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core::conformation::Residue Class Reference

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

#include <Residue.hh>

Inheritance diagram for core::conformation::Residue:
Inheritance graph
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Public Types

typedef chemical::AtomType AtomType
 
typedef chemical::ResidueType ResidueType
 
typedef chemical::ResidueTypeCOP ResidueTypeCOP
 
typedef chemical::AtomIndices AtomIndices
 

Public Member Functions

 Residue (ResidueTypeCOP rsd_type_in, bool const dummy_arg)
 constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue. More...
 
 Residue (ResidueType const &rsd_type_in, bool const dummy_arg)
 constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue. More...
 
 Residue (ResidueType const &rsd_type_in, Residue const &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)
 Copy constructor. More...
 
 ~Residue () override
 Destructor. More...
 
ResidueOP clone () const
 Copy this residue( allocate actual memory for it ) More...
 
ResidueOP clone_flipping_chirality (core::chemical::ResidueTypeSet const &residue_type_set) const
 Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type. More...
 
void show (std::ostream &output=std::cout, bool output_atomic_details=false) const
 Generate string representation of Residue for debugging purposes. More...
 
ResidueCOP get_self_ptr () const
 self pointers More...
 
ResidueOP get_self_ptr ()
 
ResidueCAP get_self_weak_ptr () const
 
ResidueAP get_self_weak_ptr ()
 
AtomType const & atom_type (Size const atomno) const
 Returns the AtomType of this residue's atom with index number <atomno> More...
 
chemical::AtomTypeSet const & atom_type_set () const
 Returns the AtomTypeSet of this residue. More...
 
Size atom_type_index (Size const atomno) const
 Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType. More...
 
Real atomic_charge (Size const atomno) const
 Returns the atom charge of this residue's atom with index number <atomno> More...
 
bool is_virtual (Size const atomno) const
 Check if atom is virtual. More...
 
bool is_repulsive (Size const atomno) const
 Check if atom is repulsive. More...
 
bool is_virtual_residue () const
 Check if residue is virtual. More...
 
Size atom_index (std::string const &atm) const
 Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid. More...
 
Size natoms () const
 Returns the number of atoms in this residue. More...
 
Size n_hbond_acceptors () const
 number of hbond_donors More...
 
Size n_hbond_donors () const
 number of hbond_donors More...
 
Size nheavyatoms () const
 Returns the number of heavyatoms in this residue. More...
 
AtomIndices const & Hpos_polar () const
 Returns the AtomIndices of this residue's polar hydrogens. More...
 
AtomIndices const & all_bb_atoms () const
 Returns the AtomIndices of this residue's backbone atoms. More...
 
AtomIndices const & Haro_index () const
 Returns the AtomIndices of this residue's aromatic hydrogens. More...
 
AtomIndices const & Hpol_index () const
 Returns the AtomIndices of this residue's polar hydrogens. More...
 
AtomIndices const & Hpos_apolar () const
 Returns the AtomIndices of this residue's apolar hydrogens. More...
 
AtomIndices const & Hpos_polar_sc () const
 Returns the AtomIndices of this residue's polar sidechain hydrogens. More...
 
AtomIndices const & accpt_pos () const
 Returns the AtomIndices of this residue's h-bond acceptor atoms. More...
 
AtomIndices const & accpt_pos_sc () const
 Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms. More...
 
void get_metal_binding_atoms (AtomIndices &metal_binding_indices) const
 Gets the AtomIndices of the atoms in this residue that can bind to metals. More...
 
core::Size n_virtual_atoms () const
 Returns the number of virtual atoms in this residue. More...
 
bool heavyatom_has_polar_hydrogens (Size ind) const
 Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom) More...
 
bool heavyatom_is_an_acceptor (Size ind) const
 Is a particular atom a heavy atom acceptor? More...
 
bool atom_is_polar_hydrogen (Size ind) const
 Is a particular atom a polar hydrogen? More...
 
Atoms const & atoms () const
 Returns this residue's Atoms (const), a vector1 of Atom objects. More...
 
Atomsatoms ()
 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...
 
Atomatom (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...
 
Atomatom (std::string const &atm_name)
 Returns this residue's Atom with name <atm_name> (non-const) More...
 
Vector const & xyz (Size const atm_index) const
 Returns the position of this residue's atom with index number <atm_index> More...
 
Vector const & xyz (std::string const &atm_name) const
 Returns the position of this residue's atom with name <atm_name> More...
 
void set_xyz (core::Size const atm_index, Vector const &xyz_in)
 Sets the position of this residue's atom with index number <atm_index> More...
 
void set_xyz (std::string const &atm_name, Vector const &xyz_in)
 Sets the position of this residue's atom with name <atm_name> More...
 
Size last_backbone_atom () const
 Returns the index number of the last backbone heavyatom. More...
 
Size first_sidechain_atom () const
 Returns the index number of the first sidechain heavyatom. More...
 
Size first_sidechain_hydrogen () const
 Returns the index number of the first sidechain hydrogen. More...
 
Size attached_H_begin (Size const atom) const
 Returns the index number of the first hydrogen attached to the atom with index number <atom> More...
 
Size attached_H_end (Size const atom) const
 Returns the index number of the last hydrogen attached to the atom with index number <atom> More...
 
AtomIndices const & attached_H_begin () const
 Returns the AtomIndices of the first hydrogen attached to each heavyatom. More...
 
AtomIndices const & attached_H_end () const
 Returns the AtomIndices of the last hydrogen attached to each heavyatom. More...
 
bool has_lower_connect () const
 Returns true if residue has a valid lower connection. More...
 
Size lower_connect_atom () const
 Returns the index number of this residue's atom which connects to the residue before it in sequence. More...
 
bool has_upper_connect () const
 Returns true if residue has a valid upper connection. More...
 
Size upper_connect_atom () const
 Returns the index number of this residue's atom which connects to the residue after it in sequence. More...
 
Size connect_atom (Residue const &other) const
 Returns the index number of this residue's atom connected to the <other> Residue. More...
 
core::chemical::AtomIndices get_adjacent_heavy_atoms (uint const atom_index) const
 Get a list of heavy atoms connected to a given atom. More...
 
uint first_adjacent_heavy_atom (uint const atom_index) const
 Scan through the list of atoms connected to a given atom and return the 1st heavy atom found. More...
 
core::chemical::AtomIndices get_atoms_exocyclic_to_ring_atom (uint const atom_index) const
 Get a list of exocyclic atoms connected to a given ring atom. More...
 
core::chemical::AtomIndices get_substituents_to_ring_atom (uint const atom_index) const
 Get a list of substituent atoms connected to a given ring atom. More...
 
core::chemical::AtomIndices get_hydrogens_bonded_to_ring_atom (uint const atom_index) const
 Get a list of hydrogen atoms connected to a given ring atom. More...
 
utility::vector1< int > const & path_distance (Size atom) const
 Returns the shortest path distance from <atom> to any other atom in this residue. More...
 
utility::vector1
< utility::vector1< int >
> const & 
path_distances () const
 Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2]. More...
 
int path_distance (Size at1, Size at2) const
 Returns the number of bonds separating atom <at1> from <at2> More...
 
bool atom_is_backbone (Size const atomno) const
 Returns true if this residue's atom with index number <atomno> is a backbone atom. More...
 
bool atom_is_hydrogen (Size const atomno) const
 Returns true if this residue's atom with index number <atomno> is a hydrogen. More...
 
Size atom_base (Size const atomno) const
 Returns the atom index of the <atomno> atom's base atom. More...
 
Size abase2 (Size const atomno) const
 Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor) More...
 
AtomIndices const & bonded_neighbor (Size const atm) const
 Returns the AtomIndices for all bonded neighbor atoms of <atm> More...
 
AtomIndices const & mainchain_atoms () const
 Returns the AtomIndices of this residue's mainchain atoms. More...
 
Size mainchain_atom (Size const i) const
 Returns the atom index of the residue's ith mainchain atom. More...
 
Size n_mainchain_atoms () const
 Returns the number of the residue's mainchain atoms. More...
 
AtomIndices const & actcoord_atoms () const
 Returns the AtomIndices of atoms that will be used to define this residue's actcoord. More...
 
Vector build_atom_ideal (int const atomno, Conformation const &conformation) const
 Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms. More...
 
Size nbr_atom () const
 Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids. More...
 
Real nbr_radius () const
 Returns the distance cutoff value used as a radius for neighbor definition. More...
 
Vector const & nbr_atom_xyz () const
 
AtomIndices const & atoms_with_orb_index () const
 
Vector build_orbital_xyz (Size const orbital_index) const
 
Vector const & orbital_xyz (Size const orbital_index) const
 
void set_orbital_xyz (core::Size const orbital_index, Vector const &xyz_in)
 
Size n_orbitals () const
 Returns the number of orbitals in this residue. More...
 
utility::vector1< Size > const & bonded_orbitals (Size const atm) const
 
std::string const & orbital_name (Size const orbital_index) const
 
chemical::orbitals::OrbitalType
const & 
orbital_type (Size const orbital_index) const
 
Size orbital_type_index (Size const orbital_index) const
 
void update_orbital_coords ()
 
ResidueOP create_rotamer () const
 Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out. More...
 
ResidueOP create_residue () const
 Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out. More...
 
ResidueType const & type () const
 Returns this residue's ResidueType. More...
 
ResidueTypeCOP type_ptr () const
 Returns this residue's ResidueType as a COP. More...
 
chemical::ResidueConnection const & upper_connect () const
 Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue. More...
 
chemical::ResidueConnection const & lower_connect () const
 Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue. More...
 
bool connections_match (Residue const &other) const
 Returns true if ??? More...
 
Size n_possible_residue_connections () const
 Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType. More...
 
Size n_current_residue_connections () const
 Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!! More...
 
Size n_polymeric_residue_connections () const
 Returns the number of polymeric ResidueConnections on this residue. More...
 
Size n_non_polymeric_residue_connections () const
 Returns the number of non-polymeric ResidueConnections on this residue. More...
 
chemical::ResidueConnection const & residue_connection (Size const resconn_index) const
 Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue. More...
 
Size residue_connect_atom_index (Size const resconn_id) const
 
chemical::ResConnID connect_map (Size resconn_index) const
 
void mark_connect_incomplete (Size resconn_index)
 
core::Size connect_map_size () const
 Returns the size (number of elements) in the connect_map_ object. More...
 
void clear_residue_connections ()
 
void update_connections_to_other_residue (Residue const &other_rsd)
 Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number). More...
 
void copy_residue_connections_from (Residue const &src)
 
bool has_incomplete_connection () const
 
bool has_incomplete_connection (core::Size const atomno) const
 Returns true is <atomno> has complete connectivity? More...
 
bool connection_incomplete (Size resconnid) const
 
chemical::ResConnID actual_residue_connection (Size resconnid) const
 Get the residue connection. How is this different than residue_connection? More...
 
id::AtomID inter_residue_connection_partner (int connid, Conformation const &conformation) const
 This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More...
 
Size connected_residue_at_resconn (Size const resconn_index) const
 Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More...
 
Size connected_residue_at_upper () const
 Returns the residue number of a residue connected to this residue at this residue's upper_connect. More...
 
Size connected_residue_at_lower () const
 Returns the residue number of a residue connected to this residue at this residue's lower_connect. More...
 
Size residue_connection_partner (Size const resconn_index) const
 Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More...
 
void copy_residue_connections (Residue const &src_rsd)
 attempt to take residue connection info from src_rsd More...
 
Size residue_connection_conn_id (Size const resconn_index) const
 Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index. More...
 
void residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid)
 set a connection to this residue by adding its partner's residue number More...
 
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 (Size const atm) const
 atom indices for bonded neighbors to which atom-tree connections are disallowed. More...
 
core::Size n_bonded_neighbor_all_res (core::Size const atomno, bool virt=false) const
 Returns the number of atoms bonded to <atomno> in all residues? More...
 
AtomIndices const & nbrs (Size const atm) const
 Convenience synonym for bonded_neighbor. More...
 
utility::vector1< Real > const & mainchain_torsions () const
 Returns the mainchain torsion angles of this residue (const) More...
 
utility::vector1< Real > & mainchain_torsions ()
 Returns the mainchain torsion angles of this residue (non-const) More...
 
void mainchain_torsions (utility::vector1< Real > const &torsions)
 Sets the mainchain torsion angles of this residue to <torsions> More...
 
Real mainchain_torsion (Size const torsion) const
 Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid. More...
 
Size nchi () const
 Returns the number of chi angles this residue has. More...
 
utility::vector1< Real > const & chi () const
 Returns the chi torsion angles of this residue (const) More...
 
utility::vector1< Real > & chi ()
 Returns the chi torsion angles of this residue (non-const) More...
 
void chi (utility::vector1< Real > const &chis)
 Sets the chi torsion angles of this residue. More...
 
Real chi (Size const chino) const
 get a specific chi torsion angle More...
 
utility::vector1< AtomIndices >
const & 
chi_atoms () const
 Returns the AtomIndices of each set of four atoms defining each chi angle. More...
 
AtomIndices const & chi_atoms (Size const chino) const
 Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle. More...
 
Size n_nus () const
 Return the number of nu (internal ring) angles this residue has. More...
 
utility::vector1< core::Angle >
const & 
nus () const
 Return the nu (internal ring) torsion angles of this residue. More...
 
utility::vector1< core::Angle > & nus ()
 Return the nu (internal ring) torsion angles of this residue. (non-const) More...
 
core::Angle nu (core::uint const index) const
 Get a specific nu (internal ring) torsion angle by index. More...
 
utility::vector1< AtomIndices >
const 
nu_atoms () const
 Return the AtomIndices of each set of four atoms defining each nu angle. More...
 
AtomIndices const nu_atoms (core::uint const index) const
 Return the AtomIndices of the four atoms defining the specified nu angle. More...
 
chemical::rings::RingConformer
const & 
ring_conformer (core::uint const ring_num, core::Real limit=90.0) const
 Return the current RingConformer of this residue's nth ring. More...
 
Size seqpos () const
 Returns the sequence position of this residue. More...
 
void seqpos (Size const setting)
 Sets this residue's sequence position to <setting> More...
 
Size polymeric_sequence_distance (Residue const &other) const
 Returns the sequence separation distance between this residue and <other> More...
 
int polymeric_oriented_sequence_distance (Residue const &other) const
 Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence. More...
 
core::Size chain () const
 Returns this residue's chain id. More...
 
void chain (core::Size const setting)
 Sets this residue's chain id. More...
 
bool requires_actcoord () const
 does this residue require an actcoord? More...
 
void update_actcoord ()
 Updates actcoord for this residue. More...
 
Vector const & actcoord () const
 Returns the coordinates used for pairE calculations (amino acids only) More...
 
Vectoractcoord ()
 Returns the coordinates used for pairE calculations (amino acids only) More...
 
void update_sequence_numbering (utility::vector1< Size > const &old2new)
 Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped. More...
 
void update_nus ()
 Calculate the set of nu dihedrals from the xyz coordinates and store them. More...
 
bool is_polymer () const
 Returns true if this residue is a polymer. More...
 
bool is_protein () const
 Returns true if this residue is an amino acid. More...
 
bool is_peptoid () const
 Returns if this residue is a peptoid. More...
 
bool is_sri () const
 Is this one of SRI's special heteropolymer building blocks? More...
 
bool is_triazolemer () const
 Returns true if and only if this residue is a triazolemer. More...
 
bool is_DNA () const
 Returns true if this residue is a DNA residue. More...
 
bool is_RNA () const
 Returns true if this residue is a RNA residue. More...
 
bool is_TNA () const
 Returns true if this residue is a TNA residue. More...
 
bool is_l_rna () const
 Returns true if this residue is a L-RNA residue. More...
 
bool is_d_rna () const
 Returns true if this residue is a D-RNA residue. More...
 
bool is_NA () const
 Returns true if this residue is a nucleic acid. More...
 
bool is_purine () const
 Returns true if this residue is a purine. More...
 
bool is_pyrimidine () const
 Returns true if this residue is a pyrimidine. More...
 
bool is_carbohydrate () const
 Returns true if this residue is a carbohydrate. More...
 
bool is_water () const
 Returns true if this residue is water. More...
 
bool is_ligand () const
 Returns true if this residue is a ligand. More...
 
bool is_metal () const
 Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES. More...
 
bool is_metalbinding () const
 Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES. More...
 
bool 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_branch_point () const
 Return true if the residue is a branch point variant. More...
 
bool is_similar_rotamer (Residue const &other) const
 Returns true if the chi angles of another residue all fall within 5 deg. More...
 
bool is_similar_aa (Residue const &other) const
 Returns true if the aa residue types are the same. More...
 
bool has_shadow_atoms () const
 Return true if and only if this residue's type has shadow atoms. More...
 
bool has_property (std::string const &property) const
 Return true if the residue has <property>. More...
 
bool has_variant_type (chemical::VariantType const variant_type) const
 Generic variant access. More...
 
std::string const & atom_name (Size const atm) const
 Returns the name of this residue's atom with index number <atm> More...
 
std::string const & mm_atom_name (Size const atom) const
 Returns the mm_atom_name of this residue's atom with index number <atom> More...
 
std::string const & name () const
 Returns this residue's ResidueType name. More...
 
std::string const & name3 () const
 Returns this residue's 3-letter representation. More...
 
char name1 () const
 Returns this residue's 1-letter representation. More...
 
std::string annotated_name (bool const show_all_variants=true) const
 Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D]. More...
 
chemical::AA const & aa () const
 Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration. More...
 
chemical::AA const & backbone_aa () const
 Returns this residue's backbone_aa type, if any. More...
 
chemical::AA const & na_analogue () const
 Returns the nucleic acid type to be used for fragment sampling. More...
 
chemical::AtomICoor const & icoor (Size const atm) const
 Returns the internal coordinates of this residue's atom with index number <atm> More...
 
bool atom_depends_on_lower (core::Size const atom_index) const
 Does this atom depend on the LOWER_CONNECT? More...
 
bool atom_depends_on_upper (core::Size const atom_index) const
 Does this atom depend on the UPPER_CONNECT? More...
 
void set_d (int const chino, Real const setting)
 bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example More...
 
void set_theta (int const chino, Real const setting)
 bondangle analog to set_chi same idea as set_d More...
 
void set_tau (Size const nuno, Real const setting)
 set_theta for nus More...
 
void set_all_nu (utility::vector1< Real > const &nus, utility::vector1< Real > const &taus)
 
void set_all_ring_nu (Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus)
 
void set_chi (int const chino, Real const setting)
 Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree. More...
 
void set_all_chi (utility::vector1< Real > const &chis)
 Sets all of this residue's chi angles using the set_chi function (wrapper function) More...
 
bool has (std::string const &atm) const
 Returns true if this residue has an atom named <atm> More...
 
bool fill_missing_atoms (utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true)
 Builds coordinates for atoms missing from this residue assuming ideal internal coordinates. More...
 
void select_orient_atoms (Size &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 orient_onto_residue_peptoid (Residue const &src, Conformation const &conformation)
 Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide. More...
 
void orient_onto_location (Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)
 Orients residue object onto atom locations. More...
 
void orient_onto_location (Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)
 Orients residue object onto atom locations. More...
 
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_Info
const & 
RNA_info () const
 Return the RNA_residueType object. This is RNA specific. More...
 
core::chemical::carbohydrates::CarbohydrateInfoCOP carbohydrate_info () const
 Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More...
 
basic::datacache::BasicDataCacheCOP data_ptr () const
 BasicDataCache indexed by enum in residue_datacache.hh. More...
 
basic::datacache::BasicDataCacheOP nonconst_data_ptr ()
 BasicDataCache indexed by enum in residue_datacache.hh. More...
 
basic::datacache::BasicDataCache
const & 
data () const
 BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More...
 
basic::datacache::BasicDataCache & nonconst_data ()
 BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More...
 
bool mirrored_relative_to_type () const
 Is this residue mirrored relative to its coordinates in the ResidueType? More...
 
void set_mirrored_relative_to_type (bool const setting)
 Set whether this residue is mirrored relative to its coordinates in the ResidueType. More...
 

Private Member Functions

 Residue (Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality)
 Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve. More...
 
void init_residue_from_other (Residue const &src)
 Function called by both copy constructors, to avoid code duplication. More...
 
void update_connections_to_residues ()
 Updates connections_to_residues_ using connect_map_. More...
 
void apply_transform_downstream (core::Size const atomno, numeric::xyzMatrix< Real > const &R, Vector const &v)
 apply transform of rotation R and translation V for all atoms downstream More...
 
void determine_nonstandard_polymer_status ()
 
Residue const & operator= (Residue const &rhs)
 Assignment operator does not work for class Residue. This function is intentionally unimplemented and private. More...
 
void orient_onto_residue (Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2)
 Orient coords onto those of <src>, using the specified atoms. More...
 
void assign_orbitals ()
 Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors. More...
 

Private Attributes

ResidueTypeCOP rsd_type_ptr_
 Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed. More...
 
ResidueType const & rsd_type_
 our Residue type More...
 
Atoms atoms_
 our conformation atoms (not kinematic atom pointers) with xyz positions and atom type More...
 
utility::vector1
< orbitals::OrbitalXYZCoords
orbitals_
 
Size seqpos_
 the sequence position More...
 
bool mirrored_relative_to_type_
 Is this residue mirrored relative to its coordinates in the ResidueType? More...
 
core::Size chain_
 the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. More...
 
utility::vector1< Realchi_
 our chi (side chain) torsion angles More...
 
utility::vector1< Anglenus_
 our nu (internal ring) torsion angles More...
 
utility::vector1< Realmainchain_torsions_
 our (possibly empty) backbone torsion angles More...
 
Vector actcoord_
 the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair More...
 
basic::datacache::BasicDataCacheOP data_cache_
 
bool 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, e.g., Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:

Member Typedef Documentation

Constructor & Destructor Documentation

core::conformation::Residue::Residue ( ResidueTypeCOP  rsd_type_in,
bool const  dummy_arg 
)

constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue.

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

Note
Dummmy arg to prevent secret type conversions from ResidueTypeCOP to Residue

References assign_orbitals(), core::chemical::ResidueType::atom(), core::chemical::Atom::atom_type_index(), atoms_, core::chemical::Atom::ideal_xyz(), core::chemical::Atom::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().

Referenced by clone(), and clone_flipping_chirality().

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

constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue.

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

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

References assign_orbitals(), core::chemical::ResidueType::atom(), core::chemical::Atom::atom_type_index(), atoms_, core::chemical::Atom::ideal_xyz(), core::chemical::Atom::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().

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 position, chain id and mainchain torsion angles as current_rsd. It has a ResidueType as defined by rsd_type_in. Its side-chain chi angles are uninitialized as all 0.0 and sidechain atom coords are from ideal coords. Its backbone is aligned with that of current_rsd. Its residue connections and its pseudobonds must be initialized from the original residue.

References assign_orbitals(), core::chemical::ResidueType::atom(), atom(), core::chemical::Atom::atom_type_index(), atoms_, 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_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), place(), pseudobonds_, rsd_type_, core::conformation::TR(), type(), update_nus(), and xyz().

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

Copy constructor.

References init_residue_from_other().

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

Destructor.

core::conformation::Residue::Residue ( Residue const &  src,
core::chemical::ResidueTypeCOP  new_restype,
bool  flip_chirality 
)
private

Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve.

References atom(), chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), init_residue_from_other(), mirrored_relative_to_type(), nchi(), rsd_type_, set_mirrored_relative_to_type(), type(), and xyz().

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.

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

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::hybridization::add_non_protein_cst(), protocols::denovo_design::components::advance_past_virtual_residues(), protocols::simple_moves::VirtualRootMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::protein_interface_design::Revert::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::idealize::basic_idealize(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::denovo_design::components::StructureData::check_pose(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), core::scoring::rna::check_watson_crick_sequence(), protocols::loops::Loop::choose_cutpoint(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), core::scoring::dssp::Dssp::compute(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::constraint_generator::compute_hnq_atoms(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::relax::AtomCoordinateCstMover::compute_residue_subset(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::methods::ProClosureEnergy::defines_intrares_energy_for_residue(), core::scoring::electron_density::FastDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::PointWaterEnergy::defines_score_for_residue_pair(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_proline_design(), core::scoring::constraints::ResidueTypeLinkingConstraint::dist(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::eval_atom_derivative(), core::scoring::cryst::XtalMLEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), 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(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_intrares_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::scoring::methods::MembraneLipo::finalize_total_energy(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), core::pose::motif::get_backbone_reference_frame_atomids(), core::scoring::hackaro::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::pack::interaction_graph::SimpleEdge::get_bb_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::scoring::hackaro::HackAroEnergy::get_centroid(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::data::RNA_DMS_Potential::get_features(), core::pose::motif::get_frame_ala(), core::pose::motif::get_frame_arg(), core::pose::motif::get_frame_asn(), core::pose::motif::get_frame_asp(), core::pose::motif::get_frame_cys(), core::pose::motif::get_frame_gln(), core::pose::motif::get_frame_glu(), core::pose::motif::get_frame_gly(), core::pose::motif::get_frame_his(), core::pose::motif::get_frame_ile(), core::pose::motif::get_frame_leu(), core::pose::motif::get_frame_lys(), core::pose::motif::get_frame_met(), core::pose::motif::get_frame_phe(), core::pose::motif::get_frame_pro(), core::pose::motif::get_frame_ser(), core::pose::motif::get_frame_thr(), core::pose::motif::get_frame_trp(), core::pose::motif::get_frame_tyr(), core::pose::motif::get_frame_val(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hybridization::get_num_residues_nonvirt(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::sic_dock::get_rg(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pose::motif::get_sidechain_reference_frame(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream(), protocols::hybridization::CartesianSampler::get_transform(), core::scoring::dna::get_z_axis(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), core::io::serialization::is_pseudoresidue(), is_similar_aa(), is_similar_rotamer(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::simple_filters::ResidueDepthFilter::make_context(), core::pack::make_symmetric_task(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), core::conformation::missing_stubs_build(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::ncbb::ncbb_design_main_loop(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::conformation::WatsonCrickResidueMatcher::operator()(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::PairEPotential::pair_term_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::P_AA_ss_Energy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), protocols::dna::PDBOutput::residues_are_different(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::scoring::rna::chemical_shift::ring_current_effect(), core::scoring::rna::chemical_shift::ring_current_effect_individual_ring(), core::scoring::rna::chemical_shift::ring_pos(), core::pack::dunbrack::rotamer_from_chi(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::MembranePotential::score_normal_center(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::hbnet::HBNet::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::scoring::methods::Abego::setup_for_scoring(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), protocols::scoring::Interface::show(), protocols::hybridization::DDomainParse::split(), core::fragment::SingleResidueFragData::steal(), protocols::denovo_design::symmetric_fold_tree(), core::scoring::MembranePotential::termini_penalty(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

Size core::conformation::Residue::abase2 ( Size 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)

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

Referenced by core::scoring::hbonds::assign_abase_derivs(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::magnesium::get_cos_theta(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), and protocols::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

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

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_acceptor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_acceptor(), core::pose::rna::atom_is_acceptor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), 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::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().

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

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

Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().

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

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

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.

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
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

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

Referenced by protocols::legacy_sewing::scoring::LegacyClashScorer::score().

std::string core::conformation::Residue::annotated_name ( bool const  show_all_variants = true) const
void core::conformation::Residue::apply_transform_downstream ( core::Size 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 side chain recursively. it assumes that the atom_base array will not get us into any infinite loops!

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

References atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), protocols::sic_dock::scores::nbr, nbrs(), rsd_type_, core::conformation::TR(), core::conformation::Atom::xyz(), and xyz().

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

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

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

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

void core::conformation::Residue::assign_orbitals ( )
private

Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors.

References core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueType::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, rsd_type_, and type().

Referenced by Residue().

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

References atoms_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::rigid::RollMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), apply_transform_downstream(), protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::atomic_depth::atomic_depth(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), build_orbital_xyz(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), core::conformation::build_residue_tree(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::methods::ProQ_Energy::calculateZ(), core::select::util::cbeta_vector(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::geometry::center_of_mass(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::relax::RangeRelaxMover::constrain_to_reference(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), protocols::legacy_sewing::create_model_from_pose(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), 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::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::scoring::methods::BranchEnergy::finalize_total_energy(), core::scoring::methods::LinearBranchEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::simple_moves::WaterBoxMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::features::strand_assembly::find_sheet(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::electron_density::findLoopFromDensity(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands(), protocols::membrane::get_chain_and_z(), protocols::features::strand_assembly::get_closest_distance_between_strands(), core::scoring::magnesium::get_cos_theta(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::hybridization::get_superposition_transformation(), protocols::hybridization::CartesianSampler::get_transform(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), protocols::cryst::getMW(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::strand_assembly::is_this_strand_at_edge(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::simple_moves::BBConRotMover::make_move(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::motifs::Motif::Motif(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), place(), protocols::motifs::Motif::place_atom_(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::motifs::Motif::place_residue_helper(), core::scoring::PQR::PQR(), core::scoring::elec::FA_GrpElecEnergy::precalc_context(), protocols::viewer::print_node(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::features::SmotifFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), Residue(), core::conformation::symmetry::residue_center_of_mass(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::membrane::FaMPEnvEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H(), core::scoring::residue_fast_pair_energy_attached_H(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), core::select::util::select_coord_for_residue(), set_all_ring_nu(), set_chi(), protocols::hbnet::HBNet::set_constraints(), set_d(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_tau(), set_theta(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::hybridization::DDomainParse::split(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), update_nus(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_starting_loop(), core::chemical::ICoorAtomID::xyz(), and xyz().

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

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

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

References atom_index(), and atoms_.

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

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

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

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::scoring::hbonds::assign_abase_derivs(), core::scoring::elec::assign_rna_atom_type(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), core::pose::rna::bases_form_a_hydrogen_bond(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::pack::interaction_graph::create_hbonds_one_way(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::hbonds::determine_atom_level_edge_info(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::hbonds::HBond::get_AHDangle(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::hbonds::HBond::get_BAHangle(), core::scoring::hbonds::HBond::get_BAtorsion(), core::scoring::magnesium::get_cos_theta(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), protocols::protein_interface_design::hbonded_atom(), core::pose::rna::heavy_atom_is_polar(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_row(), core::scoring::elec::is_base_2(), core::scoring::elec::is_phosphate_2(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::scoring::elec::is_sugar_2(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), and core::scoring::hbonds::HBond::show().

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

References atoms_.

bool core::conformation::Residue::atom_depends_on_lower ( core::Size const  atom_index) const

Does this atom depend on the LOWER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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

Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().

bool core::conformation::Residue::atom_depends_on_upper ( core::Size const  atom_index) const

Does this atom depend on the UPPER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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

Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().

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

end interator, to iterate over atoms

References atoms_.

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

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

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

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

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::seeded_abinitio::add_dist_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::antibody::constraints::add_harmonic_dihedral_cst_general(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::pose::ncbb::add_oop_constraint(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::pose::ncbb::add_triazole_constraint(), protocols::loops::addScoresForLoopParts(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_residue(), core::pose::Pose::append_residue_by_atoms(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::splice::Splice::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), atom(), protocols::hydrate::atom_is_hydratable(), core::scoring::FACTSPotential::atompair_scale(), protocols::motifs::backbone_stub_match(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::conformation::build_residue_tree(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::scoring::methods::GoapEnergy::calculate_dipoles(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), protocols::loop_grower::LoopGrower::check_coordinates(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), protocols::flxbb::constraints_sheet(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::pose::correctly_add_2prime_connection_variants(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::relax::cyclize_pose(), core::conformation::Conformation::declare_chemical_bond(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::DNA_DihedralEnergy::eval_residue_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), fill_missing_atoms(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), core::conformation::Conformation::fix_disulfides(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::form_disulfide(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::pose::get_constraints_from_link_records(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), protocols::simple_moves::BBConRotMover::get_L_move(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::protein_interface_design::hbonded_atom(), core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), core::pose::make_atom_map(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), core::conformation::named_atom_id_to_atom_id(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::constraint_generator::parse_custom_torsion(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::viewer::print_node(), protocols::match::output::print_node(), core::conformation::print_node(), core::scoring::constraints::AngleConstraint::read_def(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), core::scoring::rna::chemical_shift::ring_pos(), protocols::rbsegment_relax::set_constraints(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::simple_moves::DisulfideInsertionMover::setup_constraints(), protocols::star::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::conformation::setup_links(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::loop_grower::LoopGrower::single_grow(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::grafting::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::docking::ConformerSwitchMover::switch_conformer(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

bool core::conformation::Residue::atom_is_backbone ( Size 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

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

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::hbnet::UnsatSelector::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::FACTSPotential::atompair_scale(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::HolesFilter::compute(), protocols::hbnet::UnsatSelector::compute(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::hbnet::HBNet::find_unsats(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::is_scatom(), protocols::pockets::PocketGrid::recenter(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

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

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

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::elec::assign_rna_atom_type(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::contact_map::ContactMap::fill_contacts(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), get_adjacent_heavy_atoms(), 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_PolarNonPolarEnergy::get_base_vector(), get_hydrogens_bonded_to_ring_atom(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), get_substituents_to_ring_atom(), core::scoring::ResidueNblistData::initialize(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::scoring::elec::is_base_2(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::is_non_peptide_heavy_atom(), core::scoring::elec::is_phosphate_2(), core::scoring::is_polymer_heavyatom(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::scoring::elec::is_sugar_2(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), 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
std::string const& core::conformation::Residue::atom_name ( Size const  atm) const
inline

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

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

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::util::add_constraints_to_metal(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::loops::add_single_cutpoint_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::conformation::Conformation::append_residue_by_bond(), protocols::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::ligand_docking::AddHydrogen::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), protocols::hydrate::atom_is_hydratable(), core::scoring::FACTSPotential::atompair_scale(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::constraints::combine_NMR_atom_string(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::pose::declare_cutpoint_chemical_bond(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::environment::dof_id_to_string(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), 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(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::magnesium::MgEnergy::eval_residue_pair(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::contact_map::ContactMap::fill_contacts(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_helper(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::select::get_pymol_selection_for_atoms(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::conformation::idealize_hydrogens(), core::conformation::improper_build(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::forge::methods::make_star_foldtree(), core::conformation::missing_stubs_build(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), place(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), core::conformation::print_atom(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::viewer::print_node(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::SASAShouldItCount(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), core::conformation::setup_corresponding_atoms(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), core::scoring::ShouldItCount(), show(), core::scoring::hbonds::HBond::show(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and core::scoring::VdWShouldItCount().

AtomType const& core::conformation::Residue::atom_type ( Size 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

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

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::hbnet::UnsatSelector::apply(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::elec::atom_is_aro(), core::scoring::elec::atom_is_aro2(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), core::scoring::automorphic_rmsd(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_single_edge_waters(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), core::chemical::sdf::MolWriter::compose_atoms(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::APBSWrapper::count_atoms(), core::scoring::hbonds::create_acc_orientation_vector(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::pose_metric_calculators::fast_clash_check(), protocols::forge::remodel::fast_clash_check(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_for_complex(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::ligand_docking::frac_atoms_within(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::magnesium::get_cos_theta(), core::scoring::hbonds::get_hb_acc_chem_type(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::select::get_pymol_selection_for_atoms(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::chemical::rna::get_rna_base_centroid(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::sic_dock::SICFast::init(), core::scoring::GenBornResidueInfo::initialize(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_site_row(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::protein_interface_design::make_hotspot_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), protocols::motifs::Motif::Motif(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::viewer::print_node(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::WaterAdductIntraEnergy::residue_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), core::conformation::setup_links(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

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

References atoms_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::chemical::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), 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::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), and protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection().

chemical::AtomTypeSet const& core::conformation::Residue::atom_type_set ( ) const
inline
Real core::conformation::Residue::atomic_charge ( Size 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

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

Referenced by protocols::qsar::scoring_grid::ChargeGrid::atom_score(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::elec::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::hbnet::HBNet::find_unsats(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::GenBornPotential::get_res_res_elecE(), core::chemical::rna::get_rna_base_centroid(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::elec::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::qsar::scoring_grid::ChargeGrid::score(), core::scoring::elec::RNA_FA_ElecEnergy::score_atom_pair(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().

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

References atoms_.

AtomIndices const& core::conformation::Residue::atoms_with_orb_index ( ) const
inline
Size core::conformation::Residue::attached_H_begin ( Size const  atom) const
inline
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

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

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

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

chemical::AA const& core::conformation::Residue::backbone_aa ( ) const
inline
AtomIndices const& core::conformation::Residue::bonded_neighbor ( Size const  atm) const
inline

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

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

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::chemical::sdf::MolWriter::compose_bonds(), protocols::cartesian::MolecularDynamics::createBondList(), fill_missing_atoms(), get_adjacent_heavy_atoms(), get_atoms_exocyclic_to_ring_atom(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), n_bonded_neighbor_all_res(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::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< Size > const& core::conformation::Residue::bonded_orbitals ( Size const  atm) const
inline
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.

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

Referenced by protocols::splice::Splice::apply(), and core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs().

Vector core::conformation::Residue::build_orbital_xyz ( Size const  orbital_index) const
inline
core::chemical::carbohydrates::CarbohydrateInfoCOP core::conformation::Residue::carbohydrate_info ( ) const
core::Size core::conformation::Residue::chain ( ) const
inline

Returns this residue's chain id.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References chain_.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), core::pose::Pose::chain(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::matdes::dup_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), protocols::minimization_packing::ChainGroupDiscriminator::group_id(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::forge::build::ConnectRight::modify_impl(), orient_onto_residue_peptoid(), core::pose::PDBInfo::PDBInfo(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), core::scoring::PQR::PQR(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::antibody::AntibodyFeatures::report_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::rna::RNA_BulgeEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::PoissonBoltzmannEnergy::residue_in_chains(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::methods::MotifDockEnergy::residue_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::conformation::Conformation::sequence_matches(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::docking::DockingHighResLegacy::setup_packing(), core::conformation::Conformation::update_polymeric_connection(), and core::io::serialization::write_binary().

void core::conformation::Residue::chain ( core::Size const  setting)
inline

Sets this residue's chain id.

Don't call directly – In almost all situations, this should be set by the owning Conformation

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References chain_.

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

References chi_.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pose::Pose::chi(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::legacy_sewing::create_model_from_pose(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::dna::DNABase::DNABase(), protocols::metal_interface::dump_chis(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), protocols::indexed_structure_store::extract_residue_entry(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::chemical::rna::get_residue_base_state(), core::pack::get_residue_current_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::get_rotamer_angle_diffs(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), is_similar_rotamer(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::splice::printChi(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::pack::dunbrack::rotamer_from_chi(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), 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)

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

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

References chi_.

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

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

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>

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

Referenced by core::pack::rotamer_set::build_rotamers_from_rotamer_bins().

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

References Residue().

Referenced by core::pack::rotamer_set::RotamerSubset::add_rotamer(), core::pack::rotamer_set::RotamerSet_::add_rotamer(), core::pack::rotamer_set::RotamerSubset::add_rotamer_into_existing_group(), core::pack::rotamer_set::RotamerSet_::add_rotamer_into_existing_group(), core::pose::add_variant_type_to_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::motifs::MotifHit::build_rotamer(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::seeded_abinitio::combine_two_poses(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), create_residue(), create_rotamer(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::io::pdb::dump_pdb_residue(), protocols::matdes::dup_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::splice::RotLibOut::find_matching_res(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::ligand_docking::get_ligand_torsion_constraints(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::magnesium::MgHydrater::hydrate_magnesium(), core::conformation::Conformation::insert_conformation_by_jump(), core::conformation::Conformation::insert_residue_by_bond(), protocols::motifs::BuildPosition::keep_rotamer(), protocols::stepwise::modeler::merge_two_poses(), protocols::hbnet::HBNet::minimize_network(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), core::pose::remove_variant_type_from_residue(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), protocols::denovo_design::components::Segment::set_template_pose(), core::pack::setup_bgres_cops(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::stepwise::modeler::slice(), protocols::motifs::MotifHit::target_conformer(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and protocols::vip::VIP_Mover::try_point_mutants().

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

Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.

Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues. The passed ResidueTypeSet is the ResidueTypeSet you want the mirrored type to come from.

Note
This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart. It assumes that you've already mirrored all of the coordinates, and just allows you to generate a replacement residue of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms, variant types, etc.).
Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueTypeSet::get_mirrored_type(), Residue(), and rsd_type_ptr_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner().

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):

See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Residue.upper_connect_atom Pose

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

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

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

Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::conformation::form_disulfide(), core::io::pose_from_sfr::is_connected(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), and protocols::viewer::print_interres_bond().

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

References connect_map_.

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::chemical::ICoorAtomID::atom_id(), 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::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::get_disulf_partner(), core::conformation::is_disulfide_bond(), core::pose::Pose::real_to_virtual(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::methods::LK_hack::residue_pair_energy(), core::conformation::Conformation::show_residue_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), and core::pose::Pose::virtual_to_real().

core::Size core::conformation::Residue::connect_map_size ( ) const
inline
Size core::conformation::Residue::connected_residue_at_lower ( ) const
Size core::conformation::Residue::connected_residue_at_resconn ( Size const  resconn_index) const
inline

Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.

For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6. Exactly the same as residue_connection_partner

References connect_map_.

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), connected_residue_at_lower(), connected_residue_at_upper(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::forge::methods::fold_tree_from_pose(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), core::conformation::get_second_atom_from_connection(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_current_residue_connections(), core::pose::Pose::real_to_virtual(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().

Size core::conformation::Residue::connected_residue_at_upper ( ) const
Distance core::conformation::Residue::connection_distance ( conformation::Conformation const &  conf,
Size const  resconn_index,
Vector const &  matchpoint 
) const
bool core::conformation::Residue::connection_incomplete ( Size  resconnid) const
bool core::conformation::Residue::connections_match ( Residue const &  other) const

Returns true if ???

References connect_map_, and pseudobonds_.

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

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.

References seqpos().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::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(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::conformation::get_chemical_root_and_anchor_atomnos(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

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.

References connections_to_residues_.

void core::conformation::Residue::copy_residue_connections ( Residue const &  src_rsd)
void core::conformation::Residue::copy_residue_connections_from ( Residue const &  src)
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.

References clone().

ResidueOP core::conformation::Residue::create_rotamer ( ) const
inline
AtomIndices const& core::conformation::Residue::cut_bond_neighbor ( Size const  atm) const
inline

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

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

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

basic::datacache::BasicDataCache const& core::conformation::Residue::data ( ) const
inline
basic::datacache::BasicDataCacheCOP core::conformation::Residue::data_ptr ( ) const
void core::conformation::Residue::determine_nonstandard_polymer_status ( )
private
bool core::conformation::Residue::fill_missing_atoms ( utility::vector1< bool > &  missing,
Conformation const &  conformation,
bool  fail = true 
)

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

If fail is false, will return true if we can fill all the missing atoms, and false if we can't.

missing is passed by non-const ref: it will be updated for the atoms which are filled. (If fail is false, it will end up all false, or you'll get a utility_exit()

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

References atom_index(), atom_name(), bonded_neighbor(), core::chemical::AtomICoor::build(), icoor(), core::conformation::improper_build(), core::chemical::ICoorAtomID::INTERNAL, core::conformation::missing_stubs_build(), name(), natoms(), core::chemical::pretty_print_atomicoor(), seqpos(), seqpos_, set_xyz(), core::chemical::ResidueType::show_all_atom_names(), core::chemical::AtomICoor::stub_atom(), core::conformation::TR(), and type().

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

uint core::conformation::Residue::first_adjacent_heavy_atom ( uint const  atom_index) const

Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.

Returns
The atom index of the 1st heavy atom next to the given atom (by index) or 0 if no heavy atom is found

This method does not count virtual atoms as heavy atoms.

Remarks
This method is crucial for determining atoms defining non-standard torsion angles, such as those found across branch connections or in glycosidic linkages.
Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References get_adjacent_heavy_atoms(), and core::conformation::TR().

Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), and core::conformation::Conformation::branch_connection_torsion_angle_atoms().

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

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

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::elec::assign_rna_atom_type(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pose::rna::bases_form_a_hydrogen_bond(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::relax::derive_sc_sc_restraints(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), core::pose::rna::figure_out_number_base_contacts(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::cryst::fix_bfactorsMissing(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::hackaro::HackAroEnergy::get_centroid(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::scoring::elec::is_sugar_2(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::pack::scmin::CartSCMinMinimizerMap::setup(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), sidechainAtoms_begin(), protocols::hybridization::DDomainParse::split(), protocols::stepwise::modeler::rna::suite_square_deviation(), and protocols::dna::z_axis_dist().

Size core::conformation::Residue::first_sidechain_hydrogen ( ) const
inline
utility::vector1< uint > core::conformation::Residue::get_adjacent_heavy_atoms ( uint const  atom_index) const

Get a list of heavy atoms connected to a given atom.

Returns
The atom indices of all heavy atoms bonded to the given atom (by index)

This method does not count virtual atoms as heavy atoms.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), bonded_neighbor(), and is_virtual().

Referenced by first_adjacent_heavy_atom(), core::conformation::position_of_atom_on_ring(), and show().

core::chemical::AtomIndices core::conformation::Residue::get_atoms_exocyclic_to_ring_atom ( uint const  atom_index) const

Get a list of exocyclic atoms connected to a given ring atom.

Returns
The atom indices of all atoms bonded to the given atom (by index) that are not a part of the ring.

This method does not count virtual atoms as atoms.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References bonded_neighbor(), is_virtual(), and type().

Referenced by get_hydrogens_bonded_to_ring_atom(), and get_substituents_to_ring_atom().

core::chemical::AtomIndices core::conformation::Residue::get_hydrogens_bonded_to_ring_atom ( uint const  atom_index) const

Get a list of hydrogen atoms connected to a given ring atom.

Returns
The atom indices of hydrogens bonded to the given ring atom (by index).

This method does not count virtual atoms as atoms.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().

void core::conformation::Residue::get_metal_binding_atoms ( AtomIndices metal_binding_indices) const
inline

Gets the AtomIndices of the atoms in this residue that can bind to metals.

Note
: AtomIndices == vector1< Size >
Author
: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Referenced by core::util::find_metalbinding_atoms_helper().

PseudoBondCollectionCOP core::conformation::Residue::get_pseudobonds_to_residue ( Size  resid) const
ResidueCOP core::conformation::Residue::get_self_ptr ( ) const
inline

self pointers

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::scoring::aa_repeat_energy::AARepeatEnergy::finalize_total_energy(), core::scoring::aa_composition_energy::AACompositionEnergy::finalize_total_energy(), core::scoring::netcharge_energy::NetChargeEnergy::finalize_total_energy(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::finalize_total_energy(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::carbohydrates::get_glycosidic_bond_residues(), protocols::ligand_docking::get_ligand_grid_scores(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), and protocols::ligand_docking::Transform::setup_conformers().

ResidueOP core::conformation::Residue::get_self_ptr ( )
inline
ResidueCAP core::conformation::Residue::get_self_weak_ptr ( ) const
inline
ResidueAP core::conformation::Residue::get_self_weak_ptr ( )
inline
core::chemical::AtomIndices core::conformation::Residue::get_substituents_to_ring_atom ( uint const  atom_index) const

Get a list of substituent atoms connected to a given ring atom.

Returns
The atom indices of all heavy atoms bonded to the given atom (by index) that are not a part of the ring.

This method does not count virtual atoms as atoms.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().

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

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

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

Referenced by core::pose::motif::a(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), core::pose::Pose::append_residue_by_atoms(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::scoring::FACTSPotential::atompair_scale(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::mpi_refinement::CA_Sscore(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), 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::select::util::cbeta_vector(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::sic_dock::count_CBs(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pose::declare_cutpoint_chemical_bond(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), protocols::constraint_generator::existing_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::abinitio::abscript::find_disulfide_partner(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::helical_bundle::FitSimpleHelixMultiFunc::FitSimpleHelixMultiFunc(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::sic_dock::get_CB_Vecs_from_pose(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_beta_aminoacid(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::denovo_design::rebuild_missing_atoms(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::sic_dock::XfoxmScore::score(), core::select::util::select_coord_for_residue(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::ligand_docking::set_repulsive_bb_cores(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

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

Returns true is <atomno> has complete connectivity?

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

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

bool core::conformation::Residue::has_lower_connect ( ) const
inline

Returns true if residue has a valid lower connection.

example(s): residue.has_lower_connect()

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

Referenced by core::conformation::Conformation::append_residue(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), connected_residue_at_lower(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), 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_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::pose::set_reasonable_fold_tree(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().

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

Returns true if the residue has side chain orbitals.

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

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

bool core::conformation::Residue::has_shadow_atoms ( ) const
inline
bool core::conformation::Residue::has_upper_connect ( ) const
inline

Returns true if residue has a valid upper connection.

example(s): residue.has_upper_connect()

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

Referenced by core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), connected_residue_at_upper(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), 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_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pose::set_reasonable_fold_tree(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().

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

Generic variant access.

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

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::forge::methods::add_cutpoint_variants(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), core::pose::ncbb::add_oop_constraint(), core::pose::ncbb::add_triazole_constraint(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::fold_from_loops::selectors::CutpointResidueSelector::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::splice::Splice::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), protocols::stepwise::screener::SugarInstantiator::check_moving_sugar(), core::scoring::rna::check_rna_loop(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), protocols::denovo_design::components::compute_cutpoints(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::abinitio::copy_side_chains(), core::pose::correctly_add_2prime_connection_variants(), protocols::relax::cyclize_pose(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::rna::StackElecEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::rna::RNA_TorsionEnergy::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::rna::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::rna::TNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::splice::RBOutMover::find_disulfide_postions(), protocols::splice::SpliceOutAntibody::find_disulfide_postions(), protocols::splice::RBInMover::find_disulfide_postions(), protocols::splice::SpliceInAntibody::find_disulfide_postions(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::splice::find_disulfs_in_range(), protocols::rosetta_scripts::find_nearest_disulfide(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_uninstantiated_phosphates(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::splice::Splice::fold_tree(), core::conformation::form_disulfide(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree(), core::pose::rna::get_stub_stub(), core::scoring::SecondaryStructurePotential::identify_ss(), core::pose::ncbb::initialize_hbs(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base(), core::pose::ncbb::initialize_ncbbs(), core::pose::ncbb::initialize_oops(), protocols::recces::sampler::initialize_thermal_sampler(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close(), core::scoring::methods::is_lower_cutpoint(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), core::scoring::rna::RNA_BulgeEnergy::is_RNA_bulge(), protocols::stepwise::modeler::rna::sugar::is_sugar_virtual(), core::scoring::methods::is_upper_cutpoint(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous(), protocols::antibody::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), orient_onto_residue_peptoid(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), protocols::scoring::methods::SpecialRotamerEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::FreeDOF_Energy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::rna::RNA_SuiteEnergy::residue_pair_energy(), core::scoring::rna::TNA_SuiteEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::rna::RNA_JR_SuiteEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionEnergy::residue_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::StackElecEnergy::residue_pair_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::rbsegment_relax::setup_disconnected(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::conformation::setup_links(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), protocols::splice::Splice::tail_fold_tree(), core::conformation::Conformation::update_polymeric_connection(), core::conformation::Conformation::update_residue_torsions(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition(), and core::pose::rna::virtualize_free_rna_moieties().

bool core::conformation::Residue::heavyatom_has_polar_hydrogens ( Size  ind) const
inline
bool core::conformation::Residue::heavyatom_is_an_acceptor ( Size  ind) const
inline
Atoms::const_iterator core::conformation::Residue::heavyAtoms_end ( ) const
inline
AtomIndices const& core::conformation::Residue::Hpol_index ( ) const
inline
AtomIndices const& core::conformation::Residue::Hpos_apolar ( ) const
inline
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

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

Referenced by core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_donor_h(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_donor_h(), core::pose::rna::atom_is_polar(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::pose::rna::heavy_atom_is_polar(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), and protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition().

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

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

Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().

chemical::AtomICoor const& core::conformation::Residue::icoor ( Size const  atm) const
inline
void core::conformation::Residue::init_residue_from_other ( Residue const &  src)
private

Function called by both copy constructors, to avoid code duplication.

As private member variables are added, add them to this to copy them.

Author
Vikram K. Mulligan.

References actcoord_, atoms_, chain_, chi_, connect_map_, connections_to_residues_, data_cache_, mainchain_torsions_, mirrored_relative_to_type_, nonstandard_polymer_, nus_, orbitals_, pseudobonds_, and seqpos_.

Referenced by Residue().

id::AtomID core::conformation::Residue::inter_residue_connection_partner ( int  connid,
Conformation const &  conformation 
) const
bool core::conformation::Residue::is_apolar ( ) const
inline

true if the residue is apolar

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

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

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

References connections_to_residues_, and seqpos().

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::simple_filters::AveragePathLengthFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), protocols::simple_filters::DisulfideEntropyFilter::compute(), protocols::simple_filters::DisulfideEntropyFilter::compute_residual(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::toolbox::CovalentResidueNetwork::generate_edges(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::scoring::methods::LK_PolarNonPolarEnergy::get_count_pair_function(), core::scoring::rna::StackElecEnergy::get_count_pair_function(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(), core::scoring::elec::FA_GrpElecEnergy::get_count_pair_function(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::generalized_kinematic_closure::GeneralizedKIC::has_geometric_connection(), core::scoring::trie::initialize_cpdata_for_atom(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pose::set_reasonable_fold_tree(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

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.

References connections_to_residues_.

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

Returns true if this residue is a carbohydrate.

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

Referenced by protocols::loops::add_single_cutpoint_variant(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::select::residue_selector::GlycanResidueSelector::apply(), core::select::residue_selector::RandomGlycanFoliageSelector::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::electron_density::calculate_rama(), core::pose::carbohydrates::create_glycan_movemap_from_residue_selector(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::io::carbohydrates::dump_gws(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::scoring::methods::LinearBranchEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::loops::fold_tree_from_loops(), core::pose::get_bb_torsion(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::carbohydrates::get_distance_to_start(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_glycan_start_points(), core::conformation::carbohydrates::get_glycosidic_TorsionIDs(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::pose::carbohydrates::get_resnums_in_leaf(), core::pose::carbohydrates::get_resnums_in_leaf_on_the_fly(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), protocols::carbohydrates::GlycanTreeSampler::init_objects(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::is_protein_CA_or_equiv(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), protocols::denovo_design::components::residue_is_compatible(), core::pose::set_bb_torsion(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::carbohydrates::GlycanTreeSampler::setup_movers(), and core::conformation::carbohydrates::GlycanNode::update_connectivity_data().

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

Returns true if the residue is charged.

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

bool core::conformation::Residue::is_coarse ( ) const
inline
bool core::conformation::Residue::is_d_rna ( ) const
inline
bool core::conformation::Residue::is_DNA ( ) const
inline

Returns true if this residue is a DNA residue.

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

Referenced by core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::motifs::Motif::apply_check(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::dna::DNAParameters::calculate(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_interres(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intrares(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::DNA_DihedralEnergy::defines_score_for_residue(), core::scoring::elec::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::dna::DNABase::DNABase(), protocols::dna::DNABasepair::DNABasepair(), protocols::dna::DNABasestep::DNABasestep(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNAChiEnergy::eval_dof_derivative(), core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy_ext(), core::scoring::methods::SASAEnergy::eval_intrares_energy_ext(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy_ext(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::dna::get_z_axis(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::relax::make_dna_rigid(), protocols::motifs::Motif::Motif(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::fold_from_loops::NubInitioMover::post_process(), core::scoring::dna::DNAChiEnergy::residue_energy(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), core::scoring::methods::FACTSEnergy::residue_pair_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy(), core::scoring::methods::SASAEnergy::residue_pair_energy(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy(), core::scoring::methods::SASAEnergy::residue_pair_energy_ext(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy_ext(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy_ext(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::conformation::setup_corresponding_atoms(), and core::scoring::dna::DNA_DihedralPotential::skip_torsion().

bool core::conformation::Residue::is_l_rna ( ) const
inline

Returns true if this residue is a L-RNA residue.

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

Referenced by core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().

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

Returns true if this residue is a ligand.

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

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::conformation::Conformation::append_residue(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), protocols::scoring::Interface::calculate(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::hbnet::HBNet::get_native_networks(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::sic_dock::make_Cx(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::motifs::Motif::Motif(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNet::rec_trav_native(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::features::ResidueConformationFeatures::report_features(), protocols::denovo_design::components::residue_is_compatible(), protocols::ligand_docking::restrict_to_protein_residues(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::denovo_design::components::SegmentCounts::SegmentCounts(), protocols::scoring::Interface::set_pack(), protocols::hbnet::HBNet::traverse_native(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

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

Returns true if the residue has a lower terminus variant.

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

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::loops::add_single_cutpoint_variant(), protocols::denovo_design::components::add_to_pose(), protocols::frags::add_vall_cheating_fragments(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue(), core::pose::append_subpose_to_pose(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::chemical::ICoorAtomID::atom_id(), protocols::idealize::basic_idealize(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), connect_atom(), protocols::topology_broker::copy_internal_coords(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms(), protocols::forge::methods::count_cutpoints(), protocols::relax::cyclize_pose(), determine_nonstandard_polymer_status(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), 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_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_don_chem_type(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), protocols::forge::methods::grow_left_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::conformation::Conformation::insert_polymer_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::pose::is_lower_terminus(), core::scoring::Ramachandran::is_normally_connected(), protocols::loops::Loop::is_terminal(), protocols::denovo_design::loop_stop_without_overlap(), protocols::sic_dock::make_Cx(), 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::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::denovo_design::components::pose_matches_description(), protocols::denovo_design::components::prepend_new_residues(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), core::scoring::dna::DNA_DihedralPotential::skip_torsion(), protocols::fldsgn::CircularPermutation::split_chains(), and core::conformation::Conformation::update_polymeric_connection().

bool core::conformation::Residue::is_metal ( ) const
inline

Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Referenced by core::util::add_covalent_linkages_to_metal(), core::util::auto_setup_all_metal_bonds(), core::util::auto_setup_all_metal_constraints(), protocols::simple_moves::SetupMetalsMover::find_metal_resnums(), and core::util::find_metalbinding_atoms().

bool core::conformation::Residue::is_metalbinding ( ) const
inline

Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), and core::util::find_metalbinding_atoms_helper().

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