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Rosetta
2020.11
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Rosetta
2020.11
|
A class for defining a type of residue. More...
#include <ResidueType.hh>
Public Member Functions | |
| ~ResidueType () override | |
| destructor More... | |
| ResidueTypeCOP | get_self_ptr () const |
| self pointers More... | |
| ResidueTypeOP | get_self_ptr () |
| ResidueTypeCAP | get_self_weak_ptr () const |
| ResidueTypeAP | get_self_weak_ptr () |
| Size | natoms () const override |
| number of atoms More... | |
| Size | nheavyatoms () const override |
| number of heavy atoms More... | |
| Size | n_hbond_acceptors () const |
| number of hbond_acceptors More... | |
| Size | n_hbond_donors () const |
| number of hbond_donors More... | |
| Size | nbonds () const override |
| number of bonds More... | |
| Size | n_virtual_atoms () const override |
| Counts the number of virtual atoms and returns the count. More... | |
| Size | last_backbone_atom () const |
| index of the last backbone heavy atom More... | |
| Size | first_sidechain_atom () const |
| index of the first sidechain atom (heavy or hydrogen) More... | |
| Size | first_sidechain_hydrogen () const |
| index of the first sidehchain hydrogen More... | |
| Size | nbr_atom () const |
| get nbr_atom used to define residue-level neighbors More... | |
| Real | nbr_radius () const |
| get nbr_radius_ used to define residue-level neighbors More... | |
| core::Real | mass () const |
| get the molecular weight of this residue More... | |
| bool | has_shadow_atoms () const |
| Returns true if this residue has shadow atoms, false otherwise. More... | |
| Size | atom_being_shadowed (Size atom_shadowing) const |
| Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone. More... | |
| AtomIndices const & | attached_H_begin () const |
| for all heavy atoms, index numbers of their first attached Hydrogen More... | |
| AtomIndices const & | attached_H_end () const |
| for all heavy atoms, index numbers of their last attached Hydrogen More... | |
| void | get_metal_binding_atoms (AtomIndices &metal_binding_indices) const |
| Gets indices of all atoms that can form bonds to metals. More... | |
| AtomIndices const & | all_bb_atoms () const |
| Indices of all backbone atoms, hydrogens and heavyatoms. More... | |
| AtomIndices const & | all_sc_atoms () const |
| Indices of all sidechain atoms, hydrogens and heavyatoms. More... | |
| AtomIndices const & | Haro_index () const |
| return indices of aromatic Hydrogens More... | |
| AtomIndices const & | Hpol_index () const |
| return indices of polar Hydrogens More... | |
| AtomIndices const & | Hpos_polar () const |
| indices of polar hydrogens as Hbond donors More... | |
| AtomIndices const & | Hpos_apolar () const |
| indices of non-polar hydrogens as potential carbon Hbond donors More... | |
| AtomIndices const & | Hpos_polar_sc () const |
| AtomIndices const & | accpt_pos () const |
| indices of atoms as Hbond acceptors More... | |
| AtomIndices const & | accpt_pos_sc () const |
| indices of atoms as Hbond acceptors More... | |
| bool | has (std::string const &atom_name) const override |
| is this atom present in this residue? More... | |
| std::string const & | atom_name (Size const atomno) const |
| get atom name by index More... | |
| Size | atom_index (std::string const &atom_name) const |
| get atom index by name More... | |
| AtomType const & | atom_type (Size const atomno) const |
| Get the chemical atom_type for this atom by it index number in this residue. More... | |
| core::Size | atom_type_index (core::Size atomno) const |
| ElementCOP | element_type (core::Size atomno) const |
| core::chemical::element::Elements | element (core::Size atomno) const |
| Convenience function to go directly to the element enum. More... | |
| int | path_distance (Size at1, Size at2) const |
| path distance (number of bonds separated) between a pair of atoms More... | |
| utility::vector1< int > const & | path_distance (Size atom) const |
| shortest path distance for an atom to all other residue atoms More... | |
| utility::vector1 < utility::vector1< int > > const & | path_distances () const |
| accessor of path_distance_ data for this residue, which is a 2D array More... | |
| Size | attached_H_begin (Size const atom) const |
| index number of the first attached Hydrogen on an atom More... | |
| Size | attached_H_end (Size const atom) const |
| index number of the last attached Hydrogen on an atom More... | |
| bool | heavyatom_has_polar_hydrogens (Size atomno) const |
| bool | heavyatom_is_an_acceptor (Size atomno) const |
| bool | atom_is_polar_hydrogen (Size atomno) const |
| bool | atom_is_aro_hydrogen (Size atomno) const |
| AtomIndices const & | mainchain_atoms () const |
| indices of all mainchain atoms More... | |
| Size | mainchain_atom (Size const mainchain_index) const |
| index of mainchain atom More... | |
| int | formal_charge (Size const atomno) const |
| core::Real | atom_charge (Size const atomno) const |
| core::Vector | ideal_xyz (Size const atomno) const |
| core::Vector | ideal_xyz (std::string const &atomname) const |
| bool | atom_is_backbone (Size const atomno) const |
| is a backbone atom (heavy or hydrogen)? More... | |
| bool | atom_is_sidechain (Size const atomno) const |
| bool | atom_is_hydrogen (Size const atomno) const |
| quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last. More... | |
| bool | is_virtual (Size const atomno) const |
| Check if atom is virtual. More... | |
| bool | is_repulsive (Size const atomno) const |
| Check if atom is repulsive. More... | |
| bool | atom_has_property (Size const atomno, AtomProperty const property) const |
| AtomProperties const & | atom_properties (Size const atomno) const |
| Get the AtomicProperities object for the atom. (Note this is only the manually set properties, not all the properties of the atom.) More... | |
| void | show_all_atom_names (std::ostream &out) const override |
| Size | nbonds (Size atom) const |
| number of bonds for given atom More... | |
| Size | number_bonded_hydrogens (Size const atomno) const |
| indicates how many proton bonded neighbors an atom has More... | |
| Size | number_bonded_heavyatoms (Size const atomno) const |
| indicates how many heavyatom bonded neighbors an atom has More... | |
| AtomIndices const & | bonded_neighbor (Size const atomno) const |
| indices of the bonded neighbors for an atom More... | |
| utility::vector1< std::pair < core::Size, core::Size > > | bonds () const |
| Returns a list of all pairs of atoms which are bonded. This returned list should only have only one entry per bond (So [1,2] and [2,1] will not both be present.) More... | |
| bool | atoms_are_bonded (core::Size const atomindex1, core::Size const atomindex2) const |
| Indicates whether or not two atom indices have a chemical bond linking them. More... | |
| utility::vector1< BondName > const & | bonded_neighbor_types (Size const atomno) const |
| utility::vector1< BondRingness > const & | bonded_neighbor_ringnesses (Size const atomno) const |
| BondName | bond_type (core::Size const atomindex1, core::Size const atomindex2) const |
| Returns the type of bond between the atoms Will return UnknownBond for something which isn't bonded. More... | |
| BondRingness | bond_ringness (core::Size const atomindex1, core::Size const atomindex2) const |
| Returns whether the bond between the atoms is in a ring. Will return UnknownRingness for something which isn't bonded. More... | |
| AtomIndices const & | cut_bond_neighbor (Size const atomno) const |
| indices of the bonded neighbors for an atom More... | |
| AtomIndices const & | nbrs (Size const atomno) const |
| indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno) More... | |
| Size | nchi () const |
| number of chi angles More... | |
| Size | n_nus () const |
| Return number of nu (internal ring) angles. More... | |
| Size | n_rings () const |
| Return the number of rings in this residue. More... | |
| Size | ndihe () const |
| Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms. More... | |
| Size | n_proton_chi () const |
| number of proton chis More... | |
| bool | is_proton_chi (Size const chino) const |
| number of proton chis More... | |
| Size | proton_chi_2_chi (Size proton_chi_id) const |
| translate proton_chi to global chi More... | |
| Size | chi_2_proton_chi (Size chi_index) const |
| utility::vector1< Real > const & | proton_chi_samples (Size proton_chi) const |
| utility::vector1< Real > const & | proton_chi_extra_samples (Size proton_chi) const |
| utility::vector1< std::pair < Real, Real > > const & | chi_rotamers (Size const chino) const |
| all rotamers bins (mean, std) for a given chi angle More... | |
| AtomIndices const & | chi_atoms (Size const chino) const |
| indices of the atoms which are used to define a given chi angle (chino) More... | |
| utility::vector1< AtomIndices > const & | chi_atoms () const |
| indices of the atoms which are used to define all the chi angles More... | |
| AtomIndices const & | nu_atoms (core::uint const nu_index) const |
| Return indices of the atoms used to define a given nu (internal ring) angle. More... | |
| utility::vector1< AtomIndices > const & | nu_atoms () const |
| Return list of indices of the atoms used to define all the nu (internal ring) angles. More... | |
| AtomIndices const & | ring_atoms (uint const ring_num) const |
| Return list of indices of the atoms within this residue's nth cycle, not counting virtual atoms. More... | |
| utility::vector1< AtomIndices > const & | ring_atoms () const |
| Return list of indices of the atoms within this residue's cycles, not counting virtual atoms. More... | |
| bool | is_ring_atom (uint const ring_num, uint const atom_id) const |
| Return whether this atom is in a particular ring. More... | |
| core::chemical::rings::RingSaturationType | ring_saturation_type (uint const ring_num) const |
| Return the saturation level of this residue's nth cycle. More... | |
| utility::vector1 < core::chemical::rings::RingSaturationType > const & | ring_saturation_types () const |
| Return the saturation level for all of this residue's cycles. More... | |
| utility::vector1< std::string > const & | lowest_ring_conformers () const |
| For each ring, what's the lowest conformer? More... | |
| utility::vector1 < utility::vector1 < std::string > > const & | low_ring_conformers () const |
| Low-energy ring conformers for each ring. More... | |
| utility::vector1< Size > const & | last_controlling_chi () const |
| Read access to the last_controlling_chi_ array. More... | |
| Size | last_controlling_chi (Size atomno) const |
| The last_controlling_chi for an atom. 0 if an atom is controlled by no chi. More... | |
| utility::vector1< AtomIndices > const & | atoms_last_controlled_by_chi () const |
| Read access to the atoms_last_controlled_by_chi_ array. More... | |
| AtomIndices const & | atoms_last_controlled_by_chi (Size chi) const |
| Read access to the Atoms last controlled by a particular chi. More... | |
| core::Size | root_atom () const |
| get root_atom used as the base of the icoor tree. More... | |
| AtomICoor const & | icoor (Size const atm) const |
| AtomICoord of an atom. More... | |
| Size | atom_base (Size const atomno) const |
| get index of an atom's base atom More... | |
| Size | abase2 (Size const atomno) const |
| get index of an atom's second base atom More... | |
| void | debug_dump_icoor () const |
| Dump out atomnames and icoor values. More... | |
| MMAtomType const & | mm_atom_type (Size const atomno) const |
| Get the MM atom_type for this atom by its index number in this residue. More... | |
| std::string const & | mm_name (core::Size atomno) const |
| core::Size | mm_atom_type_index (core::Size atomno) const |
| gasteiger::GasteigerAtomTypeDataCOP | gasteiger_atom_type (core::Size atomno) const |
| Get the Gasteiger atom type for this atom Can be null if the atom type isn't set. More... | |
| utility::vector1< core::Size > const & | bonded_orbitals (Size const atomno) const |
| indices of the orbitals bonded to an atom More... | |
| AtomIndices const & | atoms_with_orb_index () const |
| orbitals::ICoorOrbitalData const & | orbital_icoor_data (Size const orbital_index) const |
| orbitals::ICoorOrbitalData const & | new_orbital_icoor_data (Size const orbital_index) const |
| core::chemical::rings::RingConformerSetCOP | ring_conformer_set (core::uint ring_num) const |
| Return a pointer to the object containing the set of ring conformers possible for this residue's nth cycle. More... | |
| core::Size | n_ring_conformer_sets () const |
| ResidueConnection const & | lower_connect () const |
| Size | lower_connect_id () const |
| Size | lower_connect_atom () const |
| index number of the atom which connects to the lower connection More... | |
| ResidueConnection const & | upper_connect () const |
| Size | upper_connect_id () const |
| Size | upper_connect_atom () const |
| index number of the atom which connects to the upper connection More... | |
| utility::vector1< uint > | branch_connect_atoms () const |
| Return a list of indices of atoms at non-polymer connections. More... | |
| utility::vector1< std::string > | branch_connect_atom_names () const |
| Return a list of names of atoms at non-polymer connections. More... | |
| Size | n_possible_residue_connections () const |
| number of ResidueConnections, counting polymeric residue connections More... | |
| Size | n_polymeric_residue_connections () const |
| Size | n_non_polymeric_residue_connections () const |
| ResidueConnection const & | residue_connection (Size const i) const |
| Get a ResidueConection. More... | |
| bool | atom_forms_residue_connection (Size const atomid) const |
| Does an atom form any inter-residue chemical bonds? More... | |
| Size | n_residue_connections_for_atom (Size const atomid) const |
| How many inter-residue chemical bonds does a particular atom form? More... | |
| Size | residue_connection_id_for_atom (Size const atomid) const |
| Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom. More... | |
| utility::vector1< Size > const & | residue_connections_for_atom (Size const atomid) const |
| bool | residue_connection_is_polymeric (Size const resconn_id) const |
| Size | residue_connect_atom_index (Size const resconn_id) const |
| bool | atom_depends_on_lower_polymeric_connection (core::Size const atom_index) const |
| Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection? More... | |
| bool | atom_depends_on_upper_polymeric_connection (core::Size const atom_index) const |
| Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection? More... | |
| bool | atom_depends_on_polymeric_connection (core::Size const atom_index) const |
| Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection? More... | |
| bool | atom_depends_on_connection (core::Size const atom_index, core::Size const connection_id) const |
| Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID? More... | |
| bool | requires_actcoord () const |
| require actcoord? More... | |
| AtomIndices const & | actcoord_atoms () const |
| get indices for atoms used to define actcoord More... | |
| bool | is_sidechain_thiol () const |
| is thiol? More... | |
| bool | is_disulfide_bonded () const |
| is disulfide? More... | |
| bool | is_sidechain_amine () const |
| is sidechain amine? More... | |
| bool | is_alpha_aa () const |
| Is this an alpha-amino acid? More... | |
| bool | is_beta_aa () const |
| Is this a beta-amino acid? More... | |
| bool | is_gamma_aa () const |
| Is this a gamma-amino acid? More... | |
| bool | is_water () const |
| is this a water residue type? More... | |
| bool | is_virtualizable_by_packer () const |
| Is this a residue type that can be virtualized or devirtualized by the packer? More... | |
| bool | is_oligourea () const |
| Is this an oligourea? More... | |
| bool | is_aramid () const |
| Is this an aramid? More... | |
| bool | is_ortho_aramid () const |
| Is this an ortho-aramid? More... | |
| bool | is_meta_aramid () const |
| Is this a meta-aramid? More... | |
| bool | is_para_aramid () const |
| Is this a para-aramid? More... | |
| bool | is_pre_methylene_ortho_aramid () const |
| Is this an ortho-aramid? More... | |
| bool | is_pre_methylene_meta_aramid () const |
| Is this a meta-aramid? More... | |
| bool | is_pre_methylene_para_aramid () const |
| Is this a para-aramid? More... | |
| bool | is_post_methylene_ortho_aramid () const |
| Is this an ortho-aramid? More... | |
| bool | is_post_methylene_meta_aramid () const |
| Is this a meta-aramid? More... | |
| bool | is_post_methylene_para_aramid () const |
| Is this a para-aramid? More... | |
| bool | is_pre_methylene_post_methylene_ortho_aramid () const |
| Is this an ortho-aramid? More... | |
| bool | is_pre_methylene_post_methylene_meta_aramid () const |
| Is this a meta-aramid? More... | |
| bool | is_pre_methylene_post_methylene_para_aramid () const |
| Is this a para-aramid? More... | |
| bool | is_sri () const |
| Is this one of SRI's special heteropolymer building blocks? More... | |
| bool | is_triazolemer () const |
| Is this a triazolemer? More... | |
| bool | is_mirrored_type () const |
| Is this a D_AA, R_PEPTOID, or L_RNA? More... | |
| bool | is_n_methylated () const |
| Is this residue N-methylated? More... | |
| bool | is_TNA () const |
| is TNA? More... | |
| bool | is_PNA () const |
| is PNA? More... | |
| bool | is_coarse () const |
| is coarse? More... | |
| bool | is_NA () const |
| is Nucleic Acid? More... | |
| bool | is_purine () const |
| is purine? More... | |
| bool | is_pyrimidine () const |
| is pyrimidine? More... | |
| bool | is_solvent () const |
| Is this a solvent molecule (SOLVENT property)? More... | |
| bool | is_canonical_nucleic () const |
| Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)? More... | |
| bool | is_canonical_aa () const |
| Is this a canonical amino acid (CANONICAL_AA property)? More... | |
| bool | is_canonical () const |
| Is this a canonical residue type (nucleic acid or amino acid)? More... | |
| bool | is_carbohydrate () const |
| is carbohydrate? More... | |
| bool | is_ligand () const |
| is ligand? More... | |
| bool | is_lipid () const |
| is lipid? More... | |
| bool | is_metal () const |
| Return true if this residue type is a metal ion, false otherwise. More... | |
| bool | is_metalbinding () const |
| Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.), false otherwise. More... | |
| bool | is_membrane () const |
| is membrane? More... | |
| bool | is_surface () const |
| is surface? (e.g. enamel) More... | |
| bool | has_sc_orbitals () const |
| does this residue have sidechain orbitals? More... | |
| bool | is_polar () const |
| is polar? More... | |
| bool | is_charged () const |
| is charged? More... | |
| bool | is_aromatic () const |
| is aromatic? More... | |
| bool | is_cyclic () const |
| is cyclic? More... | |
| bool | is_terminus () const |
| is terminus? More... | |
| bool | is_lower_terminus () const |
| is lower terminus? More... | |
| bool | is_upper_terminus () const |
| is upper terminus? More... | |
| bool | is_branch_point () const |
| is a branch-point residue? More... | |
| bool | is_acetylated_nterminus () const |
| is acetylated n terminus More... | |
| bool | is_methylated_cterminus () const |
| is methylated c terminus More... | |
| bool | is_virtual_residue () const |
| Check if residue is 'VIRTUAL_RESIDUE' This ONLY checks the VIRTUAL_RESIDUE PROPERTY! More... | |
| bool | is_inverted_virtual_residue () const |
| Check if atom is an inverted virtual. More... | |
| bool | is_VRT1 () const |
| Check if residue is 'VRT1'. More... | |
| bool | is_TP3 () const |
| Check if residue is a TP3 water. More... | |
| bool | is_adduct () const |
| is an adduct-modified residue? More... | |
| bool | has_polymer_dependent_groups () const |
| Does this type have groups (not just single atoms) that are polymer-bond dependent? More... | |
| bool | is_base_type () const override |
| Is this ResidueTypeBase a base type? More... | |
| ResidueTypeCOP | get_base_type_cop () const override |
| Get a pointer to this ResidueTypeBase's base ResidueTypeBase. More... | |
| core::chemical::rna::RNA_Info const & | RNA_info () const |
| core::chemical::carbohydrates::CarbohydrateInfoCOP | carbohydrate_info () const |
| Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More... | |
| dihedral_atom_set const & | dihedral (Size const dihe) const |
| Return the indices for the set of atoms that define a particular intraresidue dihedral. More... | |
| utility::vector1< Size > const & | dihedrals_for_atom (Size atomno) const |
| Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom. More... | |
| bondangle_atom_set const & | bondangle (Size const bondang) const |
| Return the indices for the set of atoms that define a particular intraresidue angle. More... | |
| utility::vector1< Size > const & | bondangles_for_atom (Size atomno) const |
| Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More... | |
| Size | num_bondangles () const |
| get number of intraresidue bond angles More... | |
| void | print_bondangles () const |
| print intraresidue bond angles to standard out More... | |
| void | print_pretty_path_distances () const |
| print chemical-bond path distances to standard out More... | |
| utility::vector1< two_atom_set > const & | atoms_within_one_bond_of_a_residue_connection (Size resconn) const |
| Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1< std::pair < Size, Size > > const & | within1bonds_sets_for_atom (Size atomid) const |
| Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More... | |
| utility::vector1 < three_atom_set > const & | atoms_within_two_bonds_of_a_residue_connection (Size resconn) const |
| Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn. More... | |
| utility::vector1< std::pair < Size, Size > > | within2bonds_sets_for_atom (Size atomid) const |
| Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More... | |
| void | select_orient_atoms (Size ¢er, Size &nbr1, Size &nbr2) const |
| Selects three atoms for orienting this residue type. More... | |
| void | select_orient_atoms_standard_logic (Size ¢er, Size &nbr1, Size &nbr2, bool const ignore_virtuals) const |
| Pick atoms to use for orienting one Residue onto another, using standard logic. More... | |
| std::tuple< Size, Size, Size > | select_orient_atoms () const |
| Selects three atoms for orienting this residue type. More... | |
| void | show (std::ostream &output=std::cout, bool output_atomic_details=false) const override |
| Generate string representation of ResidueType for debugging purposes. More... | |
| template<typename MemFn , typename Ptr > | |
| utility::signals::Link | attach_destruction_obs (MemFn fn, Ptr ptr) const |
| attach RestypeDestructionEvent observer function More... | |
| template<typename MemFn , typename Ptr > | |
| bool | detach_destruction_obs (MemFn fn, Ptr ptr) const |
| detach RestypeDestructionEvent observer function More... | |
 Public Member Functions inherited from core::chemical::ResidueTypeBase | |
| TypeSetMode | mode () const |
| AtomTypeSet const & | atom_type_set () const |
| access by reference the atomset for which this residue is constructed More... | |
| AtomTypeSetCOP | atom_type_set_ptr () const |
| access by const pointer the atomset for which this residue is constructed More... | |
| ElementSet const & | element_set () const |
| access by reference the element set for which this residue is constructed More... | |
| ElementSetCOP | element_set_ptr () const |
| access by const pointer the element set for which this residue is constructed More... | |
| MMAtomTypeSetCOP | mm_atom_types_ptr () const |
| gasteiger::GasteigerAtomTypeSetCOP | gasteiger_atom_typeset () const |
| void | set_gasteiger_atom_typeset (gasteiger::GasteigerAtomTypeSetCOP setting) |
| orbitals::OrbitalTypeSetCOP | orbital_types_ptr () const |
| Get the MM atom_type for this atom by its index number in this residue. More... | |
| void | set_orbital_typeset (orbitals::OrbitalTypeSetCOP setting) |
| bool | has_orbital_types () const |
| Does this residue type define orbital types? More... | |
| signed long int | net_formal_charge () const |
| Get the nominal net formal charge on this residue type. More... | |
| void | net_formal_charge (signed long int charge_in) |
| Set the nominal net formal charge on this residue type. More... | |
| utility::vector1< std::string > const & | get_metal_binding_atoms () const |
| std::string const & | get_disulfide_atom_name () const |
| Gets disulfide atom name. More... | |
| void | set_disulfide_atom_name (std::string const &n) |
| Sets disulfide atom name. More... | |
| std::map< std::string, std::string > const & | atom_aliases () const |
| returns atom aliases More... | |
| std::string const & | atom_alias (std::string const &name) const |
| returns atom alias More... | |
| std::map< std::string, std::string > const & | canonical_atom_aliases () const |
| returns atom aliases More... | |
| std::string const & | canonical_atom_alias (std::string const &name) const |
| returns atom alias More... | |
| Orbital const & | orbital (Size const orbital_index) const |
| Orbital const & | orbital (std::string const &orbital_name) const |
| orbitals::OrbitalType const & | orbital_type (Size const orbital_index) const |
| Size | n_orbitals () const |
| number of orbitals More... | |
| bool | has_orbital (std::string const &orbital_name) const |
| is this orbital present in this residue? More... | |
| core::Size | orbital_index (std::string const &name) const |
| get orbital index by name More... | |
| ResidueProperties const & | properties () const |
| Access the collection of properties for this ResidueTypeBase. More... | |
| void | set_properties (ResiduePropertiesOP properties) |
| Set the collection of properties for this ResidueTypeBase. More... | |
| void | add_property (std::string const &property) |
| Add a property to this ResidueTypeBase. More... | |
| void | add_property (core::chemical::ResidueProperty const property) |
| Add a property to this ResidueType, by properties enum. More... | |
| void | set_adduct_flag (bool adduct_in) |
| void | add_numeric_property (std::string const &tag, core::Real value) |
| Add a numeric property. More... | |
| void | add_string_property (std::string const &tag, std::string value) |
| Add a string property. More... | |
| void | delete_property (std::string const &property) |
| Delete a property of this ResidueType. More... | |
| void | delete_property (core::chemical::ResidueProperty const property) |
| Delete a property of this ResidueType, by properties enum. More... | |
| void | set_metapatched () |
| Set that this is a metapatched ResidueType. More... | |
| bool | is_metapatched () const |
| Get whether this is a metapatched ResidueType. More... | |
| bool | is_polymer () const |
| is polymer? More... | |
| bool | is_protein () const |
| is protein? More... | |
| bool | is_DNA () const |
| is DNA? More... | |
| bool | is_RNA () const |
| is RNA? More... | |
| bool | is_d_aa () const |
| is this a d-amino acid? More... | |
| bool | is_l_aa () const |
| is this an l-amino acid? More... | |
| bool | is_d_rna () const |
| is this a d-RNA? More... | |
| bool | is_l_rna () const |
| is this an l-RNA? More... | |
| bool | is_peptoid () const |
| is peptoid? More... | |
| bool | is_r_peptoid () const |
| Is this a peptoid with a chiral side-chain with "R" chirality? More... | |
| bool | is_s_peptoid () const |
| Is this a peptoid with a chiral side-chain with "S" chirality? More... | |
| bool | is_achiral_backbone () const |
| is this an achiral backbone? More... | |
| bool | is_achiral_sidechain () const |
| Does this have an achiral sidechain? More... | |
| bool | has_property (std::string const &property) const |
| Generic property access. More... | |
| bool | has_property (ResidueProperty const property) const |
| Generic property access, by ResidueProperty. More... | |
| core::Real | get_numeric_property (std::string const &tag) const |
| Get a numeric property, if it exists. More... | |
| std::string | get_string_property (std::string const &tag) const |
| Get a string property, if it exists. More... | |
| void | add_variant_type (VariantType const variant_type) |
| Add a variant type to this ResidueTypeBase. More... | |
| void | add_variant_type (std::string const &variant_type) |
| Add a variant type to this ResidueTypeBase by string. More... | |
| void | remove_variant_type (VariantType const variant_type) |
| Remove a variant type to this ResidueTypeBase. More... | |
| void | remove_variant_type (std::string const &variant_type) |
| Remove a variant type to this ResidueTypeBase by string. More... | |
| bool | has_variant_type (VariantType const variant_type) const |
| Generic variant access. More... | |
| bool | has_variant_type (std::string const &variant_type) const |
| Generic variant access by string. More... | |
| void | enable_custom_variant_types () |
| Turn on the ability to create VariantTypes "on-the-fly". More... | |
| utility::vector1< std::string > | variant_types () const |
| get all the variant types for this ResidueTypeBase More... | |
| utility::vector1< VariantType > | variant_type_enums () const |
| Get a vector of VariantType enums for this ResidueTypeBase. More... | |
| utility::vector1< std::string > const & | custom_variant_types () const |
| Get a list of custom VariantType strings for this ResidueTypeBase (by const reference). More... | |
| void | aa (AA const &type) |
| set our aa-type (could be "UNK") More... | |
| void | aa (std::string const &type) |
| set our aa-type (could be "UNK") More... | |
| void | backbone_aa (std::string const &type) |
| AA to use for backbone scoring. More... | |
| void | base_analogue (std::string const &type) |
| NA to use for base-specific generalization (can be more forgiving than na_analogue for new NA backbones) More... | |
| void | na_analogue (std::string const &type) |
| NA to use for fragment sampling and some scoring purposes. More... | |
| std::string const & | base_name () const |
| Get this ResidueTypeBase's base name (shared with other residue types with the same base type). More... | |
| std::string const & | name () const |
| get our (unique) residue name More... | |
| void | base_name (std::string const &base_name_in) |
| Set this ResidueTypeBase's base name (shared with other residue types with the same base type). More... | |
| void | name (std::string const &name_in) |
| set our (unique) residue name More... | |
| std::string const & | name3 () const |
| get our 3letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More... | |
| void | name3 (std::string const &name_in) |
| set our 3letter code More... | |
| char | name1 () const |
| get our 1letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name3 string. More... | |
| void | name1 (char const code) |
| set our 1letter code More... | |
| std::string | interchangeability_group () const |
| get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag. More... | |
| void | interchangeability_group (std::string setting) |
| set our interchangeability-group id More... | |
| void | remap_pdb_atom_names (bool rename) |
| Turn on geometry-based atom renaming when loading this residue type from PDB files. More... | |
| bool | remap_pdb_atom_names () const |
| Are we using geometry-based atom renaming when loading this residue type from PDB. More... | |
| AA const & | aa () const |
| our traditional residue type, if any More... | |
| AA const & | backbone_aa () const |
| Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More... | |
| AA const & | base_analogue () const |
| Returns the nucleic acid type to be used for base features. More... | |
| AA const & | na_analogue () const |
| Returns the nucleic acid type to be used for fragment sampling/scoring. More... | |
| void | rotamer_library_specification (rotamers::RotamerLibrarySpecificationOP) |
| rotamers::RotamerLibrarySpecificationCOP | rotamer_library_specification () const |
| rotamers::RotamerLibrarySpecificationOP | rotamer_library_specification_nonconst () |
| Nonconst access to the RotamerLibrarySpecification. More... | |
| void | strip_rotamer_library_specification () |
| Remove any rotamer library specifications attached to this ResidueTypeBase. More... | |
| bool | force_nbr_atom_orient () const |
| dihedral methods More... | |
| void | force_nbr_atom_orient (bool force_orient) |
| Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More... | |
| std::string const & | get_rama_prepro_mainchain_torsion_potential_name (bool const pre_proline_position) const |
| Get the key name for the mainchain torsion potential used by the RamaPrePro score term. More... | |
| bool | mainchain_potentials_match (ResidueTypeBase const &other) const |
| Do the rama_prepro mainchain torsion potentials of this residue match another? More... | |
| void | set_rama_prepro_mainchain_torsion_potential_name (std::string const &name_in, bool const pre_proline_position) |
| Set the key name for the mainchain torsion potential used by the RamaPrePro score term. More... | |
| std::string const & | get_rama_prepro_map_file_name (bool const pre_proline_position) const |
| Get the file name for the mainchain torsion potential used by the RamaPrePro score term. More... | |
| void | set_rama_prepro_map_file_name (std::string const &filename_in, bool const pre_proline_position) |
| Set the file name for the mainchain torsion potential used by the RamaPrePro score term. More... | |
| bool | defines_custom_rama_prepro_map (bool const pre_proline_position) const |
| Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueTypeBase (which is presumably different from that of the base type). More... | |
| void | reset_mainchain_torsion_potential_names () |
| Set the names of the mainchain torsion potential maps to use to "". More... | |
| utility::vector1< Adduct > const & | defined_adducts () const |
| get the adducts defined for this residue More... | |
| void | add_adduct (Adduct &adduct_in) |
| void | report_adducts () const |
Static Public Member Functions | |
| static ResidueTypeCOP | make (MutableResidueType const &residue_type) |
| Make a ResidueType from a Modifiable residue type. More... | |
Private Member Functions | |
| ResidueType () | |
| ResidueType (MutableResidueType const &residue_type) | |
| Make (most of) a ResidueType from a MutableResidueType Use ResidueType::make() instead. More... | |
| ResidueType (ResidueType const &residue_type)=delete | |
| make a copy of this ResidueType More... | |
| ResidueTypeOP | clone () const =delete |
| make a copy More... | |
| ResidueTypeOP | placeholder_clone () const =delete |
| make a copy More... | |
| ResidueType & | operator= (ResidueType const &src)=delete |
| Copies <src> into the ResidueType. More... | |
| utility::vector1< core::Size > | setup_atom_ordering (MutableResidueType const &source) |
| Determine how to map the numeric indices of MutableResidueType to this ResidueType. ( As the MutableResidueType is const, we can assume a decent mapping here. ) More... | |
| void | copy_atom_info (MutableResidueType const &source, utility::vector1< core::Size > const &old_to_new) |
| Iterate through the atoms, filling out the various atom info vectors. More... | |
| void | copy_other_info (MutableResidueType const &source, utility::vector1< core::Size > const &old_to_new) |
| Fill in various other information which is being copied over from the MutableResidueType. More... | |
| void | initialize_derived_data () |
| Precalculate other derived data from data already present. More... | |
| void | update_derived_data () |
| Do other pre-calculation checks, not for otherwise uninitialized variables, but for data consistency or otherwise "incorrectly" set values. More... | |
| void | auto_assign_nu_atoms () |
| If a ring has been added but no nu angles have been defined, automatically assign them. More... | |
| void | define_mainchain_atoms () |
| If a polymer without explicitly set mainchain atoms, determine a list of main chain atoms by shortest path from LOWER to UPPER. More... | |
| void | update_ring_conformer_sets () |
| Update the ring conformer sets derived information. More... | |
| void | update_last_controlling_chi () |
| compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom. More... | |
| void | note_chi_controls_atom (Size chi, Size atomno) |
| Recursive subroutine invoked by update_last_controlling_chi(). More... | |
| void | update_polymer_dependent_groups () |
| Determine which atoms are polymer bond-dependent. More... | |
| void | update_nonpolymer_dependent_groups () |
| Determine which atoms are nonpolymer bond-dependent. More... | |
| void | update_ncaa_rotamer_library_specification_if_present () |
| If there is an NCAARotamerLibrarySpecification, ensure that the rotamer backbone dependicies have been set. If they have not, set them to all mainchain torsions except omega (the final, inter-residue torsion). More... | |
| void | self_pointer_updates () |
| Do updates which need a valid get_self_ptr() (And thus can't be called from the constructor.) More... | |
| void | perform_checks () const |
| Final check of ResidueType data, called by ResidueType::make(). More... | |
Private Attributes | |
| Size | natoms_ |
| Size | nbonds_ |
| Size | nheavyatoms_ |
| The number of heavy atoms. More... | |
| Size | n_hbond_acceptors_ |
| The number of hbond_acceptors. More... | |
| Size | n_hbond_donors_ |
| number of hbond_donors More... | |
| Size | n_backbone_heavyatoms_ |
| number of backbone heavy atoms More... | |
| Size | first_sidechain_hydrogen_ |
| the index of first sidechain hydrogen atom More... | |
| utility::vector1< std::string > | atom_names_ |
| std::map< std::string, core::Size > | atom_name_to_index_ |
| utility::vector1< AtomType > | vec_atom_types_ |
| The types for each atom. More... | |
| utility::vector1< core::Size > | vec_atom_type_indexes_ |
| utility::vector1< ElementCOP > | elements_ |
| utility::vector1< core::Size > | mm_atom_type_index_ |
| utility::vector1< core::Size > | gasteiger_atom_type_index_ |
| utility::vector1< int > | formal_charge_ |
| utility::vector1< core::Real > | partial_charge_ |
| utility::vector1< core::Vector > | ideal_xyz_ |
| utility::vector1 < AtomPropertiesOP > | atomic_properties_ |
| utility::vector1< AtomICoor > | icoor_ |
| Internal coordinates on how to build the given atom. More... | |
| utility::vector1< AtomIndices > | bonded_neighbor_ |
| For each atom, list the other atom indices it's bonded to. More... | |
| utility::vector1 < utility::vector1< BondName > > | bonded_neighbor_type_ |
| What is the bond type of the bond connecting the equivalent entry in bonded_neighbor_? More... | |
| utility::vector1 < utility::vector1 < BondRingness > > | bonded_neighbor_ringness_ |
| What is the ringness type of the bond connecting the equivalent entry in bonded_neighbor_? More... | |
| utility::vector1< Size > | attached_H_begin_ |
| indices of each heavyatom's first attached hydrogen More... | |
| utility::vector1< Size > | attached_H_end_ |
| indices of each heavyatom's last attached hydrogen More... | |
| utility::vector1 < dihedral_atom_set > | dihedral_atom_sets_ |
| Data for the mm potentials. List all of the intra-residue dihedral angles and bond angles. vector of sets of atoms that make up dihedral angles in the residue Data for the mm potentials. More... | |
| utility::vector1 < utility::vector1< Size > > | dihedrals_for_atom_ |
| all intra-residue dihedral angles that each atom "participates" in More... | |
| utility::vector1 < bondangle_atom_set > | bondangle_atom_sets_ |
| vector of sets of atoms that make up bond angles in the residue More... | |
| utility::vector1 < utility::vector1< Size > > | bondangles_for_atom_ |
| ??? More... | |
| utility::vector1< Size > | last_controlling_chi_ |
| Data for controlling chi. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi. More... | |
| utility::vector1< AtomIndices > | atoms_last_controlled_by_chi_ |
| for chi i, the list of atoms last controlled by i E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1 More... | |
| utility::vector1 < utility::vector1< Size > > | bonded_orbitals_ |
| For each atom, which orbitals are bonded to it. More... | |
| AtomIndices | atoms_with_orb_index_ |
| indices of atoms with orbitals More... | |
| AtomIndices | Haro_index_ |
| indices of haro hydrogens More... | |
| AtomIndices | Hpol_index_ |
| indices of hpolar hydrogens More... | |
| AtomIndices | accpt_pos_ |
| indices of Hbond acceptor positions More... | |
| AtomIndices | Hpos_polar_ |
| indices of polar Hydrogens for Hbond donors More... | |
| AtomIndices | Hpos_apolar_ |
| indices of apolar hydrogens More... | |
| AtomIndices | accpt_pos_sc_ |
| indices of Hbond acceptor positions that are part of the sidechain must be a subset of the atoms listed in the accpt_pos_ array More... | |
| AtomIndices | Hpos_polar_sc_ |
| indices of polar Hydrogens for Hbond donors that are part of the sidechain must be a subset of the atoms listed in the Hpos_polar_ array More... | |
| AtomIndices | all_bb_atoms_ |
| Indices of all backbone atoms, hydrogens and heavyatoms. More... | |
| AtomIndices | all_sc_atoms_ |
| Indices of all sidechain atoms, hydrogens and heavyatoms. More... | |
| utility::vector1< bool > | heavyatom_has_polar_hydrogens_ |
| Is this atom a heavyatom with polar hydrogens attached? More... | |
| utility::vector1 < utility::vector1< core::Size > > | chi_atoms_ |
| utility::vector1< bool > | is_proton_chi_ |
| Is the corresponding chi in chi_atoms_ a proton chi? More... | |
| utility::vector1< Size > | proton_chis_ |
| Indices of the chi_atoms_ vector for proton chis. More... | |
| utility::vector1< Size > | chi_2_proton_chi_ |
| A "map" of chi indices to proteon_chi indices. More... | |
| utility::vector1 < utility::vector1< Real > > | proton_chi_samples_ |
| For a proton chi, the primary samples to diversify the rotamer library with. More... | |
| utility::vector1 < utility::vector1< Real > > | proton_chi_extra_samples_ |
| For a proton chi, how to handle extra ex_ levels. More... | |
| utility::vector1 < utility::vector1< std::pair < Real, Real > > > | chi_rotamers_ |
| Additional non-Dunbrack rotamer bins. More... | |
| utility::vector1< AtomIndices > | nu_atoms_ |
| AtomIndex of four atoms to build each nu angle. More... | |
| utility::vector1< AtomIndices > | ring_atoms_ |
| AtomIndex of all ring atoms, not counting virtual atoms. More... | |
| utility::vector1 < core::chemical::rings::RingSaturationType > | ring_saturation_types_ |
| The saturation type of each ring in this residue. More... | |
| utility::vector1 < rings::RingConformerSetOP > | ring_conformer_sets_ |
| The sets of all possible ring conformers, one per ring. More... | |
| utility::vector1< std::string > | lowest_ring_conformer_ |
| Lowest-energy ring conformer for each ring. More... | |
| utility::vector1 < utility::vector1 < std::string > > | low_ring_conformers_ |
| Low-energy ring conformers for each ring. More... | |
| utility::vector1 < utility::vector1< int > > | path_distance_ |
| number of bonds separated between any pair of atoms in this residue More... | |
| core::Size | root_atom_ |
| Atom at the nominal root of the ICOOR tree. More... | |
| core::Size | nbr_atom_ |
| Real | nbr_radius_ |
| radius cutoff to define neighbors More... | |
| Real | mass_ |
| utility::vector1 < ResidueConnection > | residue_connections_ |
| Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections. More... | |
| utility::vector1 < utility::vector1< Size > > | atom_2_residue_connection_map_ |
| Mapping of atom indicies to residue connections. More... | |
| utility::vector1 < utility::vector1 < two_atom_set > > | atoms_within_one_bond_of_a_residue_connection_ |
| For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1 < utility::vector1< std::pair < Size, Size > > > | within1bonds_sets_for_atom_ |
| For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. More... | |
| utility::vector1 < utility::vector1 < three_atom_set > > | atoms_within_two_bonds_of_a_residue_connection_ |
| For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. More... | |
| utility::vector1 < utility::vector1< std::pair < Size, Size > > > | within2bonds_sets_for_atom_ |
| For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. More... | |
| Size | lower_connect_id_ |
| Polymer lower connections. More... | |
| Size | upper_connect_id_ |
| Polymer upper connections. More... | |
| Size | n_non_polymeric_residue_connections_ |
| Number of non-polymeric residue connections. More... | |
| Size | n_polymeric_residue_connections_ |
| Number of polymeric residue connections. More... | |
| ResidueTypeCOP | base_type_cop_ |
| Const-access owning pointer to the base residue type. More... | |
| core::chemical::rna::RNA_InfoOP | rna_info_ |
| A container for properties unique to RNA. More... | |
| core::chemical::carbohydrates::CarbohydrateInfoOP | carbohydrate_info_ |
| A container for residue properties unique to carbohydrates. More... | |
| utility::vector1< Size > | atom_base_indices_ |
| Index version of atom_base_. More... | |
| utility::vector1< Size > | abase2_indices_ |
| Index version of abase2_. More... | |
| AtomIndices | mainchain_atoms_indices_ |
| Index version of mainchain_atoms_. More... | |
| AtomIndices | actcoord_atoms_indices_ |
| Index version of actcoord_atoms_. More... | |
| utility::vector1< AtomIndices > | cut_bond_neighbor_indices_ |
| Index version of cut_bond_neighbor_. More... | |
| utility::vector1< Size > | atom_shadowed_indices_ |
| Index version of atom_shadowed_. More... | |
| bool | has_polymer_dependent_groups_ |
| Does this ResidueType have groups with icoors that depend, directly or indirectly, on polymeric bonds? More... | |
| utility::vector1< bool > | atom_depends_on_lower_polymeric_connection_ |
| vector of length corresponding to number of atoms indicating whether each atom is dependent on the lower polymer bond. More... | |
| utility::vector1< bool > | atom_depends_on_upper_polymeric_connection_ |
| vector of length corresponding to number of atoms indicating whether each atom is dependent on the upper polymer bond. More... | |
| utility::vector1 < utility::vector1< bool > > | atom_depends_on_connection_ |
| An outer vector indexed to connection ID, and an inner vector indexed to atom ids. "True" means that the atom id for the inner vector depends on the connection ID for the outer. More... | |
| utility::signals::BufferedSignalHub < void, RestypeDestructionEvent > | destruction_obs_hub_ |
| Who needs to be told if this ResidueType is destroyed? More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from core::chemical::ResidueTypeBase | |
| ResidueTypeBase () | |
| ResidueTypeBase (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types) | |
| constructor More... | |
| ResidueTypeBase (ResidueTypeBase const &)=default | |
| ResidueTypeBase & | operator= (ResidueTypeBase const &)=default |
| Copies <src> into the ResidueTypeBase. More... | |
| void | atom_type_set (AtomTypeSetCOP setting) |
| utility::vector1< std::string > & | metal_binding_atoms () |
| std::map< std::string, std::string > & | atom_aliases () |
| returns atom aliases More... | |
| std::map< std::string, std::string > & | canonical_atom_aliases () |
| returns atom aliases More... | |
| utility::vector1< Orbital > & | get_orbitals () |
| std::map< std::string, int > & | get_orbitals_index () |
| AA const & | backbone_aa_raw () const |
| AA const & | base_analogue_raw () const |
| AA const & | na_analogue_raw () const |
A class for defining a type of residue.
This class contains the "chemical" information for residues as well as the ideal xyz and internal coordinates for a residue (generated xyz coordinates are found in core/conformation/Residue.hh). A ResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. ResidueTypes are generated through .params files, which are read from the database chemical/residue_types. For ligands, a parameter has to be provided to rosetta through the -extra_res_fa flag. Primary data are set through the residue_io.cc class. The primary data that are set are: atoms, mmatoms, orbitals, and properties of the particular ResidueType. These properties can be modified through patches, which create new ResidueTypes, and are controlled through PatchOperations.cc.
When a ResidueType is initially created, it's created as a MutableResidueType, which represents the data as an atom graph, which facilitates atomistic modification. This class (the plain ResidueType class) is a "finalized" version of the ResidueType, which doesn't permit modification, and is the main class used by most Rosetta simulations. It's created from a MutableResidueType, and for efficiency represents the data as a "struct of vectors" representation.
Correspondingly, the main representation of atoms is different between the classes. Whereas the MutableResidueType uses an opaque "vertex descriptor" to identify atoms, the plain ResidueType class uses an integer index. The order of atoms is well-defined, with heavy atoms coming before hydrogens, and backbone atoms coming before sidechain atoms. (and hydrogens in the same order as the heavyatoms they're connected to).
Properties: Properties of a residue include things like DNA, PROTEIN, CHARGED, etc. These properties indicate the type of residue it is and what properties are associated with the residue. They are set when read in. To add new ResidueProperties, add them to core/chemical/residue_properties/general_properties.list.
Orbitals: Orbitals are indexed separately from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. (I haven't figured out how to get the reverse to work because of the separate indices.) Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals.
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Referenced by make().
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Make (most of) a ResidueType from a MutableResidueType Use ResidueType::make() instead.
The construction of a ResidueType from a MutableResidueType happens in several stages
References copy_atom_info(), copy_other_info(), initialize_derived_data(), core::chemical::ResidueTypeBase::name(), setup_atom_ordering(), update_derived_data(), and core::chemical::MutableResidueType::validate_residue_type().
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make a copy of this ResidueType
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destructor
References destruction_obs_hub_.
get index of an atom's second base atom
References abase2_indices_, and atom_base_indices_.
Referenced by core::conformation::Residue::abase2(), and core::chemical::residue_types_identical().
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indices of atoms as Hbond acceptors
References accpt_pos_.
Referenced by core::conformation::Residue::accpt_pos(), and core::chemical::residue_types_identical().
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indices of atoms as Hbond acceptors
References accpt_pos_sc_.
Referenced by core::conformation::Residue::accpt_pos_sc(), and core::chemical::residue_types_identical().
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get indices for atoms used to define actcoord
References actcoord_atoms_indices_.
Referenced by core::conformation::Residue::actcoord_atoms(), core::chemical::MutableResidueType::copy_other_info(), core::chemical::residue_types_identical(), core::conformation::Residue::update_actcoord(), and core::chemical::write_topology_file().
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Indices of all backbone atoms, hydrogens and heavyatoms.
References all_bb_atoms_.
Referenced by core::conformation::Residue::all_bb_atoms(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::sasa::get_sc_bb_sasa(), core::scoring::sasa::get_sc_bb_sasa_per_res(), and core::chemical::residue_types_identical().
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Indices of all sidechain atoms, hydrogens and heavyatoms.
References all_sc_atoms_.
Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), core::scoring::sasa::get_sc_bb_sasa(), core::scoring::sasa::get_sc_bb_sasa_per_res(), core::chemical::residue_types_identical(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().
get index of an atom's base atom
References atom_base_indices_.
Referenced by core::util::add_constraints_to_metal(), core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::atom_base(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), note_chi_controls_atom(), perform_checks(), core::chemical::residue_types_identical(), core::chemical::rna::RNA_Info::rna_note_chi_controls_atom(), core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(), select_orient_atoms(), select_orient_atoms_standard_logic(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), update_last_controlling_chi(), and core::chemical::ResidueTypeKinWriter::write_restype().
Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone.
References atom_shadowed_indices_.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::methods::RingClosureEnergy::residue_energy(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
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References partial_charge_.
Referenced by core::conformation::Residue::atomic_charge(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::chemical::MutableResidueType::copy_atom_info(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::PQR::PQR(), core::pose::rna::print_torsion_info(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::residue_types_identical(), show(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
| bool core::chemical::ResidueType::atom_depends_on_connection | ( | core::Size const | atom_index, |
| core::Size const | connection_id | ||
| ) | const |
Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID?
References atom_depends_on_connection_, atom_index(), n_possible_residue_connections(), and natoms().
Referenced by core::chemical::residue_types_identical().
| bool core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection | ( | core::Size const | atom_index | ) | const |
Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection?
References atom_depends_on_lower_polymeric_connection_, atom_index(), core::chemical::ResidueTypeBase::is_polymer(), and natoms().
Referenced by core::conformation::Residue::atom_depends_on_lower(), and core::chemical::residue_types_identical().
| bool core::chemical::ResidueType::atom_depends_on_polymeric_connection | ( | core::Size const | atom_index | ) | const |
Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection?
References atom_depends_on_lower_polymeric_connection_, atom_depends_on_upper_polymeric_connection_, atom_index(), core::chemical::ResidueTypeBase::is_polymer(), and natoms().
| bool core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection | ( | core::Size const | atom_index | ) | const |
Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection?
References atom_depends_on_upper_polymeric_connection_, atom_index(), core::chemical::ResidueTypeBase::is_polymer(), and natoms().
Referenced by core::conformation::Residue::atom_depends_on_upper(), and core::chemical::residue_types_identical().
Does an atom form any inter-residue chemical bonds?
References atom_2_residue_connection_map_.
| bool core::chemical::ResidueType::atom_has_property | ( | Size const | atomno, |
| AtomProperty const | property | ||
| ) | const |
References atomic_properties_.
Referenced by is_virtual(), and core::chemical::Metapatch::meets_requirements().
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get atom index by name
References atom_name(), atom_name_to_index_, is_membrane(), core::chemical::ResidueTypeBase::is_protein(), and core::chemical::ResidueTypeBase::name().
Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::hybridization::add_non_protein_cst(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::hybridization::TMalign::alignment2AtomMap(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::CreateAngleConstraint::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::nmr::pre::PREMover::apply(), protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(), atom_depends_on_connection(), atom_depends_on_lower_polymeric_connection(), atom_depends_on_polymeric_connection(), atom_depends_on_upper_polymeric_connection(), core::conformation::Residue::atom_index(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::chemical::SetPolymerConnectAtom::changes_connections_on(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::chemical::AddConnectAndTrackingVirt::changes_connections_on(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::fldsgn::MatchResidues::compute_comb(), protocols::flxbb::constraints_NtoC(), protocols::flxbb::constraints_sheet(), copy_other_info(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_constraint(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::match::Matcher::create_ds_builder(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::constraint_generator::existing_atoms(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::loops::fix_with_coord_cst(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::pose::motif::get_AIDs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::elec::CountPairRepMap::get_map(), get_metal_binding_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::chemical::ICoorAtomID::ICoorAtomID(), ideal_xyz(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Conformation::insert_residue_by_bond(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), core::pose::named_atom_id_to_atom_id(), core::chemical::Selector_UPPER_ATOM::operator[](), core::conformation::Residue::orient_onto_residue(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), core::scoring::constraints::parse_NMR_name_old(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), core::chemical::pretty_print_atomicoor(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), core::scoring::constraints::BigBinConstraint::read_def(), protocols::constraints_additional::COMCoordinateConstraint::read_def(), protocols::constraints_additional::BindingSiteConstraint::read_def(), protocols::evaluation::PCA::read_structure(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::constraints::requires_CB_mapping(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::symmetry::SymmetrySlider::rg(), core::select::util::select_coord_for_residue(), select_orient_atoms_standard_logic(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), core::pose::rna::setup_base_pair_constraints(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), core::scoring::cryst::PhenixInterface::stealBfactorsFromFile(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), protocols::chemically_conjugated_docking::ubq_ras_distance(), protocols::chemically_conjugated_docking::ubq_ras_rotation_angle(), and core::chemical::rna::RNA_Info::update_derived_rna_data().
References vec_atom_types_.
Referenced by show(), and update_derived_data().
is a backbone atom (heavy or hydrogen)?
References first_sidechain_hydrogen_, n_backbone_heavyatoms_, natoms(), and nheavyatoms_.
Referenced by core::conformation::Residue::atom_is_backbone(), core::scoring::hbonds::create_rotamer_descriptor(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Residue::place(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::constraints::requires_CB_mapping(), select_orient_atoms_standard_logic(), core::scoring::lkball::setup_water_builders_for_residue_type(), and core::scoring::orbitals::surrogate_atom_for_orbital().
quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.
References natoms(), and nheavyatoms_.
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), core::conformation::Residue::atom_is_hydrogen(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and show().
References all_sc_atoms_, and natoms().
Referenced by core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map().
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get atom name by index
References atom_names_, core::chemical::ResidueTypeBase::name(), and core::id::to_string().
Referenced by protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), atom_index(), core::conformation::Residue::atom_name(), core::chemical::Metapatch::atoms(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), branch_connect_atom_names(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), core::scoring::rna::data::RNA_DMS_Potential::check_hbonded(), core::chemical::rna::chi1_torsion_atom(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::chemical::MutableResidueType::copy_atom_info(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::chemical::rna::default_jump_atom(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), core::io::silent::BinarySilentStruct::fill_struct(), core::chemical::find_best_match(), core::chemical::rna::first_base_atom(), core::conformation::form_disulfide(), core::chemical::formatted_icoord_tree(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::chemical::rna::get_rna_base_centroid(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), core::chemical::heavy_atom_names_match(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::pose::toolbox::AtomID_Mapper::initialize_from_pose(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::pose::rna::is_cutpoint_closed_atom(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::MiniPose::MiniPose(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::chemical::ICoorAtomID::name(), core::conformation::Residue::orient_onto_residue(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), perform_checks(), core::conformation::Residue::place(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), core::chemical::pretty_print_atomicoor(), protocols::stepwise::modeler::rna::print_atom_info(), print_bondangles(), protocols::ligand_docking::print_buried_unsat_Hbonds(), core::chemical::print_chis(), protocols::rna::denovo::print_hbonds(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), print_pretty_path_distances(), core::pose::rna::print_torsion_info(), protocols::denovo_design::rebuild_missing_atoms(), core::io::pose_from_sfr::remap_names_on_geometry(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::residue_types_identical(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), core::io::pose_from_sfr::score_mapping(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::methods::GoapRsdType::setup_connectivity(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::lkball::setup_water_builders_for_residue_type(), show(), core::chemical::rna::RNA_Info::update_derived_rna_data(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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Get the AtomicProperities object for the atom. (Note this is only the manually set properties, not all the properties of the atom.)
References atomic_properties_.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), and core::chemical::residue_types_identical().
Get the chemical atom_type for this atom by it index number in this residue.
If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below
References vec_atom_types_.
Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Residue::atom_type(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::rna::movers::bump_check(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::AutomorphismIterator::can_pair(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), core::chemical::MutableResidueType::copy_atom_info(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::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(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Residue::is_repulsive(), is_repulsive(), core::conformation::Residue::is_virtual(), is_virtual(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), print_bondangles(), protocols::match::output::print_node(), core::conformation::print_node(), core::pose::rna::print_torsion_info(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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References vec_atom_type_indexes_.
Referenced by protocols::match::bump_grid_to_enclose_pose(), copy_atom_info(), core::scoring::ResidueExclParams::create_excl_info(), core::pose::rna::print_torsion_info(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), and show().
| bool core::chemical::ResidueType::atoms_are_bonded | ( | core::Size const | atom_index1, |
| core::Size const | atom_index2 | ||
| ) | const |
Indicates whether or not two atom indices have a chemical bond linking them.
Note that this assumes that the Rosetta machinery is set up so that if atom 1 is bonded to atom 2, atom 2 is bonded to atom 1. This function breaks if that assumption breaks.
References nbrs().
Referenced by core::conformation::get_second_atom_from_connection().
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Read access to the atoms_last_controlled_by_chi_ array.
References atoms_last_controlled_by_chi_.
Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::chemical::residue_types_identical(), and core::chemical::rna::RNA_Info::update_derived_rna_data().
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Read access to the Atoms last controlled by a particular chi.
References atoms_last_controlled_by_chi_.
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Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.
References atoms_within_one_bond_of_a_residue_connection_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().
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Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn.
References atoms_within_two_bonds_of_a_residue_connection_.
Referenced by core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), and core::scoring::methods::MMTorsionEnergy::residue_pair_energy().
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attach RestypeDestructionEvent observer function
| fn | pointer to observer's unary member function with signature void( RestypeDestructionEvent const & ) |
| ptr | RAW pointer to observer object |
References destruction_obs_hub_.
Referenced by core::scoring::elec::CountPairRepMap::get_map(), core::scoring::FACTSRsdTypeMap::get_type_info(), core::scoring::lkball::LKBallDatabase::initialize_residue_type(), core::scoring::methods::IdealParametersDatabase::parameters_for_restype(), and core::scoring::custom_pair_distance::PairFuncMap::set_atom_pair_func().
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for all heavy atoms, index numbers of their first attached Hydrogen
References attached_H_begin_.
Referenced by core::conformation::Residue::attached_H_begin(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::chemical::residue_types_identical(), and core::scoring::orbitals::surrogate_atom_for_orbital().
index number of the first attached Hydrogen on an atom
References attached_H_begin_.
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for all heavy atoms, index numbers of their last attached Hydrogen
References attached_H_end_.
Referenced by core::conformation::Residue::attached_H_end(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), and core::chemical::residue_types_identical().
index number of the last attached Hydrogen on an atom
References attached_H_end_.
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If a ring has been added but no nu angles have been defined, automatically assign them.
If a ring has been added but no nu angles have been defined, automatically assign them.
Don't even bother trying if there are multiple rings. The creator of the .params file needs to add the definitions manually.
References n_nus(), n_rings(), nu_atoms(), nu_atoms_, ring_atoms(), and ring_atoms_.
Referenced by copy_other_info().
| BondRingness core::chemical::ResidueType::bond_ringness | ( | core::Size const | atomindex1, |
| core::Size const | atomindex2 | ||
| ) | const |
Returns whether the bond between the atoms is in a ring. Will return UnknownRingness for something which isn't bonded.
References bonded_neighbor_, bonded_neighbor_ringness_, and core::chemical::UnknownRingness.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().
| BondName core::chemical::ResidueType::bond_type | ( | core::Size const | atomindex1, |
| core::Size const | atomindex2 | ||
| ) | const |
Returns the type of bond between the atoms Will return UnknownBond for something which isn't bonded.
References bonded_neighbor_, bonded_neighbor_type_, and core::chemical::UnknownBond.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig(), and core::chemical::write_topology_file().
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Return the indices for the set of atoms that define a particular intraresidue angle.
References bondangle_atom_sets_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), and core::chemical::residue_types_identical().
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Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.
References bondangles_for_atom_.
Referenced by core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), and core::chemical::residue_types_identical().
| AtomIndices const & core::chemical::ResidueType::bonded_neighbor | ( | Size const | atomno | ) | const |
indices of the bonded neighbors for an atom
References bonded_neighbor_.
Referenced by protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), protocols::simple_moves::chiral::ChiralMover::apply(), core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::bonded_neighbor(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), define_mainchain_atoms(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), initialize_derived_data(), nbrs(), core::conformation::Residue::nbrs(), note_chi_controls_atom(), number_bonded_heavyatoms(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::residue_types_identical(), core::chemical::rna::RNA_Info::rna_note_chi_controls_atom(), core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(), core::io::pose_from_sfr::score_mapping(), select_orient_atoms(), select_orient_atoms_standard_logic(), core::scoring::orbitals::surrogate_atom_for_orbital(), update_derived_data(), update_last_controlling_chi(), and core::chemical::ResidueTypeKinWriter::write_restype().
| utility::vector1< BondRingness > const & core::chemical::ResidueType::bonded_neighbor_ringnesses | ( | Size const | atomno | ) | const |
References bonded_neighbor_ringness_.
Referenced by core::chemical::residue_types_identical().
| utility::vector1< BondName > const & core::chemical::ResidueType::bonded_neighbor_types | ( | Size const | atomno | ) | const |
References bonded_neighbor_type_.
Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_bond(), and core::chemical::residue_types_identical().
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indices of the orbitals bonded to an atom
References bonded_orbitals_.
Referenced by core::conformation::Residue::assign_orbitals(), core::conformation::Residue::bonded_orbitals(), core::chemical::MutableResidueType::copy_atom_info(), core::chemical::residue_types_identical(), and core::conformation::Residue::update_orbital_coords().
| utility::vector1< std::pair< core::Size, core::Size > > core::chemical::ResidueType::bonds | ( | ) | const |
Returns a list of all pairs of atoms which are bonded. This returned list should only have only one entry per bond (So [1,2] and [2,1] will not both be present.)
References bonded_neighbor_, and nbonds_.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::io::pose_from_sfr::remap_names_on_geometry(), and core::io::pose_from_sfr::score_mapping().
| utility::vector1< std::string > core::chemical::ResidueType::branch_connect_atom_names | ( | ) | const |
Return a list of names of atoms at non-polymer connections.
References atom_name(), and branch_connect_atoms().
Referenced by show().
| utility::vector1< uint > core::chemical::ResidueType::branch_connect_atoms | ( | ) | const |
Return a list of indices of atoms at non-polymer connections.
References lower_connect_id_, n_non_polymeric_residue_connections_, n_possible_residue_connections(), residue_connect_atom_index(), and upper_connect_id_.
Referenced by branch_connect_atom_names().
| core::chemical::carbohydrates::CarbohydrateInfoCOP core::chemical::ResidueType::carbohydrate_info | ( | ) | const |
Return the CarbohydrateInfo object containing sugar-specific properties for this residue.
References carbohydrate_info_.
Referenced by core::conformation::Residue::carbohydrate_info(), core::pose::Pose::chain_sequence(), and core::pack::palette::PackerPalette::saccharide_backbones_are_compatible().
References chi_2_proton_chi_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::MutableResidueType::copy_other_info(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), and core::chemical::residue_types_identical().
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indices of the atoms which are used to define a given chi angle (chino)
References chi_atoms_.
Referenced by protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::chemical::rna::chi1_torsion_atom_index(), core::conformation::Residue::chi_atoms(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::MutableResidueType::copy_other_info(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::chemical::rna::first_base_atom_index(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig(), core::chemical::print_chis(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), protocols::ligand_docking::torsion_constraints_from_mean_sd(), core::chemical::rna::RNA_Info::update_derived_rna_data(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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indices of the atoms which are used to define all the chi angles
References chi_atoms_.
Referenced by perform_checks(), and update_last_controlling_chi().
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all rotamers bins (mean, std) for a given chi angle
References chi_rotamers_.
Referenced by core::conformation::Residue::chi_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::MutableResidueType::copy_other_info(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::chemical::residue_types_identical(), protocols::ligand_docking::torsion_constraints_from_chi_rotamers(), and core::chemical::write_topology_file().
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make a copy
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Iterate through the atoms, filling out the various atom info vectors.
This function updates most of the atomistic data in the ResidueType, by iterating over the atoms in the proper order
References accpt_pos_, accpt_pos_sc_, core::chemical::MutableResidueType::all_atoms(), all_bb_atoms_, all_sc_atoms_, core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), atom_name_to_index_, atom_names_, core::chemical::Atom::atom_type_index(), atom_type_index(), core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::ResidueTypeBase::atom_type_set_ptr(), atomic_properties_, atoms_with_orb_index_, core::chemical::MutableResidueType::bond(), bonded_neighbor_, bonded_neighbor_ringness_, bonded_neighbor_type_, core::chemical::MutableResidueType::bonded_neighbors(), bonded_orbitals_, cut_bond_neighbor_indices_, elements_, first_sidechain_hydrogen_, formal_charge_, gasteiger_atom_type_index_, core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), Haro_index_, heavyatom_has_polar_hydrogens_, Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, ideal_xyz_, mass_, mm_atom_type_index_, core::chemical::ResidueTypeBase::mm_atom_types_ptr(), n_backbone_heavyatoms_, n_hbond_acceptors_, n_hbond_donors_, core::chemical::ResidueTypeBase::name(), natoms_, nbonds_, partial_charge_, core::chemical::TR(), vec_atom_type_indexes_, and vec_atom_types_.
Referenced by ResidueType().
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Fill in various other information which is being copied over from the MutableResidueType.
References abase2_indices_, accpt_pos_, core::chemical::MutableResidueType::actcoord_atoms(), actcoord_atoms_indices_, core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), atom_2_residue_connection_map_, core::chemical::ResidueTypeBase::atom_aliases(), atom_base_indices_, core::chemical::MutableResidueType::atom_index(), atom_index(), atom_name_to_index_, atom_names_, atom_shadowed_indices_, auto_assign_nu_atoms(), bonded_neighbor_, chi_2_proton_chi_, core::chemical::MutableResidueType::chi_atom_vds(), chi_atoms_, core::chemical::MutableResidueType::chi_rotamers(), chi_rotamers_, define_mainchain_atoms(), core::chemical::MutableResidueType::get_atom_name_to_vd_map(), icoor_, core::chemical::MutableResidueType::is_proton_chi(), is_proton_chi_, core::chemical::MutableResidueType::low_ring_conformers(), low_ring_conformers_, core::chemical::MutableResidueType::lower_connect_id(), lower_connect_id_, core::chemical::MutableResidueType::lowest_ring_conformer(), lowest_ring_conformer_, core::chemical::MutableResidueType::mainchain_atoms(), mainchain_atoms_indices_, n_non_polymeric_residue_connections_, core::chemical::MutableResidueType::n_nus(), core::chemical::MutableResidueType::n_polymeric_residue_connections(), n_polymeric_residue_connections_, core::chemical::MutableResidueType::n_possible_residue_connections(), core::chemical::MutableResidueType::n_proton_chi(), core::chemical::MutableResidueType::n_rings(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), natoms_, nbr_atom_, core::chemical::MutableResidueType::nbr_radius(), nbr_radius_, core::chemical::MutableResidueType::nbr_vertex(), nbrs(), core::chemical::MutableResidueType::nchi(), core::chemical::MutableResidueType::nu_atoms(), nu_atoms_, core::scoring::pair, proton_chi_extra_samples_, core::chemical::MutableResidueType::proton_chi_extra_samples_for_chi(), proton_chi_samples_, core::chemical::MutableResidueType::proton_chi_samples_for_chi(), proton_chis_, core::chemical::MutableResidueType::residue_connection(), residue_connections_, core::chemical::MutableResidueType::ring_atoms(), ring_atoms_, core::chemical::MutableResidueType::ring_saturation_type(), ring_saturation_types_, core::chemical::MutableResidueType::root_atom(), root_atom_, core::chemical::MutableResidueType::shadow_atoms(), core::id::to_string(), core::chemical::MutableResidueType::upper_connect_id(), and upper_connect_id_.
Referenced by ResidueType().
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indices of the bonded neighbors for an atom
References cut_bond_neighbor_indices_.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::conformation::Residue::cut_bond_neighbor(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
| void core::chemical::ResidueType::debug_dump_icoor | ( | ) | const |
Dump out atomnames and icoor values.
References atom_name(), ideal_xyz(), core::chemical::ResidueTypeBase::name3(), natoms(), core::chemical::pretty_print_atomicoor(), and core::chemical::TR().
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If a polymer without explicitly set mainchain atoms, determine a list of main chain atoms by shortest path from LOWER to UPPER.
Should only be called from copy_other_data() function.
Needs connections, bonded neighbors set
References bonded_neighbor(), core::chemical::get_residue_path_distances(), core::chemical::ResidueTypeBase::is_polymer(), lower_connect(), lower_connect_atom(), lower_connect_id(), mainchain_atoms_indices_, core::chemical::ResidueTypeBase::name(), protocols::sic_dock::scores::nbr, nbrs(), core::chemical::TR(), upper_connect(), upper_connect_atom(), and upper_connect_id().
Referenced by copy_other_info().
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detach RestypeDestructionEvent observer function
| fn | pointer to observer's unary member function with signature void( RestypeDestructionEvent const & ) |
| ptr | RAW pointer to observer object |
References destruction_obs_hub_.
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Return the indices for the set of atoms that define a particular intraresidue dihedral.
References dihedral_atom_sets_.
Referenced by core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), and core::chemical::residue_types_identical().
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Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.
References dihedrals_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), and core::chemical::residue_types_identical().
| core::chemical::element::Elements core::chemical::ResidueType::element | ( | core::Size | atomno | ) | const |
Convenience function to go directly to the element enum.
References element_type(), and core::chemical::element::UnknownElement.
Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count(), and core::chemical::residue_types_identical().
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References elements_.
Referenced by core::chemical::AutomorphismIterator::can_pair(), protocols::md::CartesianMD::do_initialize(), element(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::io::pose_from_sfr::remap_names_on_geometry(), core::io::pose_from_sfr::score_mapping(), and show().
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index of the first sidechain atom (heavy or hydrogen)
References n_backbone_heavyatoms_, natoms(), and nheavyatoms_.
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::chemical::MutableResidueType::copy_atom_info(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pose::rna::detect_base_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::conformation::Residue::first_sidechain_atom(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), select_orient_atoms(), protocols::stepwise::modeler::rna::suite_square_deviation(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), and core::chemical::write_topology_file().
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index of the first sidehchain hydrogen
References first_sidechain_hydrogen_.
Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::conformation::Residue::first_sidechain_hydrogen(), and core::chemical::residue_types_identical().
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References formal_charge_.
Referenced by core::chemical::MutableResidueType::copy_atom_info(), core::chemical::residue_types_identical(), show(), and core::chemical::write_topology_file().
| gasteiger::GasteigerAtomTypeDataCOP core::chemical::ResidueType::gasteiger_atom_type | ( | core::Size | atomno | ) | const |
Get the Gasteiger atom type for this atom Can be null if the atom type isn't set.
References gasteiger_atom_type_index_, and core::chemical::ResidueTypeBase::gasteiger_atom_typeset().
Referenced by core::chemical::MutableResidueType::copy_atom_info(), and core::chemical::residue_types_identical().
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Get a pointer to this ResidueTypeBase's base ResidueTypeBase.
Get a pointer to this ResidueTypeBase's base ResidueType.
Returns the base_type_cop_ pointer if not null, self pointer if null.
Implements core::chemical::ResidueTypeBase.
References base_type_cop_, and get_self_ptr().
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::pack::palette::PackerPalette::get_base_type_raw_ptr(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), and core::chemical::residue_types_identical().
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Gets indices of all atoms that can form bonds to metals.
References atom_index(), core::chemical::ResidueTypeBase::get_metal_binding_atoms(), has(), and core::chemical::ResidueTypeBase::name().
Referenced by core::conformation::Residue::get_metal_binding_atoms(), and core::chemical::write_topology_file().
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self pointers
Referenced by core::scoring::GenBondedExclInfo::add_residue_exclude_torsions(), protocols::match::Matcher::create_ds_builder(), get_base_type_cop(), core::scoring::GenBondedExclInfo::get_residue_data(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::scoring::lkball::LKB_ResidueInfo::initialize(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::pose::residue_types_from_saccharide_sequence_recursive(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), and protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::template_atom_inds().
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Referenced by self_pointer_updates().
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return indices of aromatic Hydrogens
References Haro_index_.
Referenced by core::conformation::Residue::Haro_index(), and core::chemical::residue_types_identical().
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is this atom present in this residue?
Implements core::chemical::ResidueTypeBase.
References atom_name_to_index_.
Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), core::select::util::any_atoms_within_cutoff(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), core::scoring::elec::GroupElec::build_groupinfo(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), core::chemical::SetPolymerConnectAtom::changes_connections_on(), core::chemical::AddConnect::changes_connections_on(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::chemical::AddConnectAndTrackingVirt::changes_connections_on(), core::chemical::AddConnectDeleteChildProton::changes_connections_on(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::simple_filters::AtomicDistanceFilter::compute(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::sampler::protein::do_set_xyz(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), core::chemical::find_best_match(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::rna::movers::find_nearby_res(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::pose::motif::get_AIDs(), core::scoring::elec::CountPairRepMap::get_map(), get_metal_binding_atoms(), core::conformation::Residue::has(), core::chemical::ICoorAtomID::ICoorAtomID(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::orient_onto_residue(), protocols::hybridization::MRMover::pack_missing_sidechains(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::select::util::select_coord_for_residue(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), core::scoring::setup_matching_atoms_with_given_names(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), core::chemical::rna::RNA_Info::update_derived_rna_data(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd().
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Does this type have groups (not just single atoms) that are polymer-bond dependent?
Always returns false for non-polymeric residue types.
References has_polymer_dependent_groups_, and core::chemical::ResidueTypeBase::is_polymer().
Referenced by core::chemical::residue_types_identical().
| bool core::chemical::ResidueType::has_sc_orbitals | ( | ) | const |
does this residue have sidechain orbitals?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SC_ORBITALS.
Referenced by core::conformation::Residue::has_sc_orbitals().
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Returns true if this residue has shadow atoms, false otherwise.
References atom_shadowed_indices_.
Referenced by core::conformation::Residue::has_shadow_atoms(), and core::chemical::write_topology_file().
References heavyatom_has_polar_hydrogens_.
Referenced by core::pose::rna::detect_sugar_contacts(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::scoring::sasa::SasaMethod::is_polar_atom(), core::chemical::residue_types_identical(), and show().
References vec_atom_types_.
Referenced by core::scoring::elec::GroupElec::build_groupinfo(), core::pose::rna::detect_sugar_contacts(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::scoring::sasa::SasaMethod::is_polar_atom(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds(), and show().
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return indices of polar Hydrogens
References Hpol_index_.
Referenced by core::conformation::Residue::Hpol_index(), perform_checks(), and core::chemical::residue_types_identical().
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indices of non-polar hydrogens as potential carbon Hbond donors
References Hpos_apolar_.
Referenced by core::conformation::Residue::Hpos_apolar(), and core::chemical::residue_types_identical().
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indices of polar hydrogens as Hbond donors
References Hpos_polar_.
Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), core::conformation::Residue::Hpos_polar(), and core::chemical::residue_types_identical().
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References Hpos_polar_sc_.
Referenced by core::conformation::Residue::Hpos_polar_sc(), and core::chemical::residue_types_identical().
AtomICoord of an atom.
References icoor_.
Referenced by protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::chemical::MutableResidueType::copy_atom_info(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::chemical::formatted_icoord_tree(), core::conformation::Residue::icoor(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::residue_types_identical(), core::pack::palette::PackerPalette::saccharide_backbones_are_compatible(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), update_nonpolymer_dependent_groups(), update_polymer_dependent_groups(), and core::chemical::write_topology_file().
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References ideal_xyz_.
Referenced by core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_chirality(), core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_outgroup(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::MutableResidueType::copy_atom_info(), debug_dump_icoor(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), ideal_xyz(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), core::io::pose_from_sfr::score_mapping(), core::select::util::select_coord_for_residue(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::ICoorAtomID::xyz().
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References atom_index(), and ideal_xyz().
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Precalculate other derived data from data already present.
References atoms_last_controlled_by_chi_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor(), dihedral_atom_sets_, dihedrals_for_atom_, core::chemical::get_residue_path_distances(), core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::has_property(), last_controlling_chi_, core::chemical::ResidueTypeBase::name(), natoms(), nchi(), path_distance_, path_distances(), core::chemical::ResidueTypeBase::properties(), residue_connections_, core::chemical::RNA, rna_info_, core::chemical::TNA, core::chemical::TR(), update_last_controlling_chi(), update_nonpolymer_dependent_groups(), update_polymer_dependent_groups(), update_ring_conformer_sets(), within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.
Referenced by ResidueType().
| bool core::chemical::ResidueType::is_acetylated_nterminus | ( | ) | const |
is acetylated n terminus
References core::chemical::ACETYLATED_NTERMINUS, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
| bool core::chemical::ResidueType::is_adduct | ( | ) | const |
is an adduct-modified residue?
References core::chemical::ADDUCT, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
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Is this an alpha-amino acid?
References core::chemical::ALPHA_AA, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), core::select::residue_selector::BinSelector::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), 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_sample_cis_peptide_bond(), core::conformation::check_good_cutpoint_neighbour(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::conformation::form_disulfide_helper(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd().
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Is this an aramid?
References core::chemical::ARAMID, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::ncbb::ResidueReplacementRebuildMover::apply(), core::pack::palette::PackerPalette::aramid_backbones_are_compatible(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::check_good_cutpoint_neighbour(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::chemical::rna::default_jump_atom(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::RamaPreProEnergy::is_allowed_type(), core::conformation::Residue::is_aramid(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
| bool core::chemical::ResidueType::is_aromatic | ( | ) | const |
is aromatic?
References core::chemical::AROMATIC, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::antibody::AntibodyFeatures::calculate_cdr_aromatic_nres(), core::pack::task::ResidueLevelTask_::extrachi_sample_level(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), and core::conformation::Residue::is_aromatic().
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Is this ResidueTypeBase a base type?
Checks the base_type_cop_ pointer. If it's null, this is assumed to be a base type.
Implements core::chemical::ResidueTypeBase.
References base_type_cop_.
Referenced by core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::chemical::MutableResidueType::copy_other_info(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), and update_derived_data().
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Is this a beta-amino acid?
References core::chemical::BETA_AA, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::conformation::check_good_cutpoint_neighbour(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::conformation::form_disulfide_helper(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets().
| bool core::chemical::ResidueType::is_branch_point | ( | ) | const |
is a branch-point residue?
References core::chemical::BRANCH_POINT, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Residue::is_branch_point(), and show().
| bool core::chemical::ResidueType::is_canonical | ( | ) | const |
Is this a canonical residue type (nucleic acid or amino acid)?
Calls is_canonical_aa() and is_canonical_nucleic().
References is_canonical_aa(), and is_canonical_nucleic().
Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom().
| bool core::chemical::ResidueType::is_canonical_aa | ( | ) | const |
Is this a canonical amino acid (CANONICAL_AA property)?
Only the standard amino acid types (ACDEFGHIKLMNPQRSTVWY) are canonical.
References core::chemical::CANONICAL_AA, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::kinematics::jacobian::SeriesJacobians::determine_residue_series_type(), is_canonical(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), and core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary().
| bool core::chemical::ResidueType::is_canonical_nucleic | ( | ) | const |
Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)?
Only the standard nucliec acid types (dA, dC, dG, dT, A, C, G, U) are canonical.
References core::chemical::CANONICAL_NUCLEIC, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::rna::movers::determine_residues_to_rebuild(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), is_canonical(), and core::chemical::rna::RNA_Info::rna_update_last_controlling_chi().
| bool core::chemical::ResidueType::is_carbohydrate | ( | ) | const |
is carbohydrate?
References core::chemical::CARBOHYDRATE, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::append_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), core::select::residue_selector::GlycanLayerSelector::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric::calculate(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), core::conformation::Residue::carbohydrate_info(), core::conformation::check_good_cutpoint_neighbour(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::chemical::rna::default_jump_atom(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::scoring::methods::get_restag(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), core::conformation::Conformation::insert_polymer_residue(), core::conformation::Residue::is_carbohydrate(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().
| bool core::chemical::ResidueType::is_charged | ( | ) | const |
is charged?
References core::chemical::CHARGED, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), and core::conformation::Residue::is_charged().
| bool core::chemical::ResidueType::is_coarse | ( | ) | const |
is coarse?
References core::chemical::COARSE, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::chemical::rna::default_jump_atom(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library(), core::conformation::Residue::is_coarse(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), and core::pose::rna::setup_base_pair_constraints().
| bool core::chemical::ResidueType::is_cyclic | ( | ) | const |
is cyclic?
References core::chemical::CYCLIC, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::chemical::is_mainchain_torsion_also_ring_torsion(), core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::show(), and show().
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is disulfide?
References core::chemical::DISULFIDE_BONDED, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), core::conformation::break_disulfide(), protocols::denovo_design::construct_poly_ala_pose(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), core::conformation::get_disulf_partner(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::is_allowed_type(), core::conformation::is_disulfide_bond(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), protocols::loops::select_loop_residues(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), and core::pose::full_model_info::update_disulfides_from_full_model_info().
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Is this a gamma-amino acid?
References core::chemical::GAMMA_AA, core::chemical::ResidueProperties::has_property(), and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::conformation::check_good_cutpoint_neighbour(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype().
| bool core::chemical::ResidueType::is_inverted_virtual_residue | ( | ) | const |
Check if atom is an inverted virtual.
Check if residue is 'INVERTING_VIRTUAL_RESIDUE'.
Used by the symmetry machinery for mirror symmetry operations.
References core::chemical::ResidueProperties::has_property(), core::chemical::INVERTED_VIRTUAL_RESIDUE, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::symmetry::calculate_inverting_virtuals(), core::pose::symmetry::make_symmetric_pose(), and core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues().
| bool core::chemical::ResidueType::is_ligand | ( | ) | const |
is ligand?
References core::chemical::ResidueProperties::has_property(), core::chemical::LIGAND, and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::enzdes::EnzdesBaseProtocol::catalytic_res(), protocols::enzdes::enzutil::catalytic_res(), protocols::enzdes::LigDSasaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::get_ligand_seqpos(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::conformation::Residue::is_ligand(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::toolbox::match_enzdes_util::EnzdesCstCache::ordered_constrained_positions(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::Energies::update_neighbor_links(), and core::chemical::write_topology_file().
| bool core::chemical::ResidueType::is_lipid | ( | ) | const |
is lipid?
References core::chemical::ResidueProperties::has_property(), core::chemical::LIPID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::io::carbohydrates::chain_gws_string(), and core::io::carbohydrates::dump_gws().
| bool core::chemical::ResidueType::is_lower_terminus | ( | ) | const |
is lower terminus?
References core::chemical::ResidueProperties::has_property(), core::chemical::LOWER_TERMINUS, and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::conformation::Residue::is_lower_terminus(), is_terminus(), core::pose::make_pose_from_sequence(), core::conformation::Residue::orient_onto_residue_peptoid(), core::conformation::Residue::place(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::sewing::data_storage::SmartAssembly::to_pose().
| bool core::chemical::ResidueType::is_membrane | ( | ) | const |
is membrane?
References core::chemical::ResidueProperties::has_property(), core::chemical::MEMBRANE, and core::chemical::ResidueTypeBase::properties().
Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), and atom_index().
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Is this a meta-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::META_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_meta_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
| bool core::chemical::ResidueType::is_metal | ( | ) | const |
Return true if this residue type is a metal ion, false otherwise.
The METAL property is specified in the params file under PROPERTIES.
References core::chemical::ResidueProperties::has_property(), core::chemical::METAL, and core::chemical::ResidueTypeBase::properties().
Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::conformation::Residue::is_metal(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), perform_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().
| bool core::chemical::ResidueType::is_metalbinding | ( | ) | const |
Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.), false otherwise.
The METALBINDING property is specified in the params file under PROPERTIES.
References core::chemical::ResidueProperties::has_property(), core::chemical::METALBINDING, and core::chemical::ResidueTypeBase::properties().
Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_metalbinding(), and perform_checks().
| bool core::chemical::ResidueType::is_methylated_cterminus | ( | ) | const |
is methylated c terminus
References core::chemical::ResidueProperties::has_property(), core::chemical::METHYLATED_CTERMINUS, and core::chemical::ResidueTypeBase::properties().
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Is this a D_AA, R_PEPTOID, or L_RNA?
Convenience function to avoid quering is_d_aa(), is_r_peptoid(), and is_l_rna() repeatedly.
References core::chemical::ResidueTypeBase::is_d_aa(), core::chemical::ResidueTypeBase::is_l_rna(), and core::chemical::ResidueTypeBase::is_r_peptoid().
Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::OmegaTether::eval_omega_score_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static_voronoi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep().
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Is this residue N-methylated?
References core::chemical::ResidueProperties::has_property(), core::chemical::N_METHYLATED, and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd().
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is Nucleic Acid?
References core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueTypeBase::is_RNA(), and is_TNA().
Referenced by protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), protocols::minimization_packing::RotamerizeMover::apply(), core::conformation::check_good_cutpoint_neighbour(), protocols::stepwise::modeler::rna::figure_out_moving_rna_chain_breaks(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::pose::rna::get_suite_torsion_info(), core::conformation::Residue::is_NA(), core::conformation::Residue::place(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::stepwise::modeler::rna::suite_square_deviation(), and protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list().
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Is this an oligourea?
References core::chemical::ResidueProperties::has_property(), core::chemical::OLIGOUREA, and core::chemical::ResidueTypeBase::properties().
Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::check_good_cutpoint_neighbour(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), and core::scoring::methods::OmegaTetherEnergy::residue_energy().
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Is this an ortho-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::ORTHO_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_ortho_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a para-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PARA_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_para_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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| bool core::chemical::ResidueType::is_polar | ( | ) | const |
is polar?
References core::chemical::ResidueProperties::has_property(), core::chemical::POLAR, and core::chemical::ResidueTypeBase::properties().
Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), protocols::simple_filters::LongestContinuousApolarSegmentFilter::is_counted(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::is_counted(), core::conformation::Residue::is_polar(), and protocols::moves::PyMOLMover::send_polars().
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Is this a meta-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::POST_METHYLENE_META_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_post_methylene_meta_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this an ortho-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::POST_METHYLENE_ORTHO_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_post_methylene_ortho_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a para-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::POST_METHYLENE_PARA_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_post_methylene_para_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a meta-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_META_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_meta_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this an ortho-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_ORTHO_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_ortho_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a para-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_PARA_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_para_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a meta-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_POST_METHYLENE_META_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_post_methylene_meta_aramid(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this an ortho-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_post_methylene_ortho_aramid(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
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Is this a para-aramid?
References core::chemical::ResidueProperties::has_property(), core::chemical::PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, and core::chemical::ResidueTypeBase::properties().
Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::is_pre_methylene_post_methylene_para_aramid(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().
number of proton chis
References proton_chis_.
Referenced by protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::MutableResidueType::copy_other_info(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::print_chis(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
| bool core::chemical::ResidueType::is_purine | ( | ) | const |
is purine?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::PURINE.
Referenced by protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::stepwise::monte_carlo::rna::RNA_TorsionMover::apply_random_nucleoside_torsion(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::conformation::Residue::is_purine(), protocols::stepwise::modeler::rna::sugar::SugarModeling::set_base_and_pucker_state(), protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list(), and protocols::stepwise::sampler::rna::setup_sampler().
| bool core::chemical::ResidueType::is_pyrimidine | ( | ) | const |
Check if atom is repulsive.
References atom_type().
Return whether this atom is in a particular ring.
References core::sequence::end, and ring_atoms_.
Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives().
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is sidechain amine?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SIDECHAIN_AMINE.
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is thiol?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SIDECHAIN_THIOL.
Referenced by core::pack::task::operation::OptCysHG::apply(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::is_disulfide_bond(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::liganding_atom_from_restype(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), and core::pose::full_model_info::update_disulfides_from_full_model_info().
| bool core::chemical::ResidueType::is_solvent | ( | ) | const |
Is this a solvent molecule (SOLVENT property)?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SOLVENT.
Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom().
| bool core::chemical::ResidueType::is_sri | ( | ) | const |
Is this one of SRI's special heteropolymer building blocks?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SRI.
Referenced by core::conformation::Residue::is_sri().
| bool core::chemical::ResidueType::is_surface | ( | ) | const |
is surface? (e.g. enamel)
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::SURFACE.
Referenced by core::conformation::Residue::is_surface().
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is terminus?
References core::chemical::ResidueProperties::has_property(), is_lower_terminus(), is_upper_terminus(), core::chemical::ResidueTypeBase::properties(), and core::chemical::TERMINUS.
Referenced by protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::conformation::Residue::is_terminus(), and core::scoring::methods::GoapEnergy::setup_for_scoring().
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is TNA?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::TNA.
Referenced by protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(), core::chemical::rna::default_jump_atom(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::evaluate(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), is_NA(), core::conformation::Residue::is_TNA(), core::pose::rna::is_torsion_valid(), protocols::stepwise::sampler::rna::setup_sampler(), core::chemical::rna::RNA_Info::update_derived_rna_data(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().
| bool core::chemical::ResidueType::is_TP3 | ( | ) | const |
Check if residue is a TP3 water.
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::TP3.
| bool core::chemical::ResidueType::is_triazolemer | ( | ) | const |
Is this a triazolemer?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::TRIAZOLE_LINKER.
Referenced by core::conformation::Residue::is_triazolemer().
| bool core::chemical::ResidueType::is_upper_terminus | ( | ) | const |
is upper terminus?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::UPPER_TERMINUS.
Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::loops::find_non_protein_chunks(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), is_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::make_pose_from_sequence(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::pack::palette::PackerPalette::saccharide_backbones_are_compatible(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::sewing::data_storage::SmartAssembly::to_pose().
Check if atom is virtual.
References atom_has_property(), atom_type(), and core::chemical::VIRTUAL_ATOM.
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), core::scoring::ResidueExclParams::create_excl_info(), core::pose::rna::detect_base_contacts(), core::pose::rna::detect_sugar_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::elec::GroupElec::get_group(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(), core::pose::rna::is_torsion_valid(), perform_checks(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), select_orient_atoms_standard_logic(), show(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res(), and core::chemical::rna::RNA_Info::update_derived_rna_data().
| bool core::chemical::ResidueType::is_virtual_residue | ( | ) | const |
Check if residue is 'VIRTUAL_RESIDUE' This ONLY checks the VIRTUAL_RESIDUE PROPERTY!
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::VIRTUAL_RESIDUE.
Referenced by core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), core::scoring::ResidueExclParams::create_excl_info(), core::conformation::Residue::is_virtual_residue(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues(), and protocols::stepwise::modeler::rna::suite_square_deviation().
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Is this a residue type that can be virtualized or devirtualized by the packer?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::VIRTUALIZABLE_BY_PACKER.
| bool core::chemical::ResidueType::is_VRT1 | ( | ) | const |
Check if residue is 'VRT1'.
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::VRT1.
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is this a water residue type?
References core::chemical::ResidueProperties::has_property(), core::chemical::ResidueTypeBase::properties(), and core::chemical::WATER.
Referenced by protocols::simple_task_operations::RestrictToInterface::apply(), protocols::simple_moves::ExplicitWaterMover::build_lkboverlap_rotamer_clouds(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), and core::conformation::Residue::is_water().
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index of the last backbone heavy atom
References n_backbone_heavyatoms_.
Referenced by protocols::hybridization::FragmentBiasAssigner::bfactors(), core::scoring::ResidueExclParams::create_excl_info(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::conformation::Residue::last_backbone_atom(), core::chemical::residue_types_identical(), and protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned().
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Read access to the last_controlling_chi_ array.
References last_controlling_chi_.
Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::chemical::residue_types_identical(), and core::chemical::rna::RNA_Info::update_derived_rna_data().
The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.
References last_controlling_chi_.
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Low-energy ring conformers for each ring.
References low_ring_conformers_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
| ResidueConnection const & core::chemical::ResidueType::lower_connect | ( | ) | const |
References core::chemical::ResidueTypeBase::has_property(), lower_connect_id_, core::chemical::POLYMER, core::chemical::ResidueTypeBase::properties(), and residue_connections_.
Referenced by define_mainchain_atoms(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), protocols::cyclic_peptide::PeptideCyclizeMover::get_values(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::lower_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
| Size core::chemical::ResidueType::lower_connect_atom | ( | ) | const |
index number of the atom which connects to the lower connection
References core::chemical::ResidueTypeBase::has_property(), lower_connect_id_, core::chemical::POLYMER, core::chemical::ResidueTypeBase::properties(), and residue_connections_.
Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), core::scoring::ResidueExclParams::create_excl_info(), define_mainchain_atoms(), core::conformation::Residue::lower_connect_atom(), and core::chemical::ResidueDatabaseIO::report_residue_type().
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References lower_connect_id_.
Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::connected_residue_at_lower(), core::chemical::MutableResidueType::copy_other_info(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), define_mainchain_atoms(), core::scoring::Ramachandran::eval_rama_score_residue(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::is_polymer_bonded(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::chemical::residue_types_identical(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), and core::chemical::write_topology_file().
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For each ring, what's the lowest conformer?
References lowest_ring_conformer_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
index of mainchain atom
References mainchain_atoms_indices_.
Referenced by protocols::helical_bundle::align_mainchain_atoms(), protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::mainchain_atom(), and protocols::helical_bundle::place_atom_positions().
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indices of all mainchain atoms
References mainchain_atoms_indices_.
Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_bondangle_perturbation(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_bondlength_perturbation(), protocols::helical_bundle::align_mainchain_atoms(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::chemical::rotamers::NCAARotamerLibrarySpecification::cache_tag(), protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), core::chemical::MutableResidueType::copy_other_info(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::chemical::is_mainchain_torsion_also_ring_torsion(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), core::pack::palette::PackerPalette::saccharide_backbones_are_compatible(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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Make a ResidueType from a Modifiable residue type.
In practice, this is the only way to create (or change) a ResidueType object.
By using a static function and not a constructor, this ensures that all ResidueTypes are on the heap (and can shared_from_this()), and allows us to do OP-requiring subobject updates in self_pointer_updates().
References ResidueType().
Referenced by core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), core::chemical::GlobalResidueTypeSet::deal_with_patch_special_cases(), core::chemical::ResidueTypeSet::force_add_base_residue_type_already_write_locked(), core::chemical::PoseResidueTypeSet::generate_residue_type_write_locked(), core::chemical::ResidueTypeSet::generate_residue_type_write_locked(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::hacky_parser_init_workaround(), core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround(), and core::pose::Pose::real_to_virtual().
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get the molecular weight of this residue
References mass_.
Referenced by core::pose::mass(), protocols::qsar::scoring_grid::MolecularWeightNormalization::operator()(), and core::chemical::residue_types_identical().
| MMAtomType const & core::chemical::ResidueType::mm_atom_type | ( | Size const | atomno | ) | const |
Get the MM atom_type for this atom by its index number in this residue.
References mm_atom_type_index(), and core::chemical::ResidueTypeBase::mm_atom_types_ptr().
Referenced by print_bondangles(), and core::chemical::write_topology_file().
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References mm_atom_type_index_, and natoms_.
Referenced by core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), mm_atom_type(), mm_name(), core::conformation::Residue::Residue(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_types_identical(), and show().
| std::string const & core::chemical::ResidueType::mm_name | ( | core::Size | atomno | ) | const |
References mm_atom_type_index(), and core::chemical::ResidueTypeBase::mm_atom_types_ptr().
Referenced by core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::MutableResidueType::copy_atom_info(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::Residue::mm_atom_name(), print_bondangles(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), show(), update_derived_data(), and core::chemical::ResidueTypeKinWriter::write_restype().
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number of hbond_acceptors
References n_hbond_acceptors_.
Referenced by core::conformation::Residue::n_hbond_acceptors(), and core::chemical::residue_types_identical().
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number of hbond_donors
References n_hbond_donors_.
Referenced by core::conformation::Residue::n_hbond_donors(), and core::chemical::residue_types_identical().
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Return number of nu (internal ring) angles.
References nu_atoms_.
Referenced by auto_assign_nu_atoms(), core::chemical::MutableResidueType::copy_other_info(), core::chemical::is_mainchain_torsion_also_ring_torsion(), core::conformation::Residue::n_nus(), core::conformation::Residue::Residue(), core::conformation::Residue::update_nus(), and core::chemical::write_topology_file().
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References n_polymeric_residue_connections_.
Referenced by core::conformation::Residue::n_polymeric_residue_connections(), and core::chemical::residue_types_identical().
| Size core::chemical::ResidueType::n_possible_residue_connections | ( | ) | const |
number of ResidueConnections, counting polymeric residue connections
References residue_connections_.
Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), atom_depends_on_connection(), branch_connect_atoms(), core::chemical::MutableResidueType::copy_other_info(), core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::viewer::dump_residue_kinemage(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::conformation::get_disulf_partner(), core::conformation::get_second_atom_from_connection(), core::chemical::ICoorAtomID::ICoorAtomID(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::is_disulfide_bond(), core::conformation::Residue::n_possible_residue_connections(), core::pose::Pose::real_to_virtual(), core::pose::remove_variant_type_from_pose_residue(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), core::conformation::Residue::update_connections_to_other_residue(), update_nonpolymer_dependent_groups(), core::pose::Pose::virtual_to_real(), and core::chemical::write_topology_file().
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number of proton chis
References proton_chis_.
Referenced by protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::residue_types_identical().
How many inter-residue chemical bonds does a particular atom form?
References atom_2_residue_connection_map_.
Referenced by core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().
| core::Size core::chemical::ResidueType::n_ring_conformer_sets | ( | ) | const |
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Return the number of rings in this residue.
References ring_atoms_.
Referenced by auto_assign_nu_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::chemical::MutableResidueType::copy_other_info(), protocols::ligand_docking::ga_ligand_dock::crossover(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), protocols::ligand_docking::ga_ligand_dock::mutate(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize(), core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::show(), show(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), update_ring_conformer_sets(), and core::chemical::write_topology_file().
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Counts the number of virtual atoms and returns the count.
The virtual count is not stored in the resiude type. This count is performed on the fly, and can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.
The virtual count is not stored in the residue type. This count is performed on the fly, and can hurt performance if repeatedly carried out. Not intended for use in large loops – instead, call once and store the value.
Implements core::chemical::ResidueTypeBase.
References vec_atom_types_.
Referenced by core::conformation::Residue::n_virtual_atoms().
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number of atoms
Implements core::chemical::ResidueTypeBase.
References natoms_.
Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::mpi_refinement::add_movemap_from_loopres(), protocols::loop_grower::LoopGrower::addnativesolution(), core::conformation::annotated_atom_graph_from_conformation(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::toolbox::apply_superposition_transform(), protocols::hybridization::CartesianSampler::apply_transform(), protocols::electron_density::DockIntoDensityMover::apply_transform(), core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), core::conformation::Residue::apply_transform_Rx_plus_v(), protocols::simple_filters::RepeatParameterFilter::apply_transformation(), protocols::forge::methods::apply_transformation(), protocols::hybridization::apply_transformation(), atom_depends_on_connection(), atom_depends_on_lower_polymeric_connection(), atom_depends_on_polymeric_connection(), atom_depends_on_upper_polymeric_connection(), core::conformation::atom_graph_from_conformation(), atom_is_backbone(), atom_is_hydrogen(), atom_is_sidechain(), core::chemical::Metapatch::atoms(), core::chemical::AutomorphismIterator::AutomorphismIterator(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), protocols::toolbox::CA_superimpose(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pose::toolbox::AtomLevelDomainMap::calculate_atom_id_domain_map(), core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms(), protocols::hybridization::InsertChunkMover::check_overlap(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_bounding_box(), core::chemical::MutableResidueType::copy_atom_info(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::pose::toolbox::AtomLevelDomainMap::disallow_movement_of_input_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::select::movemap::MoveMapFactory::edit_movemap_given_pose(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::chemical::find_best_match(), protocols::rna::movers::find_nearby_res(), first_sidechain_atom(), core::chemical::formatted_icoord_tree(), protocols::ligand_docking::frac_atoms_within(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::scoring::elec::GroupElec::get_group(), core::chemical::get_residue_path_distances(), protocols::motif_grafting::movers::MotifGraftMover::get_rotated_and_translated_pose(), protocols::magnesium::MgScanner::get_score(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::pose::toolbox::AtomLevelDomainMap::initialize(), core::pose::initialize_atomid_map(), initialize_derived_data(), core::pose::toolbox::AtomID_Mapper::initialize_from_pose(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::natoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::conformation::Residue::orient_onto_location(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig(), protocols::rna::movers::RNAIdealizeMover::perturb_pose(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), core::conformation::Residue::place(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::chemical::pretty_print_atomicoor(), print_pretty_path_distances(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), protocols::mpi_refinement::ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig(), protocols::denovo_design::rebuild_missing_atoms(), core::conformation::symmetry::recenter(), core::io::pose_from_sfr::remap_names_on_geometry(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), protocols::fibril::reorient_extended_fibril(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::conformation::Residue::Residue(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::chemical::residue_types_identical(), core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(), protocols::matdes::rot_pose(), protocols::sic_dock::rot_pose(), protocols::toolbox::rigid_body::rotate(), core::io::pose_from_sfr::score_mapping(), select_orient_atoms(), select_orient_atoms_standard_logic(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::toolbox::rigid_body::set_to_origin(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::lkball::setup_water_builders_for_residue_type(), show(), protocols::loop_grower::LoopPartialSolution::store_coordinates(), core::scoring::superimpose_pose(), core::pose::Pose::total_atoms(), protocols::matdes::trans_pose(), protocols::sic_dock::trans_pose(), protocols::toolbox::rigid_body::translate(), protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body(), protocols::rna::movers::ErraserMinimizerMover::turn_off_for_chunks(), update_derived_data(), core::chemical::rna::RNA_Info::update_derived_rna_data(), update_last_controlling_chi(), update_nonpolymer_dependent_groups(), update_polymer_dependent_groups(), core::scoring::methods::Burial_v2Energy::using_atom_distance(), core::chemical::ResidueTypeKinWriter::write_restype(), core::chemical::write_topology_file(), core::scoring::motif::xform_pose(), protocols::sic_dock::xform_pose(), core::fragment::xform_pose(), and protocols::sic_dock::xform_pose_rev().
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number of bonds
Implements core::chemical::ResidueTypeBase.
References nbonds_.
Referenced by core::chemical::residue_types_identical().
number of bonds for given atom
References bonded_neighbor_.
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get nbr_atom used to define residue-level neighbors
References nbr_atom_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::residue_types_identical(), select_orient_atoms(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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get nbr_radius_ used to define residue-level neighbors
References nbr_radius_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::different_resgroup(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::Energies::require_context_graph_(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::chemical::residue_types_identical(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), core::scoring::Energies::update_neighbor_links(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)
References bonded_neighbor().
Referenced by atoms_are_bonded(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::chemical::AutomorphismIterator::can_pair(), copy_other_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), define_mainchain_atoms(), core::chemical::AutomorphismIterator::edges_match(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::chemical::get_residue_path_distances(), note_chi_controls_atom(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), select_orient_atoms(), select_orient_atoms_standard_logic(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::scoring::orbitals::surrogate_atom_for_orbital(), and core::chemical::write_topology_file().
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number of chi angles
References chi_atoms_.
Referenced by protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), core::pose::add_variant_type_to_residue(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), protocols::simple_moves::CombinePoseMover::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), protocols::comparative_modeling::chis_from_pose(), core::chemical::MutableResidueType::copy_other_info(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::enumerate_chi_sets(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::chemical::rna::RNA_Info::figure_out_chi_order(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_carbohydrate_bond_sampler(), initialize_derived_data(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_ligand_bond_sampler(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), core::conformation::Residue::nchi(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::stepwise::modeler::output_movemap(), protocols::canonical_sampling::MetricRecorder::parse_my_tag(), perform_checks(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::perturb_lig(), core::chemical::print_chis(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::randomize_lig(), protocols::minimization_packing::MinimalRotamer::record_chi(), core::pose::remove_variant_type_from_residue(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::conformation::Residue::Residue(), core::chemical::residue_types_identical(), core::chemical::rna::RNA_Info::rna_note_chi_controls_atom(), core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::carbohydrates::set_glycan_iupac_chi_torsions(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), core::chemical::rna::RNA_Info::update_derived_rna_data(), update_last_controlling_chi(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().
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Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms.
References dihedral_atom_sets_.
Referenced by core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), and core::chemical::residue_types_identical().
| orbitals::ICoorOrbitalData const & core::chemical::ResidueType::new_orbital_icoor_data | ( | Size const | orbital_index | ) | const |
References core::chemical::Orbital::new_icoor(), and core::chemical::ResidueTypeBase::orbital().
Referenced by core::conformation::Residue::build_orbital_xyz().
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number of heavy atoms
Implements core::chemical::ResidueTypeBase.
References nheavyatoms_.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::align_with_offset(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), core::chemical::AutomorphismIterator::AutomorphismIterator(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::rna::movers::com_of_true_residues(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map(), core::pose::rna::detect_base_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), core::chemical::heavy_atom_names_match(), core::pose::initialize_atomid_map_heavy_only(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::nheavyatoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), core::conformation::Residue::place(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::chemical::residue_types_identical(), select_orient_atoms(), select_orient_atoms_standard_logic(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), protocols::stepwise::modeler::rna::suite_square_deviation(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().
Recursive subroutine invoked by update_last_controlling_chi().
O(N) recursive algorithm for determining the last chi for each atom. Each atom is visited at most twice.
References atom_base(), bonded_neighbor(), last_controlling_chi_, and nbrs().
Referenced by update_last_controlling_chi().
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Return indices of the atoms used to define a given nu (internal ring) angle.
References nu_atoms_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), core::chemical::is_mainchain_torsion_also_ring_torsion(), core::conformation::Residue::nu_atoms(), core::chemical::residue_types_identical(), core::conformation::Residue::set_all_ring_nu(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::set_tau(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), core::conformation::Residue::update_nus(), and core::chemical::write_topology_file().
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Return list of indices of the atoms used to define all the nu (internal ring) angles.
References nu_atoms_.
Referenced by auto_assign_nu_atoms().
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get number of intraresidue bond angles
References bondangle_atom_sets_.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), and core::chemical::residue_types_identical().
indicates how many heavyatom bonded neighbors an atom has
References bonded_neighbor(), and number_bonded_hydrogens().
Referenced by core::scoring::orbitals::surrogate_atom_for_orbital().
indicates how many proton bonded neighbors an atom has
References attached_H_begin_, and attached_H_end_.
Referenced by number_bonded_heavyatoms(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), and core::scoring::orbitals::surrogate_atom_for_orbital().
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Copies <src> into the ResidueType.
| orbitals::ICoorOrbitalData const & core::chemical::ResidueType::orbital_icoor_data | ( | Size const | orbital_index | ) | const |
path distance (number of bonds separated) between a pair of atoms
References path_distance_.
Referenced by core::chemical::AutomorphismIterator::bonded2(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), and core::conformation::Residue::path_distance().
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shortest path distance for an atom to all other residue atoms
References path_distance_.
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accessor of path_distance_ data for this residue, which is a 2D array
References path_distance_.
Referenced by initialize_derived_data(), core::conformation::Residue::path_distances(), and core::chemical::residue_types_identical().
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Final check of ResidueType data, called by ResidueType::make().
Final check of ResidueType data, called by constuctor.
These checks are meant to be quick and low-expense, and are only called on ResidueType creation, so they shouldn't generally add much to Rosetta processing time.
References core::chemical::aa_unk, core::chemical::aa_unp, core::chemical::ALPHA_AA, atom_base(), atom_name(), core::chemical::ResidueTypeBase::backbone_aa_raw(), core::chemical::BETA_AA, core::chemical::CANONICAL_NUCLEIC, chi_atoms(), core::chemical::D_AA, core::chemical::ResidueTypeBase::get_metal_binding_atoms(), core::chemical::ResidueTypeBase::has_property(), Hpol_index(), Hpol_index_, Hpos_polar_, is_metal(), is_metalbinding(), is_virtual(), core::chemical::L_AA, core::chemical::ResidueTypeBase::na_analogue_raw(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), nchi(), nheavyatoms_, core::chemical::ResidueTypeBase::properties(), core::chemical::RNA, and vec_atom_types_.
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make a copy
| void core::chemical::ResidueType::print_bondangles | ( | ) | const |
print intraresidue bond angles to standard out
References atom_name(), atom_type(), bondangle_atom_sets_, mm_atom_type(), mm_name(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), and core::chemical::TR().
| void core::chemical::ResidueType::print_pretty_path_distances | ( | ) | const |
print chemical-bond path distances to standard out
References atom_name(), natoms(), path_distance_, and core::chemical::TR().
translate proton_chi to global chi
References proton_chis_.
Referenced by protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::residue_types_identical().
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References proton_chi_extra_samples_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::chemical::MutableResidueType::copy_other_info(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
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References proton_chi_samples_.
Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::chemical::MutableResidueType::copy_other_info(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
| bool core::chemical::ResidueType::requires_actcoord | ( | ) | const |
require actcoord?
References actcoord_atoms_indices_, core::chemical::AROMATIC, core::chemical::ResidueProperties::has_property(), core::chemical::POLAR, core::chemical::ResidueTypeBase::properties(), and core::chemical::PROTEIN.
Referenced by core::conformation::Residue::requires_actcoord().
References residue_connections_.
Referenced by core::chemical::ICoorAtomID::atom_id(), branch_connect_atoms(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::get_second_atom_from_connection(), core::conformation::Residue::inter_residue_connection_partner(), and core::conformation::Residue::residue_connect_atom_index().
| ResidueConnection const & core::chemical::ResidueType::residue_connection | ( | Size const | i | ) | const |
Get a ResidueConection.
References residue_connections_.
Referenced by protocols::cyclic_peptide::PeptideStubMover::apply(), core::conformation::Residue::connect_atom(), core::conformation::Residue::connection_distance(), core::chemical::MutableResidueType::copy_other_info(), core::conformation::Residue::copy_residue_connections(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::conformation::get_disulf_partner(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::is_disulfide_bond(), core::conformation::Residue::residue_connection(), core::chemical::residue_types_identical(), core::conformation::setup_corresponding_atoms(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom.
References atom_2_residue_connection_map_.
Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::conformation::Residue::copy_residue_connections(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::Conformation::fix_disulfides(), and core::conformation::Conformation::insert_residue_by_bond().
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References lower_connect_id_, and upper_connect_id_.
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References atom_2_residue_connection_map_.
Referenced by core::conformation::Residue::copy_residue_connections(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().
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Return list of indices of the atoms within this residue's nth cycle, not counting virtual atoms.
References ring_atoms_.
Referenced by core::chemical::MutableResidueType::copy_other_info(), protocols::ligand_docking::ga_ligand_dock::crossover(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), protocols::ligand_docking::ga_ligand_dock::mutate(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize(), core::chemical::residue_types_identical(), core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::show(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), and core::chemical::write_topology_file().
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Return list of indices of the atoms within this residue's cycles, not counting virtual atoms.
References ring_atoms_.
Referenced by auto_assign_nu_atoms().
| core::chemical::rings::RingConformerSetCOP core::chemical::ResidueType::ring_conformer_set | ( | core::uint | ring_num | ) | const |
Return a pointer to the object containing the set of ring conformers possible for this residue's nth cycle.
References ring_conformer_sets_.
Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_carbohydrate_bond_sampler(), protocols::ligand_docking::ga_ligand_dock::mutate(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize(), core::chemical::residue_types_identical(), and core::conformation::Residue::ring_conformer().
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Return the saturation level of this residue's nth cycle.
References ring_saturation_types_.
Referenced by core::conformation::Residue::ring_conformer(), and core::chemical::write_topology_file().
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Return the saturation level for all of this residue's cycles.
References ring_saturation_types_.
Referenced by core::chemical::MutableResidueType::copy_other_info().
| core::chemical::rna::RNA_Info const & core::chemical::ResidueType::RNA_info | ( | ) | const |
References rna_info_.
Referenced by protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), core::pose::rna::get_sugar_centroid(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_tna_chainbreak(), core::conformation::Residue::RNA_info(), core::pose::rna::setup_base_pair_constraints(), and protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::virtualize_poor_scoring_o2prime_hydrogens().
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get root_atom used as the base of the icoor tree.
References root_atom_.
Referenced by core::conformation::Residue::apply_transform_downstream(), core::chemical::MutableResidueType::copy_other_info(), core::conformation::get_root_atomno(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), core::chemical::pretty_print_atomicoor(), and core::chemical::residue_types_identical().
| void core::chemical::ResidueType::select_orient_atoms | ( | Size & | center, |
| Size & | nbr1, | ||
| Size & | nbr2 | ||
| ) | const |
Selects three atoms for orienting this residue type.
References atom_base(), bonded_neighbor(), first_sidechain_atom(), core::chemical::ResidueTypeBase::force_nbr_atom_orient(), core::chemical::ResidueTypeBase::name(), natoms(), protocols::sic_dock::scores::nbr, nbr_atom(), nbrs(), nheavyatoms(), and select_orient_atoms_standard_logic().
Referenced by core::conformation::Residue::select_orient_atoms().
Selects three atoms for orienting this residue type.
References core::conformation::membrane::center, protocols::sic_dock::scores::nbr1(), and protocols::sic_dock::scores::nbr2().
| void core::chemical::ResidueType::select_orient_atoms_standard_logic | ( | Size & | center, |
| Size & | nbr1, | ||
| Size & | nbr2, | ||
| bool const | ignore_virtuals | ||
| ) | const |
Pick atoms to use for orienting one Residue onto another, using standard logic.
Standard logic applies to case in which (a) the residue has backbone atoms, and (b) the residue has sidechain atoms, and (c) the orient mode has not been set explicitly to force_nbr_atom_orient. We loop through all backbone atoms and find the first atom that is bonded to a sidechain atom AND two other backbone atoms. The first such atom becomes "center", and its two backbone neighbors become "nbr1" and "nbr2".
References atom_base(), atom_index(), atom_is_backbone(), bonded_neighbor(), is_virtual(), natoms(), protocols::sic_dock::scores::nbr, nbrs(), and nheavyatoms().
Referenced by select_orient_atoms().
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Do updates which need a valid get_self_ptr() (And thus can't be called from the constructor.)
References core::chemical::CARBOHYDRATE, carbohydrate_info_, get_self_weak_ptr(), core::chemical::ResidueTypeBase::has_property(), and core::chemical::ResidueTypeBase::properties().
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Determine how to map the numeric indices of MutableResidueType to this ResidueType. ( As the MutableResidueType is const, we can assume a decent mapping here. )
Because there isn't necessarily any consistent order in the MutableResidueType (particularly because patching often adds and removes atoms) we need to reorder the atoms. The atoms are reordered with the backbone atoms coming first, sidechain atoms second, and finally hydrogens last.
We attempt to keep the atom ordering more-or-less the same as the implicit ordering in the MutableResidueType.
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), attached_H_begin_, attached_H_end_, core::chemical::MutableResidueType::bonded_hydrogens(), first_sidechain_hydrogen_, core::chemical::MutableResidueType::is_backbone_heavyatom(), n_backbone_heavyatoms_, natoms_, and nheavyatoms_.
Referenced by ResidueType().
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Generate string representation of ResidueType for debugging purposes.
Implements core::chemical::ResidueTypeBase.
References all_bb_atoms_, all_sc_atoms_, atom_charge(), atom_is_aro_hydrogen(), atom_is_hydrogen(), atom_is_polar_hydrogen(), atom_name(), atom_type_index(), core::chemical::ResidueTypeBase::base_name(), branch_connect_atom_names(), core::chemical::CARBOHYDRATE, carbohydrate_info_, element_type(), formal_charge(), gasteiger_atom_type_index_, core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), core::chemical::ResidueProperties::has_property(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), is_branch_point(), is_cyclic(), is_virtual(), mainchain_atoms_indices_, mm_atom_type_index(), mm_name(), n_rings(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), natoms(), core::chemical::ResidueTypeBase::properties(), ring_atoms_, and core::chemical::ResidueProperties::show().
Referenced by core::scoring::hbonds::get_hb_acc_chem_type(), core::chemical::operator<<(), and core::conformation::Residue::show().
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Implements core::chemical::ResidueTypeBase.
References atom_names_.
Referenced by core::conformation::Residue::fill_missing_atoms(), and core::pose::named_atom_id_to_atom_id().
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Do other pre-calculation checks, not for otherwise uninitialized variables, but for data consistency or otherwise "incorrectly" set values.
References core::chemical::AROMATIC_CARBON_WITH_FREE_VALENCE, atom_is_aro_hydrogen(), atomic_properties_, bonded_neighbor(), core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(), core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(), is_base_type(), mm_name(), core::chemical::ResidueTypeBase::name(), natoms(), core::chemical::ResidueTypeBase::set_rama_prepro_mainchain_torsion_potential_name(), and update_ncaa_rotamer_library_specification_if_present().
Referenced by ResidueType().
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compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom.
Should only be called from initialize_derived_data() function.
References atom_base(), atoms_last_controlled_by_chi_, bonded_neighbor(), chi_atoms(), last_controlling_chi_, natoms(), nchi(), and note_chi_controls_atom().
Referenced by initialize_derived_data().
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If there is an NCAARotamerLibrarySpecification, ensure that the rotamer backbone dependicies have been set. If they have not, set them to all mainchain torsions except omega (the final, inter-residue torsion).
Should only be called from update_derived_data() function.
References mainchain_atoms_indices_, core::chemical::ResidueTypeBase::rotamer_library_specification(), and core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst().
Referenced by update_derived_data().
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Determine which atoms are nonpolymer bond-dependent.
Should only be called from initialize_derived_data() function.
Should only be called from update_derived_data() function.
References atom_depends_on_connection_, icoor(), n_possible_residue_connections(), and natoms().
Referenced by initialize_derived_data().
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Determine which atoms are polymer bond-dependent.
Should only be called from initialize_derived_data() function.
Should only be called from update_derived_data() function.
References atom_depends_on_lower_polymeric_connection_, atom_depends_on_upper_polymeric_connection_, has_polymer_dependent_groups_, icoor(), core::chemical::ResidueTypeBase::is_polymer(), and natoms().
Referenced by initialize_derived_data().
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Update the ring conformer sets derived information.
References core::chemical::CYCLIC, core::chemical::ResidueTypeBase::has_property(), low_ring_conformers_, lowest_ring_conformer_, n_rings(), core::chemical::ResidueTypeBase::properties(), ring_atoms_, ring_conformer_sets_, and ring_saturation_types_.
Referenced by initialize_derived_data().
| ResidueConnection const & core::chemical::ResidueType::upper_connect | ( | ) | const |
References core::chemical::ResidueTypeBase::has_property(), core::chemical::POLYMER, core::chemical::ResidueTypeBase::properties(), residue_connections_, and upper_connect_id_.
Referenced by define_mainchain_atoms(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), protocols::cyclic_peptide::PeptideCyclizeMover::get_values(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::upper_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().
| Size core::chemical::ResidueType::upper_connect_atom | ( | ) | const |
index number of the atom which connects to the upper connection
References core::chemical::ResidueTypeBase::has_property(), core::chemical::POLYMER, core::chemical::ResidueTypeBase::properties(), residue_connections_, and upper_connect_id_.
Referenced by protocols::denovo_design::connection::AreConnectablePredicate::check_distance(), core::scoring::ResidueExclParams::create_excl_info(), define_mainchain_atoms(), core::chemical::Selector_UPPER_ATOM::operator[](), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::conformation::Residue::upper_connect_atom().
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References upper_connect_id_.
Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Residue::connected_residue_at_upper(), core::chemical::MutableResidueType::copy_other_info(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), define_mainchain_atoms(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer_bonded(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::chemical::Selector_UPPER_ATOM::operator[](), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::chemical::residue_types_identical(), and core::chemical::write_topology_file().
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Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.
References within1bonds_sets_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), and core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().
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Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.
References within2bonds_sets_for_atom_.
Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().
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Index version of abase2_.
Referenced by abase2(), and copy_other_info().
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indices of Hbond acceptor positions
Referenced by accpt_pos(), copy_atom_info(), and copy_other_info().
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indices of Hbond acceptor positions that are part of the sidechain must be a subset of the atoms listed in the accpt_pos_ array
Referenced by accpt_pos_sc(), and copy_atom_info().
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Index version of actcoord_atoms_.
Referenced by actcoord_atoms(), copy_other_info(), and requires_actcoord().
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Indices of all backbone atoms, hydrogens and heavyatoms.
Referenced by all_bb_atoms(), copy_atom_info(), and show().
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Indices of all sidechain atoms, hydrogens and heavyatoms.
Referenced by all_sc_atoms(), atom_is_sidechain(), copy_atom_info(), and show().
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Mapping of atom indicies to residue connections.
Referenced by atom_forms_residue_connection(), copy_other_info(), n_residue_connections_for_atom(), residue_connection_id_for_atom(), and residue_connections_for_atom().
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Index version of atom_base_.
Referenced by abase2(), atom_base(), and copy_other_info().
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An outer vector indexed to connection ID, and an inner vector indexed to atom ids. "True" means that the atom id for the inner vector depends on the connection ID for the outer.
Referenced by atom_depends_on_connection(), and update_nonpolymer_dependent_groups().
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vector of length corresponding to number of atoms indicating whether each atom is dependent on the lower polymer bond.
empty if this is a ligand instead of a polymer bond.
Referenced by atom_depends_on_lower_polymeric_connection(), atom_depends_on_polymeric_connection(), and update_polymer_dependent_groups().
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vector of length corresponding to number of atoms indicating whether each atom is dependent on the upper polymer bond.
empty if this is a ligand instead of a polymer bond.
Referenced by atom_depends_on_polymeric_connection(), atom_depends_on_upper_polymeric_connection(), and update_polymer_dependent_groups().
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Referenced by atom_index(), copy_atom_info(), copy_other_info(), and has().
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Referenced by atom_name(), copy_atom_info(), copy_other_info(), and show_all_atom_names().
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Index version of atom_shadowed_.
Referenced by atom_being_shadowed(), copy_other_info(), and has_shadow_atoms().
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Referenced by atom_has_property(), atom_properties(), copy_atom_info(), and update_derived_data().
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for chi i, the list of atoms last controlled by i E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1
Referenced by atoms_last_controlled_by_chi(), initialize_derived_data(), and update_last_controlling_chi().
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indices of atoms with orbitals
Referenced by atoms_with_orb_index(), and copy_atom_info().
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For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.
Referenced by atoms_within_one_bond_of_a_residue_connection(), and initialize_derived_data().
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For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i.
Referenced by atoms_within_two_bonds_of_a_residue_connection(), and initialize_derived_data().
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indices of each heavyatom's first attached hydrogen
Referenced by attached_H_begin(), number_bonded_hydrogens(), and setup_atom_ordering().
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indices of each heavyatom's last attached hydrogen
Referenced by attached_H_end(), number_bonded_hydrogens(), and setup_atom_ordering().
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Const-access owning pointer to the base residue type.
NULL if this ResidueType is a base type. If this ResidueType is cloned or copied from a base type, this will point to the base type. If this ResidueType is cloned or copied from a non-base type, this will point to the non-base type's base type. The test for whether something is a base type is whether this owning pointer is NULL.
Referenced by get_base_type_cop(), and is_base_type().
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vector of sets of atoms that make up bond angles in the residue
Referenced by bondangle(), initialize_derived_data(), num_bondangles(), and print_bondangles().
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???
Referenced by bondangles_for_atom(), and initialize_derived_data().
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For each atom, list the other atom indices it's bonded to.
Referenced by bond_ringness(), bond_type(), bonded_neighbor(), bonds(), copy_atom_info(), copy_other_info(), and nbonds().
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What is the ringness type of the bond connecting the equivalent entry in bonded_neighbor_?
Referenced by bond_ringness(), bonded_neighbor_ringnesses(), and copy_atom_info().
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What is the bond type of the bond connecting the equivalent entry in bonded_neighbor_?
Referenced by bond_type(), bonded_neighbor_types(), and copy_atom_info().
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For each atom, which orbitals are bonded to it.
Referenced by bonded_orbitals(), and copy_atom_info().
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A container for residue properties unique to carbohydrates.
Referenced by carbohydrate_info(), self_pointer_updates(), and show().
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A "map" of chi indices to proteon_chi indices.
Referenced by chi_2_proton_chi(), and copy_other_info().
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Referenced by chi_atoms(), copy_other_info(), and nchi().
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Additional non-Dunbrack rotamer bins.
pair<Real,Real> ==> mean,sdev for each chi angle i and rotamer j: chi_rotamers_[i][j]
Referenced by chi_rotamers(), and copy_other_info().
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Index version of cut_bond_neighbor_.
Referenced by copy_atom_info(), and cut_bond_neighbor().
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Who needs to be told if this ResidueType is destroyed?
Referenced by attach_destruction_obs(), detach_destruction_obs(), and ~ResidueType().
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Data for the mm potentials. List all of the intra-residue dihedral angles and bond angles. vector of sets of atoms that make up dihedral angles in the residue Data for the mm potentials.
Referenced by dihedral(), initialize_derived_data(), and ndihe().
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all intra-residue dihedral angles that each atom "participates" in
Referenced by dihedrals_for_atom(), and initialize_derived_data().
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Referenced by copy_atom_info(), and element_type().
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the index of first sidechain hydrogen atom
Referenced by atom_is_backbone(), copy_atom_info(), first_sidechain_hydrogen(), and setup_atom_ordering().
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Referenced by copy_atom_info(), and formal_charge().
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Referenced by copy_atom_info(), gasteiger_atom_type(), and show().
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indices of haro hydrogens
Referenced by copy_atom_info(), and Haro_index().
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Does this ResidueType have groups with icoors that depend, directly or indirectly, on polymeric bonds?
Referenced by has_polymer_dependent_groups(), and update_polymer_dependent_groups().
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Is this atom a heavyatom with polar hydrogens attached?
Referenced by copy_atom_info(), and heavyatom_has_polar_hydrogens().
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indices of hpolar hydrogens
Referenced by copy_atom_info(), Hpol_index(), and perform_checks().
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indices of apolar hydrogens
Referenced by copy_atom_info(), and Hpos_apolar().
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indices of polar Hydrogens for Hbond donors
Referenced by copy_atom_info(), Hpos_polar(), and perform_checks().
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indices of polar Hydrogens for Hbond donors that are part of the sidechain must be a subset of the atoms listed in the Hpos_polar_ array
Referenced by copy_atom_info(), and Hpos_polar_sc().
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Internal coordinates on how to build the given atom.
Referenced by copy_other_info(), and icoor().
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Referenced by copy_atom_info(), and ideal_xyz().
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Is the corresponding chi in chi_atoms_ a proton chi?
Referenced by copy_other_info().
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Data for controlling chi. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi.
Referenced by initialize_derived_data(), last_controlling_chi(), note_chi_controls_atom(), and update_last_controlling_chi().
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Low-energy ring conformers for each ring.
used for setting up the RingConformerSets
Referenced by copy_other_info(), low_ring_conformers(), and update_ring_conformer_sets().
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Polymer lower connections.
Referenced by branch_connect_atoms(), copy_other_info(), lower_connect(), lower_connect_atom(), lower_connect_id(), and residue_connection_is_polymeric().
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Lowest-energy ring conformer for each ring.
used for setting up the RingConformerSets
Referenced by copy_other_info(), lowest_ring_conformers(), and update_ring_conformer_sets().
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Index version of mainchain_atoms_.
Referenced by copy_other_info(), define_mainchain_atoms(), mainchain_atom(), mainchain_atoms(), show(), and update_ncaa_rotamer_library_specification_if_present().
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Referenced by copy_atom_info(), and mass().
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Referenced by copy_atom_info(), and mm_atom_type_index().
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number of backbone heavy atoms
Referenced by atom_is_backbone(), copy_atom_info(), first_sidechain_atom(), last_backbone_atom(), and setup_atom_ordering().
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The number of hbond_acceptors.
Referenced by copy_atom_info(), and n_hbond_acceptors().
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number of hbond_donors
Referenced by copy_atom_info(), and n_hbond_donors().
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Number of non-polymeric residue connections.
Referenced by branch_connect_atoms(), copy_other_info(), and n_non_polymeric_residue_connections().
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Number of polymeric residue connections.
Referenced by copy_other_info(), and n_polymeric_residue_connections().
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Referenced by copy_atom_info(), copy_other_info(), mm_atom_type_index(), natoms(), and setup_atom_ordering().
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Referenced by bonds(), copy_atom_info(), and nbonds().
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Referenced by copy_other_info(), and nbr_atom().
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radius cutoff to define neighbors
Should be the maximum distance from the nbr_atom_ to any heavy atom in any valid rotamer.
Referenced by copy_other_info(), and nbr_radius().
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The number of heavy atoms.
Referenced by atom_is_backbone(), atom_is_hydrogen(), first_sidechain_atom(), nheavyatoms(), perform_checks(), and setup_atom_ordering().
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AtomIndex of four atoms to build each nu angle.
Referenced by auto_assign_nu_atoms(), copy_other_info(), n_nus(), and nu_atoms().
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Referenced by atom_charge(), and copy_atom_info().
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number of bonds separated between any pair of atoms in this residue
Referenced by initialize_derived_data(), path_distance(), path_distances(), and print_pretty_path_distances().
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For a proton chi, how to handle extra ex_ levels.
Referenced by copy_other_info(), and proton_chi_extra_samples().
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For a proton chi, the primary samples to diversify the rotamer library with.
Referenced by copy_other_info(), and proton_chi_samples().
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Indices of the chi_atoms_ vector for proton chis.
Referenced by copy_other_info(), is_proton_chi(), n_proton_chi(), and proton_chi_2_chi().
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Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections.
Referenced by copy_other_info(), initialize_derived_data(), lower_connect(), lower_connect_atom(), n_possible_residue_connections(), residue_connect_atom_index(), residue_connection(), upper_connect(), and upper_connect_atom().
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AtomIndex of all ring atoms, not counting virtual atoms.
Referenced by auto_assign_nu_atoms(), copy_other_info(), is_ring_atom(), n_rings(), ring_atoms(), show(), and update_ring_conformer_sets().
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The sets of all possible ring conformers, one per ring.
Referenced by n_ring_conformer_sets(), ring_conformer_set(), and update_ring_conformer_sets().
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The saturation type of each ring in this residue.
Referenced by copy_other_info(), ring_saturation_type(), ring_saturation_types(), and update_ring_conformer_sets().
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A container for properties unique to RNA.
Referenced by initialize_derived_data(), and RNA_info().
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Atom at the nominal root of the ICOOR tree.
Referenced by copy_other_info(), and root_atom().
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Polymer upper connections.
Referenced by branch_connect_atoms(), copy_other_info(), residue_connection_is_polymeric(), upper_connect(), upper_connect_atom(), and upper_connect_id().
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Referenced by atom_type_index(), and copy_atom_info().
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The types for each atom.
Referenced by atom_is_aro_hydrogen(), atom_is_polar_hydrogen(), atom_type(), copy_atom_info(), heavyatom_is_an_acceptor(), n_virtual_atoms(), and perform_checks().
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For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array.
Referenced by initialize_derived_data(), and within1bonds_sets_for_atom().
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For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array.
Referenced by initialize_derived_data(), and within2bonds_sets_for_atom().
1.8.7