate_, core::chemical::AtomType::is_haro(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), is_RNA_, last_controlling_chi_, n_backbone_heavyatoms_, natoms_, ndihe_, nheavyatoms_, path_distance_, path_distances(), residue_connections_, rna_residuetype_, core::chemical::rna::RNA_ResidueType::rna_update_last_controlling_chi(), core::chemical::rna::RNA_ResidueType::update_derived_rna_data(), update_last_controlling_chi(), within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.
Referenced by finalize().
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compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom.
Definition at line 2354 of file ResidueType.cc.
References atom_base_, atoms_last_controlled_by_chi_, bonded_neighbor_, chi_atoms_, last_controlling_chi_, natoms_, nchi(), and note_chi_controls_atom().
Referenced by update_derived_data().
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Definition at line 2342 of file ResidueType.cc.
References atom_2_residue_connection_map_, natoms_, and residue_connections_.
Referenced by add_residue_connection(), reorder_primary_data(), set_lower_connect_atom(), and set_upper_connect_atom().
| ResidueConnection const & core::chemical::ResidueType::upper_connect | ( | ) | const |
Definition at line 296 of file ResidueType.cc.
References is_polymer_, residue_connections_, and upper_connect_id_.
Referenced by core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::upper_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
| Size core::chemical::ResidueType::upper_connect_atom | ( | ) | const |
index number of the atom which connects to the upper connection
Definition at line 323 of file ResidueType.cc.
References is_polymer_, residue_connections_, and upper_connect_id_.
Referenced by core::chemical::ICoorAtomID::atom_id(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ICoorAtomID::xyz().
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Definition at line 726 of file ResidueType.hh.
References upper_connect_id_.
Referenced by core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), and core::conformation::Residue::is_polymer_bonded().
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get all the variant types for this ResidueType
Definition at line 1317 of file ResidueType.hh.
References variant_types_.
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::chemical::ResidueSelector::match_variants(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::chemical::Selector_NO_VARIANTS::operator[](), protocols::swa::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), core::pose::residue_types_from_sequence(), and protocols::hybridization::FoldTreeHybridize::revert_loops_to_original().
| bool core::chemical::ResidueType::variants_match | ( | ResidueType const & | other) | const |
Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property.
Definition at line 1692 of file ResidueType.cc.
References core::chemical::DEPROTONATED, has_variant_type(), core::chemical::PROTONATED, and variant_types_.
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), and core::pack::task::ResidueLevelTask_::ResidueLevelTask_().
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Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.
Definition at line 1620 of file ResidueType.hh.
References within1bonds_sets_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), and core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().
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Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.
Definition at line 1642 of file ResidueType.hh.
References within2bonds_sets_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().
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standard rosetta aa-type for knowledge-based potentials, may be aa_unk
Definition at line 1976 of file ResidueType.hh.
Referenced by aa(), and rotamer_aa().
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indices of each atom's second base atom, for acceptors atom only
Definition at line 1823 of file ResidueType.hh.
Referenced by abase2(), and update_derived_data().
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Definition at line 1863 of file ResidueType.hh.
Referenced by accpt_pos(), and update_derived_data().
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indices of Hbond acceptor positions that are part of the sidechain must be a subset of the atoms listed in the accpt_pos_ array
Definition at line 1870 of file ResidueType.hh.
Referenced by accpt_pos_sc(), and update_derived_data().
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indices of action coordinate centers
the geometric center of the atoms listed defined the residue's "action coordinate"
Definition at line 1895 of file ResidueType.hh.
Referenced by actcoord_atoms(), add_actcoord_atom(), reorder_primary_data(), and update_actcoord().
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Indices of all backbone atoms, hydrogens and heavyatoms.
Definition at line 1875 of file ResidueType.hh.
Referenced by all_bb_atoms(), and update_derived_data().
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Indices of all sidechain atoms, hydrogens and heavyatoms.
Definition at line 1877 of file ResidueType.hh.
Referenced by all_sc_atoms(), and update_derived_data().
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Definition at line 2018 of file ResidueType.hh.
Referenced by add_atom(), atom_forms_residue_connection(), n_residue_connections_for_atom(), reorder_primary_data(), residue_connection_id_for_atom(), residue_connections_for_atom(), and update_residue_connection_mapping().
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indices of each atom's base atom
Definition at line 1821 of file ResidueType.hh.
Referenced by add_atom(), atom_base(), note_chi_controls_atom(), reorder_primary_data(), set_atom_base(), set_icoor(), update_derived_data(), and update_last_controlling_chi().
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atom index lookup by atom name string
Definition at line 1911 of file ResidueType.hh.
Referenced by add_atom(), add_bond(), add_chi(), add_cut_bond(), add_orbital_bond(), atom_index(), has(), has_atom_name(), redefine_chi(), reorder_primary_data(), set_atom_base(), and set_orbital_icoor_id().
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Definition at line 1883 of file ResidueType.hh.
Referenced by atom_is_polar_hydrogen(), and update_derived_data().
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AtomTypeSet Object.
used to define the set of allowed atomtypes for this residue and their properties
Definition at line 1743 of file ResidueType.hh.
Referenced by add_atom(), atom_type(), atom_type_set(), atom_type_set_ptr(), set_atom_type(), setup_atom_ordering(), and update_derived_data().
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vector of atoms:
Atom order rules: (1) heavyatoms before hydrogens (2) backbone heavyatoms before sidechain heavyatoms (3) hydrogens are grouped by the heavyatom they are attached to and come in the order of those heavyatoms (4) as a consequence of (2)+(3) –> backbone hydrogens come before sidechain hydrogens (5) atom order in the residue file is preserved subject to rules 1-4 see finalize() for the logic to determine the atom order
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If you add new properties that are associated with atoms and therefore depend on the atom order, and that get set during Residue creation before the call to finalize(), then you have to make sure to update them in finalize() if the atom order changes
in general, anything that might be sensitive to atom order should be updated in finalize using the old2new mapping
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Definition at line 1787 of file ResidueType.hh.
Referenced by add_atom(), assign_neighbor_atom(), atom(), atom_name(), atom_type(), icoor(), mm_atom_type(), print_bondangles(), print_dihedrals(), print_pretty_path_distances(), reorder_primary_data(), set_atom_type(), set_icoor(), set_ideal_xyz(), set_mm_atom_type(), setup_atom_ordering(), show_all_atom_names(), and update_derived_data().
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for chi i, the list of atoms last controlled by i. E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1
Definition at line 1851 of file ResidueType.hh.
Referenced by atoms_last_controlled_by_chi(), update_derived_data(), and update_last_controlling_chi().
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indices of Hbond acceptor positions
Definition at line 1858 of file ResidueType.hh.
Referenced by atoms_with_orb_index(), and update_derived_data().
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For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.
Definition at line 2024 of file ResidueType.hh.
Referenced by atoms_within_one_bond_of_a_residue_connection(), and update_derived_data().
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For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i.
Definition at line 2037 of file ResidueType.hh.
Referenced by atoms_within_two_bonds_of_a_residue_connection(), and update_derived_data().
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indices of each heavyatom's first attached hydrogen
Definition at line 1825 of file ResidueType.hh.
Referenced by attached_H_begin(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().
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indices of each heavyatom's last attached hydrogen
Definition at line 1827 of file ResidueType.hh.
Referenced by attached_H_end(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().
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Definition at line 2103 of file ResidueType.hh.
Referenced by base_restype_name().
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vector of sets of atoms that make up bond angles in the residue
Definition at line 1839 of file ResidueType.hh.
Referenced by bondangle(), num_bondangles(), print_bondangles(), and update_derived_data().
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all intra-residue bond angles that each atom "participates" in.
Definition at line 1841 of file ResidueType.hh.
Referenced by bondangles_for_atom(), and update_derived_data().
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indices of each atom's bonded neighbors
Definition at line 1815 of file ResidueType.hh.
Referenced by add_atom(), add_bond(), assign_internal_coordinates(), bonded_neighbor(), nbrs(), note_chi_controls_atom(), number_bonded_heavyatoms(), reorder_primary_data(), set_atom_base(), setup_atom_ordering(), update_derived_data(), and update_last_controlling_chi().
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indices of each atom's bonded neighbor type (uses the same indexing scheme and order as bonded_neighbor_
Definition at line 1817 of file ResidueType.hh.
Referenced by add_atom(), add_bond(), bonded_neighbor_types(), and reorder_primary_data().
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Definition at line 2060 of file ResidueType.hh.
Referenced by is_branch_point().
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Definition at line 2074 of file ResidueType.hh.
Referenced by carbohydrate_info(), and update_derived_data().
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Definition at line 1903 of file ResidueType.hh.
Referenced by add_chi(), chi_2_proton_chi(), redefine_chi(), and set_proton_chi().
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indices of four atoms to build each chi angle
Definition at line 1900 of file ResidueType.hh.
Referenced by add_chi(), chi_atoms(), nchi(), redefine_chi(), reorder_primary_data(), and update_last_controlling_chi().
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Additional non-dunbrack rotamer bins.
pair<Real,Real> ==> mean,sdev for each chi angle i and rotamer j: chi_rotamers_[i][j]
Definition at line 1921 of file ResidueType.hh.
Referenced by add_chi(), add_chi_rotamer(), and chi_rotamers().
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indices of each atom's bonded neighbors
Definition at line 1819 of file ResidueType.hh.
Referenced by add_atom(), add_cut_bond(), cut_bond_neighbor(), reorder_primary_data(), and set_atom_base().
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Definition at line 2088 of file ResidueType.hh.
Referenced by add_adduct(), defined_adducts(), and report_adducts().
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a list of atom indices to be deleted
in the next call to finalize(), used in delete_atom which is called during patching
Definition at line 2066 of file ResidueType.hh.
Referenced by delete_atom(), finalize(), and setup_atom_ordering().
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vector of sets of atoms that make up dihedral angles in the residue
Definition at line 1835 of file ResidueType.hh.
Referenced by dihedral(), print_dihedrals(), and update_derived_data().
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all intra-residue dihedral angles that each atom "participates" in.
Definition at line 1837 of file ResidueType.hh.
Referenced by dihedrals_for_atom(), and update_derived_data().
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Definition at line 1744 of file ResidueType.hh.
Referenced by add_atom(), and element_set().
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status
Definition at line 2078 of file ResidueType.hh.
Referenced by add_actcoord_atom(), add_atom(), add_bond(), add_chi(), add_cut_bond(), add_orbital(), add_orbital_bond(), add_property(), add_residue_connection(), atom_is_backbone(), atom_is_hydrogen(), atom_is_polar_hydrogen(), delete_atom(), delete_property(), finalize(), first_sidechain_hydrogen(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), redefine_chi(), require_final(), set_atom_base(), set_backbone_heavyatom(), set_lower_connect_atom(), and set_upper_connect_atom().
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the index of first sidechain hydrogen atom
Definition at line 1805 of file ResidueType.hh.
Referenced by atom_is_backbone(), first_sidechain_hydrogen(), and update_derived_data().
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atom indices forced to be considered backbone
Definition at line 2068 of file ResidueType.hh.
Referenced by finalize(), set_backbone_heavyatom(), and setup_atom_ordering().
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Definition at line 1995 of file ResidueType.hh.
Referenced by force_nbr_atom_orient().
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Definition at line 1860 of file ResidueType.hh.
Referenced by Haro_index(), and update_derived_data().
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Definition at line 1949 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and has_sc_orbitals().
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Vectors of booleans, represented as integers for speed (since vector1<bool> is optimized for space and is slow to read from) 1 for true, 0 for false
Definition at line 1881 of file ResidueType.hh.
Referenced by heavyatom_has_polar_hydrogens(), and update_derived_data().
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Definition at line 1882 of file ResidueType.hh.
Referenced by heavyatom_is_an_acceptor(), and update_derived_data().
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Definition at line 1862 of file ResidueType.hh.
Referenced by Hpol_index(), and update_derived_data().
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indices of apolar hydrogens
Definition at line 1867 of file ResidueType.hh.
Referenced by Hpos_apolar(), and update_derived_data().
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indices of polar Hydrogens for Hbond donors
Definition at line 1865 of file ResidueType.hh.
Referenced by Hpos_polar(), and update_derived_data().
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indices of polar Hydrogens for Hbond donors that are part of the sidechain must be a subset of the atoms listed in the Hpos_polar_ array
Definition at line 1873 of file ResidueType.hh.
Referenced by Hpos_polar_sc(), and update_derived_data().
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Definition at line 1962 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_acetylated_nterminus().
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Definition at line 1965 of file ResidueType.hh.
Referenced by is_adduct(), and set_adduct_flag().
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Definition at line 1950 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_aromatic(), and requires_actcoord().
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Definition at line 1954 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_carbohydrate(), and update_derived_data().
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Definition at line 1946 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_charged().
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Definition at line 1964 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_coarse().
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Definition at line 1951 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_DNA().
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Definition at line 1955 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_ligand().
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Definition at line 1958 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_lower_terminus().
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Definition at line 1963 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_methylated_cterminus().
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Definition at line 1953 of file ResidueType.hh.
Referenced by add_property(), and is_NA().
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Definition at line 1960 of file ResidueType.hh.
Referenced by add_property(), and delete_property().
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Definition at line 1961 of file ResidueType.hh.
Referenced by add_property(), and delete_property().
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Definition at line 1947 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_polar(), and requires_actcoord().
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Definition at line 1944 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_polymer(), lower_connect(), lower_connect_atom(), upper_connect(), and upper_connect_atom().
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Definition at line 1945 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_protein(), and requires_actcoord().
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Definition at line 1901 of file ResidueType.hh.
Referenced by add_chi(), redefine_chi(), and set_proton_chi().
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Definition at line 1952 of file ResidueType.hh.
Referenced by add_property(), delete_property(), is_RNA(), and update_derived_data().
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Definition at line 1956 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_surface().
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Definition at line 1957 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_terminus().
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Definition at line 1959 of file ResidueType.hh.
Referenced by add_property(), delete_property(), and is_upper_terminus().
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for each atom, the last controlling chi angle for that atom. a chi of 0 represents an atom whose location is not determined by any chi.
Definition at line 1847 of file ResidueType.hh.
Referenced by last_controlling_chi(), note_chi_controls_atom(), update_derived_data(), and update_last_controlling_chi().
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Polymer lower connections.
Definition at line 2050 of file ResidueType.hh.
Referenced by lower_connect(), lower_connect_atom(), lower_connect_id(), residue_connection_is_polymeric(), set_icoor(), set_lower_connect_atom(), and set_upper_connect_atom().
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indices of all mainchain atoms
mainchain_atoms are those atoms on the shortest path from polymer lower_connect to upper_connect. For protein, this will be N, CA and C.
Definition at line 1889 of file ResidueType.hh.
Referenced by mainchain_atom(), mainchain_atoms(), reorder_primary_data(), and set_mainchain_atoms().
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Definition at line 1746 of file ResidueType.hh.
Referenced by add_atom(), mm_atom_type(), and set_mm_atom_type().
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the unprocessed metadata
Definition at line 2007 of file ResidueType.hh.
Referenced by get_mol_data(), and set_mol_data().
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Definition at line 1998 of file ResidueType.hh.
Referenced by add_atom(), and molar_mass().
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Definition at line 1997 of file ResidueType.hh.
Referenced by add_atom(), and molecular_mass().
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number of actcoord atoms
the geometric center of the atoms listed defined the residue's "action coordinate"
Definition at line 2004 of file ResidueType.hh.
Referenced by add_actcoord_atom(), reorder_primary_data(), requires_actcoord(), and update_actcoord().
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number of backbone heavy atoms
Definition at line 1803 of file ResidueType.hh.
Referenced by atom_is_backbone(), first_sidechain_atom(), last_backbone_atom(), set_backbone_heavyatom(), setup_atom_ordering(), and update_derived_data().
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number of hbond_acceptors
Definition at line 1797 of file ResidueType.hh.
Referenced by add_atom(), and n_hbond_acceptors().
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number of hbond_donors
Definition at line 1799 of file ResidueType.hh.
Referenced by add_atom(), and n_hbond_donors().
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Definition at line 2056 of file ResidueType.hh.
Referenced by add_residue_connection(), and n_non_polymeric_residue_connections().
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number of orbitals
Definition at line 1801 of file ResidueType.hh.
Referenced by add_orbital(), and n_orbitals().
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Definition at line 2057 of file ResidueType.hh.
Referenced by n_polymeric_residue_connections(), set_lower_connect_atom(), and set_upper_connect_atom().
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one-letter code, also not necessarily unique
Definition at line 1985 of file ResidueType.hh.
Referenced by name1().
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pdb-file id, need not be unique
Definition at line 1982 of file ResidueType.hh.
Referenced by name3().
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unique residue id
Definition at line 1979 of file ResidueType.hh.
Referenced by add_actcoord_atom(), and name().
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number of atoms
Definition at line 1793 of file ResidueType.hh.
Referenced by add_atom(), atom_is_backbone(), atom_is_hydrogen(), first_sidechain_atom(), natoms(), print_pretty_path_distances(), reorder_primary_data(), set_atom_base(), setup_atom_ordering(), update_derived_data(), update_last_controlling_chi(), and update_residue_connection_mapping().
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atom used for calculating residue-level neighbors
Definition at line 1989 of file ResidueType.hh.
Referenced by assign_internal_coordinates(), nbr_atom(), and reorder_primary_data().
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radius cutoff to define neighors
Definition at line 1991 of file ResidueType.hh.
Referenced by nbr_radius().
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the number of rotamer bins for each chi angle in the NCAA rotlib
Definition at line 1933 of file ResidueType.hh.
Referenced by get_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_bin_per_rot().
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the number of non-hydrogen chi angles in the NCAA rotlib
Definition at line 1931 of file ResidueType.hh.
Referenced by set_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_rotameric_bins().
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path to the NCAA rotlib
Definition at line 1929 of file ResidueType.hh.
Referenced by get_ncaa_rotlib_path(), and set_ncaa_rotlib_path().
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number of dihedral angle atom sets
Definition at line 1807 of file ResidueType.hh.
Referenced by ndihe(), print_dihedrals(), and update_derived_data().
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number of heavy atoms
Definition at line 1795 of file ResidueType.hh.
Referenced by atom_is_backbone(), atom_is_hydrogen(), first_sidechain_atom(), nheavyatoms(), setup_atom_ordering(), and update_derived_data().
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Definition at line 2102 of file ResidueType.hh.
Referenced by nondefault().
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indices of the atoms psuedo bonded atoms. Used in orbital code
Definition at line 1813 of file ResidueType.hh.
Referenced by add_atom(), add_orbital_bond(), bonded_orbitals(), and reorder_primary_data().
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Orbital types.
Definition at line 1748 of file ResidueType.hh.
Referenced by add_orbital(), and orbital_type().
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Definition at line 1788 of file ResidueType.hh.
Referenced by add_orbital(), new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), reorder_primary_data(), and set_orbital_icoor_id().
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atom index lookup by atom name string
Definition at line 1914 of file ResidueType.hh.
Referenced by add_orbital(), add_orbital_bond(), has_orbital(), and orbital_index().
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atom parents
Definition at line 1830 of file ResidueType.hh.
Referenced by add_atom(), assign_internal_coordinates(), and reorder_primary_data().
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number of bonds separated between any pair of atoms in this residue
Definition at line 1908 of file ResidueType.hh.
Referenced by path_distance(), path_distances(), print_pretty_path_distances(), and update_derived_data().
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residue properties as defined in the residue param files
Definition at line 1943 of file ResidueType.hh.
Referenced by add_property(), delete_property(), has_property(), and properties().
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Definition at line 1905 of file ResidueType.hh.
Referenced by proton_chi_extra_samples(), and set_proton_chi().
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Definition at line 1904 of file ResidueType.hh.
Referenced by proton_chi_samples(), and set_proton_chi().
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Definition at line 1902 of file ResidueType.hh.
Referenced by is_proton_chi(), n_proton_chi(), proton_chi_2_chi(), and set_proton_chi().
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Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections.
Definition at line 2017 of file ResidueType.hh.
Referenced by add_residue_connection(), lower_connect(), lower_connect_atom(), n_residue_connections(), reorder_primary_data(), residue_connect_atom_index(), residue_connection(), set_icoor(), set_lower_connect_atom(), set_upper_connect_atom(), update_derived_data(), update_residue_connection_mapping(), upper_connect(), and upper_connect_atom().
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Definition at line 1753 of file ResidueType.hh.
Referenced by residue_type_set().
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Definition at line 2071 of file ResidueType.hh.
Referenced by RNA_type(), and update_derived_data().
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Definition at line 1976 of file ResidueType.hh.
Referenced by rotamer_aa().
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Definition at line 1923 of file ResidueType.hh.
Referenced by get_RotamerLibraryName(), and set_RotamerLibraryName().
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Definition at line 2110 of file ResidueType.hh.
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Polymer upper connections.
Definition at line 2054 of file ResidueType.hh.
Referenced by residue_connection_is_polymeric(), set_icoor(), set_lower_connect_atom(), set_upper_connect_atom(), upper_connect(), upper_connect_atom(), and upper_connect_id().
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NCAA rotlib stuff some of this is hardcoded elsewhere for the CAAs whether or not we should use the NCAA rotlib if it exists
Definition at line 1927 of file ResidueType.hh.
Referenced by get_use_ncaa_rotlib(), and set_use_ncaa_rotlib().
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here we store the patch operations/variant types that describe this residue
Definition at line 1969 of file ResidueType.hh.
Referenced by add_variant_type(), has_variant_type(), nonadduct_variants_match(), variant_types(), and variants_match().
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For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array.
Definition at line 2031 of file ResidueType.hh.
Referenced by update_derived_data(), and within1bonds_sets_for_atom().
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For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array.
Definition at line 2044 of file ResidueType.hh.
Referenced by update_derived_data(), and within2bonds_sets_for_atom().
1.8.4