Instance Residue class, used for placed residues and rotamers. More...
#include <Residue.hh>
Public Types | |
| typedef chemical::AtomType | AtomType |
| typedef chemical::ResidueType | ResidueType |
| typedef chemical::ResidueTypeCOP | ResidueTypeCOP |
| typedef chemical::AtomIndices | AtomIndices |
Public Member Functions | |
| Residue (ResidueTypeCOP rsd_type_in, bool const dummy_arg) | |
| constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue. More... | |
| Residue (ResidueType const &rsd_type_in, bool const dummy_arg) | |
| constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue. More... | |
| Residue (ResidueType const &rsd_type_in, Residue const ¤t_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false) | |
| Rotamer-style constructor; orients ideal coords onto backbone of current_rsd. More... | |
| Residue (Residue const &src) | |
| Copy constructor. More... | |
| ~Residue () override | |
| Destructor. More... | |
| ResidueOP | clone () const |
| Copy this residue( allocate actual memory for it ) More... | |
| ResidueOP | clone_flipping_chirality (core::chemical::ResidueTypeSet const &residue_type_set) const |
| Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type. More... | |
| void | show (std::ostream &output=std::cout, bool output_atomic_details=false) const |
| Generate string representation of Residue for debugging purposes. More... | |
| ResidueCOP | get_self_ptr () const |
| self pointers More... | |
| ResidueOP | get_self_ptr () |
| ResidueCAP | get_self_weak_ptr () const |
| ResidueAP | get_self_weak_ptr () |
| AtomType const & | atom_type (Size const atomno) const |
| Returns the AtomType of this residue's atom with index number <atomno> More... | |
| chemical::AtomTypeSet const & | atom_type_set () const |
| Returns the AtomTypeSet of this residue. More... | |
| Size | atom_type_index (Size const atomno) const |
| Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType. More... | |
| Real | atomic_charge (Size const atomno) const |
| Returns the atom charge of this residue's atom with index number <atomno> More... | |
| bool | is_virtual (Size const atomno) const |
| Check if atom is virtual. AMW TODO: somehow SWA spends literally 3.7% of its time calling this function. More... | |
| bool | is_repulsive (Size const atomno) const |
| Check if atom is repulsive. More... | |
| bool | is_virtual_residue () const |
| Check if residue is virtual. More... | |
| Size | atom_index (std::string const &atm) const |
| Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid. More... | |
| Size | natoms () const |
| Returns the number of atoms in this residue. More... | |
| Size | n_hbond_acceptors () const |
| number of hbond_donors More... | |
| Size | n_hbond_donors () const |
| number of hbond_donors More... | |
| Size | nheavyatoms () const |
| Returns the number of heavyatoms in this residue. More... | |
| AtomIndices const & | Hpos_polar () const |
| Returns the AtomIndices of this residue's polar hydrogens. More... | |
| AtomIndices const & | all_bb_atoms () const |
| Returns the AtomIndices of this residue's backbone atoms. More... | |
| AtomIndices const & | Haro_index () const |
| Returns the AtomIndices of this residue's aromatic hydrogens. More... | |
| AtomIndices const & | Hpol_index () const |
| Returns the AtomIndices of this residue's polar hydrogens. More... | |
| AtomIndices const & | Hpos_apolar () const |
| Returns the AtomIndices of this residue's apolar hydrogens. More... | |
| AtomIndices const & | Hpos_polar_sc () const |
| Returns the AtomIndices of this residue's polar sidechain hydrogens. More... | |
| AtomIndices const & | accpt_pos () const |
| Returns the AtomIndices of this residue's h-bond acceptor atoms. More... | |
| AtomIndices const & | accpt_pos_sc () const |
| Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms. More... | |
| void | get_metal_binding_atoms (AtomIndices &metal_binding_indices) const |
| Gets the AtomIndices of the atoms in this residue that can bind to metals. More... | |
| core::Size | n_virtual_atoms () const |
| Returns the number of virtual atoms in this residue. More... | |
| bool | heavyatom_has_polar_hydrogens (Size ind) const |
| Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom) More... | |
| bool | heavyatom_is_an_acceptor (Size ind) const |
| Is a particular atom a heavy atom acceptor? More... | |
| bool | atom_is_polar_hydrogen (Size ind) const |
| Is a particular atom a polar hydrogen? More... | |
| Atoms const & | atoms () const |
| Returns this residue's Atoms (const), a vector1 of Atom objects. More... | |
| Atoms & | atoms () |
| Returns this residue's Atoms (non-const), a vector1 of Atom objects. More... | |
| Atoms::iterator | atom_begin () |
| begin interator, to iterate over atoms More... | |
| Atoms::iterator | atom_end () |
| end interator, to iterate over atoms More... | |
| Atoms::const_iterator | atom_begin () const |
| Atoms::const_iterator | atom_end () const |
| Atoms::const_iterator | sidechainAtoms_begin () const |
| should be safe, given the atom ordering rules? More... | |
| Atoms::const_iterator | heavyAtoms_end () const |
| Atom const & | atom (Size const atm_index) const |
| Returns this residue's Atom with index number <atm_index> (const) More... | |
| Atom & | atom (Size const atm_index) |
| Returns this residue's Atom with index number <atm_index> (non-const) More... | |
| Atom const & | atom (std::string const &atm_name) const |
| Returns this residue's Atom with name <atm_name> (const) More... | |
| Atom & | atom (std::string const &atm_name) |
| Returns this residue's Atom with name <atm_name> (non-const) More... | |
| Vector const & | xyz (Size const atm_index) const |
| Returns the position of this residue's atom with index number <atm_index> More... | |
| Vector const & | xyz (std::string const &atm_name) const |
| Returns the position of this residue's atom with name <atm_name> More... | |
| void | set_xyz (core::Size const atm_index, Vector const &xyz_in) |
| Sets the position of this residue's atom with index number <atm_index> More... | |
| void | set_xyz (std::string const &atm_name, Vector const &xyz_in) |
| Sets the position of this residue's atom with name <atm_name> More... | |
| Size | last_backbone_atom () const |
| Returns the index number of the last backbone heavyatom. More... | |
| Size | first_sidechain_atom () const |
| Returns the index number of the first sidechain heavyatom. More... | |
| Size | first_sidechain_hydrogen () const |
| Returns the index number of the first sidechain hydrogen. More... | |
| Size | attached_H_begin (Size const atom) const |
| Returns the index number of the first hydrogen attached to the atom with index number <atom> More... | |
| Size | attached_H_end (Size const atom) const |
| Returns the index number of the last hydrogen attached to the atom with index number <atom> More... | |
| AtomIndices const & | attached_H_begin () const |
| Returns the AtomIndices of the first hydrogen attached to each heavyatom. More... | |
| AtomIndices const & | attached_H_end () const |
| Returns the AtomIndices of the last hydrogen attached to each heavyatom. More... | |
| bool | has_lower_connect () const |
| Returns true if residue has a valid lower connection. More... | |
| Size | lower_connect_atom () const |
| Returns the index number of this residue's atom which connects to the residue before it in sequence. More... | |
| bool | has_upper_connect () const |
| Returns true if residue has a valid upper connection. More... | |
| Size | upper_connect_atom () const |
| Returns the index number of this residue's atom which connects to the residue after it in sequence. More... | |
| Size | connect_atom (Residue const &other) const |
| Returns the index number of this residue's atom connected to the <other> Residue. More... | |
| core::chemical::AtomIndices | get_adjacent_heavy_atoms (uint const atom_index) const |
| Get a list of heavy atoms connected to a given atom. More... | |
| uint | first_adjacent_heavy_atom (uint const atom_index) const |
| Scan through the list of atoms connected to a given atom and return the 1st heavy atom found. More... | |
| core::chemical::AtomIndices | get_atoms_exocyclic_to_ring_atom (uint const atom_index) const |
| Get a list of exocyclic atoms connected to a given ring atom. More... | |
| core::chemical::AtomIndices | get_substituents_to_ring_atom (uint const atom_index) const |
| Get a list of substituent atoms connected to a given ring atom. More... | |
| core::chemical::AtomIndices | get_hydrogens_bonded_to_ring_atom (uint const atom_index) const |
| Get a list of hydrogen atoms connected to a given ring atom. More... | |
| utility::vector1< int > const & | path_distance (Size atom) const |
| Returns the shortest path distance from <atom> to any other atom in this residue. More... | |
| utility::vector1< utility::vector1< int > > const & | path_distances () const |
| Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2]. More... | |
| int | path_distance (Size at1, Size at2) const |
| Returns the number of bonds separating atom <at1> from <at2> More... | |
| bool | atom_is_backbone (Size const atomno) const |
| Returns true if this residue's atom with index number <atomno> is a backbone atom. More... | |
| bool | atom_is_hydrogen (Size const atomno) const |
| Returns true if this residue's atom with index number <atomno> is a hydrogen. More... | |
| Size | atom_base (Size const atomno) const |
| Returns the atom index of the <atomno> atom's base atom. More... | |
| Size | abase2 (Size const atomno) const |
| Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor) More... | |
| AtomIndices const & | bonded_neighbor (Size const atm) const |
| Returns the AtomIndices for all bonded neighbor atoms of <atm> More... | |
| AtomIndices const & | mainchain_atoms () const |
| Returns the AtomIndices of this residue's mainchain atoms. More... | |
| Size | mainchain_atom (Size const i) const |
| Returns the atom index of the residue's ith mainchain atom. More... | |
| Size | n_mainchain_atoms () const |
| Returns the number of the residue's mainchain atoms. More... | |
| AtomIndices const & | actcoord_atoms () const |
| Returns the AtomIndices of atoms that will be used to define this residue's actcoord. More... | |
| Vector | build_atom_ideal (int const atomno, Conformation const &conformation) const |
| Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms. More... | |
| Size | nbr_atom () const |
| Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids. More... | |
| Real | nbr_radius () const |
| Returns the distance cutoff value used as a radius for neighbor definition. More... | |
| Vector const & | nbr_atom_xyz () const |
| AtomIndices const & | atoms_with_orb_index () const |
| Vector | build_orbital_xyz (Size const orbital_index) const |
| Vector const & | orbital_xyz (Size const orbital_index) const |
| void | set_orbital_xyz (core::Size const orbital_index, Vector const &xyz_in) |
| Size | n_orbitals () const |
| Returns the number of orbitals in this residue. More... | |
| utility::vector1< Size > const & | bonded_orbitals (Size const atm) const |
| std::string const & | orbital_name (Size const orbital_index) const |
| chemical::orbitals::OrbitalType const & | orbital_type (Size const orbital_index) const |
| Size | orbital_type_index (Size const orbital_index) const |
| void | update_orbital_coords () |
| bool | misplaced () const |
| Return whether or not the Residue was incorrectly oriented and placed within the polymer when created. More... | |
| ResidueOP | create_rotamer () const |
| Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out. More... | |
| ResidueOP | create_residue () const |
| Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out. More... | |
| ResidueType const & | type () const |
| Returns this residue's ResidueType. More... | |
| ResidueTypeCOP | type_ptr () const |
| Returns this residue's ResidueType as a COP. More... | |
| chemical::ResidueConnection const & | upper_connect () const |
| Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue. More... | |
| chemical::ResidueConnection const & | lower_connect () const |
| Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue. More... | |
| bool | connections_match (Residue const &other) const |
| Returns true if ??? More... | |
| Size | n_possible_residue_connections () const |
| Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType. More... | |
| Size | n_current_residue_connections () const |
| Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!! More... | |
| Size | n_polymeric_residue_connections () const |
| Returns the number of polymeric ResidueConnections on this residue. More... | |
| Size | n_non_polymeric_residue_connections () const |
| Returns the number of non-polymeric ResidueConnections on this residue. More... | |
| chemical::ResidueConnection const & | residue_connection (Size const resconn_index) const |
| Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue. More... | |
| Size | residue_connect_atom_index (Size const resconn_id) const |
| chemical::ResConnID | connect_map (Size resconn_index) const |
| void | mark_connect_incomplete (Size resconn_index) |
| core::Size | connect_map_size () const |
| Returns the size (number of elements) in the connect_map_ object. More... | |
| void | clear_residue_connections () |
| void | update_connections_to_other_residue (Residue const &other_rsd) |
| Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number). More... | |
| void | copy_residue_connections_from (Residue const &src) |
| bool | has_incomplete_connection () const |
| bool | has_incomplete_connection (core::Size const atomno) const |
| Returns true is <atomno> has complete connectivity? More... | |
| bool | connection_incomplete (Size resconnid) const |
| chemical::ResConnID | actual_residue_connection (Size resconnid) const |
| Get the residue connection. How is this different than residue_connection? More... | |
| id::AtomID | inter_residue_connection_partner (int connid, Conformation const &conformation) const |
| This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More... | |
| Size | connected_residue_at_resconn (Size const resconn_index) const |
| Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More... | |
| Size | connected_residue_at_upper () const |
| Returns the residue number of a residue connected to this residue at this residue's upper_connect. More... | |
| Size | connected_residue_at_lower () const |
| Returns the residue number of a residue connected to this residue at this residue's lower_connect. More... | |
| Size | residue_connection_partner (Size const resconn_index) const |
| Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More... | |
| void | copy_residue_connections (Residue const &src_rsd, bool const suppress_warnings=false) |
| Attempt to take residue connection info from src_rsd. More... | |
| Size | residue_connection_conn_id (Size const resconn_index) const |
| Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index. More... | |
| void | residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid) |
| set a connection to this residue by adding its partner's residue number More... | |
| id::AtomID | resolve_partial_atom_id (id::PartialAtomID const &partial_id) const |
| Resolve a partial atom ID into an AtomID for this residue. More... | |
| Distance | connection_distance (conformation::Conformation const &conf, Size const resconn_index, Vector const &matchpoint) const |
| Distance between a potential residue connection match and the position of the expected atom. More... | |
| bool | is_bonded (Residue const &other) const |
| Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides) More... | |
| bool | is_pseudo_bonded (Residue const &other) const |
| Do I have any pseudobonds to other? More... | |
| bool | is_bonded (Size const other_residue_index) const |
| Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic. More... | |
| bool | is_pseudo_bonded (Size const other_index) const |
| Do I have any pseudobonds to other? More... | |
| bool | is_polymer_bonded (Residue const &other) const |
| Am I polymer bonded to other? More... | |
| bool | is_polymer_bonded (Size const other_index) const |
| Am I polymer-bonded to other? checks lower and upper connections. More... | |
| utility::vector1< Size > const & | connections_to_residue (Residue const &other) const |
| Returns the vector1 of resconn ids that connect this residue to other. More... | |
| utility::vector1< Size > const & | connections_to_residue (Size const other_resid) const |
| Returns the vector1 of resconn ids that connect this residue to other. More... | |
| PseudoBondCollectionCOP | get_pseudobonds_to_residue (Size resid) const |
| std::map< Size, PseudoBondCollectionCOP > const & | pseudobonds () const |
| void | set_pseudobonds_to_residue (Size resid, PseudoBondCollectionCOP pbs) |
| utility::vector1< std::pair< Real, Real > > const & | chi_rotamers (Size const chino) const |
| Returns the chi rotamers available for this residue's chi angle <chino> More... | |
| AtomIndices const & | cut_bond_neighbor (Size const atm) const |
| atom indices for bonded neighbors to which atom-tree connections are disallowed. More... | |
| core::Size | n_bonded_neighbor_all_res (core::Size const atomno, bool virt=false) const |
| Returns the number of atoms bonded to <atomno> in all residues? More... | |
| AtomIndices const & | nbrs (Size const atm) const |
| Convenience synonym for bonded_neighbor. More... | |
| utility::vector1< Real > const & | mainchain_torsions () const |
| Returns the mainchain torsion angles of this residue (const) More... | |
| utility::vector1< Real > & | mainchain_torsions () |
| Returns the mainchain torsion angles of this residue (non-const) More... | |
| void | mainchain_torsions (utility::vector1< Real > const &torsions) |
| Sets the mainchain torsion angles of this residue to <torsions> More... | |
| Real | mainchain_torsion (Size const torsion) const |
| Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid. More... | |
| Size | nchi () const |
| Returns the number of chi angles this residue has. More... | |
| utility::vector1< Real > const & | chi () const |
| Returns the chi torsion angles of this residue (const) More... | |
| utility::vector1< Real > & | chi () |
| Returns the chi torsion angles of this residue (non-const) More... | |
| void | chi (utility::vector1< Real > const &chis) |
| Sets the chi torsion angles of this residue. More... | |
| Real | chi (Size const chino) const |
| get a specific chi torsion angle More... | |
| utility::vector1< AtomIndices > const & | chi_atoms () const |
| Returns the AtomIndices of each set of four atoms defining each chi angle. More... | |
| AtomIndices const & | chi_atoms (Size const chino) const |
| Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle. More... | |
| Size | n_nus () const |
| Return the number of nu (internal ring) angles this residue has. More... | |
| utility::vector1< core::Angle > const & | nus () const |
| Return the nu (internal ring) torsion angles of this residue. More... | |
| utility::vector1< core::Angle > & | nus () |
| Return the nu (internal ring) torsion angles of this residue. (non-const) More... | |
| core::Angle | nu (core::uint const index) const |
| Get a specific nu (internal ring) torsion angle by index. More... | |
| utility::vector1< AtomIndices > const | nu_atoms () const |
| Return the AtomIndices of each set of four atoms defining each nu angle. More... | |
| AtomIndices const | nu_atoms (core::uint const index) const |
| Return the AtomIndices of the four atoms defining the specified nu angle. More... | |
| chemical::rings::RingConformer const & | ring_conformer (core::uint const ring_num, core::Real limit=90.0) const |
| Return the current RingConformer of this residue's nth ring. More... | |
| Size | seqpos () const |
| Returns the sequence position of this residue. More... | |
| void | seqpos (Size const setting) |
| Sets this residue's sequence position to <setting> More... | |
| Size | polymeric_sequence_distance (Residue const &other) const |
| Returns the sequence separation distance between this residue and <other> More... | |
| int | polymeric_oriented_sequence_distance (Residue const &other) const |
| Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence. More... | |
| core::Size | chain () const |
| Returns this residue's chain id. More... | |
| void | chain (core::Size const setting) |
| Sets this residue's chain id. More... | |
| bool | requires_actcoord () const |
| does this residue require an actcoord? More... | |
| void | update_actcoord () |
| Updates actcoord for this residue. More... | |
| Vector const & | actcoord () const |
| Returns the coordinates used for pairE calculations (amino acids only) More... | |
| Vector & | actcoord () |
| Returns the coordinates used for pairE calculations (amino acids only) More... | |
| void | update_sequence_numbering (utility::vector1< Size > const &old2new) |
| Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped. More... | |
| void | update_nus () |
| Calculate the set of nu dihedrals from the xyz coordinates and store them. More... | |
| bool | is_polymer () const |
| Returns true if this residue is a polymer. More... | |
| bool | is_protein () const |
| Returns true if this residue is an amino acid. More... | |
| bool | is_peptoid () const |
| Returns if this residue is a peptoid. More... | |
| bool | is_aramid () const |
| Returns if this residue is an aramid. More... | |
| bool | is_ortho_aramid () const |
| Returns if this residue is an ortho aramid. More... | |
| bool | is_pre_methylene_ortho_aramid () const |
| Returns if this residue is a pre methylene ortho aramid. More... | |
| bool | is_post_methylene_ortho_aramid () const |
| Returns if this residue is a post methylene ortho aramid. More... | |
| bool | is_pre_methylene_post_methylene_ortho_aramid () const |
| Returns if this residue is a post methylene ortho aramid. More... | |
| bool | is_meta_aramid () const |
| Returns if this residue is a meta aramid. More... | |
| bool | is_pre_methylene_meta_aramid () const |
| Returns if this residue is a pre methylene meta aramid. More... | |
| bool | is_post_methylene_meta_aramid () const |
| Returns if this residue is a post methylene meta aramid. More... | |
| bool | is_pre_methylene_post_methylene_meta_aramid () const |
| Returns if this residue is a post methylene meta aramid. More... | |
| bool | is_para_aramid () const |
| Returns if this residue is a para aramid. More... | |
| bool | is_pre_methylene_para_aramid () const |
| Returns if this residue is a pre methylene para aramid. More... | |
| bool | is_post_methylene_para_aramid () const |
| Returns if this residue is a post methylene para aramid. More... | |
| bool | is_pre_methylene_post_methylene_para_aramid () const |
| Returns if this residue is a post methylene para aramid. More... | |
| bool | is_sri () const |
| Is this one of SRI's special heteropolymer building blocks? More... | |
| bool | is_triazolemer () const |
| Returns true if and only if this residue is a triazolemer. More... | |
| bool | is_DNA () const |
| Returns true if this residue is a DNA residue. More... | |
| bool | is_RNA () const |
| Returns true if this residue is a RNA residue. More... | |
| bool | is_TNA () const |
| Returns true if this residue is a TNA residue. More... | |
| bool | is_l_rna () const |
| Returns true if this residue is a L-RNA residue. More... | |
| bool | is_d_rna () const |
| Returns true if this residue is a D-RNA residue. More... | |
| bool | is_NA () const |
| Returns true if this residue is a nucleic acid. More... | |
| bool | is_purine () const |
| Returns true if this residue is a purine. More... | |
| bool | is_pyrimidine () const |
| Returns true if this residue is a pyrimidine. More... | |
| bool | is_carbohydrate () const |
| Returns true if this residue is a carbohydrate. More... | |
| bool | is_water () const |
| Returns true if this residue is water. More... | |
| bool | is_ligand () const |
| Returns true if this residue is a ligand. More... | |
| bool | is_metal () const |
| Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES. More... | |
| bool | is_metalbinding () const |
| Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES. More... | |
| bool | is_surface () const |
| Returns true if this residue is a surface residue. More... | |
| bool | has_sc_orbitals () const |
| Returns true if the residue has side chain orbitals. More... | |
| bool | is_polar () const |
| Returns true if the residue is polar. More... | |
| bool | is_apolar () const |
| bool | is_charged () const |
| Returns true if the residue is charged. More... | |
| bool | is_aromatic () const |
| Returns true if the residue is aromatic. More... | |
| bool | is_coarse () const |
| residue is coarse (used for RNA right now) More... | |
| bool | is_terminus () const |
| Returns true if the residue has a terminus property. More... | |
| bool | is_upper_terminus () const |
| Return true if the residue has an upper terminus property. More... | |
| bool | is_lower_terminus () const |
| Returns true if the residue has a lower terminus property. More... | |
| bool | is_branch_point () const |
| Return true if the residue is a branch point variant. More... | |
| bool | is_similar_rotamer (Residue const &other) const |
| Returns true if the chi angles of another residue all fall within 5 deg. More... | |
| bool | is_similar_aa (Residue const &other) const |
| Returns true if the aa residue types are the same. More... | |
| bool | has_shadow_atoms () const |
| Return true if and only if this residue's type has shadow atoms. More... | |
| bool | has_property (std::string const &property) const |
| Return true if the residue has <property>. More... | |
| bool | has_variant_type (chemical::VariantType const variant_type) const |
| Generic variant access. More... | |
| std::string const & | atom_name (Size const atm) const |
| Returns the name of this residue's atom with index number <atm> More... | |
| std::string const & | mm_atom_name (Size const atom) const |
| Returns the mm_atom_name of this residue's atom with index number <atom> More... | |
| std::string const & | name () const |
| Returns this residue's ResidueType name. More... | |
| std::string const & | name3 () const |
| Returns this residue's 3-letter representation. More... | |
| char | name1 () const |
| Returns this residue's 1-letter representation. More... | |
| std::string | annotated_name (bool const show_all_variants=true) const |
| Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D]. More... | |
| chemical::AA const & | aa () const |
| Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration. More... | |
| chemical::AA const & | backbone_aa () const |
| Returns this residue's backbone_aa type, if any. More... | |
| chemical::AA const & | na_analogue () const |
| Returns the nucleic acid type to be used for fragment sampling. More... | |
| chemical::AtomICoor const & | icoor (Size const atm) const |
| Returns the internal coordinates of this residue's atom with index number <atm> More... | |
| bool | atom_depends_on_lower (core::Size const atom_index) const |
| Does this atom depend on the LOWER_CONNECT? More... | |
| bool | atom_depends_on_upper (core::Size const atom_index) const |
| Does this atom depend on the UPPER_CONNECT? More... | |
| void | set_d (int const chino, Real const setting) |
| bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example More... | |
| void | set_theta (int const chino, Real const setting) |
| bondangle analog to set_chi same idea as set_d More... | |
| void | set_tau (Size const nuno, Real const setting) |
| set_theta for nus More... | |
| void | set_all_nu (utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) |
| void | set_all_ring_nu (Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus) |
| void | set_chi (int const chino, Real const setting) |
| Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree. More... | |
| void | set_all_chi (utility::vector1< Real > const &chis) |
| Sets all of this residue's chi angles using the set_chi function (wrapper function) More... | |
| bool | has (std::string const &atm) const |
| Returns true if this residue has an atom named <atm> More... | |
| bool | fill_missing_atoms (utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true) |
| Builds coordinates for atoms missing from this residue assuming ideal internal coordinates. More... | |
| void | select_orient_atoms (Size ¢er, Size &nbr1, Size &nbr2) const |
| Selects three atoms for orienting this residue. More... | |
| void | orient_onto_residue (Residue const &src) |
| Orient our coords onto those of <src>, using the atoms from select_orient_atoms. More... | |
| void | orient_onto_residue (Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) |
| Orient our coords onto those of <src>, using the three atom pairs specified in the input. More... | |
| void | orient_onto_residue_peptoid (Residue const &src, Conformation const &conformation) |
| Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide. More... | |
| void | orient_onto_location (Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) |
| Orients residue object onto atom locations. More... | |
| void | orient_onto_location (Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton) |
| Orients residue object onto atom locations. More... | |
| bool | place (Residue const &src, Conformation const &conformation, bool preserve_c_beta=false) |
| Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match. More... | |
| void | apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > R, Vector v) |
| Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space. More... | |
| core::chemical::rna::RNA_Info const & | RNA_info () const |
| Return the RNA_residueType object. This is RNA specific. More... | |
| core::chemical::carbohydrates::CarbohydrateInfoCOP | carbohydrate_info () const |
| Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More... | |
| basic::datacache::BasicDataCacheCOP | data_ptr () const |
| BasicDataCache indexed by enum in residue_datacache.hh. More... | |
| basic::datacache::BasicDataCacheOP | nonconst_data_ptr () |
| BasicDataCache indexed by enum in residue_datacache.hh. More... | |
| basic::datacache::BasicDataCache const & | data () const |
| BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More... | |
| basic::datacache::BasicDataCache & | nonconst_data () |
| BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More... | |
| bool | mirrored_relative_to_type () const |
| Is this residue mirrored relative to its coordinates in the ResidueType? More... | |
| void | set_mirrored_relative_to_type (bool const setting) |
| Set whether this residue is mirrored relative to its coordinates in the ResidueType. More... | |
Private Member Functions | |
| Residue (Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality) | |
| Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve. More... | |
| void | init_residue_from_other (Residue const &src) |
| Function called by both copy constructors, to avoid code duplication. More... | |
| void | update_connections_to_residues () |
| Updates connections_to_residues_ using connect_map_. More... | |
| void | apply_transform_downstream (core::Size const atomno, core::Size const upstream_atomno, numeric::xyzMatrix< Real > const &R, Vector const &v) |
| apply transform of rotation R and translation V for all atoms downstream More... | |
| void | determine_nonstandard_polymer_status () |
| Residue const & | operator= (Residue const &rhs) |
| Assignment operator does not work for class Residue. This function is intentionally unimplemented and private. More... | |
| void | orient_onto_residue (Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2) |
| Orient coords onto those of <src>, using the specified atoms. More... | |
| void | assign_orbitals () |
| Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors. More... | |
Private Attributes | |
| ResidueTypeCOP | rsd_type_ptr_ |
| Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed. More... | |
| ResidueType const & | rsd_type_ |
| our Residue type More... | |
| Atoms | atoms_ |
| our conformation atoms (not kinematic atom pointers) with xyz positions and atom type More... | |
| utility::vector1< orbitals::OrbitalXYZCoordsOP > | orbitals_ |
| Size | seqpos_ |
| the sequence position More... | |
| bool | mirrored_relative_to_type_ |
| Is this residue mirrored relative to its coordinates in the ResidueType? More... | |
| core::Size | chain_ |
| the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. More... | |
| utility::vector1< Real > | chi_ |
| our chi (side chain) torsion angles More... | |
| utility::vector1< Angle > | nus_ |
| our nu (internal ring) torsion angles More... | |
| utility::vector1< Real > | mainchain_torsions_ |
| our (possibly empty) backbone torsion angles More... | |
| Vector | actcoord_ |
| the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair More... | |
| basic::datacache::BasicDataCacheOP | data_cache_ |
| bool | misplaced_ = false |
| Inter-residue connection data. More... | |
| bool | nonstandard_polymer_ |
| true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1 More... | |
| utility::vector1< chemical::ResConnID > | connect_map_ |
| map between connection ids on this residue and the connection points on other residues to which its bonded More... | |
| std::map< Size, utility::vector1< Size > > | connections_to_residues_ |
| lists for each connected residue of the connection points on this residue that connect the pair. More... | |
| std::map< Size, PseudoBondCollectionCOP > | pseudobonds_ |
| other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds) More... | |
Detailed Description
Instance Residue class, used for placed residues and rotamers.
This class is designed to be lightweight. It holds a const-reference ("rsd_type_") to a ResidueType object for access to information common to all instances of a single type, e.g., Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:
- a vector1 of Atoms, which holds the positions (and also the atom-types for fast access during scoring);
- the sequence position and chain number, both integers (See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.)
- the backbone, side-chain, and internal ring (if applicable) torsion angles (of course backbone torsions are not unique to a rotamer, and the chi angles are derivable from the coordinates, but storing them in the residue is convenient for scoring purposes).
- the coordinates of an interaction center or centroid, used e.g., in the knowledge-based full-atom pair term ("actcoord_"). Maybe this will also hold the centroid position for centroid-mode scoring??
Member Typedef Documentation
◆ AtomIndices
◆ AtomType
◆ ResidueType
◆ ResidueTypeCOP
Constructor & Destructor Documentation
◆ Residue() [1/5]
| core::conformation::Residue::Residue | ( | ResidueTypeCOP | rsd_type_in, |
| bool const | dummy_arg | ||
| ) |
constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue.
Constructor from ResidueTypeCOP; sets coords to ideal values create a residue of type residue_type_in.
- Note
- Dummmy arg to prevent secret type conversions from ResidueTypeCOP to Residue
References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().
Referenced by clone_flipping_chirality().
◆ Residue() [2/5]
| core::conformation::Residue::Residue | ( | ResidueType const & | rsd_type_in, |
| bool const | dummy_arg | ||
| ) |
constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue.
Constructor from residue type; sets coords to ideal values create a residue of type residue_type_in.
- Note
- Dummmy arg to prevent secret type conversions from ResidueType to Residue
References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().
◆ Residue() [3/5]
| core::conformation::Residue::Residue | ( | ResidueType const & | rsd_type_in, |
| Residue const & | current_rsd, | ||
| Conformation const & | conformation, | ||
| bool | preserve_c_beta = false, |
||
| bool | allow_alternate_backbone_matching = false |
||
| ) |
Rotamer-style constructor; orients ideal coords onto backbone of current_rsd.
Create a residue/rotamer of type rsd_type_in placed at the position occupied by current_rsd Used primarily in rotamer building. The newly created Residue has the same sequence position, chain id and mainchain torsion angles as current_rsd. It has a ResidueType as defined by rsd_type_in. Its side-chain chi angles are uninitialized as all 0.0 and sidechain atom coords are from ideal coords. Its backbone is aligned with that of current_rsd. Its residue connections and its pseudobonds must be initialized from the original residue.
- Parameters
-
<allow_alternate_backbone_matching> If true, the number of main-chain atoms in the input ResidueType need not match the number in the template Residue. A function will be called that will attempt to align the Residues' connections. If successful, the new Residue will be created; if unsuccessful, an empty Residue will be returned.
References assign_orbitals(), atom(), core::chemical::ResidueType::atom_type_index(), atoms_, chi_, chi_atoms(), core::chemical::ResidueType::chi_atoms(), copy_residue_connections(), core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mainchain_atoms(), mainchain_torsions(), misplaced_, core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::n_nus(), n_nus(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), nus_, place(), pseudobonds_, rsd_type_, core::conformation::TR(), type(), update_nus(), and xyz().
◆ Residue() [4/5]
| core::conformation::Residue::Residue | ( | Residue const & | src | ) |
Copy constructor.
References init_residue_from_other().
◆ ~Residue()
|
overridedefault |
Destructor.
◆ Residue() [5/5]
|
private |
Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve.
References atom(), chi_, chi_atoms(), core::chemical::ResidueType::chi_atoms(), init_residue_from_other(), mirrored_relative_to_type(), nchi(), rsd_type_, set_mirrored_relative_to_type(), type(), and xyz().
Member Function Documentation
◆ aa()
|
inline |
Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration.
References core::chemical::ResidueTypeBase::aa(), and rsd_type_.
Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::hybridization::add_non_protein_cst(), protocols::toolbox::sample_around::add_virtual_res(), core::pose::addVirtualResAsRoot(), protocols::denovo_design::components::advance_past_virtual_residues(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::protein_interface_design::Revert::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::idealize::IdealizeMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::nmr::pre::PREMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::simple_moves::VirtualRootMover::apply(), core::pose::rna::RNA_IdealCoord::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::energy_methods::ProQ_Energy::atom13_0(), core::energy_methods::FastDensEnergy::atomistic_energy(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::atoms_with_dof_derivatives(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::idealize::basic_idealize(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::build_rna_rotamers(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), core::energy_methods::MPSpanInsertionEnergy::calc_span_score(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::energy_methods::RG_Energy_Fast::calculate_rg_score(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::rna::denovo::check_base_pair(), protocols::denovo_design::components::StructureData::check_pose(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), core::scoring::rna::check_watson_crick_sequence(), protocols::loops::Loop::choose_cutpoint(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), core::scoring::dssp::Dssp::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::sasa_scores::compute_avge_scores(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::constraint_generator::compute_hnq_atoms(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), protocols::esm_perplexity::PseudoPerplexityMetric::compute_perplexity(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::relax::AtomCoordinateCstMover::compute_residue_subset(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), protocols::sasa_scores::compute_sasapack_scores(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::energy_methods::ProClosureEnergy::defines_intrares_energy_for_residue(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::energy_methods::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensCenEnergy::defines_residue_pair_energy(), core::energy_methods::ElecDensEnergy::defines_residue_pair_energy(), core::energy_methods::FastDensEnergy::defines_residue_pair_energy(), core::energy_methods::PointWaterEnergy::defines_score_for_residue_pair(), core::energy_methods::ProClosureEnergy::defines_score_for_residue_pair(), core::energy_methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_proline_design(), core::scoring::constraints::ResidueCouplingConstraint::dist(), core::scoring::constraints::ResidueTypeLinkingConstraint::dist(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FiberDiffractionEnergy::eval_atom_derivative(), core::energy_methods::XtalMLEnergy::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::MgEnergy::eval_intrares_energy(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::energy_methods::CartesianBondedEnergy::eval_singleres_energy(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::rna::denovo::figure_out_base_pair_partner(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), core::energy_methods::MembraneLipo::finalize_total_energy(), core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::dna::find_basepairs(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), protocols::relax::fix_worst_bad_ramas(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_loops(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::pose::motif::get_backbone_reference_frame_atomids(), core::energy_methods::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pack::interaction_graph::SimpleEdge::get_bb_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::pose::get_center_of_mass(), core::energy_methods::HackAroEnergy::get_centroid(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::data::RNA_DMS_Potential::get_features(), core::pose::motif::get_frame_ala(), core::pose::motif::get_frame_arg(), core::pose::motif::get_frame_asn(), core::pose::motif::get_frame_asp(), core::pose::motif::get_frame_cys(), core::pose::motif::get_frame_gln(), core::pose::motif::get_frame_glu(), core::pose::motif::get_frame_gly(), core::pose::motif::get_frame_his(), core::pose::motif::get_frame_ile(), core::pose::motif::get_frame_leu(), core::pose::motif::get_frame_lys(), core::pose::motif::get_frame_met(), core::pose::motif::get_frame_phe(), core::pose::motif::get_frame_pro(), core::pose::motif::get_frame_ser(), core::pose::motif::get_frame_thr(), core::pose::motif::get_frame_trp(), core::pose::motif::get_frame_tyr(), core::pose::motif::get_frame_val(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hybridization::get_num_residues_nonvirt(), core::pose::rna::get_number_base_pairs(), core::pose::rna::get_number_native_base_pairs(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::sic_dock::get_rg(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pose::motif::get_sidechain_reference_frame(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream(), protocols::electron_density::get_spectrum(), core::import_pose::RNA_BasePairHandler::get_stem_residues(), core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), protocols::hybridization::CartesianSampler::get_transform(), core::scoring::dna::get_z_axis(), core::pose::carbohydrates::glycosylate_pose(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::constel::has_aromatic(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::features::ReportToDB::initialize_pose(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), core::io::serialization::is_pseudoresidue(), is_similar_aa(), is_similar_rotamer(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::simple_filters::ResidueDepthFilter::make_context(), core::pack::make_symmetric_task(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), core::conformation::missing_stubs_build(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::ShearMover::move_with_rama(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::ncbb::ncbb_design_main_loop(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::electron_density::BfactorMultifunc::operator()(), core::conformation::WatsonCrickResidueMatcher::operator()(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::PairEPotential::pair_term_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::ncbb::oop::pep_COM(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), core::scoring::electron_density::pose_has_nonzero_Bs(), core::energy_methods::FastDensEnergy::pose_is_setup_for_density_scoring(), protocols::electron_density::pose_spherical_samples(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::simple_filters::ResidueDepthCalculator::read_unit_waterbox(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::electron_density::remove_occupied_density_from_density(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::CenRotEnvEnergy::residue_energy(), core::energy_methods::EnvEnergy::residue_energy(), core::energy_methods::MembraneCbetaEnergy::residue_energy(), core::energy_methods::MembraneEnvEnergy::residue_energy(), core::energy_methods::MPCbetaEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::energy_methods::P_AA_ss_Energy::residue_energy(), core::energy_methods::RamachandranEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::SequenceDependentRefEnergy::residue_energy(), core::energy_methods::SmoothEnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::DNA_ReferenceEnergy::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), core::energy_methods::ElecDensAllAtomCenEnergy::residue_pair_energy(), core::energy_methods::ElecDensAtomwiseEnergy::residue_pair_energy(), core::energy_methods::ElecDensCenEnergy::residue_pair_energy(), core::energy_methods::ElecDensEnergy::residue_pair_energy(), core::energy_methods::FastDensEnergy::residue_pair_energy(), core::energy_methods::ProClosureEnergy::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::scoring::rna::chemical_shift::ring_current_effect(), core::scoring::rna::chemical_shift::ring_current_effect_individual_ring(), core::scoring::rna::chemical_shift::ring_pos(), core::pack::dunbrack::rotamer_from_chi(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::ResidueTypeLinkingConstraint::score(), core::scoring::MembranePotential::score_normal_center(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::hbnet::HBNet::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), core::pose::setup_dof_mask_from_move_map(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::ElecDensEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::RG_Energy_Fast::setup_for_derivatives(), core::energy_methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::energy_methods::Abego::setup_for_scoring(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensAtomwiseEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), protocols::scoring::Interface::show(), protocols::hybridization::DDomainParse::split(), core::fragment::SingleResidueFragData::steal(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), protocols::denovo_design::symmetric_fold_tree(), protocols::electron_density::symmetrizeBfactors(), protocols::fldsgn::topology::BB_Pos::take_coordinates_from_pose(), core::scoring::BB_Pos::take_coordinates_from_pose(), core::scoring::MembranePotential::termini_penalty(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::hybridization::MRMover::trim_target_pose(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(), protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().
◆ abase2()
Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor)
References core::chemical::ResidueType::abase2(), and rsd_type_.
Referenced by core::scoring::hbonds::assign_abase_derivs(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::magnesium::get_cos_theta(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::dna::PDBOutput::output_hbond_info(), and protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().
◆ accpt_pos()
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inline |
Returns the AtomIndices of this residue's h-bond acceptor atoms.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.accpt_pos() See also: Residue Residue.accpt_pos_sc Residue.atoms Pose
References core::chemical::ResidueType::accpt_pos(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::energy_methods::OccludedHbondSolEnergy::atom_is_acceptor(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_acceptor(), core::pose::rna::atom_is_acceptor(), core::energy_methods::OccludedHbondSolEnergy::atom_is_valid_base(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pose::rna::bases_form_a_hydrogen_bond(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::compute_exact_geosol(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::features::HBondFeatures::report_features(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::ExactOccludedHbondSolEnergy::residue_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().
◆ accpt_pos_sc()
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inline |
Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.accpt_pos_sc() See also: Residue Residue.accpt_pos Residue.atoms Pose
References core::chemical::ResidueType::accpt_pos_sc(), and rsd_type_.
Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().
◆ actcoord() [1/2]
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inline |
Returns the coordinates used for pairE calculations (amino acids only)
References actcoord_.
◆ actcoord() [2/2]
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inline |
Returns the coordinates used for pairE calculations (amino acids only)
References actcoord_.
Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows(), core::conformation::orient_residue_for_ideal_bond(), core::scoring::PairEPotential::pair_term_energy(), protocols::features::PairFeatures::report_residue_pairs(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), and update_actcoord().
◆ actcoord_atoms()
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inline |
Returns the AtomIndices of atoms that will be used to define this residue's actcoord.
References core::chemical::ResidueType::actcoord_atoms(), and rsd_type_.
Referenced by core::energy_methods::PairEnergy::eval_residue_pair_derivatives().
◆ actual_residue_connection()
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inline |
Get the residue connection. How is this different than residue_connection?
References connect_map_.
Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Conformation::detect_pseudobonds().
◆ all_bb_atoms()
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inline |
Returns the AtomIndices of this residue's backbone atoms.
- Note
- : heavyatoms and hydrogens, AtomIndices == vector1< Size >
example(s): residue.all_bb_atoms() See also: Residue Residue.atoms Pose
References core::chemical::ResidueType::all_bb_atoms(), and rsd_type_.
Referenced by protocols::indexed_structure_store::apply_residue_entries_to_pose().
◆ annotated_name()
| std::string core::conformation::Residue::annotated_name | ( | bool const | show_all_variants = true | ) | const |
Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D].
References core::chemical::aa_from_oneletter_code(), name(), name1(), core::chemical::name_from_aa(), and core::chemical::oneletter_code_specifies_aa().
Referenced by core::conformation::Conformation::annotated_sequence(), and core::scoring::rna::output_rna_motif().
◆ apply_transform_downstream()
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private |
apply transform of rotation R and translation V for all atoms downstream
- Note
- note this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.
xyz --> R * xyz + v
this uses information from atom_base array to transform all the downstream atoms along the side chain recursively. it assumes that the atom_base array will not get us into any infinite loops!
- Note
- this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.
References atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), protocols::sic_dock::scores::nbr, nbrs(), core::chemical::ResidueType::root_atom(), rsd_type_, core::conformation::TR(), core::conformation::Atom::xyz(), and xyz().
Referenced by set_all_ring_nu(), set_chi(), set_d(), set_tau(), and set_theta().
◆ apply_transform_Rx_plus_v()
| void core::conformation::Residue::apply_transform_Rx_plus_v | ( | numeric::xyzMatrix< Real > | R, |
| Vector | v | ||
| ) |
Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space.
References core::chemical::ResidueType::natoms(), set_xyz(), type(), and xyz().
◆ assign_orbitals()
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private |
Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors.
References core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueTypeBase::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, rsd_type_, and type().
Referenced by Residue().
◆ atom() [1/4]
Returns this residue's Atom with index number <atm_index> (non-const)
- Note
- : Atom object is xyz and atom_type
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atoms_.
◆ atom() [2/4]
Returns this residue's Atom with index number <atm_index> (const)
- Note
- : Atom object is xyz and atom_type
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atoms_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::energy_methods::add_to_individual_sol_energies(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::RollMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::contact_map::ContactMap::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), apply_transform_downstream(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::energy_methods::ProQ_Energy::atom_feature(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::atomic_depth::atomic_depth(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), attached_H_begin(), attached_H_end(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), build_orbital_xyz(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), core::conformation::build_residue_tree(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::membrane::calc_helix_axis(), core::select::util::calc_sc_neighbors(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), protocols::pose_sewing::calculate_distance_score_bt_residues(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::energy_methods::ProQ_Energy::calculateZ(), core::select::util::cbeta_vector(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::geometry::center_of_mass(), core::pose::center_of_mass(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::rbsegment_relax::ConfChangeMover::check_gaps(), core::scoring::MembranePotential::check_spanning(), protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::relax::RangeRelaxMover::constrain_to_reference(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::energy_methods::ProQ_Energy::crd(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), protocols::legacy_sewing::create_model_from_pose(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), core::conformation::Conformation::debug_residue_torsions(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::energy_methods::LinearChainbreakEnergy::do_score_dev(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::energy_methods::BranchEnergy::finalize_total_energy(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearBranchEnergy::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::features::strand_assembly::find_sheet(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::electron_density::findLoopFromDensity(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), core::pose::get_center_of_mass(), protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands(), protocols::membrane::get_chain_and_z(), protocols::features::strand_assembly::get_closest_distance_between_strands(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), core::scoring::magnesium::get_cos_theta(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::matdes::get_matching_subunits(), protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::electron_density::get_spectrum(), protocols::hybridization::get_superposition_transformation(), protocols::hybridization::CartesianSampler::get_transform(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), protocols::cryst::getMW(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), core::pose::rna::is_rna_chainbreak(), protocols::features::strand_assembly::is_this_strand_at_edge(), core::pose::rna::is_tna_chainbreak(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), mm_atom_name(), protocols::motifs::Motif::Motif(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::dna::PDBOutput::output_hbond_info(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), path_distance(), protocols::ncbb::oop::pep_COM(), place(), protocols::motifs::Motif::place_atom_(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::motifs::Motif::place_residue_helper(), protocols::electron_density::pose_spherical_samples(), core::scoring::PQR::PQR(), core::energy_methods::FA_GrpElecEnergy::precalc_context(), protocols::viewer::print_node(), core::energy_methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::pose::radius_of_gyration(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::SmotifFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::simple_filters::res_res_min_distance(), Residue(), core::conformation::symmetry::residue_center_of_mass(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::Fa_MbenvEnergy::residue_energy(), core::energy_methods::FaMPEnvEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::residue_fast_pair_energy_attached_H(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::toolbox::pose_manipulation::rigid_body_move(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), core::select::util::select_coord_for_residue(), set_all_ring_nu(), set_chi(), protocols::hbnet::HBNet::set_constraints(), set_d(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::design_opt::Supercharge::set_surface(), set_tau(), set_theta(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::NeighborList::setup(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_dis_by_terminals(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::hybridization::DDomainParse::split(), protocols::rbsegment_relax::ConfChangeMover::stage2(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), core::util::switch_to_centroid_rot_set(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), core::scoring::MembranePotential::tm_projection_penalty(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), update_nus(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), core::scoring::epr_deer::EPRSpinLabel::weight(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), core::scoring::PoissonBoltzmannPotential::write_pqr(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_starting_loop(), core::chemical::ICoorAtomID::xyz(), and xyz().
◆ atom() [3/4]
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Returns this residue's Atom with name <atm_name> (non-const)
- Note
- : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atom_index(), and atoms_.
◆ atom() [4/4]
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Returns this residue's Atom with name <atm_name> (const)
- Note
- : Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom
example(s): residue.atom(3) See also: Residue Residue.atoms Pose
References atom_index(), and atoms_.
◆ atom_base()
Returns the atom index of the <atomno> atom's base atom.
References core::chemical::ResidueType::atom_base(), and rsd_type_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), core::energy_methods::add_to_individual_sol_energies(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::hbonds::assign_abase_derivs(), core::energy_methods::assign_rna_atom_type(), core::energy_methods::OccludedHbondSolEnergy::atom_is_valid_base(), core::energy_methods::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::pose::rna::bases_form_a_hydrogen_bond(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::energy_methods::compute_exact_geosol(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::pack::interaction_graph::create_hbonds_one_way(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::hbonds::determine_atom_level_edge_info(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), protocols::pockets::PocketGrid::findExemplars(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::magnesium::get_cos_theta(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), protocols::protein_interface_design::hbonded_atom(), core::pose::rna::heavy_atom_is_polar(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::HBondFeatures::insert_site_row(), core::energy_methods::is_base_2(), core::energy_methods::is_phosphate_2(), core::energy_methods::StackElecEnergy::is_rna_base(), core::energy_methods::is_sugar_2(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::dna::PDBOutput::output_hbond_info(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(), protocols::features::HBondFeatures::report_features(), core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::energy_methods::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), and protocols::md::Rattle::setup_constraint().
◆ atom_begin() [1/2]
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begin interator, to iterate over atoms
References atoms_.
Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::environment::com_calc(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs(), and core::scoring::interface_::DDPscore::residue_pair_energy().
◆ atom_begin() [2/2]
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References atoms_.
◆ atom_depends_on_lower()
| bool core::conformation::Residue::atom_depends_on_lower | ( | core::Size const | atom_index | ) | const |
Does this atom depend on the LOWER_CONNECT?
Now based on a simple lookup, based on data initialized during ResidueType::finalize().
References core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(), atom_index(), and rsd_type_.
Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().
◆ atom_depends_on_upper()
| bool core::conformation::Residue::atom_depends_on_upper | ( | core::Size const | atom_index | ) | const |
Does this atom depend on the UPPER_CONNECT?
Now based on a simple lookup, based on data initialized during ResidueType::finalize().
References core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(), atom_index(), and rsd_type_.
Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().
◆ atom_end() [1/2]
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end interator, to iterate over atoms
References atoms_.
Referenced by protocols::simple_filters::AtomicContactFilter::compute(), and protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs().
◆ atom_end() [2/2]
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References atoms_.
◆ atom_index()
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Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid.
example(s): residue.atom_index("CA") See also: Residue AtomType Pose
References core::chemical::ResidueType::atom_index(), and rsd_type_.
Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts_to_rb(), protocols::seeded_abinitio::add_dist_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), core::pose::ncbb::add_generic_hbs_constraint(), protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), protocols::antibody::constraints::add_harmonic_dihedral_cst_general(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::pose::ncbb::add_oop_constraint(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::pose::ncbb::add_triazole_constraint(), protocols::loops::addScoresForLoopParts(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_residue(), core::pose::Pose::append_residue_by_atoms(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::splice::Splice::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_dihedral_bbg(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), protocols::constel::PresenceCommon::are_atoms_pres(), atom(), atom_depends_on_lower(), atom_depends_on_upper(), protocols::hydrate::atom_is_hydratable(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::conformation::build_residue_tree(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), core::select::util::calc_sc_neighbors(), core::energy_methods::GoapEnergy::calculate_dipoles(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::antibody::cdr_backbone_rmsds(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), protocols::loop_grower::LoopGrower::check_coordinates(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), protocols::flxbb::constraints_sheet(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::pose::correctly_add_2prime_connection_variants(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::relax::cyclize_pose(), core::conformation::Conformation::declare_chemical_bond(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), first_adjacent_heavy_atom(), protocols::splice::fix_chain_break_residue(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::form_disulfide(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), get_adjacent_heavy_atoms(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), get_atoms_exocyclic_to_ring_atom(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond(), core::pose::get_constraints_from_link_records(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), get_hydrogens_bonded_to_ring_atom(), protocols::simple_moves::BBConRotMover::get_L_move(), core::scoring::loop_graph::get_loop_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::lDDT_Calculator::get_matching_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), get_substituents_to_ring_atom(), protocols::constel::has_aromatic(), protocols::constel::FilterBySASA::has_low_per_atom_sasa(), protocols::protein_interface_design::hbonded_atom(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::frags::TorsionFragment::insert(), core::pose::Pose::insert_residue_by_atoms(), core::io::pose_from_sfr::is_connected(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::constel::HBondCommon::is_rmoi_hbonded(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), core::pose::make_atom_map(), protocols::simple_moves::BBConRotMover::make_move(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), core::conformation::named_atom_id_to_atom_id(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::tcr::orient_tcr_chain(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::constraint_generator::parse_custom_torsion(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate(), protocols::viewer::print_node(), core::conformation::print_node(), protocols::match::output::print_node(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), core::scoring::constraints::AngleConstraint::read_def(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::features::SaltBridgeFeatures::report_features(), core::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), core::scoring::rna::chemical_shift::ring_pos(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::rbsegment_relax::set_constraints(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::star::setup_constraints(), protocols::simple_moves::DisulfideInsertionMover::setup_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::ChemicalShiftAnisotropyEnergy::setup_for_minimizing(), core::energy_methods::DipolarCouplingEnergy::setup_for_minimizing(), core::energy_methods::ResidualDipolarCouplingEnergy::setup_for_minimizing(), core::conformation::setup_links(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::loop_grower::LoopGrower::single_grow(), protocols::constel::SingResCnlCrea::strip_atoms(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::grafting::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::docking::ConformerSwitchMover::switch_conformer(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::fldsgn::topology::BB_Pos::update_indices(), core::scoring::BB_Pos::update_indices(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), core::scoring::epr_deer::EPRSpinLabel::weight(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().
◆ atom_is_backbone()
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Returns true if this residue's atom with index number <atomno> is a backbone atom.
example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose
References core::chemical::ResidueType::atom_is_backbone(), and rsd_type_.
Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::hbnet::UnsatSelector::apply(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::scoring::calc_per_atom_sasa_sc(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::HolesFilter::compute(), core::energy_methods::ProQ_Energy::crd(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), core::pack::guidance_scoreterms::sap::SapDatabase::generate_max_sasa(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::dna::get_base_pair_stub_slow(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::is_scatom(), protocols::dna::PDBOutput::output_hbond_info(), protocols::minimization_packing::PertMinMover::pert(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), protocols::pockets::PocketGrid::recenter(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), core::scoring::constraints::remove_nonbb_constraints(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and protocols::constel::SingResCnlCrea::zero_occ_bb_h().
◆ atom_is_hydrogen()
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Returns true if this residue's atom with index number <atomno> is a hydrogen.
example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose
References core::chemical::ResidueType::atom_is_hydrogen(), and rsd_type_.
Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::energy_methods::add_to_individual_sol_energies(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::energy_methods::assign_rna_atom_type(), core::scoring::constraints::auto_detect_atoms(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::energy_methods::LK_hack::eval_atom_derivative(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_DomeEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), get_adjacent_heavy_atoms(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), get_hydrogens_bonded_to_ring_atom(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), get_substituents_to_ring_atom(), core::scoring::ResidueNblistData::initialize(), core::energy_methods::is_base_2(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::is_non_peptide_heavy_atom(), core::energy_methods::is_phosphate_2(), core::scoring::is_polymer_heavyatom(), core::energy_methods::StackElecEnergy::is_rna_base(), core::energy_methods::is_sugar_2(), core::scoring::IsHeavyAtomPredicate::operator()(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::NeighborList::setup(), protocols::md::Rattle::setup_constraint(), core::scoring::NeighborList::update_from_wide_nblist(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and protocols::constel::SingResCnlCrea::zero_occ_bb_h().
◆ atom_is_polar_hydrogen()
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Is a particular atom a polar hydrogen?
References core::chemical::ResidueType::atom_is_polar_hydrogen(), and rsd_type_.
Referenced by protocols::hbnet::UnsatSelector::apply(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::hbonds::weights_and_derivs_for_hbonds(), and core::scoring::hbonds::weights_for_hbonds().
◆ atom_name()
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inline |
Returns the name of this residue's atom with index number <atm>
References core::chemical::ResidueType::atom_name(), and rsd_type_.
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), core::util::add_constraints_to_metal(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::nmr::ParaNMRScoreMover::add_pcs_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_pre_scores_to_scorefile(), protocols::nmr::ParaNMRScoreMover::add_rdc_scores_to_scorefile(), protocols::loops::add_single_cutpoint_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_multipole_axes(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::annotated_atom_graph_from_conformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::Conformation::append_residue_by_bond(), core::conformation::Conformation::append_residues(), protocols::ligand_docking::AddHydrogen::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::energy_methods::ProQ_Energy::atom13_0(), core::conformation::atom_graph_from_conformation(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), protocols::hydrate::atom_is_hydratable(), protocols::qsar::scoring_grid::LipidMemGrid::atom_score(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::constraints::auto_detect_atoms(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::rna::movers::bump_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::electron_density::DensityZscores::calc_avg_residue_bfac(), core::scoring::calc_per_atom_sasa_sc(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::import_pose::RNA_JumpMover::check_forward_backward(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::constraints::combine_NMR_atom_string(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), core::energy_methods::compute_exact_geosol(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pose::correctly_add_2prime_connection_variants(), core::energy_methods::ProQ_Energy::crd(), core::pose::create_chemical_edge(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::pose::declare_cutpoint_chemical_bond(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::environment::dof_id_to_string(), core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::SymmetricLigandEnergy::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::energy_methods::MgEnergy::eval_residue_pair(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::magnesium::filter_water_ligands(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_helper(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::pockets::PocketGrid::findExemplars(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), IdentifyLigandMotifs::get_atom_trios(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::lDDT_Calculator::get_matching_atom(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::select::get_pymol_selection_for_atoms(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), core::conformation::idealize_hydrogens(), core::conformation::improper_build(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::conformation::is_ideal_position(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_residues_in_contact(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::forge::methods::make_star_foldtree(), core::conformation::missing_stubs_build(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), protocols::dna::PDBOutput::output_hbond_info(), core::pose::rna::output_other_contacts(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), core::chemical::sdf::MolWriter::output_residue(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), place(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::normalmode::NormalMode::prepare_coord(), core::conformation::print_atom(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_info(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::viewer::print_node(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::SASAShouldItCount(), protocols::qsar::scoring_grid::LipidMemGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::hbnet::HBNet::set_constraints(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), core::scoring::ShouldItCount(), show(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), protocols::nmr::pre::PREEnergy::show_additional_info(), protocols::nmr::rdc::RDCEnergy::show_additional_info(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::backrub::BackrubSidechainMover::update_segments(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), core::scoring::VdWShouldItCount(), protocols::metal_interface::AddZincSiteConstraints::view_constraints_in_pymol(), and core::scoring::PoissonBoltzmannPotential::write_pqr().
◆ atom_type()
Returns the AtomType of this residue's atom with index number <atomno>
example(s): residue.atom_type(3) See also: Residue Residue.atom_index AtomType Pose
References core::chemical::ResidueType::atom_type(), and rsd_type_.
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::hbnet::UnsatSelector::apply(), core::energy_methods::ProQ_Energy::atom13_0(), core::conformation::atom_graph_from_conformation(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::energy_methods::atom_is_aro(), core::energy_methods::atom_is_aro2(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_single_edge_waters(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac(), protocols::electron_density::DensityZscores::calc_avg_residue_bfac(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::hbnet::HBNet::estimate_saturation(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FiberDiffractionEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::forge::remodel::fast_clash_check(), protocols::pose_metric_calculators::fast_clash_check(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), protocols::magnesium::filter_acceptor_ligands(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_for_complex(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::pockets::PocketGrid::findExemplars(), protocols::ligand_docking::frac_atoms_within(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), IdentifyLigandMotifs::get_atom_trios(), core::scoring::magnesium::get_cos_theta(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::hbonds::get_hb_acc_chem_type(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::select::get_pymol_selection_for_atoms(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::chemical::rna::get_rna_base_centroid(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::relax::RangeRelaxMover::idealize_pose(), protocols::sic_dock::SICFast::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), core::scoring::GenBornResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_site_row(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::magnesium::is_ligand(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), core::scoring::lkball::LKD_ResidueInfo::LKD_ResidueInfo(), protocols::protein_interface_design::make_hotspot_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), protocols::motifs::Motif::Motif(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::dna::PDBOutput::output_hbond_info(), core::energy_methods::parcs_ccs(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::viewer::print_node(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::energy_methods::SAXSEnergy::rehash_form_factors(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::energy_methods::WaterAdductIntraEnergy::residue_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), core::conformation::setup_links(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulphur_bond_check(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::conformation::ResidueKinWriter::write_rsd_coords(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().
◆ atom_type_index()
Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType.
example(s): residue.atom_type_index(3) See also: Residue Residue.atom_index AtomType Pose
References atoms_.
Referenced by core::energy_methods::add_to_individual_sol_energies(), protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::energy_methods::compute_exact_geosol(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::chemical::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::electron_density::BfactorMultifunc::operator()(), core::conformation::orient_residue_for_ideal_bond(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::electron_density::pose_spherical_samples(), core::scoring::packing::PoseBalls::PoseBalls(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::electron_density::remove_occupied_density_from_density(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), protocols::legacy_sewing::scoring::LegacyClashScorer::score(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection(), core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc(), and core::scoring::epr_deer::EPRSpinLabel::weight().
◆ atom_type_set()
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Returns the AtomTypeSet of this residue.
example(s): residue.atom_type_set() See also: Residue Residue.atom_type_index AtomType Pose
References core::chemical::ResidueTypeBase::atom_type_set(), and rsd_type_.
Referenced by protocols::electron_density::ReportFSC::apply(), protocols::electron_density::ScaleMapIntensities::apply(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::electron_density::pose_spherical_samples(), protocols::electron_density::remove_occupied_density_from_density(), protocols::features::AtomTypesFeatures::report_features(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().
◆ atomic_charge()
Returns the atom charge of this residue's atom with index number <atomno>
example(s): residue.atomic_charge(3) See also: Residue Residue.atom_index Pose
References core::chemical::ResidueType::atom_charge(), and rsd_type_.
Referenced by protocols::qsar::scoring_grid::ChargeGrid::atom_score(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::elec::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::hbnet::HBNet::find_unsats(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), core::scoring::GenBornPotential::get_res_res_elecE(), core::chemical::rna::get_rna_base_centroid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::cryst::ReportGradientsMover::normalization(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::qsar::scoring_grid::ChargeGrid::score(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::energy_methods::RNA_FA_ElecEnergy::score_atom_pair(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().
◆ atoms() [1/2]
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◆ atoms() [2/2]
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Returns this residue's Atoms (const), a vector1 of Atom objects.
example(s): residue.atoms() See also: Residue Pose
References atoms_.
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::pose_sewing::movers::SewAnythingAddMover::align(), core::conformation::atom_id_to_named_atom_id(), protocols::pose_sewing::calculate_motif_score_bt_residues(), core::pose::compare_atom_coordinates(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::loops::loop_rmsd(), orient_onto_location(), orient_onto_residue_peptoid(), place(), protocols::pose_sewing::filters::CoreScorer::report_sm(), core::conformation::setup_corresponding_atoms(), core::util::switch_to_centroid_rot_set(), update_actcoord(), core::io::serialization::write_binary(), and protocols::environment::claims::XYZClaim::yield_elements().
◆ atoms_with_orb_index()
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References core::chemical::ResidueType::atoms_with_orb_index(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), update_orbital_coords(), and core::conformation::Conformation::update_orbital_coords().
◆ attached_H_begin() [1/2]
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Returns the AtomIndices of the first hydrogen attached to each heavyatom.
example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Residue.nheavyatoms Pose
References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.
◆ attached_H_begin() [2/2]
Returns the index number of the first hydrogen attached to the atom with index number <atom>
example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Pose
References atom(), core::chemical::ResidueType::attached_H_begin(), and rsd_type_.
Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().
◆ attached_H_end() [1/2]
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Returns the AtomIndices of the last hydrogen attached to each heavyatom.
example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Residue.nheavyatoms Pose
References core::chemical::ResidueType::attached_H_end(), and rsd_type_.
◆ attached_H_end() [2/2]
Returns the index number of the last hydrogen attached to the atom with index number <atom>
example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Pose
References atom(), core::chemical::ResidueType::attached_H_end(), and rsd_type_.
Referenced by core::energy_methods::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().
◆ backbone_aa()
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Returns this residue's backbone_aa type, if any.
This is used for noncanonical alpha-amino acids that are templated on canonicals. For example, 4,5-dihydroxyisoleucine uses the ramachandran and p_aa_pp scoring of isoleucine.
References core::chemical::ResidueTypeBase::backbone_aa(), and rsd_type_.
Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), core::energy_methods::RamachandranEnergy::atoms_with_dof_derivatives(), protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), core::energy_methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::energy_methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), and core::energy_methods::RamachandranEnergy::residue_energy().
◆ bonded_neighbor()
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Returns the AtomIndices for all bonded neighbor atoms of <atm>
References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.
Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::bonded_neighbor_all_res(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), fill_missing_atoms(), get_adjacent_heavy_atoms(), IdentifyLigandMotifs::get_atom_trios(), get_atoms_exocyclic_to_ring_atom(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), n_bonded_neighbor_all_res(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::energy_methods::LK_hack::residue_pair_energy(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::HbaGrid::score(), and protocols::features::OrbitalsFeatures::set_OrbH_features_data().
◆ bonded_orbitals()
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References core::chemical::ResidueType::bonded_orbitals(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), and core::conformation::Conformation::update_orbital_coords().
◆ build_atom_ideal()
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Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms.
References core::chemical::AtomICoor::build(), and icoor().
Referenced by protocols::splice::Splice::apply(), protocols::splice::fix_chain_break_residue(), core::energy_methods::CartesianBondedEnergy::idealize_proline_nvs(), and protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned().
◆ build_orbital_xyz()
References atom(), core::chemical::orbitals::ICoorOrbitalData::build(), core::chemical::orbitals::ICoorOrbitalData::get_stub1(), core::chemical::orbitals::ICoorOrbitalData::get_stub2(), core::chemical::orbitals::ICoorOrbitalData::get_stub3(), core::chemical::ResidueType::new_orbital_icoor_data(), rsd_type_, and core::conformation::Atom::xyz().
Referenced by assign_orbitals(), update_orbital_coords(), and core::conformation::Conformation::update_orbital_coords().
◆ carbohydrate_info()
| core::chemical::carbohydrates::CarbohydrateInfoCOP core::conformation::Residue::carbohydrate_info | ( | ) | const |
Return the CarbohydrateInfo object containing sugar-specific properties for this residue.
References core::chemical::ResidueType::carbohydrate_info(), core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), core::scoring::carbohydrates::get_CHI_energy_function_linkage_type_for_phi_for_residue_in_pose(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::energy_methods::SugarBackboneEnergy::residue_energy(), core::io::carbohydrates::residue_range_gws_string(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), and core::pose::carbohydrates::tautomerize_anomer().
◆ chain() [1/2]
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Returns this residue's chain id.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_.
Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::scoring::sc::ElectrostaticSimilarityCalculator::Calc(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::sc::ShapeSimilarityCalculator::CalcSs(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), core::pose::Pose::chain(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::io::pdb::create_pdb_info_for_single_residue_pose(), core::pose::create_subpose(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::matdes::dup_residue(), core::pose::symmetry::extract_asymmetric_unit(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::forge::methods::fold_tree_from_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), protocols::minimization_packing::ChainGroupDiscriminator::group_id(), protocols::antibody::AntibodyInfo::identify_antibody(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::forge::build::ConnectRight::modify_impl(), orient_onto_residue_peptoid(), core::pose::PDBInfo::PDBInfo(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), core::scoring::PQR::PQR(), protocols::enzdes::enzutil::read_pose_from_file(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::antibody::AntibodyFeatures::report_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::energy_methods::RNA_BulgeEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::energy_methods::PoissonBoltzmannEnergy::residue_in_chains(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::RamachandranEnergy2B::residue_pair_energy(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::conformation::Conformation::sequence_matches(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), core::energy_methods::PoissonBoltzmannEnergy::setup_for_scoring(), protocols::docking::DockingHighResLegacy::setup_packing(), core::conformation::Conformation::update_polymeric_connection(), core::io::serialization::write_binary(), and core::scoring::PoissonBoltzmannPotential::write_pqr().
◆ chain() [2/2]
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Sets this residue's chain id.
Don't call directly – In almost all situations, this should be set by the owning Conformation
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_.
◆ chi() [1/4]
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Returns the chi torsion angles of this residue (non-const)
References chi_.
◆ chi() [2/4]
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Returns the chi torsion angles of this residue (const)
example(s): residue.chi() See also: Residue Residue.nchi Pose Pose.chi
References chi_.
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::pose::Pose::chi(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::legacy_sewing::create_model_from_pose(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::idealize::dihedral_distance(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::dna::DNABase::DNABase(), protocols::metal_interface::dump_chis(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::energy_methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), protocols::indexed_structure_store::extract_residue_entry(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_packed_rotno(), core::chemical::rna::get_residue_base_state(), core::pack::get_residue_current_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::get_rotamer_angle_diffs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::conformation::idealize_position(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), is_similar_rotamer(), protocols::motifs::make_base_pair_mutation(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::pack::optimize_H_and_notify(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::splice::printChi(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::RotamerFeatures::report_features(), core::energy_methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::pack::dunbrack::rotamer_from_chi(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::ligand_docking::LigandDockProtocol::shear_min_protocol(), protocols::dna::show_dna_geometry(), protocols::dna::show_dna_geometry_extra_details(), protocols::dna::substitute_residue(), core::conformation::Conformation::torsion(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_flexscs(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), and core::conformation::Conformation::update_residue_torsions().
◆ chi() [3/4]
◆ chi() [4/4]
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Sets the chi torsion angles of this residue.
CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.
example(s):
See also: Residue Pose Pose.set_chi
References chi_.
◆ chi_atoms() [1/2]
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Returns the AtomIndices of each set of four atoms defining each chi angle.
References core::chemical::ResidueType::chi_atoms(), and rsd_type_.
Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::energy_methods::DNA_DihedralEnergy::atoms_with_dof_derivatives(), core::energy_methods::YHHPlanarityEnergy::atoms_with_dof_derivatives(), core::energy_methods::chi2_torsion_atom_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::pack::scmin::CartSCMinMultifunc::dfunc(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::scoring::dna::get_base_pair_stub_slow(), core::pack::get_residue_current_energy(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::pack::optimize_H_and_notify(), place(), Residue(), set_chi(), core::conformation::set_chi_according_to_coordinates(), set_d(), set_theta(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), core::conformation::setup_corresponding_atoms(), core::conformation::setup_links(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().
◆ chi_atoms() [2/2]
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Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle.
References core::chemical::ResidueType::chi_atoms(), and rsd_type_.
◆ chi_rotamers()
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Returns the chi rotamers available for this residue's chi angle <chino>
References core::chemical::ResidueType::chi_rotamers(), and rsd_type_.
Referenced by core::pack::rotamer_set::build_rotamers_from_rotamer_bins().
◆ clear_residue_connections()
| void core::conformation::Residue::clear_residue_connections | ( | ) |
References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.
◆ clone()
| ResidueOP core::conformation::Residue::clone | ( | ) | const |
Copy this residue( allocate actual memory for it )
make a copy of this residue( allocate actual memory for it )
Referenced by core::util::add_covalent_linkage_helper(), core::pose::add_variant_type_to_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::seeded_abinitio::combine_two_poses(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), create_residue(), create_rotamer(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::io::pdb::dump_pdb_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::matdes::dup_residue(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::splice::RotLibOut::find_matching_res(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::ligand_docking::get_ligand_torsion_constraints(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::magnesium::MgHydrater::hydrate_magnesium(), core::conformation::idealize_position(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::initialize(), core::conformation::Conformation::insert_conformation_by_jump(), core::conformation::Conformation::insert_residue_by_bond(), protocols::motifs::BuildPosition::keep_rotamer(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::modeler::merge_two_poses(), protocols::hbnet::HBNet::minimize_network(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), core::pose::remove_variant_type_from_residue(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), protocols::denovo_design::components::Segment::set_template_pose(), core::pack::setup_bgres_cops(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::stepwise::modeler::slice(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), protocols::vip::VIP_Mover::try_point_mutants(), and protocols::hydrate::water_specific_hbond_energy().
◆ clone_flipping_chirality()
| ResidueOP core::conformation::Residue::clone_flipping_chirality | ( | core::chemical::ResidueTypeSet const & | residue_type_set | ) | const |
Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.
Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues. The passed ResidueTypeSet is the ResidueTypeSet you want the mirrored type to come from.
- Note
- This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart. It assumes that you've already mirrored all of the coordinates, and just allows you to generate a replacement residue of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms, variant types, etc.).
References core::chemical::ResidueTypeSet::get_mirrored_type(), Residue(), and rsd_type_ptr_.
Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner().
◆ connect_atom()
Returns the index number of this residue's atom connected to the <other> Residue.
Returns the atom-index of my atom which is connected to the other residue.
example(s):
See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Residue.upper_connect_atom Pose
so long as there is only a single connection to other... if there are multiple connections this will fail. If there are no connections this will fail. This is a convenience function that can fail; be careful! Fails if I'm not bonded to the other residue.
- Note
- not well defined if multiple connections to another residue – need more general function
References core::chemical::ResidueConnection::atomno(), connections_to_residues_, is_lower_terminus(), is_polymer(), is_upper_terminus(), lower_connect_atom(), core::chemical::ResidueTypeBase::name(), nonstandard_polymer_, core::chemical::ResidueType::residue_connection(), rsd_type_, seqpos(), seqpos_, core::conformation::TR(), type(), and upper_connect_atom().
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::pose::symmetry::extract_asymmetric_unit(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::form_disulfide(), core::io::pose_from_sfr::is_connected(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), and protocols::viewer::print_interres_bond().
◆ connect_map()
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inline |
References connect_map_.
Referenced by core::util::add_constraints_to_metal(), core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::chemical::ICoorAtomID::atom_id(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::energy_methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::mm::connection_indices(), copy_residue_connections(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::energy_methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::conformation::disulfide_bonds(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::cyclic_peptide::dump_debug_output(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::energy_methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::get_disulf_partner(), core::pose::Pose::real_to_virtual(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::energy_methods::LK_hack::residue_pair_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::io::pose_from_sfr::show_residue_connections(), core::conformation::Conformation::show_residue_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().
◆ connect_map_size()
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inline |
Returns the size (number of elements) in the connect_map_ object.
References connect_map_.
Referenced by core::chemical::ICoorAtomID::atom_id(), core::energy_methods::SugarBackboneEnergy::atoms_with_dof_derivatives(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), core::scoring::Ramachandran::is_normally_connected(), core::scoring::methods::lower_upper_connected_across_cutpoint(), and core::pose::show_adjacent_nt_connections().
◆ connected_residue_at_lower()
| Size core::conformation::Residue::connected_residue_at_lower | ( | ) | const |
Returns the residue number of a residue connected to this residue at this residue's lower_connect.
This function returns 0 if this residue lacks a lower_connect or if it's not connected to anything at its lower_connect.
References connected_residue_at_resconn(), has_lower_connect(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_thioether_residues_from_selection(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), orient_onto_residue_peptoid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::pose::set_reasonable_fold_tree(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), protocols::cyclic_peptide::crosslinker::set_up_thioether_variants(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ connected_residue_at_resconn()
|
inline |
Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.
For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6. Exactly the same as residue_connection_partner
References connect_map_.
Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::CrankshaftFlipMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Conformation::atoms_are_bonded(), connected_residue_at_lower(), connected_residue_at_upper(), core::pose::correctly_add_2prime_connection_variants(), core::pose::create_chemical_edge(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::pose::declare_cutpoint_chemical_bond(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::cyclic_peptide::dump_debug_output(), core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::energy_methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::io::silent::BinarySilentStruct::fill_struct(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::forge::methods::fold_tree_from_pose(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::generate_allowed_partners(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), core::scoring::methods::get_lower_cutpoint_partner_for_upper(), core::conformation::get_second_atom_from_connection(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::scoring::methods::get_upper_cutpoint_partner_for_lower(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), protocols::cyclic_peptide::CycpepSymmetryFilter::is_cyclic_peptide(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_current_residue_connections(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::pose::Pose::real_to_virtual(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::energy_methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), core::pose::show_adjacent_nt_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().
◆ connected_residue_at_upper()
| Size core::conformation::Residue::connected_residue_at_upper | ( | ) | const |
Returns the residue number of a residue connected to this residue at this residue's upper_connect.
This function returns 0 if this residue lacks an upper_connect or if it's not connected to anything at its upper_connect.
References connected_residue_at_resconn(), has_upper_connect(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), protocols::backbone_moves::RandomizeBBByRamaPrePro::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::pose::symmetry::extract_asymmetric_unit(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::set_reasonable_fold_tree(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().
◆ connection_distance()
| Distance core::conformation::Residue::connection_distance | ( | conformation::Conformation const & | conf, |
| Size const | resconn_index, | ||
| Vector const & | matchpoint | ||
| ) | const |
Distance between a potential residue connection match and the position of the expected atom.
References core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), name(), core::chemical::ResidueType::residue_connection(), core::conformation::TR(), and type().
Referenced by core::conformation::Conformation::detect_bonds().
◆ connection_incomplete()
| bool core::conformation::Residue::connection_incomplete | ( | Size | resconnid | ) | const |
References connect_map_.
Referenced by protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::backrub::connected_mainchain_atomids(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::detect_bonds(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), has_incomplete_connection(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), core::scoring::Ramachandran::is_normally_connected(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), n_bonded_neighbor_all_res(), core::energy_methods::polymeric_termini_incomplete(), core::scoring::polymeric_termini_incomplete(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), and protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms().
◆ connections_match()
| bool core::conformation::Residue::connections_match | ( | Residue const & | other | ) | const |
Returns true if ???
References connect_map_, and pseudobonds_.
◆ connections_to_residue() [1/2]
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inline |
Returns the vector1 of resconn ids that connect this residue to other.
References seqpos().
Referenced by core::conformation::Conformation::atoms_are_bonded(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::pose::create_chemical_edge(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::conformation::get_chemical_root_and_anchor_atomnos(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), protocols::simple_moves::CyclizationMover::setup_constraints(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().
◆ connections_to_residue() [2/2]
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inline |
Returns the vector1 of resconn ids that connect this residue to other.
References connections_to_residues_.
◆ copy_residue_connections()
| void core::conformation::Residue::copy_residue_connections | ( | Residue const & | src_rsd, |
| bool const | suppress_warnings = false |
||
| ) |
Attempt to take residue connection info from src_rsd.
If suppress_warnings is true, we don't warn if residue connections on other residues are invalidated by a change of residue connection numbering in this residue. (Useful if we're calling this function from a context in which we know that we're going to update residue connections after the function call.) Note that warnings are never suppressed if high verbosity is set (TR.Debug.visible() == true).
References atom_index(), atom_name(), core::chemical::ResidueConnection::atomno(), connect_map(), connect_map_, connections_to_residues_, core::chemical::ResConnID::connid(), has(), core::chemical::ResidueType::n_possible_residue_connections(), n_possible_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), pseudobonds_, core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_connection_partner(), core::chemical::ResidueType::residue_connections_for_atom(), seqpos(), core::conformation::TR(), and type().
Referenced by Residue().
◆ copy_residue_connections_from()
| void core::conformation::Residue::copy_residue_connections_from | ( | Residue const & | src | ) |
◆ create_residue()
|
inline |
◆ create_rotamer()
|
inline |
Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out.
References clone().
Referenced by core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), and core::pack::hbonds::hbond_graph_from_partial_rotsets().
◆ cut_bond_neighbor()
|
inline |
atom indices for bonded neighbors to which atom-tree connections are disallowed.
References core::chemical::ResidueType::cut_bond_neighbor(), and rsd_type_.
Referenced by core::conformation::setup_links_simple().
◆ data()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time.
References data_cache_.
Referenced by core::scoring::lkball::LK_BallEnergy::atomistic_pair_energy(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::LK_DomeEnergy::residue_pair_energy(), core::scoring::lkball::retrieve_lkb_resdata(), core::scoring::lkball::retrieve_lkd_resdata(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().
◆ data_ptr()
|
inline |
BasicDataCache indexed by enum in residue_datacache.hh.
Return a COP to the data cache
- Note
- Might be a null pointer if the cache has not been initialized
References data_cache_.
Referenced by core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::conformation::Conformation::residue_data(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().
◆ determine_nonstandard_polymer_status()
|
private |
References connect_map_, is_lower_terminus(), is_polymer(), is_upper_terminus(), nonstandard_polymer_, seqpos(), and type().
Referenced by residue_connection_partner(), and update_sequence_numbering().
◆ fill_missing_atoms()
| bool core::conformation::Residue::fill_missing_atoms | ( | utility::vector1< bool > & | missing, |
| Conformation const & | conformation, | ||
| bool | fail = true |
||
| ) |
Builds coordinates for atoms missing from this residue assuming ideal internal coordinates.
If fail is false, will return true if we can fill all the missing atoms, and false if we can't.
missing is passed by non-const ref: it will be updated for the atoms which are filled. (If fail is false, it will end up all false, or you'll get a utility_exit()
this uses ideal internal coords to build any missing atom from its three stub atoms. If any of the stub atoms are missing, build them first. Unable to build a missing atom whose stub atoms are from non-existing polymer connection and its input bogus value will not be changed.
References atom_name(), bonded_neighbor(), core::chemical::AtomICoor::build(), icoor(), core::conformation::improper_build(), core::chemical::INTERNAL, core::conformation::missing_stubs_build(), name(), natoms(), core::chemical::pretty_print_atomicoor(), seqpos(), seqpos_, set_xyz(), core::chemical::ResidueType::show_all_atom_names(), core::chemical::AtomICoor::stub_atom(), core::conformation::TR(), and type().
Referenced by core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), place(), and protocols::denovo_design::rebuild_missing_atoms().
◆ first_adjacent_heavy_atom()
Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.
- Returns
- The atom index of the 1st heavy atom next to the given atom (by index) or 0 if no heavy atom is found
This method does not count virtual atoms as heavy atoms.
- Remarks
- This method is crucial for determining atoms defining non-standard torsion angles, such as those found across branch connections or in glycosidic linkages.
References atom_index(), get_adjacent_heavy_atoms(), and core::conformation::TR().
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), and core::conformation::Conformation::branch_connection_torsion_angle_atoms().
◆ first_sidechain_atom()
|
inline |
Returns the index number of the first sidechain heavyatom.
example(s): residue.first_sidechain_atom() See also: Residue Residue.atom Residue.atoms Residue.last_backbone_atom Pose
References core::chemical::ResidueType::first_sidechain_atom(), and rsd_type_.
Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::membrane::AqueousPoreFinder::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::energy_methods::assign_rna_atom_type(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pose::rna::bases_form_a_hydrogen_bond(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::select::util::calc_sc_neighbors(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::energy_methods::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::relax::derive_sc_sc_restraints(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::pose::rna::figure_out_number_base_contacts(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::cryst::fix_bfactorsMissing(), core::scoring::dna::get_base_pair_stub_slow(), core::energy_methods::HackAroEnergy::get_centroid(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::energy_methods::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::energy_methods::is_sugar_2(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::dna::RotamerDNAHBondFilter::operator()(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::pose::rna::residue_is_bulge(), core::energy_methods::RNA_LJ_BaseEnergy::residue_pair_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::self_scsc(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), protocols::design_opt::Supercharge::set_surface(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), sidechainAtoms_begin(), protocols::hybridization::DDomainParse::split(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::util::switch_to_centroid_rot_set(), and protocols::dna::z_axis_dist().
◆ first_sidechain_hydrogen()
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Returns the index number of the first sidechain hydrogen.
example(s): residue.first_sidechain_hydrogen() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose
References core::chemical::ResidueType::first_sidechain_hydrogen(), and rsd_type_.
Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_hbond_map(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), core::pack::scmin::CartSCMinMinimizerMap::setup(), and core::optimization::CartesianMinimizerMap::setup().
◆ get_adjacent_heavy_atoms()
| utility::vector1< uint > core::conformation::Residue::get_adjacent_heavy_atoms | ( | uint const | atom_index | ) | const |
Get a list of heavy atoms connected to a given atom.
- Returns
- The atom indices of all heavy atoms bonded to the given atom (by index)
This method does not count virtual atoms as heavy atoms.
References atom_index(), atom_is_hydrogen(), bonded_neighbor(), and is_virtual().
Referenced by first_adjacent_heavy_atom(), core::conformation::position_of_atom_on_ring(), and show().
◆ get_atoms_exocyclic_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_atoms_exocyclic_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of exocyclic atoms connected to a given ring atom.
- Returns
- The atom indices of all atoms bonded to the given atom (by index) that are not a part of the ring.
This method does not count virtual atoms as atoms.
References atom_index(), bonded_neighbor(), is_virtual(), and type().
Referenced by get_hydrogens_bonded_to_ring_atom(), and get_substituents_to_ring_atom().
◆ get_hydrogens_bonded_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_hydrogens_bonded_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of hydrogen atoms connected to a given ring atom.
- Returns
- The atom indices of hydrogens bonded to the given ring atom (by index).
This method does not count virtual atoms as atoms.
References atom_index(), atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().
◆ get_metal_binding_atoms()
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Gets the AtomIndices of the atoms in this residue that can bind to metals.
- Note
- : AtomIndices == vector1< Size >
References core::chemical::ResidueType::get_metal_binding_atoms(), and rsd_type_.
Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), and core::util::find_metalbinding_atoms_helper().
◆ get_pseudobonds_to_residue()
| PseudoBondCollectionCOP core::conformation::Residue::get_pseudobonds_to_residue | ( | Size | resid | ) | const |
◆ get_self_ptr() [1/2]
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◆ get_self_ptr() [2/2]
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self pointers
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::convert_block_sasa_to_sasa_score(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_block_params(), core::energy_methods::AACompositionEnergy::finalize_total_energy(), core::energy_methods::AARepeatEnergy::finalize_total_energy(), core::energy_methods::MHCEpitopeEnergy::finalize_total_energy(), core::energy_methods::NetChargeEnergy::finalize_total_energy(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::carbohydrates::get_glycosidic_bond_residues(), protocols::ligand_docking::get_ligand_grid_scores(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::pack::guidance_scoreterms::sap::rotamer_sets_from_pose(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(), core::energy_methods::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::ligand_docking::Transform::setup_conformers(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_lightning(), and protocols::motifs::IRCollection::try_for_more().
◆ get_self_weak_ptr() [1/2]
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◆ get_self_weak_ptr() [2/2]
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◆ get_substituents_to_ring_atom()
| core::chemical::AtomIndices core::conformation::Residue::get_substituents_to_ring_atom | ( | uint const | atom_index | ) | const |
Get a list of substituent atoms connected to a given ring atom.
- Returns
- The atom indices of all heavy atoms bonded to the given atom (by index) that are not a part of the ring.
This method does not count virtual atoms as atoms.
References atom_index(), atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().
◆ Haro_index()
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Returns the AtomIndices of this residue's aromatic hydrogens.
- Note
- : AtomIndices == vector1< Size >
example(s): residue.Haro_index() See also: Residue Residue.atoms Residue.Hpol_index Pose
References core::chemical::ResidueType::Haro_index(), and rsd_type_.
Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().
◆ has()
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Returns true if this residue has an atom named <atm>
References core::chemical::ResidueType::has(), and rsd_type_.
Referenced by core::pose::motif::a(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), core::pose::Pose::append_residue_by_atoms(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::nmr::pre::PREMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::constel::PresenceCommon::are_atoms_pres(), core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::facts::FACTSPotential::atompair_scale(), core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::simple_moves::Ca_coord(), protocols::mpi_refinement::CA_Sscore(), core::energy_methods::GoapEnergy::calculate_dipoles(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), core::select::util::cbeta_vector(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::sic_dock::count_CBs(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pose::declare_cutpoint_chemical_bond(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), core::energy_methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), protocols::constraint_generator::existing_atoms(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::abinitio::abscript::find_disulfide_partner(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::helical_bundle::FitSimpleHelixMultiFunc::FitSimpleHelixMultiFunc(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::sic_dock::get_CB_Vecs_from_pose(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::scoring::loop_graph::get_loop_atom(), core::scoring::lDDT_Calculator::get_matching_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), core::pose::carbohydrates::glycosylate_pose(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::pose::Pose::insert_residue_by_atoms(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_beta_aminoacid(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::constel::HBondCommon::is_rmoi_hbonded(), core::pose::make_atom_map(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::denovo_design::rebuild_missing_atoms(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::SiteGrid::refresh(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), protocols::sic_dock::XfoxmScore::score(), core::select::util::select_coord_for_residue(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::ligand_docking::set_repulsive_bb_cores(), core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::dna::show_dna_geometry_extra_details(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().
◆ has_incomplete_connection() [1/2]
| bool core::conformation::Residue::has_incomplete_connection | ( | ) | const |
References connect_map_, and connection_incomplete().
Referenced by core::pose::append_pose_with_glycan_residues(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::conformation::Conformation::detect_bonds(), protocols::ligand_docking::find_unconnected_residues(), protocols::ligand_docking::has_incomplete_connections(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
◆ has_incomplete_connection() [2/2]
| bool core::conformation::Residue::has_incomplete_connection | ( | core::Size const | atomno | ) | const |
Returns true is <atomno> has complete connectivity?
determine whether an atom is completely connected to all possible bonded partners
References connection_incomplete(), n_possible_residue_connections(), and residue_connect_atom_index().
◆ has_lower_connect()
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Returns true if residue has a valid lower connection.
example(s): residue.has_lower_connect()
References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.
Referenced by core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residues(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives(), core::scoring::constraints::auto_detect_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), connected_residue_at_lower(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pose::declare_cutpoint_chemical_bond(), core::scoring::Ramachandran::defines_score_for_residue(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::energy_methods::CartesianBondedEnergy::eval_intrares_energy(), core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::dunbrack::PeptideTorsionReporter::get_dof(), protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_ligand_resids(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), core::pack::dunbrack::MainchainTorsionRepo