Instance Residue class, used for placed residues and rotamers. More...

#include <Residue.hh>

Inheritance diagram for core::conformation::Residue:

Collaboration diagram for core::conformation::Residue:

Public Types
typedef chemical::AtomType	AtomType

typedef chemical::ResidueType	ResidueType

typedef chemical::AtomIndices	AtomIndices

Public Member Functions
	Residue (ResidueType const &rsd_type_in, bool const dummy_arg)
	constructors Residue( Residue const & ); // user defined copy ctor to avoid #including PseudoBond.hh Residue const & operator = ( Residue const & ) // user defined assignment operator for same reason More...

	Residue (ResidueType const &rsd_type_in, bool const , bool const )

	Residue (ResidueType const &rsd_type_in, Residue const &current_rsd, Conformation const &conformation, bool preserve_c_beta=false)
	Rotamer-style constructor; orients ideal coords onto backbone of current_rsd. More...

	Residue (Residue const &src)

	~Residue ()

ResidueOP	clone () const
	Copy this residue( allocate actual memory for it ) More...

AtomType const &	atom_type (int const atomno) const
	Returns the AtomType of this residue's atom with index number <atomno> More...

chemical::AtomTypeSet const &	atom_type_set () const
	Returns the AtomTypeSet of this residue. More...

Size	atom_type_index (Size const atomno) const
	Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType. More...

Real	atomic_charge (int const atomno) const
	Returns the atom charge of this residue's atom with index number <atomno> More...

bool	is_virtual (Size const &atomno) const
	Check if atom is virtual. More...

bool	is_virtual_residue () const
	Check if residue is virtual. More...

Size	atom_index (std::string const &atm) const
	Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid. More...

Size	natoms () const
	Returns the number of atoms in this residue. More...

Size	n_hbond_acceptors () const
	number of hbond_donors More...

Size	n_hbond_donors () const
	number of hbond_donors More...

Size	nheavyatoms () const
	Returns the number of heavyatoms in this residue. More...

AtomIndices const &	Hpos_polar () const
	Returns the AtomIndices of this residue's polar hydrogens. More...

AtomIndices const &	all_bb_atoms () const
	Returns the AtomIndices of this residue's backbone atoms. More...

AtomIndices const &	Haro_index () const
	Returns the AtomIndices of this residue's aromatic hydrogens. More...

AtomIndices const &	Hpol_index () const
	Returns the AtomIndices of this residue's polar hydrogens. More...

AtomIndices const &	Hpos_apolar () const
	Returns the AtomIndices of this residue's apolar hydrogens. More...

AtomIndices const &	Hpos_polar_sc () const
	Returns the AtomIndices of this residue's polar sidechain hydrogens. More...

AtomIndices const &	accpt_pos () const
	Returns the AtomIndices of this residue's h-bond acceptor atoms. More...

AtomIndices const &	accpt_pos_sc () const
	Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms. More...

bool	heavyatom_has_polar_hydrogens (Size ind) const
	Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom) More...

bool	heavyatom_is_an_acceptor (Size ind) const
	Is a particular atom a heavy atom acceptor? More...

bool	atom_is_polar_hydrogen (Size ind) const
	Is a particular atom a polar hydrogen? More...

Atoms const &	atoms () const
	Returns this residue's Atoms (const), a vector1 of Atom objects. More...

Atoms &	atoms ()
	Returns this residue's Atoms (non-const), a vector1 of Atom objects. More...

Atoms::iterator	atom_begin ()
	begin interator, to iterate over atoms More...

Atoms::iterator	atom_end ()
	end interator, to iterate over atoms More...

Atoms::const_iterator	atom_begin () const

Atoms::const_iterator	atom_end () const

Atoms::const_iterator	sidechainAtoms_begin () const
	should be safe, given the atom ordering rules? More...

Atoms::const_iterator	heavyAtoms_end () const

Atom const &	atom (Size const atm_index) const
	Returns this residue's Atom with index number <atm_index> (const) More...

Atom &	atom (Size const atm_index)
	Returns this residue's Atom with index number <atm_index> (non-const) More...

Atom const &	atom (std::string const &atm_name) const
	Returns this residue's Atom with name <atm_name> (const) More...

Atom &	atom (std::string const &atm_name)
	Returns this residue's Atom with name <atm_name> (non-const) More...

Vector const &	xyz (Size const atm_index) const
	Returns the position of this residue's atom with index number <atm_index> More...

Vector const &	xyz (std::string const &atm_name) const
	Returns the position of this residue's atom with name <atm_name> More...

void	set_xyz (core::Size const atm_index, Vector const &xyz_in)
	Sets the position of this residue's atom with index number <atm_index> More...

void	set_xyz (std::string const &atm_name, Vector const &xyz_in)
	Sets the position of this residue's atom with name <atm_name> More...

Size	last_backbone_atom () const
	Returns the index number of the last backbone heavyatom. More...

Size	first_sidechain_atom () const
	Returns the index number of the first sidechain heavyatom. More...

Size	first_sidechain_hydrogen () const
	Returns the index number of the first sidechain hydrogen. More...

Size	attached_H_begin (int const atom) const
	Returns the index number of the first hydrogen attached to the atom with index number <atom> More...

Size	attached_H_end (int const atom) const
	Returns the index number of the last hydrogen attached to the atom with index number <atom> More...

AtomIndices const &	attached_H_begin () const
	Returns the AtomIndices of the first hydrogen attached to each heavyatom. More...

AtomIndices const &	attached_H_end () const
	Returns the AtomIndices of the last hydrogen attached to each heavyatom. More...

Size	lower_connect_atom () const
	Returns the index number of this residue's atom which connects to the residue before it in sequence. More...

Size	upper_connect_atom () const
	Returns the index number of this residue's atom which connects to the residue after it in sequence. More...

Size	connect_atom (Residue const &other) const
	Returns the index number of this residue's atom connected to the <other> Residue. More...

utility::vector1< int > const &	path_distance (int atom) const
	Returns the shortest path distance from <atom> to any other atom in this residue. More...

utility::vector1 < utility::vector1< int > > const &	path_distances () const
	Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2]. More...

int	path_distance (int at1, int at2) const
	Returns the number of bonds separating atom <at1> from <at2> More...

bool	atom_is_backbone (int const atomno) const
	Returns true if this residue's atom with index number <atomno> is a backbone atom. More...

bool	atom_is_hydrogen (Size const atomno) const
	Returns true if this residue's atom with index number <atomno> is a hydrogen. More...

Size	atom_base (int const atomno) const
	Returns the atom index of the <atomno> atom's base atom. More...

Size	abase2 (int const atomno) const
	Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor) More...

AtomIndices const &	bonded_neighbor (int const atm) const
	Returns the AtomIndices for all bonded neighbor atoms of <atm> More...

Size	nchi () const
	Returns the number of chi angles this residue has. More...

AtomIndices const &	mainchain_atoms () const
	Returns the AtomIndices of this residue's mainchain atoms. More...

Size	mainchain_atom (Size const atm) const
	??? Returns the number of the residue's mainchain atoms More...

Size	n_mainchain_atoms () const
	Returns the number of the residue's mainchain atoms. More...

AtomIndices const &	actcoord_atoms () const
	Returns the AtomIndices of atoms that will be used to define this residue's actcoord. More...

Vector	build_atom_ideal (int const atomno, Conformation const &conformation) const
	Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms. More...

Size	nbr_atom () const
	Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids. More...

Real	nbr_radius () const
	Returns the distance cutoff value used as a radius for neighbor definition. More...

Vector const &	nbr_atom_xyz () const

AtomIndices const &	atoms_with_orb_index () const

Vector	build_orbital_xyz (Size const orbital_index) const

Vector const &	orbital_xyz (Size const orbital_index) const

void	set_orbital_xyz (core::Size const orbital_index, Vector const &xyz_in)

Size	n_orbitals () const
	Returns the number of orbitals in this residue. More...

utility::vector1< core::Size > const &	bonded_orbitals (int const atm) const

std::string const &	orbital_name (int const orbital_index) const

chemical::orbitals::OrbitalType const &	orbital_type (int const orbital_index) const

Size	orbital_type_index (Size const orbital_index) const

void	update_orbital_coords ()

ResidueOP	create_rotamer () const
	Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out. More...

ResidueOP	create_residue () const
	Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out. More...

ResidueType const &	type () const
	Returns this residue's ResidueType. More...

chemical::ResidueTypeSet const &	residue_type_set () const
	Returns this residue's ResidueTypeSet. More...

chemical::ResidueConnection const &	upper_connect () const
	Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue. More...

chemical::ResidueConnection const &	lower_connect () const
	Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue. More...

bool	connections_match (Residue const &other) const
	Returns true if ??? More...

Size	n_residue_connections () const
	Returns the number of ResidueConnections on this residue including polymeric residue connections. More...

Size	n_polymeric_residue_connections () const
	Returns the number of polymeric ResidueConnections on this residue. More...

Size	n_non_polymeric_residue_connections () const
	Returns the number of non-polymeric ResidueConnections on this residue. More...

chemical::ResidueConnection const &	residue_connection (int const resconn_index) const
	Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue. More...

Size	residue_connect_atom_index (Size const resconn_id) const

Size	connected_residue_at_resconn (Size const resconn_index) const

chemical::ResConnID	connect_map (Size resconn_index) const

void	clear_residue_connections ()

void	copy_residue_connections_from (Residue const &src)

bool	has_incomplete_connection () const

bool	has_incomplete_connection (core::Size const atomno) const
	Returns true is <atomno> has complete connectivity? More...

bool	connection_incomplete (Size resconnid) const

chemical::ResConnID	actual_residue_connection (Size resconnid) const

Size	residue_connection_partner (Size const resconn_index) const
	Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ? More...

void	copy_residue_connections (Residue const &src_rsd)
	attempt to take residue connection info from src_rsd More...

Size	residue_connection_conn_id (Size const resconn_index) const
	Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ? More...

void	residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid)
	set a connection to this residue by adding its partner's residue number More...

Distance	connection_distance (conformation::Conformation const &conf, Size const resconn_index, Vector const matchpoint) const
	Distance between a potential residue connection match and the position of the expected atom. More...

bool	is_bonded (Residue const &other) const
	Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides) More...

bool	is_pseudo_bonded (Residue const &other) const
	Do I have any pseudobonds to other? More...

bool	is_bonded (Size const other_index) const
	Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic. More...

bool	is_pseudo_bonded (Size const other_index) const
	Do I have any pseudobonds to other? More...

bool	is_polymer_bonded (Residue const &other) const
	Am I polymer bonded to other? More...

bool	is_polymer_bonded (Size const other_index) const
	Am I polymer-bonded to other? checks lower and upper connections. More...

utility::vector1< Size > const &	connections_to_residue (Residue const &other) const
	Returns the vector1 of resconn ids that connect this residue to other. More...

utility::vector1< Size > const &	connections_to_residue (Size const other_resid) const
	Returns the vector1 of resconn ids that connect this residue to other. More...

PseudoBondCollectionCOP	get_pseudobonds_to_residue (Size resid) const

std::map< Size, PseudoBondCollectionCOP > const &	pseudobonds () const

void	set_pseudobonds_to_residue (Size resid, PseudoBondCollectionCOP pbs)

utility::vector1< std::pair < Real, Real > > const &	chi_rotamers (Size const chino) const
	Returns the chi rotamers available for this residue's chi angle <chino> More...

AtomIndices const &	cut_bond_neighbor (int const atm) const
	atom indices for bonded neighbors to which atom-tree connections are disallowed. More...

core::Size	n_bonded_neighbor_all_res (core::Size const atomno, bool virt=false) const
	Returns the number of atoms bonded to <atomno> in all residues? More...

AtomIndices const &	nbrs (int const atm) const
	Convenience synonym for bonded_neighbor. More...

utility::vector1< Real > const &	mainchain_torsions () const
	Returns the mainchain torsion angles of this residue (const) More...

utility::vector1< Real > &	mainchain_torsions ()
	Returns the mainchain torsion angles of this residue (non-const) More...

void	mainchain_torsions (utility::vector1< Real > const &torsions)
	Sets the mainchain torsion angles of this residue to <torsions> More...

utility::vector1< Real > const &	chi () const
	Returns the chi torsion angles of this residue (const) More...

utility::vector1< Real > &	chi ()
	Returns the chi torsion angles of this residue (non-const) More...

void	chi (utility::vector1< Real > const &chis)
	Sets the chi torsion angles of this residue. More...

utility::vector1< AtomIndices > const &	chi_atoms () const
	Returns the AtomIndices of each four atom set defining a chi angle. More...

AtomIndices const &	chi_atoms (int const chino) const
	Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle. More...

Real	mainchain_torsion (Size const torsion) const
	Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid. More...

Real	chi (Size const chino) const
	get a specific chi torsion angle More...

Size	seqpos () const
	Returns the sequence position of this residue. More...

Size	polymeric_sequence_distance (Residue const &other) const
	Returns the sequence separation distance between this residue and <other> More...

int	polymeric_oriented_sequence_distance (Residue const &other) const
	Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence. More...

void	seqpos (Size const setting)
	Sets this residue's sequence position to <setting> More...

core::Size	chain () const
	Returns this residue's chain id. More...

void	chain (int const setting)
	Sets this residue's chain id. More...

bool	requires_actcoord () const
	does this residue require an actcoord? More...

void	update_actcoord ()
	Updates actcoord for this residue. More...

Vector const &	actcoord () const
	Returns the coordinates used for pairE calculations (amino acids only) More...

Vector &	actcoord ()
	Returns the coordinates used for pairE calculations (amino acids only) More...

void	update_sequence_numbering (utility::vector1< Size > const &old2new)
	Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped. More...

bool	is_polymer () const
	Returns true if this residue is a polymer. More...

bool	is_protein () const
	Returns true if this residue is an amino acid. More...

bool	is_DNA () const
	Returns true if this residue is a DNA residue. More...

bool	is_RNA () const
	Returns true if this residue is a RNA residue. More...

bool	is_NA () const
	Returns true if this residue is a nucleic acid. More...

bool	is_carbohydrate () const
	Returns true if this residue is a carbohydrate. More...

bool	is_ligand () const
	Returns true if this residue is a ligand. More...

bool	is_surface () const
	Returns true if this residue is a surface residue. More...

bool	has_sc_orbitals () const
	Returns true if the residue has side chain orbitals. More...

bool	is_polar () const
	Returns true if the residue is polar. More...

bool	is_apolar () const

bool	is_charged () const
	Returns true if the residue is charged. More...

bool	is_aromatic () const
	Returns true if the residue is aromatic. More...

bool	is_coarse () const
	residue is coarse (used for RNA right now) More...

bool	is_terminus () const
	Returns true if the residue has a terminus variant. More...

bool	is_upper_terminus () const
	Return true if the residue has an upper terminus variant. More...

bool	is_lower_terminus () const
	Returns true if the residue has a lower terminus variant. More...

bool	is_similar_rotamer (Residue const &other) const
	Returns true if the chi angles of another residue all fall within 5 deg. More...

bool	is_similar_aa (Residue const &other) const
	Returns true if the aa residue types are the same. More...

bool	has_property (std::string const &property) const
	Returns true if the residue has <property> Generic property access – SLOW!!!!! More...

bool	has_variant_type (chemical::VariantType const &variant_type) const
	Generic variant access – SLOW!!!!! More...

std::string const &	atom_name (int const atm) const
	Returns the name of this residue's atom with index number <atm> More...

std::string const &	mm_atom_name (int const atom) const
	Returns the mm_atom_name of this residue's atom with index number <atom> More...

std::string const &	name () const
	Returns this residue's ResidueType name. More...

std::string const &	name3 () const
	Returns this residue's 3-letter representation. More...

char	name1 () const
	Returns this residue's 1-letter representation. More...

chemical::AA const &	aa () const
	Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration. More...

chemical::AtomICoor const &	icoor (int const atm) const
	Returns the internal coordinates of this residue's atom with index number <atm> More...

void	set_d (int const chino, Real const setting)

void	set_theta (int const chino, Real const setting)
	fpd bondangle analog to set_chi (see above for details) More...

void	set_chi (int const chino, Real const setting)
	Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree. More...

void	set_all_chi (utility::vector1< Real > const &chis)
	Sets all of this residue's chi angles using the set_chi function (wrapper function) More...

bool	has (std::string const &atm) const
	Returns true if this residue has an atom named <atm> More...

void	fill_missing_atoms (utility::vector1< bool > missing, Conformation const &conformation)
	Builds coordinates for atoms missing from this residue assuming ideal internal coordinates. More...

void	select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
	Selects three atoms for orienting this residue. More...

void	orient_onto_residue (Residue const &src)
	Orient our coords onto those of <src>, using the atoms from select_orient_atoms. More...

void	orient_onto_residue (Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
	Orient our coords onto those of <src>, using the three atom pairs specified in the input. More...

void	place (Residue const &src, Conformation const &conformation, bool preserve_c_beta=false)
	Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match. More...

void	apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > R, Vector v)
	Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space. More...

core::chemical::rna::RNA_ResidueType const &	RNA_type () const
	Return the RNA_residueType object. This is RNA specific. More...

core::chemical::carbohydrates::CarbohydrateInfoCOP	carbohydrate_info () const
	Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More...

Private Member Functions
void	update_connections_to_residues ()
	Updates connections_to_residues_ using connect_map_. More...

void	apply_transform_downstream (int const atomno, numeric::xyzMatrix< Real > const &R, Vector const &v)
	apply transform of rotation R and translation V for all atoms downstream More...

void	determine_nonstandard_polymer_status ()

Residue const &	operator= (Residue const &rhs)
	Assignment operator does not work for class Residue. This function is intentionally unimplemented and private. More...

void	orient_onto_residue (Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2)
	Orient coords onto those of <src>, using the specified atoms. More...

Private Attributes
ResidueType const &	rsd_type_
	our Residue type More...

Atoms	atoms_
	our conformation atoms (not kinematic atom pointers) with xyz positiona and atom type More...

utility::vector1 < orbitals::OrbitalXYZCoords >	orbitals_

Size	seqpos_
	the sequence position More...

core::Size	chain_
	the chain id number, starting from 1 More...

utility::vector1< Real >	chi_
	our chi (sidechain) torsion angles More...

utility::vector1< Real >	mainchain_torsions_
	our (possibly empty) backbone torsion angles More...

Vector	actcoord_
	the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair More...

bool	nonstandard_polymer_
	Inter-residue connection data. More...

utility::vector1 < chemical::ResConnID >	connect_map_
	map between connection ids on this residue and the connection points on other residues to which its bonded More...

std::map< Size, utility::vector1< Size > >	connections_to_residues_
	lists for each connected residue of the connection points on this residue that connect the pair. More...

std::map< Size, PseudoBondCollectionCOP >	pseudobonds_
	other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds) More...

Detailed Description

Instance Residue class, used for placed residues and rotamers.

This class is designed to be lightweight. It holds a const-reference ("rsd_type_") to a ResidueType object for access to information common to all instances of a single type, eg. Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:

a vector1 of Atoms which hold the positions (and also the atom-types for fast access during scoring);
the sequence position and chain, both integers
the backbone and sidechain torsion angles (of course backbone torsions are not unique to a rotamer, and the chi angles are derivable from the coordinates, but storing them in the residue is convenient for scoring purposes).
the coordinates of an interaction center or centroid, used eg. in the knowledge-based fullatom pair term ("actcoord_"). Maybe this will also hold the centroid position for centroid-mode scoring??

Definition at line 93 of file Residue.hh.

Member Typedef Documentation

typedef chemical::AtomIndices core::conformation::Residue::AtomIndices

Definition at line 98 of file Residue.hh.

typedef chemical::AtomType core::conformation::Residue::AtomType

Definition at line 96 of file Residue.hh.

typedef chemical::ResidueType core::conformation::Residue::ResidueType

Definition at line 97 of file Residue.hh.

Constructor & Destructor Documentation

core::conformation::Residue::Residue	(	ResidueType const &	rsd_type_in,
		bool const	dummy_arg
	)

constructors Residue( Residue const & ); // user defined copy ctor to avoid #including PseudoBond.hh Residue const & operator = ( Residue const & ) // user defined assignment operator for same reason

Constructor from residue type; sets coords to ideal values create a residue of type residue_type_in.

Note: Dummmy arg to prevent secret type conversions from ResidueType to Residue

Definition at line 62 of file Residue.cc.

References core::chemical::ResidueType::atom(), core::chemical::Atom::atom_type_index(), atoms_, core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::Atom::ideal_xyz(), core::chemical::Atom::mm_atom_type_index(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, rsd_type_, and type().

Referenced by clone().

core::conformation::Residue::Residue	(	ResidueType const &	rsd_type_in,
		bool	const,
		bool	const
	)

inline

Definition at line 107 of file Residue.hh.

core::conformation::Residue::Residue	(	ResidueType const &	rsd_type_in,
		Residue const &	current_rsd,
		Conformation const &	conformation,
		bool	preserve_c_beta = `false`
	)

Rotamer-style constructor; orients ideal coords onto backbone of current_rsd.

Create a residue/rotamer of type rsd_type_in placed at the position occupied by current_rsd Used primarily in rotamer building. The newly created Residue has the same sequence postion, chain id and mainchain torsion angles as current_rsd. It has a ResidueType as defined by rsd_type_in. Its sidechain chi angles are uninitialized as all 0.0 and sidechain atom coords are from ideal coords. Its backbone is aligned with that of current_rsd. Its residue connections and its pseudobonds must be initialized from the original residue.

Definition at line 99 of file Residue.cc.

References core::chemical::ResidueType::atom(), atom(), core::chemical::Atom::atom_type_index(), atoms_, core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), copy_residue_connections(), core::chemical::Atom::ideal_xyz(), core::chemical::ResidueType::mainchain_atoms(), mainchain_torsions(), core::chemical::Atom::mm_atom_type_index(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), core::chemical::ResidueType::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, place(), pseudobonds_, rsd_type_, type(), and xyz().

core::conformation::Residue::Residue ( Residue const & src)

Definition at line 178 of file Residue.cc.

core::conformation::Residue::~Residue ( )

Definition at line 197 of file Residue.cc.

Member Function Documentation

chemical::AA const& core::conformation::Residue::aa ( ) const

inline

Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration.

Definition at line 1725 of file Residue.hh.

References core::chemical::ResidueType::aa(), and rsd_type_.

Size core::conformation::Residue::abase2 ( int const atomno) const

inline

Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor)

Definition at line 834 of file Residue.hh.

References core::chemical::ResidueType::abase2(), and rsd_type_.

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::hbonds::assign_abase_derivs(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), and protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

AtomIndices const& core::conformation::Residue::accpt_pos ( ) const

inline

Returns the AtomIndices of this residue's h-bond acceptor atoms.

Note: : AtomIndices == vector1< Size >

example(s): residue.accpt_pos() See also: Residue Residue.accpt_pos_sc Residue.atoms Pose

Definition at line 371 of file Residue.hh.

References core::chemical::ResidueType::accpt_pos(), and rsd_type_.

AtomIndices const& core::conformation::Residue::accpt_pos_sc ( ) const

inline

Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms.

Note: : AtomIndices == vector1< Size >

example(s): residue.accpt_pos_sc() See also: Residue Residue.accpt_pos Residue.atoms Pose

Definition at line 387 of file Residue.hh.

References core::chemical::ResidueType::accpt_pos_sc(), and rsd_type_.

Vector const& core::conformation::Residue::actcoord ( ) const

inline

Returns the coordinates used for pairE calculations (amino acids only)

Definition at line 1497 of file Residue.hh.

References actcoord_.

Referenced by core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::orient_residue_for_ideal_bond(), core::scoring::PairEPotential::pair_term_energy(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), and core::chemical::ResidueType::update_actcoord().

Vector& core::conformation::Residue::actcoord ( )

inline

Returns the coordinates used for pairE calculations (amino acids only)

Definition at line 1504 of file Residue.hh.

References actcoord_.

AtomIndices const& core::conformation::Residue::actcoord_atoms ( ) const

inline

Returns the AtomIndices of atoms that will be used to define this residue's actcoord.

Definition at line 886 of file Residue.hh.

References core::chemical::ResidueType::actcoord_atoms(), and rsd_type_.

Referenced by core::scoring::methods::PairEnergy::eval_residue_pair_derivatives().

chemical::ResConnID core::conformation::Residue::actual_residue_connection ( Size resconnid) const

inline

Definition at line 1168 of file Residue.hh.

References connect_map_.

Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Conformation::detect_pseudobonds().

AtomIndices const& core::conformation::Residue::all_bb_atoms ( ) const

inline

Returns the AtomIndices of this residue's backbone atoms.

Note: : heavyatoms and hydrogens, AtomIndices == vector1< Size >

example(s): residue.all_bb_atoms() See also: Residue Residue.atoms Pose

Definition at line 287 of file Residue.hh.

References core::chemical::ResidueType::all_bb_atoms(), and rsd_type_.

void core::conformation::Residue::apply_transform_downstream	(	int const	atomno,
		numeric::xyzMatrix< Real > const &	R,
		Vector const &	v
	)

private

apply transform of rotation R and translation V for all atoms downstream

Note: note this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.

xyz –> R * xyz + v
this uses information from atom_base array to transform all the downstream atoms along the sidechain recursively. it assumes that the atom_base array will not get us into any infinite loops!

Note: this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.

Definition at line 1075 of file Residue.cc.

References atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), nbrs(), rsd_type_, core::conformation::Atom::xyz(), and xyz().

Referenced by set_chi(), set_d(), and set_theta().

void core::conformation::Residue::apply_transform_Rx_plus_v	(	numeric::xyzMatrix< Real >	R,
		Vector	v
	)

Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space.

Definition at line 1102 of file Residue.cc.

References core::chemical::ResidueType::natoms(), set_xyz(), type(), and xyz().

Atom const& core::conformation::Residue::atom ( Size const atm_index) const

inline

Returns this residue's Atom with index number <atm_index> (const)

Note: : Atom object is xyz and atom_type

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

Definition at line 465 of file Residue.hh.

References atoms_.

Atom& core::conformation::Residue::atom ( Size const atm_index)

inline

Returns this residue's Atom with index number <atm_index> (non-const)

Note: : Atom object is xyz and atom_type

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

Definition at line 480 of file Residue.hh.

References atoms_.

Atom const& core::conformation::Residue::atom ( std::string const & atm_name) const

inline

Returns this residue's Atom with name <atm_name> (const)

Note: : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

Definition at line 496 of file Residue.hh.

References atom_index(), and atoms_.

Atom& core::conformation::Residue::atom ( std::string const & atm_name)

inline

Returns this residue's Atom with name <atm_name> (non-const)

Note: : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

Definition at line 511 of file Residue.hh.

References atom_index(), and atoms_.

Size core::conformation::Residue::atom_base ( int const atomno) const

inline

Returns the atom index of the <atomno> atom's base atom.

Definition at line 825 of file Residue.hh.

References core::chemical::ResidueType::atom_base(), and rsd_type_.

Atoms::iterator core::conformation::Residue::atom_begin ( )

inline

begin interator, to iterate over atoms

Definition at line 438 of file Residue.hh.

References atoms_.

Referenced by core::pack::task::operation::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs(), and core::scoring::interface::DDPscore::residue_pair_energy().

Atoms::const_iterator core::conformation::Residue::atom_begin ( ) const

inline

Definition at line 442 of file Residue.hh.

References atoms_.

Atoms::iterator core::conformation::Residue::atom_end ( )

inline

end interator, to iterate over atoms

Definition at line 440 of file Residue.hh.

References atoms_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs().

Atoms::const_iterator core::conformation::Residue::atom_end ( ) const

inline

Definition at line 443 of file Residue.hh.

References atoms_.

Size core::conformation::Residue::atom_index ( std::string const & atm) const

inline

Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid.

example(s): residue.atom_index("CA") See also: Residue AtomType Pose

Definition at line 210 of file Residue.hh.

References core::chemical::ResidueType::atom_index(), and rsd_type_.

bool core::conformation::Residue::atom_is_backbone ( int const atomno) const

inline

Returns true if this residue's atom with index number <atomno> is a backbone atom.

example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

Definition at line 801 of file Residue.hh.

References core::chemical::ResidueType::atom_is_backbone(), and rsd_type_.

bool core::conformation::Residue::atom_is_hydrogen ( Size const atomno) const

inline

Returns true if this residue's atom with index number <atomno> is a hydrogen.

example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

Definition at line 817 of file Residue.hh.

References core::chemical::ResidueType::atom_is_hydrogen(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::scoring::methods::LK_BallEnergy::eval_residue_pair_derivatives(), protocols::contact_map::ContactMap::fill_contacts(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), core::scoring::ResidueNblistData::initialize(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::scoring::hackelec::is_base(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::hackelec::is_phosphate(), core::scoring::is_polymer_heavyatom(), core::scoring::hackelec::is_sugar(), protocols::comparative_modeling::randomize_selected_atoms(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

bool core::conformation::Residue::atom_is_polar_hydrogen ( Size ind) const

inline

Is a particular atom a polar hydrogen?

Definition at line 406 of file Residue.hh.

References core::chemical::ResidueType::atom_is_polar_hydrogen(), and rsd_type_.

std::string const& core::conformation::Residue::atom_name ( int const atm) const

inline

Returns the name of this residue's atom with index number <atm>

Definition at line 1685 of file Residue.hh.

References core::chemical::ResidueType::atom_name(), and rsd_type_.

AtomType const& core::conformation::Residue::atom_type ( int const atomno) const

inline

Returns the AtomType of this residue's atom with index number <atomno>

example(s): residue.atom_type(3) See also: Residue Residue.atom_index AtomType Pose

Definition at line 144 of file Residue.hh.

References core::chemical::ResidueType::atom_type(), and rsd_type_.

Size core::conformation::Residue::atom_type_index ( Size const atomno) const

Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType.

example(s): residue.atom_type_index(3) See also: Residue Residue.atom_index AtomType Pose

Definition at line 209 of file Residue.cc.

References atoms_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchRes(), core::conformation::orient_residue_for_ideal_bond(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::VDW_Energy::residue_pair_energy(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

chemical::AtomTypeSet const& core::conformation::Residue::atom_type_set ( ) const

inline

Returns the AtomTypeSet of this residue.

example(s): residue.atom_type_set() See also: Residue Residue.atom_type_index AtomType Pose

Definition at line 159 of file Residue.hh.

References core::chemical::ResidueType::atom_type_set(), and rsd_type_.

Referenced by core::scoring::calc_per_atom_sasa(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::FACTSResidueInfo::initialize_parameters(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), protocols::features::AtomTypesFeatures::report_features(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

Real core::conformation::Residue::atomic_charge ( int const atomno) const

Returns the atom charge of this residue's atom with index number <atomno>

example(s): residue.atomic_charge(3) See also: Residue Residue.atom_index Pose

Definition at line 215 of file Residue.cc.

References core::chemical::ResidueType::atom(), core::chemical::Atom::charge(), and rsd_type_.

Atoms const& core::conformation::Residue::atoms ( ) const

inline

Returns this residue's Atoms (const), a vector1 of Atom objects.

example(s): residue.atoms() See also: Residue Pose

Definition at line 419 of file Residue.hh.

References atoms_.

Referenced by core::scoring::orbitals::OrbitalsAssigned::aromatic_ring_center(), core::conformation::atom_id_to_named_atom_id(), core::pose::compare_atom_coordinates(), core::scoring::orbitals::OrbitalsAssigned::cp_function(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::contact_map::ContactMap::fill_contacts(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), protocols::loops::loop_rmsd(), orient_onto_residue(), place(), core::conformation::setup_corresponding_atoms(), core::chemical::ResidueType::update_actcoord(), and core::io::serialization::write_binary().

Atoms& core::conformation::Residue::atoms ( )

inline

Returns this residue's Atoms (non-const), a vector1 of Atom objects.

example(s): residue.atoms() See also: Residue Pose

Definition at line 432 of file Residue.hh.

References atoms_.

AtomIndices const& core::conformation::Residue::atoms_with_orb_index ( ) const

inline

Definition at line 936 of file Residue.hh.

References core::chemical::ResidueType::atoms_with_orb_index(), and rsd_type_.

Size core::conformation::Residue::attached_H_begin ( int const atom) const

inline

Returns the index number of the first hydrogen attached to the atom with index number <atom>

example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Pose

Definition at line 635 of file Residue.hh.

References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.

Referenced by core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::trie::create_trie(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::hackelec::HackElecEnergy::residue_pair_energy().

AtomIndices const& core::conformation::Residue::attached_H_begin ( ) const

inline

Returns the AtomIndices of the first hydrogen attached to each heavyatom.

example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Residue.nheavyatoms Pose

Definition at line 669 of file Residue.hh.

References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.

Size core::conformation::Residue::attached_H_end ( int const atom) const

inline

Returns the index number of the last hydrogen attached to the atom with index number <atom>

example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Pose

Definition at line 652 of file Residue.hh.

References core::chemical::ResidueType::attached_H_end(), and rsd_type_.

Referenced by core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::trie::create_trie(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::hackelec::HackElecEnergy::residue_pair_energy().

AtomIndices const& core::conformation::Residue::attached_H_end ( ) const

inline

Returns the AtomIndices of the last hydrogen attached to each heavyatom.

example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Residue.nheavyatoms Pose

Definition at line 686 of file Residue.hh.

References core::chemical::ResidueType::attached_H_end(), and rsd_type_.

AtomIndices const& core::conformation::Residue::bonded_neighbor ( int const atm) const

inline

Returns the AtomIndices for all bonded neighbor atoms of <atm>

Definition at line 841 of file Residue.hh.

References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), n_bonded_neighbor_all_res(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::HbaGrid::score(), and protocols::features::OrbitalsFeatures::set_OrbH_features_data().

utility::vector1<core::Size> const& core::conformation::Residue::bonded_orbitals ( int const atm) const

inline

Definition at line 990 of file Residue.hh.

References core::chemical::ResidueType::bonded_orbitals(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::io::pdb::dump_pdb_residue(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), and core::conformation::Conformation::update_orbital_coords().

Vector core::conformation::Residue::build_atom_ideal	(	int const	atomno,
		Conformation const &	conformation
	)		const

inline

Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms.

Definition at line 895 of file Residue.hh.

References core::chemical::AtomICoor::build(), and icoor().

Referenced by core::conformation::Conformation::fill_missing_atoms(), and fill_missing_atoms().

Vector core::conformation::Residue::build_orbital_xyz ( Size const orbital_index) const

inline

Definition at line 946 of file Residue.hh.

References atom(), core::chemical::ResidueType::new_orbital_icoor_data(), rsd_type_, and xyz().

Referenced by Residue(), core::conformation::Conformation::update_orbital_coords(), and update_orbital_coords().

core::chemical::carbohydrates::CarbohydrateInfoCOP core::conformation::Residue::carbohydrate_info ( ) const

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

Definition at line 248 of file Residue.cc.

References core::chemical::ResidueType::carbohydrate_info(), core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.

Referenced by core::pose::carbohydrates::calculate_carbohydrate_phi(), core::pose::Pose::chain_sequence(), core::conformation::operator<<(), and protocols::simple_moves::carbohydrates::RingConformationMover::setup_residue_list().

core::Size core::conformation::Residue::chain ( ) const

inline

Returns this residue's chain id.

Definition at line 1468 of file Residue.hh.

References chain_.

Referenced by protocols::features::BetaTurnDetectionFeatures::all_turn_residues_are_on_the_same_chain(), core::io::pdb::FileData::append_residue(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pose::Pose::chain(), protocols::simple_filters::TerminusDistanceFilter::compute(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::io::pdb::dump_pdb_residue(), core::pack::rotamer_set::dup_residue(), core::pack::dunbrack::dup_residue(), protocols::rosetta_scripts::find_nearest_res(), protocols::forge::methods::fold_tree_from_pose(), protocols::simple_moves::ChainGroupDiscriminator::group_id(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::forge::build::ConnectRight::modify_impl(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), core::pose::PDBInfo::PDBInfo(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::methods::PoissonBoltzmannEnergy::residue_in_chains(), core::scoring::interface::DDPscore::residue_pair_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), core::import_pose::set_reasonable_fold_tree(), protocols::docking::DockingHighResLegacy::setup_packing(), core::conformation::Conformation::update_polymeric_connection(), and core::io::serialization::write_binary().

void core::conformation::Residue::chain ( int const setting)

inline

Sets this residue's chain id.

Definition at line 1475 of file Residue.hh.

References chain_.

utility::vector1< Real > const& core::conformation::Residue::chi ( ) const

inline

Returns the chi torsion angles of this residue (const)

example(s): residue.chi() See also: Residue Residue.nchi Pose Pose.chi

Definition at line 1355 of file Residue.hh.

References chi_.

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pose::Pose::chi(), protocols::simple_moves::MinimalRotamer::chi_matches_coords(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), protocols::swa::rna::copy_torsions_FROM_TO(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_rotamer_string(), protocols::swa::rna::StepWiseRNA_ResidueSampler::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::dna::DNABase::DNABase(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::get_residue_current_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), protocols::features::RotamerInitializer< T >::initialize_rotamer(), is_similar_rotamer(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::swa::rna::Print_torsion_info(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::simple_moves::MinimalRotamer::record_chi(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::pack::dunbrack::rotamer_from_chi(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), and core::conformation::Conformation::update_residue_torsions().

utility::vector1< Real >& core::conformation::Residue::chi ( )

inline

Returns the chi torsion angles of this residue (non-const)

Definition at line 1362 of file Residue.hh.

References chi_.

void core::conformation::Residue::chi ( utility::vector1< Real > const & chis)

inline

Sets the chi torsion angles of this residue.

CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.

example(s):

See also: Residue Pose Pose.set_chi

Definition at line 1380 of file Residue.hh.

References chi_.

Real core::conformation::Residue::chi ( Size const chino) const

inline

get a specific chi torsion angle

example(s): residue.chi(1) See also: Residue Pose Pose.chi

Definition at line 1428 of file Residue.hh.

References chi_.

utility::vector1< AtomIndices > const& core::conformation::Residue::chi_atoms ( ) const

inline

Returns the AtomIndices of each four atom set defining a chi angle.

Definition at line 1387 of file Residue.hh.

References core::chemical::ResidueType::chi_atoms(), and rsd_type_.

Referenced by core::scoring::rna::chi1_torsion_atom_index(), core::scoring::hackaro::chi2_torsion_atom_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::scoring::rna::first_base_atom_index(), core::scoring::dna::get_base_pair_stub_slow(), core::conformation::Conformation::get_torsion_angle_atom_ids(), place(), Residue(), set_chi(), core::conformation::set_chi_according_to_coordinates(), set_d(), set_theta(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::conformation::setup_corresponding_atoms(), core::conformation::setup_links(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().

AtomIndices const& core::conformation::Residue::chi_atoms ( int const chino) const

inline

Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle.

Definition at line 1395 of file Residue.hh.

References core::chemical::ResidueType::chi_atoms(), and rsd_type_.

utility::vector1< std::pair< Real, Real > > const& core::conformation::Residue::chi_rotamers ( Size const chino) const

inline

Returns the chi rotamers available for this residue's chi angle <chino>

Definition at line 1274 of file Residue.hh.

References core::chemical::ResidueType::chi_rotamers(), and rsd_type_.

void core::conformation::Residue::clear_residue_connections ( )

Definition at line 648 of file Residue.cc.

References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.

ResidueOP core::conformation::Residue::clone ( ) const

Copy this residue( allocate actual memory for it )

make a copy of this residue( allocate actual memory for it )

Definition at line 202 of file Residue.cc.

References Residue().

Size core::conformation::Residue::connect_atom ( Residue const & other) const

Returns the index number of this residue's atom connected to the <other> Residue.

Returns the atom-index of my atom which is connected to the other residue.

example(s):

so long as there is only a single connection to other... if there are multiple connections this will fail. If there are no connections this will fail. This is a convenience function that can fail; be careful! Fails if I'm not bonded to the other residue.

Note: not well defined if multiple connections to another residue – need more general function

Definition at line 866 of file Residue.cc.

References connections_to_residues_, is_lower_terminus(), is_polymer(), is_upper_terminus(), lower_connect_atom(), nonstandard_polymer_, core::chemical::ResidueType::residue_connection(), rsd_type_, seqpos(), seqpos_, and upper_connect_atom().

Referenced by protocols::cartesian::MolecularDynamics::createBondList(), protocols::forge::methods::fold_tree_from_pose(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::viewer::print_interres_bond(), and core::import_pose::set_reasonable_fold_tree().

chemical::ResConnID core::conformation::Residue::connect_map ( Size resconn_index) const

inline

Definition at line 1145 of file Residue.hh.

References connect_map_.

Referenced by core::scoring::mm::connection_indices(), copy_residue_connections(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::disulfide_bonds(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::is_disulfide_bond(), core::scoring::methods::LK_hack::residue_pair_energy(), core::import_pose::set_reasonable_fold_tree(), and core::conformation::Conformation::show_residue_connections().

Size core::conformation::Residue::connected_residue_at_resconn ( Size const resconn_index) const

inline

Definition at line 1140 of file Residue.hh.

References connect_map_.

Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamer(), protocols::forge::methods::fold_tree_from_pose(), and core::conformation::ConformationKinWriter::write_coords().

Distance core::conformation::Residue::connection_distance	(	conformation::Conformation const &	conf,
		Size const	resconn_index,
		Vector const	matchpoint
	)		const

Distance between a potential residue connection match and the position of the expected atom.

Definition at line 800 of file Residue.cc.

References core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::residue_connection(), and type().

Referenced by core::conformation::Conformation::detect_bonds().

bool core::conformation::Residue::connection_incomplete ( Size resconnid) const

Definition at line 698 of file Residue.cc.

References connect_map_.

Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::detect_bonds(), has_incomplete_connection(), n_bonded_neighbor_all_res(), and core::import_pose::set_reasonable_fold_tree().

bool core::conformation::Residue::connections_match ( Residue const & other) const

Returns true if ???

Definition at line 257 of file Residue.cc.

References connect_map_, and pseudobonds_.

utility::vector1< Size > const& core::conformation::Residue::connections_to_residue ( Residue const & other) const

inline

Returns the vector1 of resconn ids that connect this residue to other.

Definition at line 1245 of file Residue.hh.

References seqpos().

utility::vector1< Size > const& core::conformation::Residue::connections_to_residue ( Size const other_resid) const

inline

Returns the vector1 of resconn ids that connect this residue to other.

Definition at line 1252 of file Residue.hh.

References connections_to_residues_.

void core::conformation::Residue::copy_residue_connections ( Residue const & src_rsd)

attempt to take residue connection info from src_rsd

Definition at line 302 of file Residue.cc.

References atom_index(), atom_name(), core::chemical::ResidueConnection::atomno(), connect_map(), connect_map_, connections_to_residues_, core::chemical::ResConnID::connid(), has(), core::chemical::ResidueType::n_residue_connections(), n_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), pseudobonds_, core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_connection_partner(), core::chemical::ResidueType::residue_connections_for_atom(), seqpos(), core::io::serialization::size(), and type().

Referenced by Residue().

void core::conformation::Residue::copy_residue_connections_from ( Residue const & src)

Definition at line 661 of file Residue.cc.

References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), and core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner().

ResidueOP core::conformation::Residue::create_residue ( ) const

inline

Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out.

Definition at line 1053 of file Residue.hh.

References clone().

ResidueOP core::conformation::Residue::create_rotamer ( ) const

inline

Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out.

Definition at line 1045 of file Residue.hh.

References clone().

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers(), and core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete().

AtomIndices const& core::conformation::Residue::cut_bond_neighbor ( int const atm) const

inline

atom indices for bonded neighbors to which atom-tree connections are disallowed.

Definition at line 1285 of file Residue.hh.

References core::chemical::ResidueType::cut_bond_neighbor(), and rsd_type_.

Referenced by core::conformation::setup_links_simple().

void core::conformation::Residue::determine_nonstandard_polymer_status ( )

private

Definition at line 1113 of file Residue.cc.

References connect_map_, is_lower_terminus(), is_polymer(), is_upper_terminus(), nonstandard_polymer_, seqpos(), and type().

Referenced by residue_connection_partner(), and update_sequence_numbering().

void core::conformation::Residue::fill_missing_atoms	(	utility::vector1< bool >	missing,
		Conformation const &	conformation
	)

Builds coordinates for atoms missing from this residue assuming ideal internal coordinates.

this uses ideal internal coords to build any missing atom from its three stub atoms. If any of the stub atoms are missing, build them first. Unable to build a missing atom whose stub atoms are from non-existing polymer connection and its input bogus value will not be changed.

Definition at line 596 of file Residue.cc.

References atom_name(), build_atom_ideal(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), icoor(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::name(), natoms(), seqpos_, set_xyz(), core::conformation::Conformation::size(), core::chemical::AtomICoor::stub_atom(), and type().

Referenced by core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), and place().

Size core::conformation::Residue::first_sidechain_atom ( ) const

inline

Returns the index number of the first sidechain heavyatom.

example(s): residue.first_sidechain_atom() See also: Residue Residue.atom Residue.atoms Residue.last_backbone_atom Pose

Definition at line 601 of file Residue.hh.

References core::chemical::ResidueType::first_sidechain_atom(), and rsd_type_.

Size core::conformation::Residue::first_sidechain_hydrogen ( ) const

inline

Returns the index number of the first sidechain hydrogen.

example(s): residue.first_sidechain_hydrogen() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

Definition at line 617 of file Residue.hh.

References core::chemical::ResidueType::first_sidechain_hydrogen(), and rsd_type_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), and core::pack::scmin::CartSCMinMinimizerMap::setup().

PseudoBondCollectionCOP core::conformation::Residue::get_pseudobonds_to_residue ( Size resid) const

Definition at line 885 of file Residue.cc.

References pseudobonds_.

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

AtomIndices const& core::conformation::Residue::Haro_index ( ) const

inline

Returns the AtomIndices of this residue's aromatic hydrogens.

Note: : AtomIndices == vector1< Size >

example(s): residue.Haro_index() See also: Residue Residue.atoms Residue.Hpol_index Pose

Definition at line 302 of file Residue.hh.

References core::chemical::ResidueType::Haro_index(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

bool core::conformation::Residue::has ( std::string const & atm) const

inline

Returns true if this residue has an atom named <atm>

Definition at line 1764 of file Residue.hh.

References core::chemical::ResidueType::has(), and rsd_type_.

Referenced by protocols::seeded_abinitio::add_coordinate_constraints(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), core::pack::task::operation::util::cbeta_vector(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::sic_dock::count_CBs(), protocols::cartesian::MolecularDynamics::createDihedralList(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::topology_broker::fix_mainchain_connect(), protocols::sic_dock::get_CB_Vecs(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::swa::protein::get_pretend_phi_explicit(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), protocols::enzdes::DiffAtomSasaFilter::parse_my_tag(), place(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::sic_dock::XfoxmScore::score(), core::pack::task::operation::util::select_coord_for_residue(), protocols::ligand_docking::set_repulsive_bb_cores(), core::scoring::setup_matching_heavy_atoms(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), and protocols::rna::RNA_ChunkLibrary::zero_out_allow_insert().

bool core::conformation::Residue::has_incomplete_connection ( ) const

Definition at line 671 of file Residue.cc.

References connect_map_, and connection_incomplete().

Referenced by protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::conformation::Conformation::detect_bonds(), protocols::ligand_docking::find_unconnected_residues(), and protocols::ligand_docking::has_incomplete_connections().

bool core::conformation::Residue::has_incomplete_connection ( core::Size const atomno) const

Returns true is <atomno> has complete connectivity?

Detailed:: determine whether an atom is completely connected to all possible bonded partners

Definition at line 683 of file Residue.cc.

References connection_incomplete(), n_residue_connections(), and residue_connect_atom_index().

bool core::conformation::Residue::has_property ( std::string const & property) const

inline

Returns true if the residue has <property> Generic property access – SLOW!!!!!

Definition at line 1670 of file Residue.hh.

References core::chemical::ResidueType::has_property(), and rsd_type_.

Referenced by protocols::ligand_docking::MoveMapBuilder::build(), and protocols::ligand_docking::LigandBaseProtocol::make_movemap().

bool core::conformation::Residue::has_sc_orbitals ( ) const

inline

Returns true if the residue has side chain orbitals.

Definition at line 1581 of file Residue.hh.

References core::chemical::ResidueType::has_sc_orbitals(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

bool core::conformation::Residue::has_variant_type ( chemical::VariantType const & variant_type) const

inline

Generic variant access – SLOW!!!!!

Definition at line 1677 of file Residue.hh.

References core::chemical::ResidueType::has_variant_type(), and rsd_type_.

bool core::conformation::Residue::heavyatom_has_polar_hydrogens ( Size ind) const

inline

Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom)

Definition at line 394 of file Residue.hh.

References core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation().

bool core::conformation::Residue::heavyatom_is_an_acceptor ( Size ind) const

inline

Is a particular atom a heavy atom acceptor?

Definition at line 400 of file Residue.hh.

References core::chemical::ResidueType::heavyatom_is_an_acceptor(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), and core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way().

Atoms::const_iterator core::conformation::Residue::heavyAtoms_end ( ) const

inline

Definition at line 450 of file Residue.hh.

References atoms_, and nheavyatoms().

Referenced by core::pack::task::operation::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), and core::scoring::interface::DDPscore::residue_pair_energy().

AtomIndices const& core::conformation::Residue::Hpol_index ( ) const

inline

Returns the AtomIndices of this residue's polar hydrogens.

Note: : AtomIndices == vector1< Size >

example(s): residue.Hpol_index() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Residue.Hpos_polar Pose

Definition at line 319 of file Residue.hh.

References core::chemical::ResidueType::Hpol_index(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

AtomIndices const& core::conformation::Residue::Hpos_apolar ( ) const

inline

Returns the AtomIndices of this residue's apolar hydrogens.

Note: : AtomIndices == vector1< Size >

example(s): residue.Hpos_apolar() See also: Residue Residue.atoms Residue.Hpol_index() Residue.Hpos_polar Pose

Definition at line 335 of file Residue.hh.

References core::chemical::ResidueType::Hpos_apolar(), and rsd_type_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::atom_is_apolar_h(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().

AtomIndices const& core::conformation::Residue::Hpos_polar ( ) const

inline

Returns the AtomIndices of this residue's polar hydrogens.

Note: : AtomIndices == vector1< Size >

example(s): residue.Hpos_polar() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Pose

Definition at line 271 of file Residue.hh.

References core::chemical::ResidueType::Hpos_polar(), and rsd_type_.

AtomIndices const& core::conformation::Residue::Hpos_polar_sc ( ) const

inline

Returns the AtomIndices of this residue's polar sidechain hydrogens.

Note: : AtomIndices == vector1< Size >

example(s): residue.Hpos_polar_sc() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_polar Pose

Definition at line 352 of file Residue.hh.

References core::chemical::ResidueType::Hpos_polar_sc(), and rsd_type_.

chemical::AtomICoor const& core::conformation::Residue::icoor ( int const atm) const

inline

Returns the internal coordinates of this residue's atom with index number <atm>

Definition at line 1733 of file Residue.hh.

References core::chemical::ResidueType::icoor(), and rsd_type_.

Referenced by build_atom_ideal(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::conformation::idealize_hydrogens(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), and core::conformation::Conformation::rebuild_residue_connection_dependent_atoms().

bool core::conformation::Residue::is_apolar ( ) const

inline

true if the residue is apolar

Note: : apolar is classified as NOT polar, aromatic, or charged

Definition at line 1597 of file Residue.hh.

References core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_polar(), and rsd_type_.

bool core::conformation::Residue::is_aromatic ( ) const

inline

Returns true if the residue is aromatic.

Definition at line 1616 of file Residue.hh.

References core::chemical::ResidueType::is_aromatic(), and rsd_type_.

Referenced by core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative_aro_aro(), core::scoring::orbitals::OrbitalsScore::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::hackelec::HackElecEnergyAroAll::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergyAroAro::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergyAroAll::residue_pair_energy(), core::scoring::hackelec::HackElecEnergyAroAro::residue_pair_energy(), core::scoring::orbitals::OrbitalsScore::residue_pair_energy(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy_aro_aro(), and core::scoring::hackelec::HackElecEnergyAroAro::residue_pair_energy_aro_aro().

bool core::conformation::Residue::is_bonded ( Residue const & other) const

Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)

first check if it is polymer upper or lower connected to the other residue. then check if it is boned to the other residue through non-polymer connection.

Definition at line 816 of file Residue.cc.

References connections_to_residues_, and seqpos().

bool core::conformation::Residue::is_bonded ( Size const other_index) const

Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic.

Definition at line 836 of file Residue.cc.

References connections_to_residues_.

bool core::conformation::Residue::is_carbohydrate ( ) const

inline

Returns true if this residue is a carbohydrate.

Definition at line 1557 of file Residue.hh.

References core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.

Referenced by core::conformation::operator<<(), and protocols::simple_moves::carbohydrates::RingConformationMover::setup_residue_list().

bool core::conformation::Residue::is_charged ( ) const

inline

Returns true if the residue is charged.

Definition at line 1609 of file Residue.hh.

References core::chemical::ResidueType::is_charged(), and rsd_type_.

bool core::conformation::Residue::is_coarse ( ) const

inline

residue is coarse (used for RNA right now)

Definition at line 1623 of file Residue.hh.

References core::chemical::ResidueType::is_coarse(), and rsd_type_.

Referenced by protocols::rna::RNA_StructureParameters::check_forward_backward(), core::scoring::rna::default_jump_atom(), core::conformation::Conformation::detect_pseudobonds(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::scoring::rna::RNA_DataBackboneEnergy::get_sugar_env_score(), protocols::rna::RNA_ChunkLibrary::initialize_rna_chunk_library(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), protocols::toolbox::AllowInsert::set_phosphate_domain(), protocols::rna::setup_base_pair_constraints(), and core::io::pdb::write_additional_pdb_data().

bool core::conformation::Residue::is_DNA ( ) const

inline

Returns true if this residue is a DNA residue.

Definition at line 1536 of file Residue.hh.

References core::chemical::ResidueType::is_DNA(), and rsd_type_.

bool core::conformation::Residue::is_ligand ( ) const

inline

Returns true if this residue is a ligand.

Definition at line 1564 of file Residue.hh.

References core::chemical::ResidueType::is_ligand(), and rsd_type_.

Referenced by core::io::pdb::FileData::append_residue(), core::conformation::Conformation::append_residue(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::scoring::Interface::calculate(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::rosetta_scripts::find_nearest_res(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::motifs::Motif::Motif(), protocols::features::ResidueConformationFeatures::report_features(), protocols::ligand_docking::restrict_to_protein_residues(), protocols::scoring::Interface::set_pack(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

bool core::conformation::Residue::is_lower_terminus ( ) const

inline

Returns true if the residue has a lower terminus variant.

Definition at line 1644 of file Residue.hh.

References core::chemical::ResidueType::is_lower_terminus(), and rsd_type_.

bool core::conformation::Residue::is_NA ( ) const

inline

Returns true if this residue is a nucleic acid.

Definition at line 1550 of file Residue.hh.

References core::chemical::ResidueType::is_NA(), and rsd_type_.

Referenced by core::pack::rotamer_set::build_lib_dna_rotamers(), and protocols::scoring::Interface::calculate().

bool core::conformation::Residue::is_polar ( ) const

inline

Returns true if the residue is polar.

Definition at line 1589 of file Residue.hh.

References core::chemical::ResidueType::is_polar(), and rsd_type_.

Referenced by protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), and core::scoring::methods::PairEnergy::residue_pair_energy().

bool core::conformation::Residue::is_polymer ( ) const

inline

Returns true if this residue is a polymer.

Definition at line 1522 of file Residue.hh.

References core::chemical::ResidueType::is_polymer(), and rsd_type_.

bool core::conformation::Residue::is_polymer_bonded ( Residue const & other) const

Am I polymer bonded to other?

Am I polymer bonded to other.seqpos()?

Definition at line 843 of file Residue.cc.

References seqpos().

bool core::conformation::Residue::is_polymer_bonded ( Size const other_index) const

Am I polymer-bonded to other? checks lower and upper connections.

Am I polymer bonded to other_index?

Definition at line 850 of file Residue.cc.

References core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::lower_connect_id(), residue_connection_partner(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().

bool core::conformation::Residue::is_protein ( ) const

inline

Returns true if this residue is an amino acid.

Definition at line 1529 of file Residue.hh.

References core::chemical::ResidueType::is_protein(), and rsd_type_.

bool core::conformation::Residue::is_pseudo_bonded ( Residue const & other) const

inline

Do I have any pseudobonds to other?

Definition at line 1217 of file Residue.hh.

References seqpos().

Referenced by core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::methods::VDW_Energy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

bool core::conformation::Residue::is_pseudo_bonded ( Size const other_index) const

inline

Do I have any pseudobonds to other?

Definition at line 1229 of file Residue.hh.

References pseudobonds_.

bool core::conformation::Residue::is_RNA ( ) const

inline

Returns true if this residue is a RNA residue.

Definition at line 1543 of file Residue.hh.

References core::chemical::ResidueType::is_RNA(), and rsd_type_.

bool core::conformation::Residue::is_similar_aa ( Residue const & other) const

inline

Returns true if the aa residue types are the same.

Definition at line 1655 of file Residue.hh.

References core::chemical::ResidueType::aa(), aa(), and rsd_type_.

bool core::conformation::Residue::is_similar_rotamer ( Residue const & other) const

Returns true if the chi angles of another residue all fall within 5 deg.

Definition at line 279 of file Residue.cc.

References core::chemical::ResidueType::aa(), aa(), chi(), chi_, core::chemical::ResidueType::name3(), name3(), and rsd_type_.

bool core::conformation::Residue::is_surface ( ) const

inline

Returns true if this residue is a surface residue.

Definition at line 1572 of file Residue.hh.

References core::chemical::ResidueType::is_surface(), and rsd_type_.

Referenced by protocols::vip::VIP_Mover::cull_mutatable_residues().

bool core::conformation::Residue::is_terminus ( ) const

inline

Returns true if the residue has a terminus variant.

Definition at line 1630 of file Residue.hh.

References core::chemical::ResidueType::is_terminus(), and rsd_type_.

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), protocols::analysis::LoopAnalyzerMover::find_positions(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::P_AA::P_AA_pp_energy(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and core::scoring::MembranePotential::termini_penalty().

bool core::conformation::Residue::is_upper_terminus ( ) const

inline

Return true if the residue has an upper terminus variant.

Definition at line 1637 of file Residue.hh.

References core::chemical::ResidueType::is_upper_terminus(), and rsd_type_.

Referenced by protocols::loops::add_cutpoint_variants(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::idealize::basic_idealize(), protocols::dna::DNAParameters::calculate(), protocols::antibody::CloseOneMover::close_one_loop_stem(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), connect_atom(), protocols::topology_broker::copy_internal_coords(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::correct_termini_derivatives(), protocols::forge::methods::count_cutpoints(), protocols::forge::methods::cyclize_pose(), determine_nonstandard_polymer_status(), core::scoring::OmegaTether::eval_omega_score_residue(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_acc_chem_type(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), protocols::forge::methods::grow_right_r(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::conformation::Conformation::insert_polymer_residue(), protocols::loops::Loop::is_terminal(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::remodel::RemodelLoopMover::parse_my_tag(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::scoring::hackelec::HackElecEnergy::set_nres_mono(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), and protocols::fldsgn::CircularPermutation::split_chains().

bool core::conformation::Residue::is_virtual ( Size const & atomno) const

Check if atom is virtual.

Definition at line 1159 of file Residue.cc.

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::is_virtual(), and rsd_type_.

Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_intra_res_hbonds(), n_bonded_neighbor_all_res(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::swa::RigidBodySampler::setup_heavy_atoms(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), core::scoring::rna::RNA_TorsionPotential::Should_score_torsion(), protocols::rna::RNA_Minimizer::update_allow_insert_with_extra_minimize_res(), and protocols::rna::RNA_ChunkLibrary::zero_out_allow_insert().

bool core::conformation::Residue::is_virtual_residue ( ) const

inline

Check if residue is virtual.

Definition at line 195 of file Residue.hh.

References core::chemical::ResidueType::is_virtual_residue(), and rsd_type_.

Referenced by core::scoring::rna::default_jump_atom(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::fill_rmsd_coordinates(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::P_AA::P_AA_pp_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), and core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial().

Size core::conformation::Residue::last_backbone_atom ( ) const

inline

Returns the index number of the last backbone heavyatom.

Note: The heavyatoms come first in atom ordering, first backbone then sidechain, hydrogens follow the order of their attached heavyatom.

example(s): residue.last_backbone_atom() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

Definition at line 585 of file Residue.hh.

References core::chemical::ResidueType::last_backbone_atom(), and rsd_type_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), core::scoring::inline_residue_atom_pair_energy_backbone_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

chemical::ResidueConnection const& core::conformation::Residue::lower_connect ( ) const

inline

Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue.

Definition at line 1094 of file Residue.hh.

References core::chemical::ResidueType::lower_connect(), and rsd_type_.

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::ccd::ccd_moves(), 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(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close(), and core::conformation::Conformation::prepend_polymer_residue_before_seqpos().

Size core::conformation::Residue::lower_connect_atom ( ) const

inline

Returns the index number of this residue's atom which connects to the residue before it in sequence.

Note: : polymers only, example: for an amino acid, residue.lower_connect_atom() = atom_index("N")

example(s): residue.lower_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.upper_connect_atom Pose

Definition at line 705 of file Residue.hh.

References core::chemical::ResidueType::lower_connect_atom(), and rsd_type_.

Referenced by core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residue_by_bond(), protocols::idealize::basic_idealize(), connect_atom(), protocols::loophash::FastGapMover::find_next_gap(), core::conformation::get_anchor_atomno(), and core::conformation::get_root_atomno().

Size core::conformation::Residue::mainchain_atom ( Size const atm) const

inline

??? Returns the number of the residue's mainchain atoms

Definition at line 871 of file Residue.hh.

References core::chemical::ResidueType::mainchain_atom(), and rsd_type_.

Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::get_anchor_atomno(), and core::conformation::get_root_atomno().

AtomIndices const& core::conformation::Residue::mainchain_atoms ( ) const

inline

Returns the AtomIndices of this residue's mainchain atoms.

Definition at line 864 of file Residue.hh.

References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.

Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::loops::loop_closure::ccd::ccd_moves(), core::conformation::Conformation::debug_residue_torsions(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::setup_corresponding_atoms(), and core::conformation::setup_links().

Real core::conformation::Residue::mainchain_torsion ( Size const torsion) const

inline

Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid.

example(s): residue.mainchain_torsion(2) See also: Residue Pose Pose.omega Pose.phi Pose.psi

Definition at line 1412 of file Residue.hh.

References mainchain_torsions_.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::bb_bins_from_pose(), protocols::swa::rna::copy_torsions_FROM_TO(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_rotamer_string(), protocols::swa::rna::StepWiseRNA_ResidueSampler::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::dna::DNABase::DNABase(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::topology_broker::fix_mainchain_connect(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::P_AA::get_Paa_pp_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::pose::Pose::omega(), core::scoring::P_AA::P_AA_pp_energy(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), core::pose::Pose::phi(), protocols::swa::rna::print_backbone_torsions(), protocols::swa::rna::Print_torsion_info(), core::pose::Pose::psi(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), and protocols::rna::suite_assign().

utility::vector1< Real > const& core::conformation::Residue::mainchain_torsions ( ) const

inline

Returns the mainchain torsion angles of this residue (const)

example(s): residue.mainchain_torsions() See also: Residue Pose Pose.omega Pose.phi Pose.psi

Definition at line 1318 of file Residue.hh.

References mainchain_torsions_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::simple_moves::GreenPacker::compare_input_pose_geometry_to_reference(), protocols::swa::Figure_out_moving_residues(), core::io::silent::RNA_SilentStruct::fill_struct(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), Residue(), protocols::dna::PDBOutput::residues_are_different(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::simple_moves::GreenPacker::store_reference_pose_geometry(), core::conformation::Conformation::update_residue_torsions(), and protocols::comparative_modeling::features::TorsionFeature::values_from_pose().

utility::vector1< Real >& core::conformation::Residue::mainchain_torsions ( )

inline

Returns the mainchain torsion angles of this residue (non-const)

Definition at line 1325 of file Residue.hh.

References mainchain_torsions_.

void core::conformation::Residue::mainchain_torsions ( utility::vector1< Real > const & torsions)

inline

Sets the mainchain torsion angles of this residue to <torsions>

example(s): residue.mainchain_torsions() See also: Residue Pose Pose.set_omega Pose.set_phi Pose.set_psi

Definition at line 1341 of file Residue.hh.

References mainchain_torsions_.

std::string const& core::conformation::Residue::mm_atom_name ( int const atom) const

inline

Returns the mm_atom_name of this residue's atom with index number <atom>

Definition at line 1692 of file Residue.hh.

References core::chemical::ResidueType::atom(), core::chemical::Atom::mm_name(), and rsd_type_.

Size core::conformation::Residue::n_bonded_neighbor_all_res	(	core::Size const	atomno,
		bool	virt = `false`
	)		const

Returns the number of atoms bonded to <atomno> in all residues?

determine how many atoms n the residue and adjacent residues are bonded to the given atom (by default, intraresidue virtual atoms are excluded)

Definition at line 906 of file Residue.cc.

References bonded_neighbor(), connection_incomplete(), is_virtual(), n_residue_connections(), and residue_connect_atom_index().

Referenced by protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), and protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute().

Size core::conformation::Residue::n_hbond_acceptors ( ) const

inline

number of hbond_donors

Definition at line 230 of file Residue.hh.

References core::chemical::ResidueType::n_hbond_acceptors(), and rsd_type_.

Referenced by core::pose::num_hbond_acceptors().

Size core::conformation::Residue::n_hbond_donors ( ) const

inline

number of hbond_donors

Definition at line 237 of file Residue.hh.

References core::chemical::ResidueType::n_hbond_donors(), and rsd_type_.

Referenced by core::pose::num_hbond_donors().

Size core::conformation::Residue::n_mainchain_atoms ( ) const

inline

Returns the number of the residue's mainchain atoms.

Definition at line 878 of file Residue.hh.

References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.

Referenced by core::conformation::get_anchor_atomno(), and core::conformation::get_root_atomno().

Size core::conformation::Residue::n_non_polymeric_residue_connections ( ) const

inline

Returns the number of non-polymeric ResidueConnections on this residue.

Definition at line 1118 of file Residue.hh.

References core::chemical::ResidueType::n_non_polymeric_residue_connections(), and rsd_type_.

Referenced by core::conformation::Conformation::show_residue_connections().

Size core::conformation::Residue::n_orbitals ( ) const

inline

Returns the number of orbitals in this residue.

Definition at line 983 of file Residue.hh.

References core::chemical::ResidueType::n_orbitals(), and rsd_type_.

Size core::conformation::Residue::n_polymeric_residue_connections ( ) const

inline

Returns the number of polymeric ResidueConnections on this residue.

Definition at line 1112 of file Residue.hh.

References core::chemical::ResidueType::n_polymeric_residue_connections(), and rsd_type_.

Referenced by core::conformation::Conformation::show_residue_connections().

Size core::conformation::Residue::n_residue_connections ( ) const

inline

Returns the number of ResidueConnections on this residue including polymeric residue connections.

Definition at line 1105 of file Residue.hh.

References core::chemical::ResidueType::n_residue_connections(), and rsd_type_.

Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::mm::connection_indices(), copy_residue_connections(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::declare_chemical_bond(), protocols::forge::methods::fold_tree_from_pose(), protocols::ligand_docking::LigandDesign::fragments_to_string(), has_incomplete_connection(), n_bonded_neighbor_all_res(), core::conformation::setup_corresponding_atoms(), core::conformation::Conformation::show_residue_connections(), and update_connections_to_residues().

std::string const& core::conformation::Residue::name ( ) const

inline

Returns this residue's ResidueType name.

Note: : for proteins, this will be the amino acid type and variant type

Definition at line 1700 of file Residue.hh.

References core::chemical::ResidueType::name(), and rsd_type_.

char core::conformation::Residue::name1 ( ) const

inline

Returns this residue's 1-letter representation.

Note: : for proteins, this will be the 1-letter amino acid code

Definition at line 1716 of file Residue.hh.

References core::chemical::ResidueType::name1(), and rsd_type_.

Referenced by protocols::rna::RNA_StructureParameters::add_new_RNA_jump(), protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::idealize::basic_idealize(), protocols::forge::components::VarLengthBuild::centroid_build(), core::pose::Pose::chain_sequence(), protocols::rna::RNA_ChunkLibrary::check_res_map(), core::pose::copy_dofs(), protocols::rna::create_rna_vall_torsions(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::Antibody::detect_regular_CDR_H3_stem_type(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::ddg::ddGMover::find_nbrs(), core::scoring::gdtha(), core::scoring::gdtsc(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::rna::RNA_ChunkLibrary::get_component_sequences(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff(), protocols::antibody2::AntibodyInfo::identify_antibody(), core::scoring::rna::is_purine(), protocols::ddg::ddGMover::neighborhood_of_mutations(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), core::pack::pack_rotamers_loop(), protocols::protein_interface_design::movers::Splice::parse_my_tag(), protocols::read_in_mutations(), protocols::pmut_scan::PointMutScanDriver::read_mutants_list_file(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::methods::NMerRefEnergy::residue_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::pose::Pose::sequence(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::sequence_recovery(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_sequence(), protocols::rna::setup_base_pair_constraints(), core::conformation::setup_corresponding_atoms(), protocols::simple_moves::BBGaussianMover::setup_list(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::antibody::Antibody::update_sequence(), protocols::outputter::ResFileOutputter::write(), and core::io::pdb::write_additional_pdb_data().

std::string const& core::conformation::Residue::name3 ( ) const

inline

Returns this residue's 3-letter representation.

Note: : for proteins, this will be the 3-letter amino acid code

Definition at line 1708 of file Residue.hh.

References core::chemical::ResidueType::name3(), and rsd_type_.

Size core::conformation::Residue::natoms ( ) const

inline

Returns the number of atoms in this residue.

example(s): residue.natoms() See also: Residue Pose

Definition at line 223 of file Residue.hh.

References core::chemical::ResidueType::natoms(), and rsd_type_.

Size core::conformation::Residue::nbr_atom ( ) const

inline

Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids.

Definition at line 906 of file Residue.hh.

References core::chemical::ResidueType::nbr_atom(), and rsd_type_.

Referenced by protocols::toolbox::task_operations::DesignAroundOperation::apply(), protocols::ligand_docking::Transform::apply(), core::scoring::calc_atom_masks(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), core::scoring::is_nbr_atom(), protocols::scoring::Interface::ligand_calculate(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), core::scoring::methods::BurialEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::conformation::residue_point_graph_from_conformation(), core::scoring::methods::residues_interact(), core::pack::task::operation::util::select_coord_for_residue(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), and core::conformation::ResidueKinWriter::write_kin_header().

Vector const& core::conformation::Residue::nbr_atom_xyz ( ) const

inline

Definition at line 920 of file Residue.hh.

References atoms_, core::chemical::ResidueType::nbr_atom(), and rsd_type_.

Real core::conformation::Residue::nbr_radius ( ) const

inline

Returns the distance cutoff value used as a radius for neighbor definition.

Definition at line 913 of file Residue.hh.

References core::chemical::ResidueType::nbr_radius(), and rsd_type_.

Referenced by core::scoring::calc_atom_masks(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::pack::find_residue_max_radii(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), protocols::scoring::Interface::ligand_calculate(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::pose::pose_max_nbr_radius(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::methods::residues_interact(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), and core::scoring::NeighborList::setup().

AtomIndices const& core::conformation::Residue::nbrs ( int const atm) const

inline

Convenience synonym for bonded_neighbor.

Definition at line 1301 of file Residue.hh.

References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.

Referenced by apply_transform_downstream(), protocols::viewer::dump_residue_kinemage(), core::conformation::setup_links_simple(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

Size core::conformation::Residue::nchi ( ) const

inline

Returns the number of chi angles this residue has.

example(s): residue.nchi() See also: Residue Pose Pose.chi Pose.set_chi

Definition at line 856 of file Residue.hh.

References core::chemical::ResidueType::nchi(), and rsd_type_.

Referenced by core::pose::add_variant_type_to_residue(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_moves::sidechain_moves::SetChiMover::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_chi_for_interpolated_rotamer(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::chis_from_pose(), core::conformation::Conformation::debug_residue_torsions(), protocols::swa::Figure_out_moving_residues(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::pose::noncanonical_chi_count(), core::pose::num_chi_angles(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::pose::remove_variant_type_from_residue(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), set_all_chi(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), and core::conformation::Conformation::update_residue_torsions().

Size core::conformation::Residue::nheavyatoms ( ) const

inline

Returns the number of heavyatoms in this residue.

example(s): residue.nheavyatoms() See also: Residue Pose

Definition at line 251 of file Residue.hh.

References core::chemical::ResidueType::nheavyatoms(), and rsd_type_.

Residue const& core::conformation::Residue::operator= ( Residue const & rhs)

private

Assignment operator does not work for class Residue. This function is intentionally unimplemented and private.

std::string const& core::conformation::Residue::orbital_name ( int const orbital_index) const

inline

Definition at line 996 of file Residue.hh.

References core::chemical::Orbital::name(), core::chemical::ResidueType::orbital(), and rsd_type_.

Referenced by core::io::pdb::dump_pdb_residue().

chemical::orbitals::OrbitalType const& core::conformation::Residue::orbital_type ( int const orbital_index) const

inline

Definition at line 1001 of file Residue.hh.

References core::chemical::ResidueType::orbital_type(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), and protocols::features::OrbitalsFeatures::set_OrbOrb_features_data().

Size core::conformation::Residue::orbital_type_index ( Size const orbital_index) const

inline

Definition at line 1006 of file Residue.hh.

References orbitals_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), and core::scoring::orbitals::OrbitalsScore::get_orb_orb_E().

Vector const& core::conformation::Residue::orbital_xyz ( Size const orbital_index) const

inline

Definition at line 968 of file Residue.hh.

References orbitals_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::io::pdb::dump_pdb_residue(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

void core::conformation::Residue::orient_onto_residue ( Residue const & src)

Orient our coords onto those of <src>, using the atoms from select_orient_atoms.

Helper function: selects atoms to orient on and transforms all of my atoms to orient onto another residue. Used by place(). Need to think a bit more about the restrictions on src...

Definition at line 424 of file Residue.cc.

References atom_index(), core::chemical::ResidueType::atom_name(), rsd_type_, and select_orient_atoms().

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), orient_onto_residue(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(), place(), and core::conformation::Conformation::replace_residue().

void core::conformation::Residue::orient_onto_residue	(	Residue const &	src,
		utility::vector1< std::pair< std::string, std::string > > const &	atom_pairs
	)

Orient our coords onto those of <src>, using the three atom pairs specified in the input.

Parameters

atom_pairs

Definition at line 448 of file Residue.cc.

References atom_index(), and orient_onto_residue().

void core::conformation::Residue::orient_onto_residue	(	Residue const &	src,
		Size	center,
		Size	nbr1,
		Size	nbr2,
		Size	src_center,
		Size	src_nbr1,
		Size	src_nbr2
	)

private

Orient coords onto those of <src>, using the specified atoms.

Definition at line 470 of file Residue.cc.

References atom(), atoms(), core::chemical::ResidueType::natoms(), rsd_type_, core::conformation::Atom::xyz(), and xyz().

utility::vector1< int > const& core::conformation::Residue::path_distance ( int atom) const

inline

Returns the shortest path distance from <atom> to any other atom in this residue.

example(s):

See also: Residue Residue.atom Residue.atoms Pose

Definition at line 753 of file Residue.hh.

References core::chemical::ResidueType::path_distance(), and rsd_type_.

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::trie::initialize_cpdata_for_atom(), core::scoring::rna::Is_base_phosphate_atom_pair(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

int core::conformation::Residue::path_distance	(	int	at1,
		int	at2
	)		const

inline

Returns the number of bonds separating atom <at1> from <at2>

example(s):

Definition at line 785 of file Residue.hh.

References core::chemical::ResidueType::path_distance(), and rsd_type_.

utility::vector1< utility::vector1< int > > const& core::conformation::Residue::path_distances ( ) const

inline

Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2].

example(s):

Definition at line 770 of file Residue.hh.

References core::chemical::ResidueType::path_distances(), and rsd_type_.

void core::conformation::Residue::place	(	Residue const &	src,
		Conformation const &	conformation,
		bool	preserve_c_beta = `false`
	)

Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match.

place/orient "this" Residue onto "src" Residue by backbone superimposition Since rotamer is represented by Residue in mini now, this function is mainly used to place a rotamer onto the backbone of "src" residue. Meanwhile, it can also be used to add sidechains to one pose/conformation from another pose/conformation.
current logic: find backbone atom with bonded neighbors in sidechain, and which is the base_atom of those neighbors. Take that backbone atom and find two neighboring backbone heavyatoms. The three atoms to be superimposed with are the center/base atom, the backbone neighbor 1 and the mid-point of backbone neighbor 1 and 2. This way, we can avoid large perturbation on backbone neighbor 2 after superimpostion if the two sets of backbone atoms are not perfectly superimposable ( e.g., with slightly different backbone geometry).
after all atoms in "this" Residue is oriented, copy any corresponding backbone atom coords from "src" and if there are any backbone atom missing from "src" (for example, src is a proline with HN missing), build them using ideal internal coords (that is why "conformation" is needed as an input argument). For residues without any backbone atoms (e.g. some ligands), center on nbr_atom instead and two of its bonded neighbors (preferring heavy atoms to hydrogens if possible).

Definition at line 521 of file Residue.cc.

References atom(), atom_index(), core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_name(), atom_name(), atoms(), chi_atoms(), fill_missing_atoms(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::has(), has(), is_RNA(), natoms(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), orient_onto_residue(), rsd_type_, type(), core::conformation::Atom::xyz(), and xyz().

Referenced by Residue().

int core::conformation::Residue::polymeric_oriented_sequence_distance ( Residue const & other) const

inline

Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence.

Definition at line 1453 of file Residue.hh.

References chain(), chain_, is_polymer(), and seqpos_.

Referenced by core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), and core::scoring::hbonds::hbond_evaluation_type().

Size core::conformation::Residue::polymeric_sequence_distance ( Residue const & other) const

inline

Returns the sequence separation distance between this residue and <other>

Note: : magnitude of distance only

Definition at line 1443 of file Residue.hh.

References chain(), chain_, is_polymer(), and seqpos_.

Referenced by core::scoring::methods::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), and core::coarse::CoarseEtable::set_residue_pair().

std::map< Size, PseudoBondCollectionCOP > const& core::conformation::Residue::pseudobonds ( ) const

inline

Definition at line 1262 of file Residue.hh.

References pseudobonds_.

Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamer().

bool core::conformation::Residue::requires_actcoord ( ) const

inline

does this residue require an actcoord?

Definition at line 1482 of file Residue.hh.

References core::chemical::ResidueType::requires_actcoord(), and rsd_type_.

Size core::conformation::Residue::residue_connect_atom_index ( Size const resconn_id) const

inline

Definition at line 1134 of file Residue.hh.

References core::chemical::ResidueType::residue_connect_atom_index(), and rsd_type_.

Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), has_incomplete_connection(), core::scoring::trie::initialize_cpdata_for_atom(), n_bonded_neighbor_all_res(), core::conformation::Conformation::show_residue_connections(), and core::conformation::ConformationKinWriter::write_coords().

chemical::ResidueConnection const& core::conformation::Residue::residue_connection ( int const resconn_index) const

inline

Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue.

Definition at line 1128 of file Residue.hh.

References core::chemical::ResidueType::residue_connection(), and rsd_type_.

Size core::conformation::Residue::residue_connection_conn_id ( Size const resconn_index) const

inline

Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ?

Definition at line 1188 of file Residue.hh.

References connect_map_.

Size core::conformation::Residue::residue_connection_partner ( Size const resconn_index) const

inline

Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ?

Definition at line 1175 of file Residue.hh.

References connect_map_.

void core::conformation::Residue::residue_connection_partner	(	Size const	resconn_index,
		Size const	otherres,
		Size const	other_connid
	)

set a connection to this residue by adding its partner's residue number

Definition at line 707 of file Residue.cc.

References connect_map_, determine_nonstandard_polymer_status(), and update_connections_to_residues().

chemical::ResidueTypeSet const& core::conformation::Residue::residue_type_set ( ) const

inline

Returns this residue's ResidueTypeSet.

Definition at line 1073 of file Residue.hh.

References core::chemical::ResidueType::residue_type_set(), and rsd_type_.

core::chemical::rna::RNA_ResidueType const& core::conformation::Residue::RNA_type ( ) const

inline

Return the RNA_residueType object. This is RNA specific.

Definition at line 1818 of file Residue.hh.

References core::chemical::ResidueType::RNA_type(), and rsd_type_.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::rna::get_rna_base_centroid(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::rna::Is_base_phosphate_atom_pair(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

void core::conformation::Residue::select_orient_atoms	(	Size &	center,
		Size &	nbr1,
		Size &	nbr2
	)		const

Selects three atoms for orienting this residue.

Definition at line 414 of file Residue.cc.

References rsd_type_, and core::chemical::ResidueType::select_orient_atoms().

Referenced by orient_onto_residue().

Size core::conformation::Residue::seqpos ( ) const

inline

Returns the sequence position of this residue.

Definition at line 1435 of file Residue.hh.

References seqpos_.

void core::conformation::Residue::seqpos ( Size const setting)

inline

Sets this residue's sequence position to <setting>

Definition at line 1461 of file Residue.hh.

References seqpos_.

void core::conformation::Residue::set_all_chi ( utility::vector1< Real > const & chis)

Sets all of this residue's chi angles using the set_chi function (wrapper function)

Definition at line 1055 of file Residue.cc.

References nchi(), and set_chi().

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), and protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept().

void core::conformation::Residue::set_chi	(	int const	chino,
		Real const	setting
	)

Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree.

this assumes that change propagates according to the information from atom_base array, not from atom tree. So be sure not to get into an endless loop.

Definition at line 1005 of file Residue.cc.

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

Referenced by set_all_chi().

void core::conformation::Residue::set_d	(	int const	chino,
		Real const	setting
	)

fpd bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

Definition at line 935 of file Residue.cc.

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

void core::conformation::Residue::set_orbital_xyz	(	core::Size const	orbital_index,
		Vector const &	xyz_in
	)

inline

Definition at line 974 of file Residue.hh.

References core::chemical::ResidueType::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, and rsd_type_.

Referenced by core::conformation::Conformation::update_orbital_coords(), and update_orbital_coords().

void core::conformation::Residue::set_pseudobonds_to_residue	(	Size	resid,
		PseudoBondCollectionCOP	pbs
	)

Definition at line 895 of file Residue.cc.

References pseudobonds_.

void core::conformation::Residue::set_theta	(	int const	chino,
		Real const	setting
	)

fpd bondangle analog to set_chi (see above for details)

fpd bondangle analog to set_chi same idea as set_d

Definition at line 962 of file Residue.cc.

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

void core::conformation::Residue::set_xyz	(	core::Size const	atm_index,
		Vector const &	xyz_in
	)

Sets the position of this residue's atom with index number <atm_index>

example(s):

Definition at line 233 of file Residue.cc.

References atoms_.

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), apply_transform_Rx_plus_v(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), fill_missing_atoms(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::idealize_hydrogens(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::conformation::orient_residue_for_ideal_bond(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_coordinates(), and protocols::kinmatch::xform_rsd_gl2().

void core::conformation::Residue::set_xyz	(	std::string const &	atm_name,
		Vector const &	xyz_in
	)

Sets the position of this residue's atom with name <atm_name>

example(s):

Definition at line 239 of file Residue.cc.

References atom(), and core::conformation::Atom::xyz().

Atoms::const_iterator core::conformation::Residue::sidechainAtoms_begin ( ) const

inline

should be safe, given the atom ordering rules?

Definition at line 446 of file Residue.hh.

References atoms_, and first_sidechain_atom().

Referenced by core::pack::task::operation::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), and protocols::simple_filters::AtomicContactFilter::compute().

ResidueType const& core::conformation::Residue::type ( ) const

inline

Returns this residue's ResidueType.

example(s): residue.type() See also: Residue Residue.atom_type

Definition at line 1066 of file Residue.hh.

References rsd_type_.

void core::conformation::Residue::update_actcoord ( )

Updates actcoord for this residue.

loop over all actcoord atoms for this ResidueType, average their actual positions in this residue.

Definition at line 409 of file Residue.cc.

References rsd_type_, and core::chemical::ResidueType::update_actcoord().

Referenced by set_chi(), set_d(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_theta(), and core::conformation::Conformation::update_residue_coordinates().

void core::conformation::Residue::update_connections_to_residues ( )

private

Updates connections_to_residues_ using connect_map_.

Private function to keep the connections_to_residues_ array up to date

Note: This could be made faster – connections_to_residues_ is a std::map< > so operator[] calls are slow

Definition at line 744 of file Residue.cc.

References connect_map_, connections_to_residues_, and n_residue_connections().

Referenced by residue_connection_partner(), and update_sequence_numbering().

void core::conformation::Residue::update_orbital_coords ( )

inline

Definition at line 1012 of file Residue.hh.

References core::chemical::ResidueType::atoms_with_orb_index(), atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), rsd_type_, and set_orbital_xyz().

void core::conformation::Residue::update_sequence_numbering ( utility::vector1< Size > const & old2new)

Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped.

update sequence numbers for this residue and the numbers stored about its connections. called by our owning conformation when the sequence numbers are remapped

Definition at line 758 of file Residue.cc.

References connect_map_, determine_nonstandard_polymer_status(), pseudobonds_, seqpos_, and update_connections_to_residues().

chemical::ResidueConnection const& core::conformation::Residue::upper_connect ( ) const

inline

Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue.

Definition at line 1084 of file Residue.hh.

References rsd_type_, and core::chemical::ResidueType::upper_connect().

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::ccd::ccd_moves(), 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(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close(), and core::conformation::Conformation::prepend_polymer_residue_before_seqpos().

Size core::conformation::Residue::upper_connect_atom ( ) const

inline

Returns the index number of this residue's atom which connects to the residue after it in sequence.

Note: : polymers only, example: for an amino acid, residue.upper_connect_atom() = atom_index("C")

example(s): residue.upper_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Pose

Definition at line 723 of file Residue.hh.

References rsd_type_, and core::chemical::ResidueType::upper_connect_atom().

Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::idealize::basic_idealize(), connect_atom(), protocols::loophash::FastGapMover::find_next_gap(), core::conformation::get_anchor_atomno(), and core::conformation::get_root_atomno().

Vector const & core::conformation::Residue::xyz ( Size const atm_index) const

Returns the position of this residue's atom with index number <atm_index>

Note: : position is a Vector

example(s): residue.xyz(3) See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose

Definition at line 221 of file Residue.cc.

References atoms_.

Vector const & core::conformation::Residue::xyz ( std::string const & atm_name) const

Returns the position of this residue's atom with name <atm_name>

Note: : position is a Vector

example(s): residue.xyz("CA") See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose

Definition at line 227 of file Residue.cc.

References atom(), and core::conformation::Atom::xyz().

Member Data Documentation

Vector core::conformation::Residue::actcoord_

private

the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair

Definition at line 1913 of file Residue.hh.

Referenced by actcoord().

Atoms core::conformation::Residue::atoms_

private

our conformation atoms (not kinematic atom pointers) with xyz positiona and atom type

Definition at line 1894 of file Residue.hh.

Referenced by atom(), atom_begin(), atom_end(), atom_type_index(), atoms(), heavyAtoms_end(), nbr_atom_xyz(), Residue(), set_xyz(), sidechainAtoms_begin(), and xyz().

core::Size core::conformation::Residue::chain_

private

the chain id number, starting from 1

Definition at line 1903 of file Residue.hh.

Referenced by chain(), polymeric_oriented_sequence_distance(), and polymeric_sequence_distance().

utility::vector1< Real > core::conformation::Residue::chi_

private

our chi (sidechain) torsion angles

Definition at line 1906 of file Residue.hh.

Referenced by chi(), is_similar_rotamer(), Residue(), and set_chi().

utility::vector1< chemical::ResConnID > core::conformation::Residue::connect_map_

private

map between connection ids on this residue and the connection points on other residues to which its bonded

Definition at line 1927 of file Residue.hh.

Referenced by actual_residue_connection(), clear_residue_connections(), connect_map(), connected_residue_at_resconn(), connection_incomplete(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), determine_nonstandard_polymer_status(), has_incomplete_connection(), residue_connection_conn_id(), residue_connection_partner(), update_connections_to_residues(), and update_sequence_numbering().

std::map< Size, utility::vector1< Size > > core::conformation::Residue::connections_to_residues_

private

lists for each connected residue of the connection points on this residue that connect the pair.

Definition at line 1931 of file Residue.hh.

Referenced by clear_residue_connections(), connect_atom(), connections_to_residue(), copy_residue_connections(), copy_residue_connections_from(), is_bonded(), and update_connections_to_residues().

utility::vector1< Real > core::conformation::Residue::mainchain_torsions_

private

our (possibly empty) backbone torsion angles

Definition at line 1909 of file Residue.hh.

Referenced by mainchain_torsion(), and mainchain_torsions().

bool core::conformation::Residue::nonstandard_polymer_

private

Inter-residue connection data.

true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1

Definition at line 1923 of file Residue.hh.

Referenced by clear_residue_connections(), connect_atom(), copy_residue_connections_from(), and determine_nonstandard_polymer_status().

utility::vector1<orbitals::OrbitalXYZCoords> core::conformation::Residue::orbitals_

private

Definition at line 1896 of file Residue.hh.

Referenced by orbital_type_index(), orbital_xyz(), Residue(), and set_orbital_xyz().

std::map< Size, PseudoBondCollectionCOP > core::conformation::Residue::pseudobonds_

private

other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds)

Definition at line 1935 of file Residue.hh.

Referenced by clear_residue_connections(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), get_pseudobonds_to_residue(), is_pseudo_bonded(), pseudobonds(), Residue(), set_pseudobonds_to_residue(), and update_sequence_numbering().

ResidueType const& core::conformation::Residue::rsd_type_

private

our Residue type

Definition at line 1891 of file Residue.hh.

Referenced by aa(), abase2(), accpt_pos(), accpt_pos_sc(), actcoord_atoms(), all_bb_atoms(), apply_transform_downstream(), atom_base(), atom_index(), atom_is_backbone(), atom_is_hydrogen(), atom_is_polar_hydrogen(), atom_name(), atom_type(), atom_type_set(), atomic_charge(), atoms_with_orb_index(), attached_H_begin(), attached_H_end(), bonded_neighbor(), bonded_orbitals(), build_orbital_xyz(), carbohydrate_info(), chi_atoms(), chi_rotamers(), connect_atom(), cut_bond_neighbor(), first_sidechain_atom(), first_sidechain_hydrogen(), Haro_index(), has(), has_property(), has_sc_orbitals(), has_variant_type(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), Hpol_index(), Hpos_apolar(), Hpos_polar(), Hpos_polar_sc(), icoor(), is_apolar(), is_aromatic(), is_carbohydrate(), is_charged(), is_coarse(), is_DNA(), is_ligand(), is_lower_terminus(), is_NA(), is_polar(), is_polymer(), is_polymer_bonded(), is_protein(), is_RNA(), is_similar_aa(), is_similar_rotamer(), is_surface(), is_terminus(), is_upper_terminus(), is_virtual(), is_virtual_residue(), last_backbone_atom(), lower_connect(), lower_connect_atom(), mainchain_atom(), mainchain_atoms(), mm_atom_name(), n_hbond_acceptors(), n_hbond_donors(), n_mainchain_atoms(), n_non_polymeric_residue_connections(), n_orbitals(), n_polymeric_residue_connections(), n_residue_connections(), name(), name1(), name3(), natoms(), nbr_atom(), nbr_atom_xyz(), nbr_radius(), nbrs(), nchi(), nheavyatoms(), orbital_name(), orbital_type(), orient_onto_residue(), path_distance(), path_distances(), place(), requires_actcoord(), Residue(), residue_connect_atom_index(), residue_connection(), residue_type_set(), RNA_type(), select_orient_atoms(), set_chi(), set_d(), set_orbital_xyz(), set_theta(), type(), update_actcoord(), update_orbital_coords(), upper_connect(), and upper_connect_atom().

Size core::conformation::Residue::seqpos_

private

the sequence position

Definition at line 1900 of file Residue.hh.

Referenced by connect_atom(), fill_missing_atoms(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), seqpos(), and update_sequence_numbering().

The documentation for this class was generated from the following files:

src/core/conformation/Residue.hh
src/core/conformation/Residue.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation