Rosetta 3.4
Public Types | Public Member Functions
core::conformation::Residue Class Reference

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

#include <Residue.hh>

Inheritance diagram for core::conformation::Residue:
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List of all members.

Public Types

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

Public Member Functions

 Residue (ResidueType const &rsd_type_in, bool const dummy_arg)
 constructors Residue( Residue const & ); // user defined copy ctor to avoid #including PseudoBond.hh Residue const & operator = ( Residue const & ) // user defined assignment operator for same reason
 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.
 Residue (Residue const &src)
 ~Residue ()
ResidueOP clone () const
 Copy this residue( allocate actual memory for it )
AtomType const & atom_type (int const atomno) const
 Returns the AtomType of this residue's atom with index number <atomno>
chemical::AtomTypeSet const & atom_type_set () const
 Returns the AtomTypeSet of this residue.
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.
Real atomic_charge (int const atomno) const
 Returns the atom charge of this residue's atom with index number <atomno>
bool is_virtual (Size const &atomno) const
 Check if atom is virtual.
bool is_virtual_residue () const
 Check if residue is virtual.
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.
Size natoms () const
 Returns the number of atoms in this residue.
Size n_hbond_acceptors () const
 number of hbond_donors
Size n_hbond_donors () const
 number of hbond_donors
Size nheavyatoms () const
 Returns the number of heavyatoms in this residue.
AtomIndices const & Hpos_polar () const
 Returns the AtomIndices of this residue's polar hydrogens.
AtomIndices const & all_bb_atoms () const
 Returns the AtomIndices of this residue's backbone atoms.
AtomIndices const & Haro_index () const
 Returns the AtomIndices of this residue's aromatic hydrogens.
AtomIndices const & Hpol_index () const
 Returns the AtomIndices of this residue's polar hydrogens.
AtomIndices const & Hpos_apolar () const
 Returns the AtomIndices of this residue's apolar hydrogens.
AtomIndices const & Hpos_polar_sc () const
 Returns the AtomIndices of this residue's polar sidechain hydrogens.
AtomIndices const & accpt_pos () const
 Returns the AtomIndices of this residue's h-bond acceptor atoms.
AtomIndices const & accpt_pos_sc () const
 Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms.
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)
bool heavyatom_is_an_acceptor (Size ind) const
 Is a particular atom a heavy atom acceptor?
bool atom_is_polar_hydrogen (Size ind) const
 Is a particular atom a polar hydrogen?
Atoms const & atoms () const
 Returns this residue's Atoms (const), a vector1 of Atom objects.
Atomsatoms ()
 Returns this residue's Atoms (non-const), a vector1 of Atom objects.
Atoms::iterator atom_begin ()
 begin interator, to iterate over atoms
Atoms::iterator atom_end ()
 end interator, to iterate over atoms
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?
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)
Atomatom (Size const atm_index)
 Returns this residue's Atom with index number <atm_index> (non-const)
Atom const & atom (std::string const &atm_name) const
 Returns this residue's Atom with name <atm_name> (const)
Atomatom (std::string const &atm_name)
 Returns this residue's Atom with name <atm_name> (non-const)
Vector const & xyz (Size const atm_index) const
 Returns the position of this residue's atom with index number <atm_index>
Vector const & xyz (std::string const &atm_name) const
 Returns the position of this residue's atom with name <atm_name>
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>
void set_xyz (std::string const &atm_name, Vector const &xyz_in)
 Sets the position of this residue's atom with name <atm_name>
Size last_backbone_atom () const
 Returns the index number of the last backbone heavyatom.
Size first_sidechain_atom () const
 Returns the index number of the first sidechain heavyatom.
Size first_sidechain_hydrogen () const
 Returns the index number of the first sidechain hydrogen.
Size attached_H_begin (int const atom) const
 Returns the index number of the first hydrogen attached to the atom with index number <atom>
Size attached_H_end (int const atom) const
 Returns the index number of the last hydrogen attached to the atom with index number <atom>
AtomIndices const & attached_H_begin () const
 Returns the AtomIndices of the first hydrogen attached to each heavyatom.
AtomIndices const & attached_H_end () const
 Returns the AtomIndices of the last hydrogen attached to each heavyatom.
Size lower_connect_atom () const
 Returns the index number of this residue's atom which connects to the residue before it in sequence.
Size upper_connect_atom () const
 Returns the index number of this residue's atom which connects to the residue after it in sequence.
Size connect_atom (Residue const &other) const
 Returns the index number of this residue's atom connected to the <other> Residue.
utility::vector1< int > const & path_distance (int atom) const
 Returns the shortest path distance from <atom> to any other atom in this residue.
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].
int path_distance (int at1, int at2) const
 Returns the number of bonds separating atom <at1> from <at2>
bool atom_is_backbone (int const atomno) const
 Returns true if this residue's atom with index number <atomno> is a backbone atom.
bool atom_is_hydrogen (Size const atomno) const
 Returns true if this residue's atom with index number <atomno> is a hydrogen.
Size atom_base (int const atomno) const
 Returns the atom index of the <atomno> atom's base atom.
Size abase2 (int const atomno) const
 Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor)
AtomIndices const & bonded_neighbor (int const atm) const
 Returns the AtomIndices for all bonded neighbor atoms of <atm>
Size nchi () const
 Returns the number of chi angles this residue has.
AtomIndices const & mainchain_atoms () const
 Returns the AtomIndices of this residue's mainchain atoms.
Size mainchain_atom (Size const atm) const
 ??? Returns the number of the residue's mainchain atoms
Size n_mainchain_atoms () const
 Returns the number of the residue's mainchain atoms.
AtomIndices const & actcoord_atoms () const
 Returns the AtomIndices of atoms that will be used to define this residue's actcoord.
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.
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.
Real nbr_radius () const
 Returns the distance cutoff value used as a radius for neighbor definition.
Vector const & nbr_atom_xyz () const
AtomIndices const & atoms_with_orb_index () const
Vector const 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.
utility::vector1< core::Size >
const 
bonded_orbitals (int const atm) const
std::string const & orbital_name (int const orbital_index) const
chemical::orbitals::OrbitalType
const & 
orbital_type (int const orbital_index) const
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.
ResidueOP create_residue () const
 Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out.
ResidueType const & type () const
 Returns this residue's ResidueType.
chemical::ResidueTypeSet const & residue_type_set () const
 Returns this residue's ResidueTypeSet.
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.
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.
bool connections_match (Residue const &other) const
 Returns true if ???
Size n_residue_connections () const
 Returns the number of ResidueConnections on this residue including polymeric residue connections.
Size n_polymeric_residue_connections () const
 Returns the number of polymeric ResidueConnections on this residue.
Size n_non_polymeric_residue_connections () const
 Returns the number of non-polymeric ResidueConnections on this residue.
chemical::ResidueConnection const & residue_connection (int const resconn_index) const
 Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue.
Size residue_connect_atom_index (Size const resconn_id) const
Size connected_residue_at_resconn (Size const resconn_index) const
chemical::ResConnID connect_map (Size resconn_index) const
void clear_residue_connections ()
void copy_residue_connections_from (Residue const &src)
bool has_incomplete_connection () const
bool has_incomplete_connection (core::Size const atomno) const
 Returns true is <atomno> has complete connectivity?
bool connection_incomplete (Size resconnid) const
chemical::ResConnID actual_residue_connection (Size resconnid) const
Size residue_connection_partner (Size const resconn_index) const
 Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ?
void copy_residue_connections (Residue const &src_rsd)
 attempt to take residue connection info from src_rsd
Size residue_connection_conn_id (Size const resconn_index) const
 Returns the residue number of a residue connected to this residue with ResidueConnection <resconn_index> ?
void residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid)
 set a connection to this residue by adding its parnter's residue number
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.
bool is_bonded (Residue const &other) const
 Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)
bool is_pseudo_bonded (Residue const &other) const
 Do I have any pseudobonds to other?
bool is_bonded (Size const other_index) const
 Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic.
bool is_pseudo_bonded (Size const other_index) const
 Do I have any pseudobonds to other?
bool is_polymer_bonded (Residue const &other) const
 Am I polymer bonded to other?
bool is_polymer_bonded (Size const other_index) const
 Am I polymer-bonded to other? checks lower and upper connections.
utility::vector1< Size > const & connections_to_residue (Residue const &other) const
 Returns the vector1 of resconn ids that connect this residue to other.
utility::vector1< Size > const & connections_to_residue (Size const other_resid) const
 Returns the vector1 of resconn ids that connect this residue to other.
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>
AtomIndices const & cut_bond_neighbor (int const atm) const
 atom indices for bonded neighbors to which atom-tree connections are disallowed.
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?
AtomIndices const & nbrs (int const atm) const
 Convenience synonym for bonded_neighbor.
utility::vector1< Real > const & mainchain_torsions () const
 Returns the mainchain torsion angles of this residue (const)
utility::vector1< Real > & mainchain_torsions ()
 Returns the mainchain torsion angles of this residue (non-const)
void mainchain_torsions (utility::vector1< Real > const &torsions)
 Sets the mainchain torsion angles of this residue to <torsions>
utility::vector1< Real > const & chi () const
 Returns the chi torsion angles of this residue (const)
utility::vector1< Real > & chi ()
 Returns the chi torsion angles of this residue (non-const)
void chi (utility::vector1< Real > const &chis)
 Sets the chi torsion angles of this residue.
utility::vector1< AtomIndices >
const & 
chi_atoms () const
 Returns the AtomIndices of each four atom set defining a chi angle.
AtomIndices const & chi_atoms (int const chino) const
 Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle.
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.
Real chi (Size const chino) const
 get a specific chi torsion angle
Size seqpos () const
 Returns the sequence position of this residue.
Size polymeric_sequence_distance (Residue const &other) const
 Returns the sequence separation distance between this residue and <other>
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.
void seqpos (Size const setting)
 Sets this residue's sequence position to <setting>
core::Size chain () const
 Returns this residue's chain id.
void chain (int const setting)
 Sets this residue's chain id.
bool requires_actcoord () const
 does this residue require an actcoord?
void update_actcoord ()
 Updates actcoord for this residue.
Vector const & actcoord () const
 Returns the coordinates used for pairE calculations (amino acids only)
Vectoractcoord ()
 Returns the coordinates used for pairE calculations (amino acids only)
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.
bool is_polymer () const
 Returns true if this residue is a polymer.
bool is_protein () const
 Returns true if this residue is an amino acid.
bool is_DNA () const
 Returns true if this residue is a DNA residue.
bool is_RNA () const
 Returns true if this residue is a RNA residue.
bool is_NA () const
 Returns true if this residue is a nucleic acid.
bool is_ligand () const
 Returns true if this residue is a ligand.
bool is_surface () const
 Returns true if this residue is a surface residue.
bool has_sc_orbitals () const
 Returns true if the residue has side chain orbitals.
bool is_polar () const
 Returns true if the residue is polar.
bool is_apolar () const
bool is_charged () const
 Returns true if the residue is charged.
bool is_aromatic () const
 Returns true if the residue is aromatic.
bool is_coarse () const
 residue is coarse (used for RNA right now)
bool is_terminus () const
 Returns true if the residue has a terminus variant.
bool is_upper_terminus () const
 Return true if the residue has an upper terminus variant.
bool is_lower_terminus () const
 Returns true if the residue has a lower terminus variant.
bool is_similar_rotamer (Residue const &other) const
 Returns true if the chi angles of another residue all fall within 5 deg.
bool is_similar_aa (Residue const &other) const
 Returns true if the aa residue types are the same.
bool has_property (std::string const &property) const
 Returns true if the residue has <property> Generic property access -- SLOW!!!!!
bool has_variant_type (chemical::VariantType const &variant_type) const
 Generic variant access -- SLOW!!!!!
std::string const & atom_name (int const atm) const
 Returns the name of this residue's atom with index number <atm>
std::string const & mm_atom_name (int const atom) const
 Returns the mm_atom_name of this residue's atom with index number <atom>
std::string const & name () const
 Returns this residue's ResidueType name.
std::string const & name3 () const
 Returns this residue's 3-letter representation.
char name1 () const
 Returns this residue's 1-letter representation.
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.
chemical::AtomICoor const & icoor (int const atm) const
 Returns the internal coordinates of this residue's atom with index number <atm>
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.
void set_all_chi (utility::vector1< Real > const &chis)
 Sets all of this residue's chi angles using the set_chi function (wrapper function)
bool has (std::string const &atm) const
 Returns true if this residue has an atom named <atm>
void fill_missing_atoms (utility::vector1< bool > missing, Conformation const &conformation)
 Builds coordinates for atoms missing from this residue assuming ideal internal coordinates.
void select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
 Select three atoms for orienting.
void orient_onto_residue (Residue const &src)
 Orient our coords onto those of <src>, using the atoms from select_orient_atoms.
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 atoms specified in the input.
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.
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.
core::chemical::rna::RNA_ResidueType
const & 
RNA_type () const
 Return the RNA_residueType object. This is RNA specific.

Detailed Description

Instance Residue class, used for placed residues and rotamers.

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


Member Typedef Documentation


Constructor & Destructor Documentation

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

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

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

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

References core::chemical::ResidueType::atom_type_index(), core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), and core::chemical::ResidueType::xyz().

Referenced by clone().

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

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

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

References atom(), core::chemical::ResidueType::atom_type_index(), core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueType::chi_atoms(), chi_atoms(), copy_residue_connections(), core::chemical::ResidueType::mainchain_atoms(), mainchain_torsions(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), place(), type(), xyz(), and core::chemical::ResidueType::xyz().

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

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().

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::protein_interface_design::movers::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::swa::rna::Add_virtual_O2Star_hydrogen(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::Revert::apply(), protocols::idealize::IdealizeMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply(), core::pack::task::operation::OptCysHG::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frame(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), protocols::swa::rna::base_atoms_square_deviation(), protocols::idealize::basic_idealize(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::swa::rna::check_for_messed_up_structure(), protocols::loops::Loop::choose_cutpoint(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), protocols::swa::rna::copy_all_o2star_torsions(), protocols::swa::rna::create_alignment_id_map(), protocols::swa::rna::create_standard_o2star_pack_task(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::methods::ProClosureEnergy::defines_intrares_energy_for_residue(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::defines_residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_disulfides(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), 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::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::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::conformation::form_disulfide(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::rna::get_rna_base_coordinate_system(), protocols::rna::RNA_StructureParameters::get_stem_residues(), core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::scoring::dna::get_z_axis(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::comparative_modeling::hybridize::HybridizeProtocol::initialize_and_sample_loops(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::swa::rna::Is_close_chain_break(), core::io::serialization::is_pseudoresidue(), is_similar_aa(), is_similar_rotamer(), protocols::swa::rna::Is_virtual_base(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::make_symmetric_task(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), protocols::toolbox::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::motifs::mutate_loops_for_search(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::swa::rna::o2star_minimize(), core::conformation::WatsonCrickResidueMatcher::operator()(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), protocols::comparative_modeling::hybridize::ChunkTrialMover::pick_random_chunk(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::swa::rna::remove_all_variant_types(), protocols::swa::rna::Remove_virtual_O2Star_hydrogen(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::interface::DDPscore::residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::residue_pair_energy(), core::scoring::electron_density::PattersonCorrEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), 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::pack::dunbrack::rotamer_from_chi(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::scoring::constraints::BackboneStubConstraint::score(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::rna::setup_base_pair_constraints(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hackelec::HackElecEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::scoring::Interface::show(), core::fragment::SingleResidueFragData::steal(), protocols::swa::rna::suite_square_deviation(), core::scoring::MembranePotential::termini_penalty(), protocols::protein_interface_design::filters::RelativePoseFilter::thread_seq(), protocols::rna::update_edge_hbond_numbers(), protocols::rna::update_edge_hbond_numbers_careful_hydrogen(), and protocols::swa::rna::virtualize_energetically_unfavorable_nucleotides().

Size core::conformation::Residue::abase2 ( int const  atomno) const [inline]
AtomIndices const& core::conformation::Residue::accpt_pos ( ) const [inline]
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().

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

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

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().

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().

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().

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

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::io::pdb::FileData::append_residue(), protocols::simple_filters::SheetFilter::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frame(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::orbitals::OrbitalsAssigned::aromatic_ring_center(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), build_orbital_xyz(), 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::scoring::calc_atom_masks(), core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::pack::task::operation::util::cbeta_vector(), protocols::features::helixAssembly::HelixBundleFeatures::checkHelixContacts(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesTetrahedral(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), core::scoring::orbitals::OrbitalsAssigned::cp_function(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), core::io::pdb::dump_pdb_residue(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), 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::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::electron_density::findLoopFromDensity(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), protocols::comparative_modeling::hybridize::InsertChunkMover::get_superposition_transformation(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), 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::topology_broker::RigidChunkClaimer::initialize_dofs(), 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_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::simple_moves::BBConRotMover::make_move(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::motifs::Motif::Motif(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::conformation::operator<<(), orient_onto_residue(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), place(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::viewer::print_node(), protocols::pockets::PocketGrid::recenter(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), protocols::features::helixAssembly::HelixBundleFeatures::report_features(), protocols::features::OrbitalsFeatures::report_haro_orbital_interactions(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), Residue(), protocols::geometry::residue_center_of_mass(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H(), core::scoring::residue_fast_pair_energy_attached_H(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), protocols::geometry::return_nearest_residue(), core::conformation::symmetry::return_nearest_residue(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), protocols::pockets::PlaidFingerprint::rmsd(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::pack::task::operation::util::select_coord_for_residue(), set_chi(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair_one_way(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), core::scoring::electron_density::ElectronDensity::updateCachedDensity(), xyz(), and core::chemical::ICoorAtomID::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

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().

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().

Size core::conformation::Residue::atom_base ( int const  atomno) const [inline]

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

References core::chemical::ResidueType::atom_base().

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::hbonds::assign_abase_derivs(), protocols::rna::bases_form_a_hydrogen_bond(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::rna::heavy_atom_is_polar(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_row(), core::scoring::hackelec::is_base(), core::scoring::hackelec::is_phosphate(), core::scoring::hackelec::is_sugar(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), select_orient_atoms(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), 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]
Atoms::iterator core::conformation::Residue::atom_end ( ) [inline]

end interator, to iterate over atoms

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

Atoms::const_iterator core::conformation::Residue::atom_end ( ) const [inline]
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().

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::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_dist_constraints(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::loops::addScoresForLoopParts(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), atom(), protocols::motifs::backbone_stub_match(), core::conformation::build_residue_tree(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::flxbb::constraints_sheet(), copy_residue_connections(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::forge::methods::cyclize_pose(), core::conformation::Conformation::declare_chemical_bond(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::conformation::Conformation::fix_disulfides(), protocols::topology_broker::fix_mainchain_connect(), protocols::forge::methods::fixH(), core::conformation::form_disulfide(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), protocols::match::BfactorMPM::get_ca_bfactors(), core::io::silent::BinaryRNASilentStruct::get_debug_rmsd(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), protocols::simple_moves::BBConRotMover::get_L_move(), core::conformation::get_root_residue_root_atomno(), protocols::rna::get_sugar_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), 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::rna::is_rna_chainbreak(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::simple_moves::BBConRotMover::make_move(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), core::conformation::named_atom_id_to_atom_id(), orient_onto_residue(), place(), protocols::viewer::print_node(), protocols::match::output::print_node(), core::conformation::print_node(), core::scoring::constraints::AngleConstraint::read_def(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), select_orient_atoms(), protocols::rbsegment_relax::set_constraints(), protocols::rbsegment_relax::set_rb_constraints(), protocols::rna::setup_base_pair_constraints(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::setup_coarse_chainbreak_constraints(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::conformation::setup_links(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::docking::ConformerSwitchMover::switch_conformer(), and protocols::rna::update_edge_hbond_numbers_careful_hydrogen().

bool core::conformation::Residue::atom_is_backbone ( int const  atomno) const [inline]

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

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

References core::chemical::ResidueType::atom_is_backbone().

Referenced by core::scoring::hbonds::HBondSet::append_hbond(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::hackelec::HackElecEnergy::eval_residue_pair_derivatives(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), 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::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), 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]
bool core::conformation::Residue::atom_is_polar_hydrogen ( Size  ind) const [inline]

Is a particular atom a polar hydrogen?

References core::chemical::ResidueType::atom_is_polar_hydrogen().

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

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

References core::chemical::ResidueType::atom_name().

Referenced by core::scoring::sc::ShapeComplementarityCalculator::AddResidue(), core::io::pdb::FileData::append_residue(), core::conformation::Conformation::append_residue_by_bond(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::ligand_docking::AddHydrogen::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::orbitals::OrbitalsAssigned::aromatic_ring_center(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::scoring::rna::chi1_torsion_atom(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::constraints::combine_NMR_atom_string(), core::scoring::geometric_solvation::compute_exact_geosol(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pose::copy_dofs(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::io::pdb::dump_pdb_residue(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), fill_missing_atoms(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::rna::first_base_atom(), protocols::forge::methods::fold_tree_from_pose(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::conformation::idealize_hydrogens(), core::conformation::operator<<(), place(), core::conformation::print_atom(), protocols::swa::rna::Print_heavy_atoms(), protocols::viewer::print_node(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::hackelec::RNAHackElecEnergy::residue_pair_energy_RNA(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::import_pose::set_reasonable_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::hbonds::HBond::show(), protocols::swa::rna::suite_square_deviation(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), protocols::rna::update_edge_hbond_numbers(), and protocols::rna::update_edge_hbond_numbers_careful_hydrogen().

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

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

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

References core::chemical::ResidueType::atom_type().

Referenced by core::io::pdb::FileData::append_residue(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::hackelec::atom_is_aro(), core::scoring::hackelec::atom_is_aro2(), core::scoring::automorphic_rmsd(), protocols::swa::rna::base_atoms_square_deviation(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::calc_atom_masks(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::scoring::orbitals::OrbitalsScore::cation_pi_rules(), 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::orbitals::OrbitalsAssigned::cp_function(), core::scoring::hbonds::create_acc_orientation_vector(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::pdb::dump_pdb_residue(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), protocols::toolbox::pose_metric_calculators::fast_clash_check(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), core::conformation::Conformation::fill_missing_atoms(), protocols::ligand_docking::frac_atoms_within(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), 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::swa::rna::Is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::motifs::Motif::Motif(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), protocols::swa::rna::print_atom_info(), protocols::swa::rna::print_individual_atom_info(), protocols::viewer::print_node(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), core::scoring::methods::WaterAdductIntraEnergy::residue_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), core::conformation::setup_links(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::swa::rna::suite_square_deviation(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

Size core::conformation::Residue::atom_type_index ( Size const  atomno) const [inline]

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

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::methods::VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

chemical::AtomTypeSet const& core::conformation::Residue::atom_type_set ( ) const [inline]
Real core::conformation::Residue::atomic_charge ( int const  atomno) 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

Atoms const& core::conformation::Residue::atoms ( ) const [inline]
AtomIndices const& core::conformation::Residue::atoms_with_orb_index ( ) const [inline]
Size core::conformation::Residue::attached_H_begin ( int 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().

Size core::conformation::Residue::attached_H_end ( int 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().

AtomIndices const& core::conformation::Residue::bonded_neighbor ( int const  atm) const [inline]
utility::vector1<core::Size> const core::conformation::Residue::bonded_orbitals ( int 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 fill_missing_atoms(), and core::conformation::Conformation::fill_missing_atoms().

Vector const core::conformation::Residue::build_orbital_xyz ( Size const  orbital_index) const [inline]
core::Size core::conformation::Residue::chain ( ) const [inline]

Returns this residue's chain id.

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

void core::conformation::Residue::chain ( int const  setting) [inline]

Sets this residue's chain id.

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

Referenced by core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pose::Pose::chi(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::compute_proposal_density(), protocols::swa::rna::copy_torsions_FROM_TO(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), is_similar_rotamer(), core::pack::minimize_alt_rotamer(), protocols::swa::rna::Print_torsion_info(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::pack::dunbrack::rotamer_from_chi(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().

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

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

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

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

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

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

References core::chemical::ResidueType::chi_atoms().

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().

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::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::StealSideChainsMover::apply(), 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::pack::rotamer_set::dup_residue(), core::pack::dunbrack::dup_residue(), protocols::ligand_docking::get_ligand_torsion_constraints(), protocols::pockets::PocketGrid::getRelaxResidues(), core::conformation::Conformation::insert_conformation_by_jump(), protocols::motifs::BuildPosition::keep_rotamer(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::swa::pdbslice(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::pack::setup_bgres_cops(), protocols::swa::rna::setup_residue_at_origin_list(), protocols::motifs::MotifHit::target_conformer(), and protocols::vip::VIP_Mover::try_point_mutants().

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 is_lower_terminus(), is_polymer(), is_upper_terminus(), lower_connect_atom(), core::chemical::ResidueType::residue_connection(), seqpos(), and upper_connect_atom().

Referenced by protocols::forge::methods::fold_tree_from_pose(), protocols::viewer::print_interres_bond(), and core::import_pose::set_reasonable_fold_tree().

chemical::ResConnID core::conformation::Residue::connect_map ( Size  resconn_index) const [inline]
Size core::conformation::Residue::connected_residue_at_resconn ( Size const  resconn_index) const [inline]
Distance core::conformation::Residue::connection_distance ( conformation::Conformation const &  conf,
Size const  resconn_index,
Vector const  matchpoint 
) const

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

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

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

bool core::conformation::Residue::connection_incomplete ( Size  resconnid) const
bool core::conformation::Residue::connections_match ( Residue const &  other) const

Returns true if ???

utility::vector1< Size > const& core::conformation::Residue::connections_to_residue ( Residue const &  other) const [inline]
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.

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]

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

References clone().

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

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

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

References core::chemical::ResidueType::cut_bond_neighbor().

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

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

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

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

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

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

Size core::conformation::Residue::first_sidechain_atom ( ) const [inline]

Returns the index number of the first sidechain heavyatom.

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

References core::chemical::ResidueType::first_sidechain_atom().

Referenced by protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::swa::rna::base_atoms_square_deviation(), protocols::rna::bases_form_a_hydrogen_bond(), protocols::relax::derive_sc_sc_restraints(), 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::rna::figure_out_number_base_contacts(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::rna::get_rna_base_centroid(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), 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(), core::scoring::hackelec::is_sugar(), protocols::swa::rna::Is_virtual_base(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), protocols::swa::rna::setup_suite_atom_id_map(), sidechainAtoms_begin(), protocols::swa::rna::suite_square_deviation(), and protocols::dna::z_axis_dist().

Size core::conformation::Residue::first_sidechain_hydrogen ( ) const [inline]

Returns the index number of the first sidechain hydrogen.

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

References core::chemical::ResidueType::first_sidechain_hydrogen().

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

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::topology_broker::fix_mainchain_connect(), protocols::swa::protein::get_pretend_phi_explicit(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), protocols::enzdes::DiffAtomSasaFilter::parse_my_tag(), place(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::ligand_docking::set_repulsive_bb_cores(), core::scoring::setup_matching_heavy_atoms(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), and protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all().

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?

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

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

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

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

References core::chemical::ResidueType::has_property().

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

bool core::conformation::Residue::has_sc_orbitals ( ) const [inline]

Returns true if the residue has side chain orbitals.

References core::chemical::ResidueType::has_sc_orbitals().

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

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

Generic variant access -- SLOW!!!!!

References core::chemical::ResidueType::has_variant_type().

Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::antibody::LoopRlxMover::apply(), core::pack::task::operation::OptCysHG::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::copy_side_chains(), protocols::forge::methods::cyclize_pose(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_disulfides(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::etable::EtableEnergy::eval_intrares_energy(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_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(), protocols::swa::Figure_out_moving_residues(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::form_disulfide(), protocols::swa::rna::full_length_rmsd_over_residue_list(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::has_virtual_rna_residue_variant_type(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::methods::is_lower_cutpoint(), protocols::swa::rna::Is_ribose_virtual(), core::scoring::methods::is_upper_cutpoint(), protocols::swa::rna::Is_virtual_base(), protocols::antibody2::CDRH3Modeler2::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::swa::rna::minimize_all_sampled_floating_bases(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::loops::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::scoring::methods::SpecialRotamerEnergy::residue_energy(), core::scoring::rna::RNA_BulgeEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), protocols::swa::rna::rmsd_over_residue_list(), protocols::swa::rna::setup_FB_CC_JP_list(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::conformation::setup_links(), protocols::antibody2::Ab_RelaxCDRs_Mover::setup_objects(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::swa::rna::virtualize_energetically_unfavorable_nucleotides().

bool core::conformation::Residue::heavyatom_has_polar_hydrogens ( Size  ind) const [inline]

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

References core::chemical::ResidueType::heavyatom_has_polar_hydrogens().

bool core::conformation::Residue::heavyatom_is_an_acceptor ( Size  ind) const [inline]

Is a particular atom a heavy atom acceptor?

References core::chemical::ResidueType::heavyatom_is_an_acceptor().

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]

Returns the AtomIndices of this residue's apolar hydrogens.

Note:
: AtomIndices == vector1< Size >

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

References core::chemical::ResidueType::Hpos_apolar().

AtomIndices const& core::conformation::Residue::Hpos_polar ( ) const [inline]
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().

chemical::AtomICoor const& core::conformation::Residue::icoor ( int const  atm) const [inline]
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(), and core::chemical::ResidueType::is_polar().

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 seqpos().

Referenced by core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), core::scoring::GenBornPotential::eval_atom_derivative(), 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::conformation::get_chemical_root_and_anchor_atomnos(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::trie::initialize_cpdata_for_atom(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::scoring::methods::VDW_Energy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

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

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

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

Returns true if the residue is charged.

References core::chemical::ResidueType::is_charged().

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

Referenced by core::scoring::hbonds::HBondSet::append_hbond(), protocols::motifs::Motif::apply_check(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full(), protocols::forge::remodel::RemodelMover::confirm_sequence(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::determine_crossover_behavior(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::etable::BaseEtableEnergy< Derived >::get_intrares_countpair(), core::scoring::dna::get_z_axis(), protocols::relax::FastRelax::makeDnaRigid(), protocols::motifs::Motif::Motif(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::conformation::setup_corresponding_atoms(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy().

bool core::conformation::Residue::is_ligand ( ) const [inline]
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().

Referenced by protocols::loops::add_cutpoint_variants(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::idealize::basic_idealize(), 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(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::correct_termini_derivatives(), protocols::forge::methods::count_cutpoints(), protocols::forge::methods::cyclize_pose(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_don_chem_type(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), core::conformation::get_root_atomno(), protocols::forge::methods::grow_left_r(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::loops::Loop::is_terminal(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::Bridge::modify_impl(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), protocols::fldsgn::CircularPermutation::split_chains(), and core::conformation::Conformation::update_polymeric_connection().

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

Returns true if this residue is a nucleic acid.

References core::chemical::ResidueType::is_NA().

Referenced by protocols::scoring::Interface::calculate().

bool core::conformation::Residue::is_polar ( ) const [inline]
bool core::conformation::Residue::is_polymer ( ) const [inline]

Returns true if this residue is a polymer.

References core::chemical::ResidueType::is_polymer().

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::loops::add_cutpoint_variants(), core::pose::addVirtualResAsRoot(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), core::io::pdb::FileData::append_residue(), core::conformation::Conformation::append_residue_by_bond(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::idealize::basic_idealize(), connect_atom(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::electron_density::findLoopFromDensity(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::get_anchor_atomno(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), core::conformation::get_root_atomno(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::is_polymer_heavyatom(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only(), core::scoring::electron_density::ElectronDensity::matchRes(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::reorder_with_first_non_mobile_as_root(), protocols::protein_interface_design::star_fold_tree(), and core::conformation::Conformation::update_polymeric_connection().

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

Am I polymer bonded to other?

Am I polymer bonded to other.seqpos()?

References seqpos().

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

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

Am I polymer bonded to other_index?

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

bool core::conformation::Residue::is_protein ( ) const [inline]

Returns true if this residue is an amino acid.

References core::chemical::ResidueType::is_protein().

Referenced by protocols::loops::addScoresForLoopParts(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::swa::protein::StepWiseProteinPoseSetup::apply(), protocols::simple_moves::MakePolyXMover::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::abinitio::DomainAssembly::apply(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), protocols::loops::apply_sequence_mapping(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::enzdes::RepackWithoutLigandFilter::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::swa::create_alignment_id_map(), core::scoring::hbonds::create_rotamer_descriptor(), core::pack::rotamer_set::symmetry::SymmetricRotamerSetFactory::create_rotamer_set(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::protein_interface_design::AlaScan::ddG_for_single_residue(), core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::dssp::Dssp::Dssp(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), 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::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::electron_density::findLoopFromPatterson(), protocols::loops::fold_tree_from_loops(), protocols::comparative_modeling::gather_coords(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), protocols::simple_filters::AbinitioBaseFilter::get_protein_sstype(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::topology_broker::SequenceClaimer::initialize_residues(), 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(), protocols::loops::Loop::is_terminal(), core::pack::dunbrack::load_unboundrot(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::toolbox::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), MinimizeInterface(), protocols::motifs::Motif::Motif(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), core::scoring::methods::OmegaTetherEnergy::old_eval_dof_derivative(), protocols::abinitio::AllResiduesChanged::operator()(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::scoring::PairEPotential::pair_term_energy_exists(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), core::pose::read_psipred_ss2_file(), protocols::pockets::PocketGrid::recenter(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::AtrGrid::refresh(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_filters::AlaScan::report(), protocols::protein_interface_design::EnergyPerResidueFilter::report(), protocols::protein_interface_design::AlaScan::report(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::protein_interface_design::AlaScan::report_symmetry(), protocols::geometry::residue_center_of_mass(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::geometry::return_nearest_residue(), core::conformation::symmetry::return_nearest_residue(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), protocols::pockets::PlaidFingerprint::rmsd(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), protocols::motifs::LigandMotifSearch::run(), core::scoring::constraints::BackboneStubConstraint::score(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), protocols::loops::set_single_loop_fold_tree(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(), protocols::abinitio::AllResiduesChanged::show_unmoved(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), protocols::fldsgn::CircularPermutation::split_chains(), and SymMinimizeInterface().

bool core::conformation::Residue::is_pseudo_bonded ( Residue const &  other) const [inline]
bool core::conformation::Residue::is_pseudo_bonded ( Size const  other_index) const [inline]

Do I have any pseudobonds to other?

bool core::conformation::Residue::is_RNA ( ) const [inline]

Returns true if this residue is a RNA residue.

References core::chemical::ResidueType::is_RNA().

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::swa::create_alignment_id_map(), protocols::swa::rna::create_standard_o2star_pack_task(), core::scoring::rna::default_jump_atom(), core::scoring::methods::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::LK_CosThetaEnergy::eval_intrares_energy(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_intrares_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_intrares_energy(), core::scoring::hackelec::RNAHackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::scoring::hbonds::get_hb_acc_chem_type(), protocols::swa::rna::Get_ribose_stub(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::rna::make_phosphate_nomenclature_matches_mini(), place(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::rna::RNA_BulgeEnergy::residue_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::scoring::rna::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::hackelec::RNAHackElecEnergy::residue_pair_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy(), core::scoring::hackelec::RNAHackElecEnergy::residue_pair_energy_RNA(), core::conformation::setup_corresponding_atoms(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::use_orientation_dep_rna_ch_o_bonds().

bool core::conformation::Residue::is_similar_aa ( Residue const &  other) const [inline]

Returns true if the aa residue types are the same.

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

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

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

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

bool core::conformation::Residue::is_surface ( ) const [inline]

Returns true if this residue is a surface residue.

References core::chemical::ResidueType::is_surface().

bool core::conformation::Residue::is_terminus ( ) const [inline]
bool core::conformation::Residue::is_upper_terminus ( ) const [inline]

Return true if the residue has an upper terminus variant.

References core::chemical::ResidueType::is_upper_terminus().

Referenced by protocols::loops::add_cutpoint_variants(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::idealize::basic_idealize(), protocols::antibody::CloseOneMover::close_one_loop_stem(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), connect_atom(), protocols::topology_broker::copy_internal_coords(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::correct_termini_derivatives(), protocols::forge::methods::count_cutpoints(), protocols::forge::methods::cyclize_pose(), core::scoring::OmegaTether::eval_omega_score_residue(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_acc_chem_type(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), core::conformation::get_root_atomno(), protocols::forge::methods::grow_right_r(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::loops::Loop::is_terminal(), protocols::antibody2::CDRH3Modeler2::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::Bridge::modify_impl(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::antibody2::Ab_RelaxCDRs_Mover::setup_objects(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), and protocols::fldsgn::CircularPermutation::split_chains().

bool core::conformation::Residue::is_virtual ( Size const &  atomno) const
bool core::conformation::Residue::is_virtual_residue ( ) const [inline]
Size core::conformation::Residue::last_backbone_atom ( ) const [inline]
chemical::ResidueConnection const& core::conformation::Residue::lower_connect ( ) const [inline]
Size core::conformation::Residue::lower_connect_atom ( ) const [inline]

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

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

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

References core::chemical::ResidueType::lower_connect_atom().

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

Size core::conformation::Residue::mainchain_atom ( Size const  atm) const [inline]

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

References core::chemical::ResidueType::mainchain_atom().

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

AtomIndices const& core::conformation::Residue::mainchain_atoms ( ) const [inline]
Real core::conformation::Residue::mainchain_torsion ( Size const  torsion) const [inline]

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

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

Referenced by protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::bb_bins_from_pose(), protocols::swa::rna::copy_torsions_FROM_TO(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::topology_broker::fix_mainchain_connect(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::P_AA::get_Paa_pp_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::pose::Pose::omega(), core::scoring::P_AA::P_AA_pp_energy(), core::pose::Pose::phi(), protocols::swa::rna::print_backbone_torsions(), protocols::swa::rna::Print_torsion_info(), core::pose::Pose::psi(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), and core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().

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

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

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

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

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

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

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

References core::chemical::ResidueType::mm_atom_name().

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

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

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

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

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

Size core::conformation::Residue::n_hbond_acceptors ( ) const [inline]
Size core::conformation::Residue::n_hbond_donors ( ) const [inline]

number of hbond_donors

References core::chemical::ResidueType::n_hbond_acceptors().

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

Size core::conformation::Residue::n_mainchain_atoms ( ) const [inline]

Returns the number of the residue's mainchain atoms.

References core::chemical::ResidueType::mainchain_atoms().

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

Size core::conformation::Residue::n_non_polymeric_residue_connections ( ) const [inline]

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

References core::chemical::ResidueType::n_non_polymeric_residue_connections().

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

Size core::conformation::Residue::n_orbitals ( ) const [inline]

Returns the number of orbitals in this residue.

References core::chemical::ResidueType::n_orbitals().

Size core::conformation::Residue::n_polymeric_residue_connections ( ) const [inline]

Returns the number of polymeric ResidueConnections on this residue.

References core::chemical::ResidueType::n_polymeric_residue_connections().

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

Size core::conformation::Residue::n_residue_connections ( ) const [inline]
std::string const& core::conformation::Residue::name ( ) const [inline]

Returns this residue's ResidueType name.

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

References core::chemical::ResidueType::name().

Referenced by protocols::seeded_abinitio::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), core::pose::Pose::annotated_sequence(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::filters::CompleteConnectionsFilter::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::vip::are_seqs_different(), protocols::match::downstream::ClassicMatchAlgorithm::build(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::coarse::TranslatorSet::coarsify(), core::pose::copy_dofs(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::Conformation::detect_bonds(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::io::pdb::extract_scores(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::form_disulfide(), protocols::vip::VIP_Report::get_GOE_packstat_report(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::ligand_docking::has_incomplete_connections(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::features::ResidueFeatures::insert_residue_rows(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), core::conformation::operator<<(), core::conformation::print_atom(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep(), core::pose::symmetry::rotate_anchor_to_x_axis(), select_orient_atoms(), core::conformation::Conformation::show_residue_connections(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and core::chemical::ICoorAtomID::xyz().

char core::conformation::Residue::name1 ( ) const [inline]

Returns this residue's 1-letter representation.

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

References core::chemical::ResidueType::name1().

Referenced by core::pose::Pose::annotated_sequence(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::idealize::basic_idealize(), protocols::forge::components::VarLengthBuild::centroid_build(), core::pose::Pose::chain_sequence(), core::pose::copy_dofs(), protocols::rna::create_rna_vall_torsions(), protocols::antibody2::Ab_Info::detect_and_set_regular_CDR_H3_stem_type(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::antibody2::get_seq_from_a_loop(), core::scoring::rna::is_purine(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), core::pack::pack_rotamers_loop(), protocols::read_in_mutations(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::nv::NVscore::residue_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::pose::Pose::sequence(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::sequence_recovery(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_sequence(), protocols::rna::setup_base_pair_constraints(), protocols::antibody2::Ab_Info::setup_CDR_loops(), core::conformation::setup_corresponding_atoms(), protocols::simple_moves::BBGaussianMover::setup_list(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(), and core::io::pdb::write_additional_pdb_data().

std::string const& core::conformation::Residue::name3 ( ) const [inline]

Returns this residue's 3-letter representation.

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

References core::chemical::ResidueType::name3().

Referenced by core::scoring::sc::ShapeComplementarityCalculator::AddResidue(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::alter_rotamer_set(), core::io::pdb::FileData::append_residue(), protocols::simple_moves::MutateResidue::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::simple_filters::ResidueDistanceFilter::apply(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::simple_filters::NeighborTypeFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::ResidueDistanceFilter::apply(), protocols::protein_interface_design::ResidueBurialFilter::apply(), protocols::protein_interface_design::NeighborTypeFilter::apply(), protocols::protein_interface_design::Revert::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::motifs::Motif::apply_check(), core::scoring::orbitals::OrbitalsAssigned::aromatic_ring_center(), protocols::motifs::Motif::backward_check(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::motifs::MotifSearch::BuildPosition_from_Size(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::antibody2::CDR_H3_filter(), protocols::antibody::CDRH3Modeler::CDR_H3_filter(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::determine_largest_nbr_atom_distance(), protocols::antibody2::Ab_ModelCDRH3::display_constraint_residues(), protocols::antibody2::Ab_Assemble_Templates::display_constraint_residues(), core::io::pdb::dump_pdb_residue(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::motifs::Motif::forward_check(), protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::motifs::MotifSearch::identify_motif_BuildPositions(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::features::ResidueFeatures::insert_residue_rows(), protocols::motifs::make_dna_mutations(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::motifs::Motif::Motif(), core::io::sequence_comparation::DesignContrast::output_sqc_file(), protocols::motifs::Motif::place_atoms(), protocols::motifs::Motif::place_residue(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::rna::print_internal_coords(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::simple_filters::RotamerBoltzmannWeight::report(), protocols::simple_filters::ResidueDistanceFilter::report(), protocols::simple_filters::ResidueBurialFilter::report(), protocols::simple_filters::NeighborTypeFilter::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_filters::AlaScan::report(), protocols::protein_interface_design::EnergyPerResidueFilter::report(), protocols::protein_interface_design::ResidueDistanceFilter::report(), protocols::protein_interface_design::ResidueBurialFilter::report(), protocols::protein_interface_design::NeighborTypeFilter::report(), protocols::protein_interface_design::AlaScan::report(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::protein_interface_design::AlaScan::report_symmetry(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::multistate_design::restrict_to_canonical_aas(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::scoring::packstat::MultiProbePoseAccumulator::show(), protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_and_bonds_from_template(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

Size core::conformation::Residue::natoms ( ) const [inline]

Returns the number of atoms in this residue.

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

References core::chemical::ResidueType::natoms().

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), protocols::toolbox::AllowInsert::append_residue(), core::io::pdb::FileData::append_residue(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::protein_interface_design::movers::SetTemperatureFactor::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), protocols::rbsegment_relax::RBSegmentMover::applyRotation(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::conformation::build_residue_tree(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::scoring::calc_atom_masks(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pose::Pose::center(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), 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::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::star::copy_residues(), protocols::abinitio::copy_side_chains(), core::scoring::hbonds::create_rotamer_descriptor(), core::pack::create_scmin_minimizer_map(), core::scoring::trie::create_trie(), protocols::relax::derive_sc_sc_restraints(), core::scoring::constraints::AtomPairConstraint::dist(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::pdb::dump_pdb_residue(), protocols::viewer::dump_residue_kinemage(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative_RNA(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::methods::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), protocols::toolbox::pose_metric_calculators::fast_clash_check(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), protocols::match::fill_grid_with_residue_spheres(), fill_missing_atoms(), core::conformation::Conformation::fill_missing_atoms(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::electron_density::findLoopFromDensity(), protocols::swa::rna::get_atom_coordinates(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), core::scoring::GenBornPotential::get_res_res_elecE(), core::pack::get_residue_current_energy(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), protocols::comparative_modeling::hybridize::InsertChunkMover::get_superposition_transformation(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::conformation::idealize_hydrogens(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::scoring::ResidueNblistData::initialize(), core::scoring::GenBornResidueInfo::initialize(), core::pose::initialize_dof_id_map(), 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::ResiduePairNeighborList::initialize_from_residues(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::pose::symmetry::make_symmetric_movemap(), core::pose::symmetry::make_symmetric_pdb_info(), core::pose::MiniPose::MiniPose(), core::pose::num_atoms(), core::scoring::constraints::ResiduePairXYZ::operator()(), core::scoring::constraints::ResidueXYZ::operator()(), core::conformation::operator<<(), core::conformation::orient_residue_for_ideal_bond(), place(), protocols::motifs::Motif::place_residue_(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::NeighborList::prepare_for_scoring(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::swa::rna::print_atom_info(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::optimization::MinimizerMap::reset(), core::optimization::CartesianMinimizerMap::reset(), core::scoring::methods::WaterAdductIntraEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::methods::VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::hackelec::HackElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::hackelec::RNAHackElecEnergy::residue_pair_energy_RNA(), core::pose::PDBInfo::resize_atom_records(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::rmsd_no_super(), core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super(), core::scoring::rmsd_with_super_subset(), protocols::qsar::scoring_grid::VdwGrid::score(), select_orient_atoms(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::scoring::NeighborList::setup(), core::pack::scmin::SCMinMinimizerMap::setup(), core::conformation::setup_corresponding_atoms(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::conformation::setup_links(), core::conformation::setup_links_simple(), protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_and_bonds_from_template(), core::scoring::superimpose_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::sym_rmsd_with_super_subset(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::cartesian::MolecularDynamics::testCartesianDerivatives(), protocols::protein_interface_design::transform_pose(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and protocols::kinmatch::xform_rsd_gl2().

Size core::conformation::Residue::nbr_atom ( ) const [inline]

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

References core::chemical::ResidueType::nbr_atom().

Referenced by protocols::toolbox::task_operations::DesignAroundOperation::apply(), protocols::ligand_docking::Transform::apply(), core::scoring::calc_atom_masks(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), protocols::loops::filter_loop_neighbors_by_distance(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::scoring::is_nbr_atom(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::conformation::residue_point_graph_from_conformation(), core::scoring::methods::residues_interact(), select_orient_atoms(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), and core::conformation::ResidueKinWriter::write_kin_header().

Vector const& core::conformation::Residue::nbr_atom_xyz ( ) const [inline]
Real core::conformation::Residue::nbr_radius ( ) const [inline]
AtomIndices const& core::conformation::Residue::nbrs ( int const  atm) const [inline]
Size core::conformation::Residue::nchi ( ) const [inline]
Size core::conformation::Residue::nheavyatoms ( ) const [inline]

Returns the number of heavyatoms in this residue.

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

References core::chemical::ResidueType::nheavyatoms().

Referenced by core::scoring::sc::ShapeComplementarityCalculator::AddResidue(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::append_radius_of_gyration(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::automorphic_rmsd(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::methods::LKB_ResidueInfo::build_waters(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::packstat::cavity_distance_constraint(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), core::scoring::packstat::compute_atom_packing_scores(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), protocols::rna::figure_out_number_base_contacts(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::ligand_docking::frac_atoms_within(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::rna::get_rna_base_centroid(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), core::scoring::rna::RNA_DataBackboneEnergy::get_sugar_env_score(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), heavyAtoms_end(), core::conformation::idealize_hydrogens(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::swa::rna::Is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::pose::num_heavy_atoms(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::kinmatch::BruteFunGroupTK::place_h(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::swa::rna::Print_heavy_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), protocols::rna::residue_is_bulge(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::pockets::PlaidFingerprint::rmsd(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), protocols::qsar::scoring_grid::GridBase::score(), protocols::relax::RelaxProtocolBase::set_up_constraints(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), core::scoring::setup_matching_heavy_atoms(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::packstat::MultiProbePoseAccumulator::show(), protocols::swa::rna::suite_square_deviation(), and core::scoring::electron_density::ElectronDensity::updateCachedDensity().

std::string const& core::conformation::Residue::orbital_name ( int const  orbital_index) const [inline]
chemical::orbitals::OrbitalType const& core::conformation::Residue::orbital_type ( int const  orbital_index) const [inline]
Vector const& core::conformation::Residue::orbital_xyz ( Size const  orbital_index) const [inline]
void core::conformation::Residue::orient_onto_residue ( Residue const &  src)

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

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

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

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

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

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

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

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

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

example(s):

See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose

References core::chemical::ResidueType::path_distance().

utility::vector1< int > const& core::conformation::Residue::path_distance ( int  atom) const [inline]
utility::vector1< utility::vector1< int > > const& core::conformation::Residue::path_distances ( ) const [inline]

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

example(s):

See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose

References core::chemical::ResidueType::path_distances().

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

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

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

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

Referenced by Residue().

int core::conformation::Residue::polymeric_oriented_sequence_distance ( Residue const &  other) const [inline]

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

References chain(), and is_polymer().

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

Size core::conformation::Residue::polymeric_sequence_distance ( Residue const &  other) const [inline]
std::map< Size, PseudoBondCollectionCOP > const& core::conformation::Residue::pseudobonds ( ) const [inline]
bool core::conformation::Residue::requires_actcoord ( ) const [inline]

does this residue require an actcoord?

References core::chemical::ResidueType::requires_actcoord().

Size core::conformation::Residue::residue_connect_atom_index ( Size const  resconn_id) const [inline]
chemical::ResidueConnection const& core::conformation::Residue::residue_connection ( int const  resconn_index) const [inline]
Size core::conformation::Residue::residue_connection_conn_id ( Size const  resconn_index) const [inline]
Size core::conformation::Residue::residue_connection_partner ( Size const  resconn_index) const [inline]
void core::conformation::Residue::residue_connection_partner ( Size const  resconn_index,
Size const  otherres,
Size const  other_connid 
)

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

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

chemical::ResidueTypeSet const& core::conformation::Residue::residue_type_set ( ) const [inline]

Returns this residue's ResidueTypeSet.

References core::chemical::ResidueType::residue_type_set().

Referenced by protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::pose::add_variant_type_to_residue(), protocols::relax::add_virtual_residue_to_cterm(), protocols::kinmatch::alapose(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::MutateResidue::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::idealize::IdealizeMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::rna::assert_phosphate_nomenclature_matches_mini(), protocols::relax::coordinate_constrain_selection(), protocols::rna::ensure_phosphate_nomenclature_matches_mini(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::motifs::make_base_pair_mutation(), protocols::rna::make_phosphate_nomenclature_matches_mini(), protocols::forge::build::BuildManager::modify(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::pose::remove_variant_type_from_residue(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::revert_loops_to_original(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::set_loops_to_virt_ala(), protocols::relax::RelaxProtocolBase::set_up_constraints(), and core::conformation::symmetry::setup_symmetric_conformation().

core::chemical::rna::RNA_ResidueType const& core::conformation::Residue::RNA_type ( ) const [inline]
void core::conformation::Residue::select_orient_atoms ( Size center,
Size nbr1,
Size nbr2 
) const
Size core::conformation::Residue::seqpos ( ) const [inline]

Returns the sequence position of this residue.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::hbonds::HBondSet::append_hbond(), core::io::pdb::FileData::append_residue(), protocols::swa::rna::atom_square_deviation(), core::scoring::methods::atoms_interact(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::dna::DNA_BasePotential::base_step_score(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::conformation::build_residue_tree(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full(), core::scoring::calc_atom_masks(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), connect_atom(), core::scoring::mm::connection_indices(), connections_to_residue(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::hbonds::create_rotamer_descriptor(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::create_rotamers_from_chisets(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::io::pdb::dump_pdb_residue(), protocols::viewer::dump_residue_kinemage(), core::pack::rotamer_set::dup_residue(), core::pack::dunbrack::dup_residue(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(), protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::constraints::ConstraintSet::eval_intrares_energy(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::hackelec::HackElecEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), core::scoring::MembranePotential::evaluate_cbeta(), 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::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::methods::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_base_step_params(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), core::scoring::GenBornPotential::get_res_res_elecE(), core::conformation::get_residue_connections(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::conformation::get_root_residue_root_atomno(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::conformation::Conformation::insert_residue_by_jump(), core::conformation::insert_residue_into_atom_tree(), core::scoring::rna::Is_base_phosphate_atom_pair(), is_bonded(), protocols::scoring::Interface::is_interface(), protocols::scoring::Interface::is_pair(), is_polymer_bonded(), is_pseudo_bonded(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::constraints::ResiduePairXYZ::operator()(), core::scoring::constraints::ResidueXYZ::operator()(), core::conformation::operator<<(), protocols::kinmatch::KinFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::KinFunGroupTK::place_d(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::kinmatch::KinFunGroupTK::place_h(), protocols::kinmatch::BruteFunGroupTK::place_h(), core::conformation::print_atom(), protocols::viewer::print_interres_bond(), protocols::viewer::print_node(), core::pack::reinitialize_mingraph_neighborhood_for_residue(), core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), core::scoring::electron_density::ElectronDensity::rematchResToPatterson(), core::conformation::replace_residue_in_atom_tree(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::constraints::ResiduePairXYZ::residue(), protocols::hotspot_hashing::HotspotStub::residue(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::rna::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::PoissonBoltzmannEnergy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::interface::DDPscore::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::residue_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::residue_pair_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy_ext(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), core::conformation::setup_corresponding_atoms(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue(), protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(), core::scoring::hackelec::HackElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::scoring::Interface::show(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::scoring::MembranePotential::termini_penalty(), core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric(), core::scoring::electron_density::ElectronDensity::updateCachedDensity(), protocols::simple_moves::symmetry::SymmetrySlider::very_far_away(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and core::chemical::ICoorAtomID::xyz().

void core::conformation::Residue::seqpos ( Size const  setting) [inline]

Sets this residue's sequence position to <setting>

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

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

References nchi(), and set_chi().

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

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

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

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

Referenced by set_all_chi().

void core::conformation::Residue::set_orbital_xyz ( core::Size const  orbital_index,
Vector const &  xyz_in 
) [inline]
void core::conformation::Residue::set_pseudobonds_to_residue ( Size  resid,
PseudoBondCollectionCOP  pbs 
)
void core::conformation::Residue::set_xyz ( std::string const &  atm_name,
Vector const &  xyz_in 
) [inline]

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

example(s):

See also: Residue Residue.atom Residue.atoms Residue.xyz Pose

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

void core::conformation::Residue::set_xyz ( core::Size const  atm_index,
Vector const &  xyz_in 
) [inline]
Atoms::const_iterator core::conformation::Residue::sidechainAtoms_begin ( ) const [inline]
ResidueType const& core::conformation::Residue::type ( ) const [inline]

Returns this residue's ResidueType.

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

Referenced by protocols::seeded_abinitio::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::motifs::add_motif_bb_constraints(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::alter_rotamer_set(), core::pack::task::operation::util::any_atoms_within_cutoff(), core::conformation::Conformation::append_residue_by_bond(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::abinitio::DomainAssembly::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), protocols::loops::apply_sequence_mapping(), apply_transform_Rx_plus_v(), protocols::swa::rna::atom_square_deviation(), core::scoring::automorphic_rmsd(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), protocols::motifs::backbone_stub_match(), protocols::swa::rna::base_atoms_square_deviation(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::ClassicMatchAlgorithm::build(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::io::pdb::build_pose_as_is1(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), core::scoring::methods::LKB_ResidueInfo::build_waters(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), connection_distance(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), copy_residue_connections(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::dna::DnaInterfacePacker::current_working_sequence(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), protocols::viewer::dump_residue_kinemage(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), fill_missing_atoms(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), protocols::ligand_docking::frac_atoms_within(), core::scoring::dna::get_base_stub(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), protocols::loops::get_tenA_neighbor_residues(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::scoring::dna::get_y_axis(), core::conformation::idealize_position(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::is_disulfide_bond(), core::conformation::is_ideal_position(), core::pack::dunbrack::load_unboundrot(), protocols::rotamer_recovery::RRProtocol::measure_rotamer_recovery(), place(), protocols::swa::rna::print_atom_info(), protocols::swa::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), core::coarse::CoarseEtable::print_residue_info(), protocols::swa::rna::Print_torsion_info(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::swa::rna::remove_all_variant_types(), core::pose::remove_variant_type_from_residue(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), Residue(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::pHEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::pack::dunbrack::RotamerLibrary::rotamer_energy(), core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv(), core::pack::dunbrack::rotamer_from_chi(), protocols::constraints_additional::SequenceCouplingConstraint::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::pack::task::operation::util::select_coord_for_residue(), protocols::loops::select_loop_residues(), core::conformation::Conformation::sequence_matches(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), protocols::rna::setup_base_pair_constraints(), core::conformation::setup_corresponding_atoms(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_derivatives(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_scoring(), core::scoring::etable::EtableEnergy::setup_for_scoring_(), core::scoring::etable::CoarseEtableEnergy::setup_for_scoring_(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::swa::rna::setup_suite_atom_id_map(), core::scoring::hbonds::HBond::show(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), and core::io::serialization::write_binary().

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

Updates actcoord for this residue.

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

References core::chemical::ResidueType::update_actcoord().

Referenced by set_chi(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), and protocols::features::OrbitalsFeatures::set_OrbOrb_features_data().

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

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

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

chemical::ResidueConnection const& core::conformation::Residue::upper_connect ( ) const [inline]
Size core::conformation::Residue::upper_connect_atom ( ) const [inline]

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

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

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

References core::chemical::ResidueType::upper_connect_atom().

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

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

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

Note:
: position is a Vector

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

Referenced by protocols::seeded_abinitio::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_dist_constraints(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), core::scoring::sc::ShapeComplementarityCalculator::AddResidue(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::append_radius_of_gyration(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::toolbox::task_operations::DesignAroundOperation::apply(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::antibody2::Ab_CloseOneCDR_Mover::apply(), protocols::antibody::CloseOneMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), apply_transform_Rx_plus_v(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), protocols::motifs::atom_specific_rms(), protocols::swa::rna::atom_square_deviation(), core::scoring::methods::atoms_interact(), core::scoring::automorphic_rmsd(), core::scoring::hackelec::HackElecEnergy::backbone_backbone_energy(), core::scoring::hackelec::HackElecEnergy::backbone_sidechain_energy(), protocols::motifs::backbone_stub_match(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::match::downstream::RigidLigandBuilder::build(), core::scoring::methods::WaterBuilder::build(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), protocols::match::downstream::ClassicMatchAlgorithm::build_from_three_coords(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), build_orbital_xyz(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::packstat::cavity_distance_constraint(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::Check_chain_closable_floating_base(), protocols::swa::rna::check_floating_base_chain_closable(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), protocols::comparative_modeling::hybridize::InsertChunkMover::check_overlap(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::forge::remodel::RemodelMover::confirm_sequence(), core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::rna::create_rna_vall_torsions(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::antibody2::cutpoint_separation(), protocols::antibody::CDRH3Modeler::cutpoint_separation(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::relax::derive_sc_sc_restraints(), core::conformation::Conformation::detect_bonds(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::comparative_modeling::hybridize::discontinued_lower(), protocols::comparative_modeling::hybridize::discontinued_upper(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::hackelec::HackElecEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::MembranePotential::evaluate_env(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), protocols::rna::figure_out_number_base_contacts(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::conformation::Conformation::fill_missing_atoms(), core::io::silent::RNA_SilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::loops::filter_loop_neighbors_by_distance(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::forge::methods::fixH(), protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::ligand_docking::frac_atoms_within(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::comparative_modeling::gather_coords(), protocols::swa::rna::get_atom_coordinates(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::scoring::dna::get_base_pucker(), core::scoring::dna::get_base_stub(), protocols::swa::rna::get_C4_C3_distance_range(), protocols::simple_filters::get_contact_features(), core::io::silent::RNA_SilentStruct::get_debug_rmsd(), core::io::silent::ProteinSilentStruct_Template< T >::get_debug_rmsd(), core::io::silent::BinaryRNASilentStruct::get_debug_rmsd(), core::io::silent::BinaryProteinSilentStruct::get_debug_rmsd(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::scoring::GenBornPotential::get_res_res_elecE(), core::pack::get_residue_current_energy(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), protocols::swa::rna::Get_ribose_stub(), core::scoring::rna::get_rna_base_centroid(), core::scoring::rna::get_rna_base_coordinate_system(), protocols::swa::rna::get_specific_atom_coordinate(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::rna::get_sugar_centroid(), core::scoring::rna::RNA_DataBackboneEnergy::get_sugar_env_score(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::pose::symmetry::get_symm_axis(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::scoring::ResidueNblistData::initialize(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), core::fragment::make_pose_from_frags(), core::pack::min_pack(), MinimizeInterface(), core::pose::MiniPose::MiniPose(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), core::scoring::constraints::ResiduePairXYZ::operator()(), core::scoring::constraints::ResidueXYZ::operator()(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), orient_onto_residue(), core::conformation::orient_residue_for_ideal_bond(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::comparative_modeling::pick_loops_chainbreak(), place(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::kinmatch::BruteFunGroupTK::place_h(), protocols::motifs::Motif::place_residue_(), core::scoring::NeighborList::prepare_for_scoring(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), core::scoring::rna::prepare_scratch_residue(), protocols::match::output::print_node(), core::conformation::print_node(), core::conformation::symmetry::recenter(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::helixAssembly::HelixBundleFeatures::report_features(), Residue(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::rna::residue_is_bulge(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::VDW_Energy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::hackelec::HackElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::hackelec::RNAHackElecEnergy::residue_pair_energy_RNA(), core::conformation::residue_point_graph_from_conformation(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::scoring::methods::residues_interact(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::scoring::rmsd_no_super(), core::scoring::rmsd_no_super_subset(), core::scoring::rmsd_with_super(), core::scoring::rmsd_with_super_subset(), core::pose::symmetry::rotate_anchor_to_x_axis(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::RTMin::rtmin(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::GridBase::score(), core::scoring::constraints::BackboneStubConstraint::score(), set_chi(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::match::downstream::TargetRotamerCoords::set_coordinates_for_rotamer(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::scoring::NeighborList::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), core::scoring::hbonds::HBond::show(), core::scoring::hackelec::HackElecEnergy::sidechain_sidechain_energy(), protocols::loops::split_by_ca_ca_dist(), core::scoring::dna::strand_orientation_vector(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::swa::rna::suite_square_deviation(), core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair(), core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair_one_way(), core::scoring::superimpose_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::scoring::sym_rmsd_with_super_subset(), protocols::protein_interface_design::movers::test_res_res_aln(), core::scoring::MembranePotential::tm_projection_penalty(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), protocols::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), core::conformation::ResidueKinWriter::write_kin_header(), protocols::kinmatch::xform_rsd_gl2(), and protocols::dna::z_axis_dist().

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

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

Note:
: position is a Vector

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

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


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