Rosetta Core  2014.35
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core::chemical::ResidueType Class Reference

A class for defining a type of residue. More...

#include <ResidueType.hh>

Public Member Functions

virtual ~ResidueType ()
 destructor More...
 
 ResidueType (AtomTypeSetCAP atom_types, ElementSetCAP element_types, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types)
 constructor More...
 
 ResidueType (ResidueType const &residue_type)
 
ResidueTypeOP clone () const
 make a copy More...
 
AtomTypeSet const & atom_type_set () const
 access by reference the atomset for which this residue is constructed More...
 
ElementSet const & element_set () const
 access by reference the atomset for which this residue is constructed More...
 
AtomTypeSetCAP atom_type_set_ptr () const
 access by const pointer the atomset for which this residue is constructed More...
 
Atomatom (Size const atom_index)
 
Atom const & atom (Size const atom_index) const
 
Atomatom (std::string const &atom_name)
 
Atom const & atom (std::string const &atom_name) const
 
Atomatom (VD const atom_vd)
 
Atom const & atom (VD const atom_vd) const
 
Orbital const & orbital (Size const orbital_index) const
 
Orbital const & orbital (std::string const &orbital_name) const
 
Bondbond (ED const ed)
 
Bond const & bond (ED const ed) const
 
Bondbond (std::string const &atom1, std::string const &atom2)
 
Bond const & bond (std::string const &atom1, std::string const &atom2) const
 
AtomType const & atom_type (Size const atomno) const
 Get the chemical atom_type for this atom by it index number in this residue. More...
 
AtomType const & atom_type (VD const vd) const
 Get the chemical atom_type for this atom by it index number in this residue. More...
 
Size natoms () const
 number of atoms More...
 
Size nheavyatoms () const
 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
 number of bonds More...
 
Size nbonds (Size atom) const
 number of bonds for given atom More...
 
Size nbonds (VD atom) const
 number of bonds for given atom 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...
 
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...
 
Size n_virtual_atoms () const
 Counts the number of virtual atoms and returns the count. 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...
 
AdjacentIterPair bonded_neighbor_iterators (VD const &atom) const
 
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
 
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...
 
AtomIndices const & chi_atoms (Size const chino) const
 indices of the atoms which are used to define a given chi angle (chino) More...
 
VDs const & chi_atom_vds (Size const chino) const
 VDs 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...
 
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 heavyatom_has_polar_hydrogens (Size atomno) const
 
bool heavyatom_is_an_acceptor (Size atomno) const
 
bool atom_is_polar_hydrogen (Size atomno) const
 
AtomIndices const & mainchain_atoms () const
 indices of all mainchain atoms More...
 
Size mainchain_atom (Size const atm) const
 index of mainchain atom More...
 
void set_mainchain_atoms (AtomIndices const &mainchain)
 set indices of all mainchain atoms More...
 
bool has (std::string const &atom_name) const
 is this atom present in this residue? More...
 
bool has (VD const vd) const
 is this vertex descriptor present in this residue? More...
 
Size atom_base (Size const atomno) const
 get index of an atom's base atom More...
 
VD atom_base (VD const atomno) const
 get vd of an atom's base atom More...
 
Size abase2 (Size const atomno) const
 get index of an atom's second base atom More...
 
std::string const & atom_name (Size const index) const
 get atom name by index More...
 
std::string const & atom_name (VD const vd) const
 get atom name by vertex descriptor More...
 
Size atom_index (std::string const &name) const
 get atom index by name More...
 
Size atom_index (VD const &vd) const
 get atom index by vertex descriptor More...
 
VD atom_vertex (std::string const &name) const
 get the vertex descriptor from the name of the atom. More...
 
VD atom_vertex (Size const &atomno) const
 Get the vertex descriptor from the atom index. More...
 
ResidueGraph const & graph () const
 Constant access to the underlying graph. More...
 
void dump_vd_info () const
 
void show_all_atom_names (std::ostream &out) const
 
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...
 
VIterPair atom_iterators () const
 
EIterPair bond_iterators () const
 
OutEdgeIterPair bond_iterators (VD const &atom) const
 
bool atom_is_backbone (Size const atomno) const
 is a backbone atom (heavy or hydrogen)? More...
 
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...
 
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...
 
AtomIndices const & actcoord_atoms () const
 get indices for atoms used to define actcoord More...
 
bool is_virtual (Size const &atomno) const
 Check if atom is virtual. 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...
 
gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type (Size const atomno) const
 Get the MM atom_type index number for this atom by its index number in this residue. More...
 
chemical::orbitals::OrbitalType
const & 
orbital_type (int const orbital_index) const
 
Size n_orbitals () const
 number of orbitals More...
 
utility::vector1< core::Size >
const & 
bonded_orbitals (Size const atomno) const
 indices of the orbitals bonded to an atom More...
 
bool has_orbital (std::string const &orbital_name) const
 is this orbital present in this residue? More...
 
AtomIndices const & atoms_with_orb_index () const
 
core::Size orbital_index (std::string const &name) const
 get orbital index by name More...
 
core::chemical::RingConformerSetCOP ring_conformer_set () const
 Return a pointer to the object containing the set of ring conformers possible for this cyclic residue. More...
 
ResidueTypeSet const & residue_type_set () const
 
void residue_type_set (ResidueTypeSetCAP set_in)
 set the residue type set of origin. More...
 
Size nchi () const
 number of chi angles More...
 
Size n_nus () const
 Return number of nu (internal ring) angles. 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...
 
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...
 
void set_lower_connect_atom (std::string const &atm_name)
 set 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...
 
void set_upper_connect_atom (std::string const &atm_name)
 set the atom which connects to the upper connection More...
 
Size n_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...
 
ResidueConnectionresidue_connection (Size const i)
 
bool atom_forms_residue_connection (Size const atomid)
 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 requires_actcoord () const
 require actcoord? More...
 
void update_actcoord (conformation::Residue &rot) const
 update actcoord More...
 
VD add_atom (std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge)
 add an atom into this residue Will return the vertex descriptor of the added atom. More...
 
VD add_atom (std::string const &atom_name="")
 add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom. More...
 
void delete_atom (std::string const &name)
 flag an atom for deletion by adding its index to the delete_atom_ list More...
 
void delete_atom (Size const index)
 flag an atom for deletion by adding its index to the delete_atom_ list More...
 
void add_atom_alias (std::string const &rosetta_atom, std::string const &alias)
 Add an alias name for an atom. More...
 
void delete_atom_alias (std::string const &alias)
 Remove a given alias name for an atom. More...
 
void set_atom_type (std::string const &atom_name, std::string const &atom_type_name)
 set atom type More...
 
void set_atom_type (VD atom, std::string const &atom_type_name)
 set atom type More...
 
void set_mm_atom_type (std::string const &atom_name, std::string const &mm_atom_type_name)
 set mm atom type More...
 
void set_gasteiger_typeset (gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types)
 Manually set the gasteiger typeset - will use the default set otherwise. More...
 
void set_gasteiger_atom_type (std::string const &atom_name, std::string const &gasteiger_atom_type_name)
 set gasteiger atom type More...
 
void add_metalbinding_atom (std::string const atom_name)
 Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime). More...
 
void add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond)
 
void add_bond (VD atom1, VD atom2, BondName bondLabel=SingleBond)
 
void add_cut_bond (std::string const &atom_name1, std::string const &atom_name2)
 add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond More...
 
VD root_atom () const
 get root_atom used as the base of the icoor tree. More...
 
void nbr_atom (std::string const &atom_name)
 set nbr_atom used to define residue-level neighbors More...
 
void nbr_atom (VD vertex)
 set nbr_atom used to define residue-level neighbors More...
 
Size nbr_atom () const
 get nbr_atom used to define residue-level neighbors More...
 
VD nbr_vertex () const
 get VD used to define residue-level neighbors More...
 
void nbr_radius (Real const radius)
 set nbr_radius_ used to define residue-level neighbors More...
 
Real nbr_radius () const
 get nbr_radius_ used to define residue-level neighbors More...
 
core::Real const & mass () const
 get the molecular weight of this residue More...
 
void set_atom_base (std::string const &atom_name1, std::string const &atom_name2)
 sets atom_base[ atom1 ] = atom2 More...
 
void set_atom_base (VD const &atom1, VD const &atom2)
 sets atom_base[ atom1 ] = atom2, vertex descriptor version More...
 
void set_backbone_heavyatom (std::string const &name)
 set an atom as backbone heavy atom More...
 
void debug_dump_icoor () const
 Dump out atomnames and icoor values. More...
 
AtomICoor const & icoor (Size const atm) const
 AtomICoord of an atom. More...
 
AtomICoor const & icoor (VD const atm) const
 AtomICoord of an atom. More...
 
void set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom More...
 
void set_icoor (VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false)
 set AtomICoor for an atom, vertex descriptor version More...
 
void assign_neighbor_atom ()
 
void assign_internal_coordinates ()
 Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds. More...
 
void assign_internal_coordinates (core::chemical::VD new_root)
 
void set_ideal_xyz (std::string const &atm, Vector const &xyz_in)
 
void set_ideal_xyz (Size index, Vector const &xyz_in)
 
void set_ideal_xyz (VD atm, Vector const &xyz_in)
 
void fill_ideal_xyz_from_icoor ()
 
void set_shadowing_atom (std::string const &atom, std::string const &atom_being_shadowed)
 
void add_orbital (std::string &orbital_name, std::string &orbital_type_name)
 add an orbital onto a residue based upon atom More...
 
void add_orbital_bond (std::string const &atom_name1, std::string const &orbital_name)
 add an orbital bond between an atom and an orbital. More...
 
orbitals::ICoorOrbitalData const & orbital_icoor_data (Size const orbital_index) const
 
orbitals::ICoorOrbitalData const & new_orbital_icoor_data (Size const orbital_index) const
 
void set_orbital_icoor_id (std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)
 set OrbitalICoor for an orbital More...
 
const HeavyAtomGraph heavy_atoms ()
 
const AcceptorAtomGraph acceptor_atoms ()
 
const
HeavyAtomWithPolarHydrogensGraph 
heavy_atom_with_polar_hydrogens ()
 
const HeavyAtomWithHydrogensGraph heavy_atom_with_hydrogens ()
 
const HydrogenAtomGraph hydrogens ()
 
const PolarHydrogenGraph polar_hydrogens ()
 
const APolarHydrogenGraph apolar_hydrogens ()
 
const AromaticAtomGraph aromatic_atoms ()
 
void add_chi (Size const chino, VD atom1, VD atom2, VD atom3, VD atom4)
 Add a chi (side-chain) angle defined by four atoms. More...
 
void add_chi (VD atom1, VD atom2, VD atom3, VD atom4)
 Add a chi (side-chain) angle defined by four atoms. More...
 
void add_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 Add a chi (side-chain) angle defined by four atoms. More...
 
void add_chi (std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 Add a chi (side-chain) angle defined by four atoms to the end of the list of chis. More...
 
void add_nu (core::uint const nu_index, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 Add a nu (internal cyclic) angle defined by four atoms. More...
 
void redefine_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
 redefine a chi angle based on four atoms More...
 
void set_proton_chi (Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples)
 Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior. More...
 
void add_chi_rotamer (Size const chino, Real const mean, Real const sdev)
 Add a rotamer bin for a given chi. More...
 
void add_chi_rotamer_to_last_chi (core::Angle const mean, core::Angle const sdev)
 Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType. More...
 
void autodetermine_chi_bonds (core::Size max_proton_chi_samples=500)
 Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all. More...
 
void finalize ()
 recalculate derived data, potentially reordering atom-indices More...
 
void require_final () const
 an assertion function to ensure an ResidueType has been finalized More...
 
Size add_residue_connection (std::string const &atom_name)
 add a non-polymeric ResidueConnection More...
 
void add_actcoord_atom (std::string const &atom)
 add an atom to the list for calculating actcoord center More...
 
ResidueProperties const & properties () const
 Access the collection of properties for this ResidueType. More...
 
void add_property (std::string const &property)
 Add a property to this ResidueType. 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)
 Add a property of this ResidueType. More...
 
bool is_polymer () const
 is polymer? More...
 
bool is_protein () const
 is protein? 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_d_aa () const
 is this a d-amino acid? More...
 
bool is_l_aa () const
 is this an l-amino acid? More...
 
bool is_DNA () const
 is DNA? More...
 
bool is_RNA () const
 is RNA? More...
 
bool is_coarse () const
 is coarse? More...
 
bool is_NA () const
 is Nucleic Acid? More...
 
bool is_peptoid () const
 is peptoid? 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_lower_terminus () const
 is lower terminus of a branch? 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'. More...
 
bool is_adduct () const
 is an adduct-modified residue? More...
 
bool has_property (std::string const &property) const
 Generic property access. 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...
 
utility::vector1< VariantType >
const & 
variant_types () const
 Get all the variant types for this ResidueType. More...
 
void add_variant_type (VariantType const &variant_type)
 Add a variant type to this ResidueType. More...
 
bool has_variant_type (VariantType const &variant_type) const
 Generic variant access. More...
 
bool variants_match (ResidueType const &other) const
 Does this residue have exactly the same set of properties as residue other? More...
 
bool nonadduct_variants_match (ResidueType const &other) const
 similar to variants_match(), but allows different adduct-modified states 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 rotamer_aa (AA const &type)
 AA to use for rotamer library. More...
 
void rotamer_aa (std::string const &type)
 AA to use for rotamer library. More...
 
void backbone_aa (std::string const &type)
 AA to use for backbone scoring. More...
 
std::string const & name () const
 get our (unique) residue name 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 ResidueType .params file through the IO_STRING tag along with the name1 string 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 ResidueType .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. ResidueTypes 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 ResidueTypes .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 & rotamer_aa () const
 
AA const & backbone_aa () const
 Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More...
 
void set_RotamerLibraryName (std::string const &filename)
 
std::string get_RotamerLibraryName () const
 A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use. More...
 
dihedral_atom_set const & dihedral (Size const dihe) const
 dihedral methods More...
 
dihedral_atom_set const & improper_dihedral (Size const dihe) const
 Return the indices for the set of atoms that define a particular. 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...
 
utility::vector1< Size > const & improper_dihedrals_for_atom (Size atomno) const
 Returns the list of all of the indices of all the intraresidue. 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...
 
void print_dihedrals () const
 
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...
 
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...
 
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...
 
void set_ncaa_rotlib_path (std::string const &path)
 Sets the path for the NCAA rotlib for the ResidueType. More...
 
std::string const & get_ncaa_rotlib_path () const
 Returns the path to the NCAA rotlib for the residue type. More...
 
void set_use_ncaa_rotlib (bool flag)
 Sets whether we are using a NCAA rotlib for the residue type. More...
 
bool get_use_ncaa_rotlib () const
 Returns whether we are using a NCAA rotlib for the residue type. More...
 
void set_ncaa_rotlib_n_rotameric_bins (Size n_rots)
 Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More...
 
Size set_ncaa_rotlib_n_rotameric_bins () const
 Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi) More...
 
void set_ncaa_rotlib_n_bin_per_rot (utility::vector1< Size > n_bins_per_rot)
 Sets the number of rotamers for each rotatable bond described by the NCAA rotlib. More...
 
Size get_ncaa_rotlib_n_bin_per_rot (Size n_rot)
 Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond. More...
 
utility::vector1< Size > const & get_ncaa_rotlib_n_bin_per_rot () const
 Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds. More...
 
void set_peptoid_rotlib_path (std::string const &path)
 Sets the path for the peptoid rotlib for the ResidueType. More...
 
std::string const & get_peptoid_rotlib_path () const
 Returns the path to the peptoid rotlib for the residue type. More...
 
void set_use_peptoid_rotlib (bool flag)
 Sets whether we are using a peptoid rotlib for the residue type. More...
 
bool get_use_peptoid_rotlib () const
 Returns whether we are using a peptoid rotlib for the residue type. More...
 
void set_peptoid_rotlib_n_rotameric_bins (Size n_rots)
 Sets the number of rotatable bonds described by the peptoid rotlib (not nesesarily equal to nchi) More...
 
Size set_peptoid_rotlib_n_rotameric_bins () const
 Returns the number of rotatable bonds described by the peptoid rotlib (not nesesarily equal to nchi) More...
 
void set_peptoid_rotlib_n_bin_per_rot (utility::vector1< Size > n_bins_per_rot)
 Sets the number of rotamers for each rotatable bond described by the peptoid rotlib. More...
 
Size get_peptoid_rotlib_n_bin_per_rot (Size n_rot)
 Returns the number of rotamers for each rotatable bond described by the peptoid rotlib for a single bond. More...
 
utility::vector1< Size > const & get_peptoid_rotlib_n_bin_per_rot () const
 Returns the number of rotamers for each rotatable bond described by the peptoid rotlib for all bonds. 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...
 
core::chemical::rna::RNA_ResidueType
const & 
RNA_type () const
 
core::chemical::carbohydrates::CarbohydrateInfoCOP carbohydrate_info () const
 Return the CarbohydrateInfo object containing sugar-specific properties for this residue. 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...
 
bool force_nbr_atom_orient () const
 Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...
 
void select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
 Selects three atoms for orienting this residue type. More...
 
core::Size smallest_ring_size (VD const &atom, core::Size const &max_size=999999) const
 A graph-based function to determine the size of the smallest ring that involves a given atom. More...
 
std::list< utility::vector1
< ED > > const & 
rings ()
 
void show (std::ostream &output=std::cout, bool output_atomic_details=false) const
 Generate string representation of ResidueType for debugging purposes. 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 ()
 
void nondefault (bool in)
 
void base_restype_name (std::string const &in)
 
std::string base_restype_name () const
 

Public Attributes

bool serialized_
 

Static Public Attributes

static VD const null_vertex = boost::graph_traits<ResidueGraph>::null_vertex()
 

Private Member Functions

void setup_atom_ordering ()
 set up atom ordering map old2new, called by finalize() More...
 
void order_atoms ()
 GRAPH FUNCTION to provide backward compatibility ////////. More...
 
void generate_atom_indices ()
 reorder primary data in ResidueType given the old2new map, called by finalize() More...
 
void update_derived_data ()
 update derived data in ResidueType, called by finalize() More...
 
void perform_checks ()
 Final check of ResidueType data, called by finalize(). More...
 
void update_residue_connection_mapping ()
 
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...
 

Private Attributes

AtomTypeSetCAP atom_types_
 The type set for Rosetta Atom types. – Primary used to define the set of allowed atomtypes for this residue and their properties Needs to be non-null by the time finalize() is called. More...
 
ElementSetCAP elements_
 The set for element objects. – Primary, can be null. More...
 
MMAtomTypeSetCAP mm_atom_types_
 The set for MMAtomTypes. – Primary, can be null. More...
 
gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types_
 The set for GasteigerAtomTypes. – Primary, can be null. More...
 
orbitals::OrbitalTypeSetCAP orbital_types_
 The set for OrbitalTypes. – Primary, can be null. More...
 
RingConformerSetOP conformer_set_
 The set of all possible ring conformers – Derived, can be null. More...
 
ResidueTypeSetCAP residue_type_set_
 The owning ResidueTypeSet, if any. – Primary, can be null. More...
 
ResidueGraph graph_
 The Atoms and Bonds of the ResidueType, stored as Nodes and Edges. – Primary. More...
 
std::map< VD, Sizevd_to_index_
 A map of graph VDs to vector indexes. – Derived, valid during Mutable. More...
 
std::map< VD, VDatom_base_
 The atom "one up" in the atom tree. – Derived, valid during Mutable. Updated in set_icoor. (also set_atom_base - TODO: Fix redundancy issue. More...
 
std::map< VD, VDabase2_
 The base of the atom base – Derived. More...
 
VDs ordered_atoms_
 Vector of atoms for index->vd mapping. More...
 
utility::vector1< Orbitalorbitals_
 The orbitals on the ResidueType, if any. – Primary. More...
 
Size nheavyatoms_
 The number of heavy atoms – Derived. More...
 
Size n_hbond_acceptors_
 The number of hbond_acceptors – Derived. More...
 
Size n_hbond_donors_
 number of hbond_donors – Derived. More...
 
Size n_backbone_heavyatoms_
 number of backbone heavy atoms – Derived. More...
 
Size first_sidechain_hydrogen_
 the index of first sidechain hydrogen atom – Derived. More...
 
utility::vector1< AtomIndicesbonded_neighbor_
 indices of the atoms psuedo bonded atoms. Used in orbital code – Derived More...
 
utility::vector1
< utility::vector1< BondName > > 
bonded_neighbor_type_
 ??? – Derived More...
 
std::map< VD, utility::vector1
< VD > > 
cut_bond_neighbor_
 ??? – Derived More...
 
utility::vector1< Sizeattached_H_begin_
 indices of each heavyatom's first attached hydrogen – Derived. More...
 
utility::vector1< Sizeattached_H_end_
 indices of each heavyatom's last attached hydrogen – Derived. More...
 
std::map< VD, AtomICooricoor_
 Internal coordinates on how to build the given atom – Primary. More...
 
utility::vector1
< dihedral_atom_set
dihedral_atom_sets_
 Data for the mm potentials. – Derived 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 – Derived More...
 
utility::vector1
< dihedral_atom_set
improper_dihedral_atom_sets_
 
utility::vector1
< utility::vector1< Size > > 
improper_dihedrals_for_atom_
 
utility::vector1
< bondangle_atom_set
bondangle_atom_sets_
 vector of sets of atoms that make up bond angles in the residue – Derived More...
 
utility::vector1
< utility::vector1< Size > > 
bondangles_for_atom_
 ??? – Derived More...
 
std::map< VD, VDatom_shadowed_
 Data to describe virtual atoms that should shadow other atoms for the sake of keeping intraresidue cycles closed when working with an atom tree, e.g. NV shadows N on proline. For each atom, the following vector lists the index of the atom it is shadowing. – Primary. More...
 
utility::vector1< Sizelast_controlling_chi_
 Data for controlling chi. – Derived. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi. More...
 
utility::vector1< AtomIndicesatoms_last_controlled_by_chi_
 for chi i, the list of atoms last controlled by i – Derived E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1 More...
 
AtomIndices atoms_with_orb_index_
 indices of atoms with orbitals – Derived More...
 
AtomIndices Haro_index_
 indices of haro hydrogens – Derived More...
 
AtomIndices Hpol_index_
 indices of hpolar hydrogens – Derived More...
 
AtomIndices accpt_pos_
 indices of Hbond acceptor positions – Derived More...
 
AtomIndices Hpos_polar_
 indices of polar Hydrogens for Hbond donors – Derived More...
 
AtomIndices Hpos_apolar_
 indices of apolar hydrogens – Derived More...
 
AtomIndices accpt_pos_sc_
 indices of Hbond acceptor positions that are part of the sidechain – Derived 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 – Derived 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 – Derived. More...
 
AtomIndices all_sc_atoms_
 Indices of all sidechain atoms, hydrogens and heavyatoms – Derived. More...
 
utility::vector1< std::string > metal_binding_atoms_
 Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types. More...
 
utility::vector1< VDmainchain_atoms_
 Verticies of all mainchain atoms – Primary. More...
 
utility::vector1< VDactcoord_atoms_
 indices of action coordinate centers – Primary More...
 
utility::vector1
< utility::vector1< VD > > 
chi_atoms_
 the four atoms to build each chi angle – Primary. More...
 
utility::vector1< boolis_proton_chi_
 Is the corresponding chi in chi_atoms_ a proton chi? – Primary. More...
 
utility::vector1< Sizeproton_chis_
 Indices of the chi_atoms_ vector for proton chis – Derived, valid during Mutable. More...
 
utility::vector1< Sizechi_2_proton_chi_
 A "map" of chi indices to proteon_chi indices – Derived, valid during Mutable. More...
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_samples_
 For a proton chi, the primary samples to diversify the rotamer library with – Primary. More...
 
utility::vector1
< utility::vector1< Real > > 
proton_chi_extra_samples_
 For a proton chi, how to handle extra ex_ levels – Primary. More...
 
utility::vector1
< utility::vector1< VD > > 
nu_atoms_
 indices of four atoms to build each nu angle – Primary. More...
 
utility::vector1
< utility::vector1< int > > 
path_distance_
 number of bonds separated between any pair of atoms in this residue – Derived. More...
 
std::map< std::string, VDatom_name_to_vd_
 atom index lookup by atom name string – Derived, valid during Mutable, with caveats More...
 
std::map< std::string,
std::string > 
atom_aliases_
 A mapping of alias atom names to canonical atom names – Primary Will be added to atom_name_to_vd_ during finalization. More...
 
std::map< std::string, intorbitals_index_
 index lookup for orbitals based on atom name – Derived, valid during Mutable Updated in add_orbital() More...
 
utility::vector1
< utility::vector1< std::pair
< Real, Real > > > 
chi_rotamers_
 Additional non-Dunbrack rotamer bins – Primary. More...
 
std::string rotamer_library_name_
 The filename of the PDBRotamersLibrary – Primary. More...
 
bool use_ncaa_rotlib_
 NCAA rotlib stuff some of this is hardcoded elsewhere for the CAAs. More...
 
std::string ncaa_rotlib_path_
 path to the NCAA rotlib – Primary More...
 
Size ncaa_rotlib_n_rots_
 the number of non-hydrogen chi angles in the NCAA rotlib – Primary More...
 
utility::vector1< Sizencaa_rotlib_n_bins_per_rot_
 the number of rotamer bins for each chi angle in the NCAA rotlib – Primary More...
 
bool use_peptoid_rotlib_
 whether or not we should use the peptoid rotlib if it exists – Primary More...
 
std::string peptoid_rotlib_path_
 path to the peptoid rotlib – Primary More...
 
Size peptoid_rotlib_n_rots_
 the number of non-hydrogen chi angles in the peptoid rotlib – Primary More...
 
utility::vector1< Sizepeptoid_rotlib_n_bins_per_rot_
 the number of rotamer bins for each chi angle in the peptoid rotlib – Primary More...
 
ResiduePropertiesOP properties_
 Residue properties as defined in the residue topology (.params) files – Primary. More...
 
AA aa_
 standard rosetta aa-type for knowledge-based potentials, may be aa_unk – Primary More...
 
AA rotamer_aa_
 
AA backbone_aa_
 
std::string name_
 residue id – Primary, should be unique More...
 
std::string name3_
 pdb-file id, need not be unique – Primary More...
 
char name1_
 one-letter code, also not necessarily unique – Primary More...
 
std::string interchangeability_group_
 interchangeability group lets a ResidueType claim to be functionally interchangeable with any other ResidueType in the same group. This is used by the packer to decide which ResidueType from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueType and build rotamers for it. Primary. More...
 
VD root_atom_
 Atom at the nominal root of the ICOOR tree. More...
 
VD nbr_atom_
 atom used for calculating residue-level neighbors – Primary More...
 
Real nbr_radius_
 radius cutoff to define neighbors – Primary More...
 
bool force_nbr_atom_orient_
 
bool remap_pdb_atom_names_
 Should we attempt to rename atoms for this residue type when we read in PDB files? – Primary. More...
 
Real mass_
 The isotopically averaged mass of the residue – Derived. More...
 
utility::vector1
< ResidueConnection
residue_connections_
 Vector of inter-residue connections expected for this residuetype – Primary 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 – Derived. 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. – Derived. 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. – Derived. 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. – Derived. 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. – Derived. More...
 
Size lower_connect_id_
 Polymer lower connections – Derived, valid during Mutable Updated in set_lower_connect_atom() More...
 
Size upper_connect_id_
 Polymer upper connections – Derived valid during Mutable Updated in set_upper_connect_atom() More...
 
Size n_non_polymeric_residue_connections_
 Number of non-polymeric residue connections – Derived. More...
 
Size n_polymeric_residue_connections_
 Number of polymeric residue connections – Derived. More...
 
utility::vector1< VDforce_bb_
 atom indices forced to be considered backbone – Primary More...
 
core::chemical::rna::RNA_ResidueTypeOP rna_residue_type_
 A container for properties unique to RNA. – Derived, can be null. More...
 
core::chemical::carbohydrates::CarbohydrateInfoOP carbohydrate_info_
 A container for residue properties unique to carbohydrates. – Derived, can be null. More...
 
std::list< utility::vector1< ED > > rings_and_their_edges_
 All the rings and the edges. Defaulted to null until defined – Derived. More...
 
utility::vector1< Sizeatom_base_indices_
 Index version of atom_base_ – Derived. More...
 
utility::vector1< Sizeabase2_indices_
 Index version of abase2_ – Derived. More...
 
utility::vector1< AtomIndiceschi_atoms_indices_
 Index version of chi_atoms_ – Derived. More...
 
utility::vector1< AtomIndicesnu_atoms_indices_
 Index version of nu_atoms__ – Derived. More...
 
AtomIndices mainchain_atoms_indices_
 Index version of mainchain_atoms_ – Derived. More...
 
Size nbr_atom_indices_
 Index version of nbr_atom_ – Derived. More...
 
AtomIndices actcoord_atoms_indices_
 Index version of actcoord_atoms_ – Derived. More...
 
utility::vector1< AtomIndicescut_bond_neighbor_indices_
 Index version of cut_bond_neighbor_ – Primary - will be converted to derived (from Bond.cut_bond()) More...
 
utility::vector1< Sizeatom_shadowed_indices_
 Index version of atom_shadowed_ – Derived. More...
 
bool finalized_
 Is all the derived data appropriately updated? More...
 
utility::vector1< Adductdefined_adducts_
 Adducts defined for this residue – Primary. More...
 
bool nondefault_
 
std::string base_restype_name_
 

Detailed Description

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.

The data structure of a ResidueType is based on a boost::graph implementation. Vertex descriptors (VD, yeah, I know, the name is kind of bad) are the atoms, while the edge descriptors (ED, yet another bad name) are the bonds. Initially, when a ResidueType is constructed, the following primary data are set:

atom_base_; chi_atoms_; nu_atoms_; mainchain_atoms_; nbr_atom_; actcoord_atoms_; cut_bond_neighbor_; atom_shadowed_;

When this data is set, it is set based on vertex descriptors. Because vertex descriptors never change, like atom indices, there is no need to reorder this primary data; however, because Rosetta relies heavily on atom indices to access data, atom indices for the above data have to be generated. To do this, when finalized is called, a function specifically designed to generate the atom indices for the primary data is called: generate_atom_indices. This function iterates over the vertex descriptors assigned in the primary data and creates private data based on atom indices. For example, atom_base_ has atom_base_indices_. When the function atom_base(atomno) is called, the private datum atom_base_indices_ is called. This allows for the external interface of ResidueType to be accessed by atom indices while the internal functions in ResidueType work off of vertex descriptors. This also removes the need to have the former old2new reordering scheme.

Atoms: Setting of atoms includes indexing the atoms into vectors, saving their names into vectors/maps, saving the associated mm_atom_type into a vector, saving bond connections into vectors, etc, etc. On any given residue, the heavy atoms are put into the vector first, (their indices are first,) and hydrogens are put in last.

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.

Constructor & Destructor Documentation

core::chemical::ResidueType::~ResidueType ( )
virtual

destructor

References core::chemical::tr.

core::chemical::ResidueType::ResidueType ( AtomTypeSetCAP  atom_types,
ElementSetCAP  element_types,
MMAtomTypeSetCAP  mm_atom_types,
orbitals::OrbitalTypeSetCAP  orbital_types 
)

constructor

We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc.

Referenced by clone().

core::chemical::ResidueType::ResidueType ( ResidueType const &  residue_type)

Member Function Documentation

void core::chemical::ResidueType::aa ( AA const &  type)
inline

set our aa-type (could be "UNK")

References aa_.

Referenced by core::conformation::Residue::aa(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library(), core::scoring::methods::get_parallel_h_for_arg(), core::scoring::methods::get_restag(), core::scoring::dna::get_y_axis_atoms(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::constraints::is_aromatic(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::constraints::requires_CB_mapping(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::ProQPotential::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::aa ( std::string const &  type)
inline

set our aa-type (could be "UNK")

References aa_, and core::chemical::aa_from_name().

AA const& core::chemical::ResidueType::aa ( ) const
inline

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be "aa_unk".

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

References aa_.

Size core::chemical::ResidueType::abase2 ( Size const  atomno) const

get index of an atom's second base atom

References abase2_indices_, ordered_atoms_, and PyAssert.

Referenced by core::conformation::Residue::abase2().

const AcceptorAtomGraph core::chemical::ResidueType::acceptor_atoms ( )

References atom_types_, filter, graph(), and graph_.

AtomIndices const& core::chemical::ResidueType::accpt_pos ( ) const
inline

indices of atoms as Hbond acceptors

References accpt_pos_.

Referenced by core::conformation::Residue::accpt_pos().

AtomIndices const& core::chemical::ResidueType::accpt_pos_sc ( ) const
inline

indices of atoms as Hbond acceptors

References accpt_pos_sc_.

Referenced by core::conformation::Residue::accpt_pos_sc().

AtomIndices const& core::chemical::ResidueType::actcoord_atoms ( ) const
inline

get indices for atoms used to define actcoord

References actcoord_atoms_indices_.

Referenced by core::conformation::Residue::actcoord_atoms(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::add_actcoord_atom ( std::string const &  atom)

add an atom to the list for calculating actcoord center

add an atom to the list for calculating actcoord center

References actcoord_atoms_, atom_index(), finalized_, is_protein(), name(), name_, ordered_atoms_, and core::chemical::tr.

void core::chemical::ResidueType::add_adduct ( Adduct adduct_in)
inline

References defined_adducts_.

VD core::chemical::ResidueType::add_atom ( std::string const &  atom_name,
std::string const &  atom_type_name,
std::string const &  mm_atom_type_name,
Real const  charge 
)

add an atom into this residue Will return the vertex descriptor of the added atom.

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_atom().

VD core::chemical::ResidueType::add_atom ( std::string const &  atom_name = "")

add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom.

References atom_2_residue_connection_map_, atom_base_, atom_name(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, icoor_, ordered_atoms_, core::chemical::strip_whitespace(), and vd_to_index_.

void core::chemical::ResidueType::add_atom_alias ( std::string const &  rosetta_atom,
std::string const &  alias 
)
void core::chemical::ResidueType::add_bond ( std::string const &  atom_name1,
std::string const &  atom_name2,
BondName  bondLabel = SingleBond 
)
void core::chemical::ResidueType::add_bond ( VD  atom1,
VD  atom2,
BondName  bondLabel = SingleBond 
)
void core::chemical::ResidueType::add_chi ( Size const  chino,
VD  atom1,
VD  atom2,
VD  atom3,
VD  atom4 
)
void core::chemical::ResidueType::add_chi ( VD  atom1,
VD  atom2,
VD  atom3,
VD  atom4 
)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and nchi().

void core::chemical::ResidueType::add_chi ( Size const  chino,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and atom_vertex().

void core::chemical::ResidueType::add_chi ( std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

Add a chi (side-chain) angle defined by four atoms to the end of the list of chis.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with add_chi_rotamer_to_last_chi() that adds rotamer bins to the last chi in the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note
See also add_chi_rotamer_to_last_chi().
Author
Labonte

References add_chi(), and nchi().

void core::chemical::ResidueType::add_chi_rotamer ( Size const  chino,
Real const  mean,
Real const  sdev 
)

Add a rotamer bin for a given chi.

A rotamer bin has the mean and standard deviation.

References chi_rotamers_.

Referenced by add_chi_rotamer_to_last_chi(), core::chemical::AddChiRotamer::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer().

void core::chemical::ResidueType::add_chi_rotamer_to_last_chi ( core::Angle const  mean,
core::Angle const  sdev 
)

Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with the overloaded version of add_chi() that adds a new chi to the end of the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note
See also add_chi().
Author
Labonte

References add_chi_rotamer(), and nchi().

Referenced by core::chemical::AddChiRotamer::apply().

void core::chemical::ResidueType::add_cut_bond ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond

add a cut_bond between atom1 and atom2, which disallows an atom-tree connection, though the atoms are really bonded. update cut_bond_ and resize it as necessary

References atom_name_to_vd_, cut_bond_neighbor_, finalized_, graph_, has(), core::chemical::tr, and utility_exit_with_message.

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond().

void core::chemical::ResidueType::add_metalbinding_atom ( std::string const  atom_name)

Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime).

Add an atom to the list of atoms that can potentially form a bond to a metal ion.

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

References has(), metal_binding_atoms_, name3(), and utility_exit_with_message.

void core::chemical::ResidueType::add_nu ( core::uint const  nu_index,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

Add a nu (internal cyclic) angle defined by four atoms.

References atom_index(), finalized_, has(), nu_atoms_, ordered_atoms_, and utility_exit_with_message.

void core::chemical::ResidueType::add_numeric_property ( std::string const &  tag,
core::Real  value 
)

Add a numeric property.

References properties_.

void core::chemical::ResidueType::add_orbital ( std::string &  orbital_name,
std::string &  orbital_type_name 
)

add an orbital onto a residue based upon atom

Note
this does not set xyz coordiates for the added orbital but sets the index of the orbital and maps it to the type of orbital.

References finalized_, orbital_types_, orbitals_, orbitals_index_, core::chemical::strip_whitespace(), and type.

void core::chemical::ResidueType::add_orbital_bond ( std::string const &  atom_name1,
std::string const &  orbital_name 
)

add an orbital bond between an atom and an orbital.

Note
NOTE!!!!! This is indexed based upon atoms, not orbitals. That means that in your params file you must have the atom as the first and orbital as the second.

References atom_index(), atom_name_to_vd_, finalized_, graph_, has(), has_orbital(), orbitals_index_, ordered_atoms_, and utility_exit_with_message.

void core::chemical::ResidueType::add_property ( std::string const &  property)
Size core::chemical::ResidueType::add_residue_connection ( std::string const &  atom_name)

add a non-polymeric ResidueConnection

For polymeric connections, see set_lower_connect() and set_upper_connect() Doesn't set the ideal geometry – maybe it should?

References atom_index(), finalized_, n_non_polymeric_residue_connections_, ordered_atoms_, residue_connections_, and update_residue_connection_mapping().

Referenced by core::util::add_covalent_linkage_helper(), and core::chemical::AddConnect::apply().

void core::chemical::ResidueType::add_string_property ( std::string const &  tag,
std::string  value 
)

Add a string property.

References properties_.

Referenced by core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::add_variant_type ( VariantType const &  variant_type)
AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const
inline
AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const
inline
const APolarHydrogenGraph core::chemical::ResidueType::apolar_hydrogens ( )

References atom_types_, filter, and graph_.

const AromaticAtomGraph core::chemical::ResidueType::aromatic_atoms ( )

References atom_types_, filter, and graph_.

void core::chemical::ResidueType::assign_internal_coordinates ( )

Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds.

References nbr_atom_, null_vertex, ordered_atoms_, and root_atom_.

void core::chemical::ResidueType::assign_internal_coordinates ( core::chemical::VD  new_root)

@ recursive function to assign internal coordinates Note that it currently does not work well with polymers.

References graph_, n_residue_connections(), name(), null_vertex, core::chemical::reroot_restype(), root_atom_, core::chemical::tr, and utility_exit_with_message.

void core::chemical::ResidueType::assign_neighbor_atom ( )
Atom & core::chemical::ResidueType::atom ( Size const  atom_index)

References atom_index(), graph_, and ordered_atoms_.

Referenced by core::util::add_covalent_linkage_helper(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::conformation::Residue::atomic_charge(), attached_H_begin(), attached_H_end(), autodetermine_chi_bonds(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::chemical::AutomorphismIterator::can_pair(), core::io::pdb::check_and_correct_sister_atom_based_on_chirality(), core::io::pdb::check_and_correct_sister_atom_based_on_outgroup(), core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), debug_dump_icoor(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::RigidDistanceVisitor::examine_vertex(), core::chemical::find_chi_bonds(), core::chemical::find_nbr_dist(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::chemical::RerootRestypeVisitor::initialize_vertex(), core::chemical::RigidDistanceVisitor::is_nub(), core::conformation::Residue::mm_atom_name(), path_distance(), core::scoring::PQR::PQR(), core::chemical::rename_atoms(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::conformation::Residue::Residue(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::rosetta_recharge_fullatom(), core::io::pdb::score_mapping(), core::pack::task::operation::util::select_coord_for_residue(), set_atom_type(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), show(), update_derived_data(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::ResidueTypeKinWriter::write_restype(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

Atom const & core::chemical::ResidueType::atom ( Size const  atom_index) const

References atom_index(), graph_, and ordered_atoms_.

Atom & core::chemical::ResidueType::atom ( std::string const &  atom_name)

References atom_name(), atom_name_to_vd_, and graph_.

Atom const & core::chemical::ResidueType::atom ( std::string const &  atom_name) const

References atom_name_to_vd_, and graph_.

Atom & core::chemical::ResidueType::atom ( VD const  atom_vd)

References graph_, and has().

Atom const & core::chemical::ResidueType::atom ( VD const  atom_vd) const

References graph_, and has().

Size core::chemical::ResidueType::atom_base ( Size const  atomno) const
VD core::chemical::ResidueType::atom_base ( VD const  atomno) const

get vd of an atom's base atom

References atom_base_, has(), and PyAssert.

Size core::chemical::ResidueType::atom_being_shadowed ( Size  atom_shadowing) const
inline

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::scoring::methods::IdealParametersDatabase::create_parameters_for_restype().

bool core::chemical::ResidueType::atom_forms_residue_connection ( Size const  atomid)
inline

Does an atom form any inter-residue chemical bonds?

References atom_2_residue_connection_map_.

Size core::chemical::ResidueType::atom_index ( std::string const &  name) const

get atom index by name

References atom_name_to_vd_, graph_, is_protein(), name3(), ordered_atoms_, show_all_atom_names(), core::chemical::tr, and utility_exit_with_message.

Referenced by add_actcoord_atom(), core::coarse::Translator::add_atom(), add_bond(), add_nu(), add_orbital_bond(), add_residue_connection(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::gasteiger::assign_gasteiger_atom_types(), atom(), core::conformation::Residue::atom_index(), core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), delete_atom(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::RigidDistanceVisitor::examine_vertex(), core::io::pdb::fill_name_map(), core::chemical::find_nbr_dist(), generate_atom_indices(), get_metal_binding_atoms(), core::scoring::methods::get_parallel_h_for_arg(), core::conformation::get_root_atomno(), core::chemical::ICoorAtomID::ICoorAtomID(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::chemical::RerootRestypeVisitor::initialize_vertex(), core::conformation::Conformation::insert_residue_by_bond(), core::pose::named_atom_id_to_atom_id(), nbr_atom(), core::scoring::constraints::ConstraintIO::parse_atom_pair_constraint(), core::scoring::constraints::ConstraintIO::parse_coordinate_constraint(), core::scoring::constraints::parse_NMR_name_old(), core::scoring::methods::GoapEnergy::read_angle_definitions(), 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(), redefine_chi(), core::scoring::constraints::requires_CB_mapping(), core::chemical::RigidDistanceVisitor::RigidDistanceVisitor(), core::pack::task::operation::util::select_coord_for_residue(), select_orient_atoms(), set_ideal_xyz(), set_lower_connect_atom(), set_orbital_icoor_id(), set_shadowing_atom(), set_upper_connect_atom(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and core::scoring::cryst::PhenixInterface::stealBfactorsFromFile().

Size core::chemical::ResidueType::atom_index ( VD const &  vd) const

get atom index by vertex descriptor

References utility_exit_with_message, and vd_to_index_.

bool core::chemical::ResidueType::atom_is_backbone ( Size const  atomno) const
inline
bool core::chemical::ResidueType::atom_is_hydrogen ( Size const  atomno) const
inline

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 finalized_, natoms(), and nheavyatoms_.

Referenced by core::util::add_covalent_linkage_helper(), assign_neighbor_atom(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), and core::scoring::is_protein_sidechain_heavyatom().

bool core::chemical::ResidueType::atom_is_polar_hydrogen ( Size  atomno) const
inline
VIterPair core::chemical::ResidueType::atom_iterators ( ) const
inline
std::string const & core::chemical::ResidueType::atom_name ( Size const  index) const

get atom name by index

Get the atom name by index.

References graph_, ordered_atoms_, and PyAssert.

Referenced by core::coarse::Translator::add_atom(), add_atom(), core::util::add_covalent_linkage_helper(), atom(), core::conformation::Residue::atom_name(), core::io::pdb::build_pose_as_is1(), core::chemical::calculate_rigid_matrix(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::data::RNA_DMS_Potential::check_hbonded(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), dump_vd_info(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::chemical::fill_ideal_xyz_from_icoor(), core::io::pdb::fill_name_map(), core::io::silent::BinarySilentStruct::fill_struct(), core::chemical::find_bonds_in_rings(), core::chemical::find_chi_bonds(), core::chemical::find_nbr_dist(), core::chemical::formatted_icoord_tree(), core::chemical::rna::get_rna_base_centroid(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), 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(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), core::chemical::print_chis(), core::conformation::print_node(), core::pose::rna::print_torsion_info(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::reroot_restype(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), core::io::pdb::score_mapping(), set_atom_base(), set_gasteiger_atom_type(), set_mm_atom_type(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::methods::setup_water_builders_for_residue_type(), show(), core::chemical::RerootRestypeVisitor::start_vertex(), and core::chemical::write_topology_file().

std::string const & core::chemical::ResidueType::atom_name ( VD const  vd) const

get atom name by vertex descriptor

Get atom name by vertex descriptor.

References graph_, has(), and PyAssert.

AtomType const & core::chemical::ResidueType::atom_type ( Size const  atomno) const

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 atom_types_, graph_, ordered_atoms_, and PyAssert.

Referenced by core::conformation::Residue::atom_type(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), 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::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_virtual(), is_virtual(), print_bondangles(), print_dihedrals(), core::conformation::print_node(), 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::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::setup_water_builders_for_residue_type(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

AtomType const & core::chemical::ResidueType::atom_type ( VD const  vd) const

Get the chemical atom_type for this atom by it index number in this residue.

References atom_types_, graph_, ordered_atoms_, and PyAssert.

AtomTypeSet const& core::chemical::ResidueType::atom_type_set ( ) const
inline
AtomTypeSetCAP core::chemical::ResidueType::atom_type_set_ptr ( ) const
inline
VD core::chemical::ResidueType::atom_vertex ( std::string const &  name) const
VD core::chemical::ResidueType::atom_vertex ( Size const &  atomno) const

Get the vertex descriptor from the atom index.

References ordered_atoms_.

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.

Author
Vikram K. Mulligan

References nbrs().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( ) const
inline

Read access to the atoms_last_controlled_by_chi_ array.

References atoms_last_controlled_by_chi_.

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

AtomIndices const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( Size  chi) const
inline

Read access to the Atoms last controlled by a particular chi.

References atoms_last_controlled_by_chi_.

AtomIndices const& core::chemical::ResidueType::atoms_with_orb_index ( ) const
inline
utility::vector1< two_atom_set > const& core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection ( Size  resconn) const
inline
utility::vector1< three_atom_set > const& core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection ( Size  resconn) const
inline

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::methods::MMTorsionEnergy::residue_pair_energy().

Size core::chemical::ResidueType::attached_H_begin ( Size const  atom) const
inline
AtomIndices const& core::chemical::ResidueType::attached_H_begin ( ) const
inline

for all heavy atoms, index numbers of their first attached Hydrogen

References attached_H_begin_.

Size core::chemical::ResidueType::attached_H_end ( Size const  atom) const
inline

index number of the last attached Hydrogen on an atom

References atom(), and attached_H_end_.

Referenced by core::coarse::Translator::add_atom(), and core::conformation::Residue::attached_H_end().

AtomIndices const& core::chemical::ResidueType::attached_H_end ( ) const
inline

for all heavy atoms, index numbers of their last attached Hydrogen

References attached_H_end_.

void core::chemical::ResidueType::autodetermine_chi_bonds ( core::Size  max_proton_chi_samples = 500)

Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all.

Requires that Icoor and atom base records are up-to-date, and that ring bonds have been annotated.

References add_chi(), atom(), chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, core::chemical::find_chi_bonds(), core::chemical::element::H, is_proton_chi_, core::chemical::is_sp2_proton_chi(), name(), nchi(), proton_chi_extra_samples_, proton_chi_samples_, proton_chis_, set_proton_chi(), and core::chemical::tr.

void core::chemical::ResidueType::backbone_aa ( std::string const &  type)
inline
AA const& core::chemical::ResidueType::backbone_aa ( ) const
inline

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

References aa_, core::chemical::aa_unk, and backbone_aa_.

void core::chemical::ResidueType::base_restype_name ( std::string const &  in)
inline
std::string core::chemical::ResidueType::base_restype_name ( ) const
inline

References base_restype_name_.

Bond & core::chemical::ResidueType::bond ( ED const  ed)
Bond const & core::chemical::ResidueType::bond ( ED const  ed) const

References graph_.

Bond & core::chemical::ResidueType::bond ( std::string const &  atom1,
std::string const &  atom2 
)
Bond const & core::chemical::ResidueType::bond ( std::string const &  atom1,
std::string const &  atom2 
) const
EIterPair core::chemical::ResidueType::bond_iterators ( ) const
inline
OutEdgeIterPair core::chemical::ResidueType::bond_iterators ( VD const &  atom) const
inline

References graph_.

bondangle_atom_set const& core::chemical::ResidueType::bondangle ( Size const  bondang) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::bondangles_for_atom ( Size  atomno) const
inline

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().

AtomIndices const & core::chemical::ResidueType::bonded_neighbor ( Size const  atomno) const
AdjacentIterPair core::chemical::ResidueType::bonded_neighbor_iterators ( VD const &  atom) const
utility::vector1< BondName > const & core::chemical::ResidueType::bonded_neighbor_types ( Size const  atomno) const
utility::vector1<core::Size> const& core::chemical::ResidueType::bonded_orbitals ( Size const  atomno) const
inline
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(), and core::chemical::Selector_UPPER_POSITION::operator[]().

Size core::chemical::ResidueType::chi_2_proton_chi ( Size  chi_index) const
inline
VDs const& core::chemical::ResidueType::chi_atom_vds ( Size const  chino) const
inline

VDs of the atoms which are used to define a given chi angle (chino)

References chi_atoms_.

Referenced by core::chemical::is_sp2_proton_chi().

AtomIndices const& core::chemical::ResidueType::chi_atoms ( Size const  chino) const
inline
utility::vector1< AtomIndices > const& core::chemical::ResidueType::chi_atoms ( ) const
inline

indices of the atoms which are used to define all the chi angles

References chi_atoms_indices_.

Referenced by generate_atom_indices(), and update_last_controlling_chi().

utility::vector1< std::pair< Real, Real > > const& core::chemical::ResidueType::chi_rotamers ( Size const  chino) const
inline
ResidueTypeOP core::chemical::ResidueType::clone ( ) const
AtomIndices const& core::chemical::ResidueType::cut_bond_neighbor ( Size const  atomno) const
inline
void core::chemical::ResidueType::debug_dump_icoor ( ) const

Dump out atomnames and icoor values.

References atom(), atom_name(), atom_vertex(), core::chemical::Atom::ideal_xyz(), name3(), natoms(), and core::chemical::tr.

utility::vector1< Adduct > const& core::chemical::ResidueType::defined_adducts ( ) const
inline
void core::chemical::ResidueType::delete_atom ( std::string const &  name)

flag an atom for deletion by adding its index to the delete_atom_ list

References atom_index(), and has().

Referenced by core::chemical::DeleteAtom::apply().

void core::chemical::ResidueType::delete_atom ( Size const  index)

flag an atom for deletion by adding its index to the delete_atom_ list

References finalized_, graph_, and ordered_atoms_.

void core::chemical::ResidueType::delete_atom_alias ( std::string const &  alias)

Remove a given alias name for an atom.

References atom_aliases_, finalized_, core::chemical::strip_whitespace(), and utility_exit_with_message.

void core::chemical::ResidueType::delete_property ( std::string const &  property)

Add a property of this ResidueType.

This is needed for deleting properties, which occurs in certain PTMs.

References finalized_, and properties_.

Referenced by core::chemical::DeleteProperty::apply().

dihedral_atom_set const& core::chemical::ResidueType::dihedral ( Size const  dihe) const
inline

dihedral methods

Return the indices for the set of atoms that define a particular intraresidue dihedral

References dihedral_atom_sets_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), and core::scoring::methods::MMTorsionEnergy::eval_intrares_energy().

utility::vector1< Size > const& core::chemical::ResidueType::dihedrals_for_atom ( Size  atomno) const
inline

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().

void core::chemical::ResidueType::dump_vd_info ( ) const
ElementSet const& core::chemical::ResidueType::element_set ( ) const
inline

access by reference the atomset for which this residue is constructed

References elements_.

void core::chemical::ResidueType::fill_ideal_xyz_from_icoor ( )
void core::chemical::ResidueType::finalize ( )

recalculate derived data, potentially reordering atom-indices

recalculate derived data, potentially reordering atom-indices This routine updates all the derived data.
Atom order will probably change after this call, so if you add a new property that depends on atom-indices that will have to be updated below.

References finalized_, generate_atom_indices(), perform_checks(), setup_atom_ordering(), and update_derived_data().

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

Size core::chemical::ResidueType::first_sidechain_atom ( ) const
inline
Size core::chemical::ResidueType::first_sidechain_hydrogen ( ) const
inline

index of the first sidehchain hydrogen

References finalized_, and first_sidechain_hydrogen_.

Referenced by core::conformation::Residue::first_sidechain_hydrogen().

void core::chemical::ResidueType::force_nbr_atom_orient ( bool  force_orient)
inline

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by core::chemical::SetOrientAtom::apply(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::force_nbr_atom_orient ( ) const
inline

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by select_orient_atoms().

gasteiger::GasteigerAtomTypeDataCOP core::chemical::ResidueType::gasteiger_atom_type ( Size const  atomno) const

Get the MM atom_type index number for this atom by its index number in this residue.

Get the Gasteiger atom_type for this atom by its index number in this residue.

Get the MM atom_type for this atom by its index number in this residue

References graph_, and ordered_atoms_.

void core::chemical::ResidueType::generate_atom_indices ( )
private

reorder primary data in ResidueType given the old2new map, called by finalize()

The private data for ResidueType is based on vertex descriptors (VD). Rosetta relies on atom indices to access the private data. In order to keep this interface, the VDs must be converted into atom indices. These are called *_indices, where the primary data is a VD but the indices_data is the atom indices. Because the atom indices change during the setup atom ordering, we must regenerate the cached data. This would not have to occur if Rosetta relied on VDs instead of atom indices.

First, the private data that relies on atom ordering, atom_name_to_vd_ and vd_to_index_ is created by iterating over the total number of atoms in the graph.

Second, the bonded neighbors are generated based on the graph structure.

Finally, all the cached data is generated by iterating over the VDs.

– Assumes that ordered_atoms_ is updated appropriately. Derived data set in this method: atom_name_to_vd_ vd_to_index_ atom_base_indices_ chi_atoms_indices_ nu_atoms_indices_ mainchain_atoms_indices_ nbr_atom_indices_ actcoord_atoms_indices_ cut_bond_neighbor_indices_ atom_shadowed_indices_ bonded_neighbor_ bonded_neighbor_type_ atom_2_residue_connection_map_

References actcoord_atoms_, actcoord_atoms_indices_, atom_2_residue_connection_map_, atom_aliases_, atom_base_, atom_base_indices_, atom_index(), atom_name_to_vd_, atom_shadowed_, atom_shadowed_indices_, core::chemical::ICoorAtomID::atomno(), bond(), bonded_neighbor_, bonded_neighbor_type_, bonded_orbitals(), chi_atoms(), chi_atoms_, chi_atoms_indices_, cut_bond_neighbor_, cut_bond_neighbor_indices_, graph_, icoor_, core::chemical::ICoorAtomID::INTERNAL, mainchain_atoms_, mainchain_atoms_indices_, name(), natoms(), nbr_atom_, nbr_atom_indices_, nu_atoms_, nu_atoms_indices_, orbitals_, ordered_atoms_, residue_connections_, core::chemical::strip_whitespace(), core::chemical::AtomICoor::stub_atom(), target, core::chemical::ICoorAtomID::type(), update_residue_connection_mapping(), vd_to_index_, and core::chemical::ICoorAtomID::vertex().

Referenced by finalize().

void core::chemical::ResidueType::get_metal_binding_atoms ( AtomIndices metal_binding_indices) const
inline

Gets indices of all atoms that can form bonds to metals.

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

References atom_index(), has(), and metal_binding_atoms_.

Referenced by core::conformation::Residue::get_metal_binding_atoms().

Size core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot ( Size  n_rot)
inline

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for a single bond.

References ncaa_rotlib_n_bins_per_rot_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library().

utility::vector1<Size> const& core::chemical::ResidueType::get_ncaa_rotlib_n_bin_per_rot ( ) const
inline

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds.

References ncaa_rotlib_n_bins_per_rot_.

std::string const& core::chemical::ResidueType::get_ncaa_rotlib_path ( ) const
inline

Returns the path to the NCAA rotlib for the residue type.

References ncaa_rotlib_path_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library().

core::Real core::chemical::ResidueType::get_numeric_property ( std::string const &  tag) const

Get a numeric property, if it exists.

References name3_, and properties_.

Size core::chemical::ResidueType::get_peptoid_rotlib_n_bin_per_rot ( Size  n_rot)
inline

Returns the number of rotamers for each rotatable bond described by the peptoid rotlib for a single bond.

References peptoid_rotlib_n_bins_per_rot_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_peptoid_rotamer_library().

utility::vector1<Size> const& core::chemical::ResidueType::get_peptoid_rotlib_n_bin_per_rot ( ) const
inline

Returns the number of rotamers for each rotatable bond described by the peptoid rotlib for all bonds.

References peptoid_rotlib_n_bins_per_rot_.

std::string const& core::chemical::ResidueType::get_peptoid_rotlib_path ( ) const
inline

Returns the path to the peptoid rotlib for the residue type.

References peptoid_rotlib_path_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_peptoid_rotamer_library().

std::string core::chemical::ResidueType::get_RotamerLibraryName ( ) const

A residue parameter file can refer to a set of "pdb rotamers" that can be superimposed onto a starting position for use in the packer. These rotamers are loaded into the pack::dunbrack::RotamerLibrary at the time of their first use.

References rotamer_library_name_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library(), and core::chemical::ResidueDatabaseIO::report_residue_type().

std::string core::chemical::ResidueType::get_string_property ( std::string const &  tag) const

Get a string property, if it exists.

References name3_, and properties_.

bool core::chemical::ResidueType::get_use_ncaa_rotlib ( ) const
inline

Returns whether we are using a NCAA rotlib for the residue type.

References use_ncaa_rotlib_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library().

bool core::chemical::ResidueType::get_use_peptoid_rotlib ( ) const
inline

Returns whether we are using a peptoid rotlib for the residue type.

References use_peptoid_rotlib_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library().

ResidueGraph const& core::chemical::ResidueType::graph ( ) const
inline
AtomIndices const& core::chemical::ResidueType::Haro_index ( ) const
inline

return indices of aromatic Hydrogens

References Haro_index_.

Referenced by core::conformation::Residue::Haro_index().

bool core::chemical::ResidueType::has ( std::string const &  atom_name) const
inline

is this atom present in this residue?

References atom_name_to_vd_.

Referenced by core::coarse::Translator::add_atom(), add_atom_alias(), add_bond(), add_chi(), core::util::add_covalent_linkage_helper(), add_cut_bond(), add_metalbinding_atom(), add_nu(), add_orbital_bond(), core::pack::task::operation::util::any_atoms_within_cutoff(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddConnect::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), atom(), atom_base(), atom_name(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), delete_atom(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), dump_vd_info(), core::io::pdb::fill_name_map(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), get_metal_binding_atoms(), core::conformation::Residue::has(), core::chemical::has_assigned_coords(), icoor(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::sdf::MolFileIOMolecule::index_valid(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::is_disulfide_bond(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::place(), core::chemical::pretty_print_atomicoor(), core::scoring::methods::GoapEnergy::read_angle_definitions(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), redefine_chi(), core::chemical::reroot_restype(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::pack::task::operation::util::select_coord_for_residue(), set_atom_base(), set_atom_type(), set_backbone_heavyatom(), set_ideal_xyz(), core::scoring::setup_matching_atoms_with_given_names(), core::chemical::RerootRestypeVisitor::start_vertex(), and core::coarse::Translator::Translator().

bool core::chemical::ResidueType::has ( VD const  vd) const
inline

is this vertex descriptor present in this residue?

References graph_, and core::chemical::has().

bool core::chemical::ResidueType::has_orbital ( std::string const &  orbital_name) const
inline

is this orbital present in this residue?

References orbitals_index_.

Referenced by add_orbital_bond().

bool core::chemical::ResidueType::has_property ( std::string const &  property) const
bool core::chemical::ResidueType::has_sc_orbitals ( ) const

does this residue have sidechain orbitals?

References properties_, and core::chemical::SC_ORBITALS.

Referenced by core::conformation::Residue::has_sc_orbitals().

bool core::chemical::ResidueType::has_variant_type ( VariantType const &  variant_type) const
const HeavyAtomWithHydrogensGraph core::chemical::ResidueType::heavy_atom_with_hydrogens ( )

References atom_types_, filter, graph(), and graph_.

const HeavyAtomWithPolarHydrogensGraph core::chemical::ResidueType::heavy_atom_with_polar_hydrogens ( )

References atom_types_, filter, graph(), and graph_.

const HeavyAtomGraph core::chemical::ResidueType::heavy_atoms ( )

References atom_types_, filter, and graph_.

bool core::chemical::ResidueType::heavyatom_has_polar_hydrogens ( Size  atomno) const
inline
bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size  atomno) const
inline
AtomIndices const& core::chemical::ResidueType::Hpol_index ( ) const
inline

return indices of polar Hydrogens

References Hpol_index_.

Referenced by core::conformation::Residue::Hpol_index().

AtomIndices const& core::chemical::ResidueType::Hpos_apolar ( ) const
inline

indices of non-polar hydrogens as potential carbon Hbond donors

References Hpos_apolar_.

Referenced by core::conformation::Residue::Hpos_apolar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar ( ) const
inline

indices of polar hydrogens as Hbond donors

References Hpos_polar_.

Referenced by core::conformation::Residue::Hpos_polar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar_sc ( ) const
inline
const HydrogenAtomGraph core::chemical::ResidueType::hydrogens ( )

References atom_types_, filter, and graph_.

Referenced by setup_atom_ordering().

AtomICoor const & core::chemical::ResidueType::icoor ( Size const  atm) const
AtomICoor const & core::chemical::ResidueType::icoor ( VD const  atm) const

AtomICoord of an atom.

References has(), and icoor_.

dihedral_atom_set const& core::chemical::ResidueType::improper_dihedral ( Size const  dihe) const
inline

Return the indices for the set of atoms that define a particular.

intraresidue improper dihedral

References improper_dihedral_atom_sets_.

utility::vector1< Size > const& core::chemical::ResidueType::improper_dihedrals_for_atom ( Size  atomno) const
inline

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 improper_dihedrals_for_atom_.

std::string core::chemical::ResidueType::interchangeability_group ( ) const
inline

get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes 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 ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag.

References interchangeability_group_.

Referenced by core::chemical::SetInterchangeabilityGroup_String::apply(), core::chemical::AppendInterchangeabilityGroup_String::apply(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::interchangeability_group ( std::string  setting)
inline

set our interchangeability-group id

References interchangeability_group_.

bool core::chemical::ResidueType::is_acetylated_nterminus ( ) const

is acetylated n terminus

References core::chemical::ACETYLATED_NTERMINUS, and properties_.

bool core::chemical::ResidueType::is_adduct ( ) const

is an adduct-modified residue?

References core::chemical::ADDUCT, and properties_.

bool core::chemical::ResidueType::is_alpha_aa ( ) const
bool core::chemical::ResidueType::is_aromatic ( ) const
bool core::chemical::ResidueType::is_beta_aa ( ) const

is this a beta amino acid?

References core::chemical::BETA_AA, and properties_.

Referenced by core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_branch_lower_terminus ( ) const
bool core::chemical::ResidueType::is_carbohydrate ( ) const
bool core::chemical::ResidueType::is_charged ( ) const
bool core::chemical::ResidueType::is_coarse ( ) const
bool core::chemical::ResidueType::is_cyclic ( ) const

is cyclic?

References core::chemical::CYCLIC, and properties_.

bool core::chemical::ResidueType::is_d_aa ( ) const

is this a d-amino acid?

References core::chemical::D_AA, and properties_.

Referenced by core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_DNA ( ) const
bool core::chemical::ResidueType::is_l_aa ( ) const

is this an l-amino acid?

References core::chemical::L_AA, and properties_.

Referenced by core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_ligand ( ) const
bool core::chemical::ResidueType::is_lipid ( ) const

is lipid?

References core::chemical::LIPID, and properties_.

bool core::chemical::ResidueType::is_lower_terminus ( ) const
bool core::chemical::ResidueType::is_membrane ( ) const

is membrane?

References core::chemical::MEMBRANE, and properties_.

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.

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

References core::chemical::METAL, and properties_.

Referenced by core::util::add_covalent_linkage_helper(), core::conformation::Residue::is_metal(), perform_checks(), and core::chemical::write_topology_file().

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.

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

References core::chemical::METALBINDING, and properties_.

Referenced by core::conformation::Residue::is_metalbinding(), perform_checks(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_methylated_cterminus ( ) const

is methylated c terminus

References core::chemical::METHYLATED_CTERMINUS, and properties_.

bool core::chemical::ResidueType::is_NA ( ) const
bool core::chemical::ResidueType::is_peptoid ( ) const
bool core::chemical::ResidueType::is_polar ( ) const
bool core::chemical::ResidueType::is_polymer ( ) const
bool core::chemical::ResidueType::is_protein ( ) const
bool core::chemical::ResidueType::is_proton_chi ( Size const  chino) const
inline
bool core::chemical::ResidueType::is_RNA ( ) const
bool core::chemical::ResidueType::is_surface ( ) const
bool core::chemical::ResidueType::is_terminus ( ) const
bool core::chemical::ResidueType::is_upper_terminus ( ) const
bool core::chemical::ResidueType::is_virtual ( Size const &  atomno) const

Check if atom is virtual.

References atom_type().

Referenced by n_virtual_atoms(), and perform_checks().

bool core::chemical::ResidueType::is_virtual_residue ( ) const

Check if residue is 'VIRTUAL_RESIDUE'.

References properties_, and core::chemical::VIRTUAL_RESIDUE.

Referenced by core::conformation::Residue::is_virtual_residue().

Size core::chemical::ResidueType::last_backbone_atom ( ) const
inline

index of the last backbone heavy atom

References n_backbone_heavyatoms_.

Referenced by core::conformation::Residue::last_backbone_atom().

utility::vector1< Size > const& core::chemical::ResidueType::last_controlling_chi ( ) const
inline

Read access to the last_controlling_chi_ array.

References last_controlling_chi_.

Size core::chemical::ResidueType::last_controlling_chi ( Size  atomno) const
inline

The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.

References last_controlling_chi_.

ResidueConnection const & core::chemical::ResidueType::lower_connect ( ) const
Size core::chemical::ResidueType::lower_connect_atom ( ) const
Size core::chemical::ResidueType::lower_connect_id ( ) const
inline
Size core::chemical::ResidueType::mainchain_atom ( Size const  atm) const
inline
AtomIndices const& core::chemical::ResidueType::mainchain_atoms ( ) const
inline
core::Real const& core::chemical::ResidueType::mass ( ) const
inline

get the molecular weight of this residue

References mass_.

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

MMAtomType const & core::chemical::ResidueType::mm_atom_type ( Size const  atomno) const
Size core::chemical::ResidueType::n_hbond_acceptors ( ) const
inline

number of hbond_acceptors

References n_hbond_acceptors_.

Referenced by core::conformation::Residue::n_hbond_acceptors().

Size core::chemical::ResidueType::n_hbond_donors ( ) const
inline

number of hbond_donors

References n_hbond_donors_.

Referenced by core::conformation::Residue::n_hbond_donors().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections ( ) const
inline
Size core::chemical::ResidueType::n_nus ( ) const
inline

Return number of nu (internal ring) angles.

References nu_atoms_.

Referenced by core::conformation::Residue::n_nus(), core::conformation::Residue::Residue(), and core::chemical::write_topology_file().

Size core::chemical::ResidueType::n_orbitals ( ) const

number of orbitals

References orbitals_.

Referenced by core::conformation::Residue::n_orbitals().

Size core::chemical::ResidueType::n_polymeric_residue_connections ( ) const
inline
Size core::chemical::ResidueType::n_proton_chi ( ) const
inline
Size core::chemical::ResidueType::n_residue_connections ( ) const
Size core::chemical::ResidueType::n_residue_connections_for_atom ( Size const  atomid) const
inline
Size core::chemical::ResidueType::n_virtual_atoms ( ) const

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.

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

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.

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

References is_virtual(), and natoms().

Referenced by core::util::add_covalent_linkage_helper(), and core::conformation::Residue::n_virtual_atoms().

std::string const& core::chemical::ResidueType::name ( ) const
inline

get our (unique) residue name

References name_.

Referenced by add_actcoord_atom(), core::util::add_covalent_linkage_helper(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), core::conformation::Conformation::append_residue_by_bond(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::Patch::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::apply_adducts_to_residue(), assign_internal_coordinates(), assign_neighbor_atom(), autodetermine_chi_bonds(), core::scoring::automorphic_rmsd(), bond(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::chemical::calculate_rigid_matrix(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::pack::rotamer_set::debug_dump_rotamers(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), dump_vd_info(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::chemical::fill_ideal_xyz_from_icoor(), core::conformation::Residue::fill_missing_atoms(), core::chemical::find_nbr_dist(), generate_atom_indices(), core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::chemical::has_assigned_coords(), core::chemical::ICoorAtomID::ICoorAtomID(), core::scoring::FACTSPoseInfo::initialize(), core::scoring::FACTSRotamerSetInfo::initialize(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::methods::LKB_ResidueInfo::initialize_residue_type(), core::pack::dunbrack::load_unboundrot(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::conformation::Residue::name(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::chemical::pretty_print_atomicoor(), core::chemical::print_chis(), core::coarse::CoarseEtable::print_residue_info(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::io::pdb::remap_names_on_geometry(), core::pose::remove_virtual_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::chemical::rosetta_recharge_fullatom(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), select_orient_atoms(), set_atom_base(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::import_pose::set_reasonable_fold_tree(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::setup_water_builders_for_residue_type(), core::chemical::RerootRestypeVisitor::start_vertex(), core::util::switch_to_residue_type_set(), core::coarse::Translator::Translator(), core::coarse::TranslatorSet::TranslatorSet(), core::io::serialization::write_binary(), core::chemical::ResidueTypeKinWriter::write_kin_header(), core::chemical::ResidueDatabaseIO::write_residuetype_to_database(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::name ( std::string const &  name_in)
inline

set our (unique) residue name

References name_.

char core::chemical::ResidueType::name1 ( ) const
inline
void core::chemical::ResidueType::name1 ( char const  code)
inline

set our 1letter code

References name1_.

std::string const& core::chemical::ResidueType::name3 ( ) const
inline

get our 3letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name1 string

References name3_.

Referenced by core::util::add_covalent_linkage_helper(), add_metalbinding_atom(), core::pack::task::operation::OptCysHG::apply(), core::chemical::SetIO_String::apply(), atom_index(), atom_vertex(), core::chemical::AutomorphismIterator::can_pair(), core::pose::full_model_info::check_full_model_info_OK(), debug_dump_icoor(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::io::pdb::fill_name_map(), core::pack::dunbrack::RotamerLibrary::get_NCAA_rotamer_library(), core::pack::dunbrack::RotamerLibrary::get_peptoid_rotamer_library(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::is_similar_rotamer(), core::conformation::Residue::name3(), core::pack::task::operation::ResidueName3Is::operator()(), core::chemical::Selector_NAME3::operator[](), orbital_index(), core::scoring::constraints::parse_NMR_name_old(), core::conformation::print_node(), core::chemical::ResidueDatabaseIO::read_residue_type(), report_adducts(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::conformation::setup_corresponding_atoms(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::scoring::hbonds::HBond::show(), core::util::switch_to_residue_type_set(), core::coarse::TranslatorSet::TranslatorSet(), core::chemical::ResidueTypeKinWriter::write_kin_header(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::name3 ( std::string const &  name_in)
inline

set our 3letter code

References name3_.

Size core::chemical::ResidueType::natoms ( ) const
inline

number of atoms

References graph_.

Referenced by core::conformation::annotated_atom_graph_from_conformation(), core::pose::Pose::apply_transform_Rx_plus_v(), core::conformation::Residue::apply_transform_Rx_plus_v(), core::conformation::atom_graph_from_conformation(), atom_is_backbone(), atom_is_hydrogen(), core::scoring::automorphic_rmsd(), core::chemical::AutomorphismIterator::AutomorphismIterator(), core::pose::copydofs::blank_atom_id_domain_map(), 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::io::pdb::build_pose_as_is1(), core::scoring::calc_per_res_hydrophobic_sasa(), core::chemical::calculate_rigid_matrix(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::chemical::fill_ideal_xyz_from_icoor(), fill_ideal_xyz_from_icoor(), core::chemical::find_nbr_dist(), first_sidechain_atom(), core::chemical::formatted_icoord_tree(), generate_atom_indices(), core::scoring::methods::get_parallel_h_for_arg(), core::chemical::get_residue_path_distances(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::pose::initialize_atomid_map(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), n_virtual_atoms(), core::conformation::Residue::natoms(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::orient_onto_residue_peptoid(), 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::conformation::symmetry::recenter(), core::io::pdb::remap_names_on_geometry(), 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::chemical::reroot_restype(), core::conformation::Residue::Residue(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), ResidueType(), core::io::pdb::score_mapping(), select_orient_atoms(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::GoapRsdType::setup_connectivity(), core::scoring::methods::setup_water_builders_for_residue_type(), show(), core::scoring::superimpose_pose(), update_derived_data(), update_last_controlling_chi(), update_residue_connection_mapping(), core::chemical::ResidueTypeKinWriter::write_restype(), core::chemical::write_topology_file(), and core::fragment::xform_pose().

Size core::chemical::ResidueType::nbonds ( ) const
inline

number of bonds

References graph_.

Size core::chemical::ResidueType::nbonds ( Size  atom) const
inline

number of bonds for given atom

References graph_, and ordered_atoms_.

Size core::chemical::ResidueType::nbonds ( VD  atom) const
inline

number of bonds for given atom

References graph_.

void core::chemical::ResidueType::nbr_atom ( std::string const &  atom_name)
inline
void core::chemical::ResidueType::nbr_atom ( VD  vertex)
inline

set nbr_atom used to define residue-level neighbors

References atom_index(), nbr_atom_, and nbr_atom_indices_.

Size core::chemical::ResidueType::nbr_atom ( ) const
inline

get nbr_atom used to define residue-level neighbors

References nbr_atom_indices_.

Referenced by assign_neighbor_atom(), and select_orient_atoms().

void core::chemical::ResidueType::nbr_radius ( Real const  radius)
inline
Real core::chemical::ResidueType::nbr_radius ( ) const
inline

get nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

VD core::chemical::ResidueType::nbr_vertex ( ) const
inline

get VD used to define residue-level neighbors

References nbr_atom_.

AtomIndices const& core::chemical::ResidueType::nbrs ( Size const  atomno) const
inline
Size core::chemical::ResidueType::nchi ( ) const
inline
Size core::chemical::ResidueType::ndihe ( ) const
inline

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::methods::MMTorsionEnergy::eval_intrares_energy(), and print_dihedrals().

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::new_orbital_icoor_data ( Size const  orbital_index) const
Size core::chemical::ResidueType::nheavyatoms ( ) const
inline
bool core::chemical::ResidueType::nonadduct_variants_match ( ResidueType const &  other) const
void core::chemical::ResidueType::nondefault ( bool  in)
inline
void core::chemical::ResidueType::note_chi_controls_atom ( Size  chi,
Size  atomno 
)
private

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().

AtomIndices const& core::chemical::ResidueType::nu_atoms ( core::uint const  nu_index) const
inline

Return indices of the atoms used to define a given nu (internal ring) angle.

References nu_atoms_indices_.

Referenced by core::conformation::Residue::nu_atoms(), core::conformation::Residue::Residue(), and core::chemical::write_topology_file().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::nu_atoms ( ) const
inline

Return list of indices of the atoms used to define all the nu (internal ring) angles.

References nu_atoms_indices_.

Size core::chemical::ResidueType::num_bondangles ( ) const
inline
Size core::chemical::ResidueType::number_bonded_heavyatoms ( Size const  atomno) const

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().

Size core::chemical::ResidueType::number_bonded_hydrogens ( Size const  atomno) const
inline

indicates how many proton bonded neighbors an atom has

References attached_H_begin_, and attached_H_end_.

Referenced by number_bonded_heavyatoms(), and core::scoring::orbitals::surrogate_atom_for_orbital().

Orbital const & core::chemical::ResidueType::orbital ( Size const  orbital_index) const
Orbital const & core::chemical::ResidueType::orbital ( std::string const &  orbital_name) const

References orbital_index(), and orbitals_.

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::orbital_icoor_data ( Size const  orbital_index) const

References orbital_index(), and orbitals_.

core::Size core::chemical::ResidueType::orbital_index ( std::string const &  name) const
orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type ( int const  orbital_index) const
void core::chemical::ResidueType::order_atoms ( )
private

GRAPH FUNCTION to provide backward compatibility ////////.

int core::chemical::ResidueType::path_distance ( Size  at1,
Size  at2 
) const
inline
utility::vector1< int > const& core::chemical::ResidueType::path_distance ( Size  atom) const
inline

shortest path distance for an atom to all other residue atoms

References atom(), and path_distance_.

utility::vector1< utility::vector1< int > > const& core::chemical::ResidueType::path_distances ( ) const
inline

accessor of path_distance_ data for this residue, which is a 2D array

References path_distance_.

Referenced by core::conformation::Residue::path_distances(), and update_derived_data().

void core::chemical::ResidueType::perform_checks ( )
private

Final check of ResidueType data, called by finalize().

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

These checks are meant to be quick and low-expense, and are only called on finalize(), so they shouldn't generally add much to Rosetta processing time.

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

References core::chemical::aa_unk, core::chemical::ALPHA_AA, backbone_aa_, core::chemical::BETA_AA, core::chemical::D_AA, is_metal(), is_metalbinding(), is_virtual(), core::chemical::L_AA, metal_binding_atoms_, nheavyatoms_, properties_, and utility_exit_with_message.

Referenced by finalize().

const PolarHydrogenGraph core::chemical::ResidueType::polar_hydrogens ( )

References atom_types_, filter, and graph_.

void core::chemical::ResidueType::print_bondangles ( ) const
void core::chemical::ResidueType::print_dihedrals ( ) const
void core::chemical::ResidueType::print_pretty_path_distances ( ) const

print chemical-bond path distances to standard out

References graph_, natoms(), ordered_atoms_, path_distance_, and core::chemical::tr.

ResidueProperties const & core::chemical::ResidueType::properties ( ) const

Access the collection of properties for this ResidueType.

References properties_.

Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_properties().

Size core::chemical::ResidueType::proton_chi_2_chi ( Size  proton_chi_id) const
inline

translate proton_chi to global chi

References proton_chis_.

Referenced by core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().

utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_extra_samples ( Size  proton_chi) const
inline
utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_samples ( Size  proton_chi) const
inline
void core::chemical::ResidueType::redefine_chi ( Size const  chino,
std::string const &  atom_name1,
std::string const &  atom_name2,
std::string const &  atom_name3,
std::string const &  atom_name4 
)

redefine a chi angle based on four atoms

This function is almost an exact copy of the add_chi function except that vector resizing does NOT occur. It is needed for certain PTMs that affect proton chis (e.g., phosphorylation and sulfation).

Author
Andy M. Chen (June 2009)

References atom_index(), chi_2_proton_chi_, chi_atoms_, finalized_, has(), is_proton_chi_, ordered_atoms_, and utility_exit_with_message.

Referenced by core::chemical::RedefineChi::apply().

void core::chemical::ResidueType::remap_pdb_atom_names ( bool  rename)
inline

Turn on geometry-based atom renaming when loading this residue type from PDB files.

References remap_pdb_atom_names_.

Referenced by core::io::pdb::fill_name_map(), and core::chemical::rename_atoms().

bool core::chemical::ResidueType::remap_pdb_atom_names ( ) const
inline

Are we using geometry-based atom renaming when loading this residue type from PDB.

References remap_pdb_atom_names_.

void core::chemical::ResidueType::report_adducts ( )
void core::chemical::ResidueType::require_final ( ) const
inline

an assertion function to ensure an ResidueType has been finalized

References finalized_, and utility_exit_with_message.

bool core::chemical::ResidueType::requires_actcoord ( ) const
Size core::chemical::ResidueType::residue_connect_atom_index ( Size const  resconn_id) const
ResidueConnection const & core::chemical::ResidueType::residue_connection ( Size const  i) const
ResidueConnection & core::chemical::ResidueType::residue_connection ( Size const  i)

References residue_connections_.

Size core::chemical::ResidueType::residue_connection_id_for_atom ( Size const  atomid) const
inline
bool core::chemical::ResidueType::residue_connection_is_polymeric ( Size const  resconn_id) const
inline
utility::vector1< Size > const& core::chemical::ResidueType::residue_connections_for_atom ( Size const  atomid) const
inline
ResidueTypeSet const & core::chemical::ResidueType::residue_type_set ( ) const
void core::chemical::ResidueType::residue_type_set ( ResidueTypeSetCAP  set_in)

set the residue type set of origin.

References residue_type_set_.

core::chemical::RingConformerSetCOP core::chemical::ResidueType::ring_conformer_set ( ) const

Return a pointer to the object containing the set of ring conformers possible for this cyclic residue.

References conformer_set_.

std::list<utility::vector1<ED> > const& core::chemical::ResidueType::rings ( )
inline
core::chemical::rna::RNA_ResidueType const & core::chemical::ResidueType::RNA_type ( ) const
VD core::chemical::ResidueType::root_atom ( ) const
inline

get root_atom used as the base of the icoor tree.

References root_atom_.

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

void core::chemical::ResidueType::rotamer_aa ( AA const &  type)
inline
void core::chemical::ResidueType::rotamer_aa ( std::string const &  type)
inline

AA to use for rotamer library.

References core::chemical::aa_from_name(), and rotamer_aa_.

AA const& core::chemical::ResidueType::rotamer_aa ( ) const
inline
void core::chemical::ResidueType::select_orient_atoms ( Size center,
Size nbr1,
Size nbr2 
) const
void core::chemical::ResidueType::set_adduct_flag ( bool  adduct_in)
void core::chemical::ResidueType::set_atom_base ( std::string const &  atom_name1,
std::string const &  atom_name2 
)

sets atom_base[ atom1 ] = atom2

sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary

References atom_name_to_vd_, has(), name(), core::chemical::tr, and utility_exit_with_message.

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

void core::chemical::ResidueType::set_atom_base ( VD const &  atom1,
VD const &  atom2 
)

sets atom_base[ atom1 ] = atom2, vertex descriptor version

sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary

References atom_base_, atom_name(), cut_bond_neighbor_, finalized_, graph_, has(), core::chemical::tr, and utility_exit_with_message.

void core::chemical::ResidueType::set_atom_type ( std::string const &  atom_name,
std::string const &  atom_type_name 
)
inline
void core::chemical::ResidueType::set_atom_type ( VD  atom,
std::string const &  atom_type_name 
)
void core::chemical::ResidueType::set_backbone_heavyatom ( std::string const &  name)

set an atom as backbone heavy atom

backbone stuff is a little tricky if we want to allow newly added atoms, eg in patching, to be backbone atoms. We move any exsiting backbone heavy atoms back into force_bb_ list and add the new one. Afterwards, the new backbone heavy atom list will be generated in finalize() using info from force_bb_.

References atom_name_to_vd_, finalized_, force_bb_, has(), and utility_exit_with_message.

Referenced by core::chemical::SetBackboneHeavyatom::apply().

void core::chemical::ResidueType::set_gasteiger_atom_type ( std::string const &  atom_name,
std::string const &  gasteiger_atom_type_name 
)
void core::chemical::ResidueType::set_gasteiger_typeset ( gasteiger::GasteigerAtomTypeSetCOP  gasteiger_atom_types)

Manually set the gasteiger typeset - will use the default set otherwise.

References gasteiger_atom_types_.

void core::chemical::ResidueType::set_icoor ( std::string const &  atm,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3,
bool const  update_xyz = false 
)
void core::chemical::ResidueType::set_icoor ( VD const &  atm,
Real const  phi,
Real const  theta,
Real const  d,
VD const &  stub_atom1,
VD const &  stub_atom2,
VD const &  stub_atom3,
bool const  update_xyz = false 
)

set AtomICoor for an atom, vertex descriptor version

phi and theta are in radians

void core::chemical::ResidueType::set_ideal_xyz ( std::string const &  atm,
Vector const &  xyz_in 
)
void core::chemical::ResidueType::set_ideal_xyz ( Size  index,
Vector const &  xyz_in 
)
void core::chemical::ResidueType::set_ideal_xyz ( VD  atm,
Vector const &  xyz_in 
)
void core::chemical::ResidueType::set_lower_connect_atom ( std::string const &  atm_name)
void core::chemical::ResidueType::set_mainchain_atoms ( AtomIndices const &  mainchain)
void core::chemical::ResidueType::set_mm_atom_type ( std::string const &  atom_name,
std::string const &  mm_atom_type_name 
)
void core::chemical::ResidueType::set_ncaa_rotlib_n_bin_per_rot ( utility::vector1< Size n_bins_per_rot)

Sets the number of rotamers for each rotatable bond described by the NCAA rotlib.

References ncaa_rotlib_n_bins_per_rot_, and ncaa_rotlib_n_rots_.

void core::chemical::ResidueType::set_ncaa_rotlib_n_rotameric_bins ( Size  n_rots)
inline

Sets the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

References ncaa_rotlib_n_rots_.

Size core::chemical::ResidueType::set_ncaa_rotlib_n_rotameric_bins ( ) const
inline

Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

References ncaa_rotlib_n_rots_.

void core::chemical::ResidueType::set_ncaa_rotlib_path ( std::string const &  path)
inline

Sets the path for the NCAA rotlib for the ResidueType.

References ncaa_rotlib_path_.

Referenced by core::chemical::NCAARotLibPath::apply().

void core::chemical::ResidueType::set_orbital_icoor_id ( std::string const &  orbital,
Real const  phi,
Real const  theta,
Real const  d,
std::string const &  stub_atom1,
std::string const &  stub_atom2,
std::string const &  stub_atom3 
)

set OrbitalICoor for an orbital

References atom_index(), orbital_index(), orbitals_, ordered_atoms_, s1, and s2.

void core::chemical::ResidueType::set_peptoid_rotlib_n_bin_per_rot ( utility::vector1< Size n_bins_per_rot)

Sets the number of rotamers for each rotatable bond described by the peptoid rotlib.

References peptoid_rotlib_n_bins_per_rot_, and peptoid_rotlib_n_rots_.

void core::chemical::ResidueType::set_peptoid_rotlib_n_rotameric_bins ( Size  n_rots)
inline

Sets the number of rotatable bonds described by the peptoid rotlib (not nesesarily equal to nchi)

References peptoid_rotlib_n_rots_.

Size core::chemical::ResidueType::set_peptoid_rotlib_n_rotameric_bins ( ) const
inline

Returns the number of rotatable bonds described by the peptoid rotlib (not nesesarily equal to nchi)

References peptoid_rotlib_n_rots_.

void core::chemical::ResidueType::set_peptoid_rotlib_path ( std::string const &  path)
inline

Sets the path for the peptoid rotlib for the ResidueType.

DOUG DOUG DOUG

References peptoid_rotlib_path_.

void core::chemical::ResidueType::set_proton_chi ( Size  chino,
utility::vector1< Real > const &  dihedral_samples,
utility::vector1< Real > const &  extra_samples 
)

Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior.

Describe proton behavior for residue type; where should rotamer samples be considered, and if expanded rotamers are desired, what deviations from the original rotamer samples should be included. E.g. dihedral_samples of 60, -60, and 180 could have an extra_sample of 20 which would produce rotamers at 40 60 & 80, -40 -60 & -80, and -160, 180 & 160. Extra_samples at 10 and 20 would produce 15 different rotamer samples.

References chi_2_proton_chi_, is_proton_chi_, nchi(), proton_chi_extra_samples_, proton_chi_samples_, proton_chis_, and utility_exit_with_message.

Referenced by core::chemical::AddProtonChi::apply(), and autodetermine_chi_bonds().

void core::chemical::ResidueType::set_RotamerLibraryName ( std::string const &  filename)
void core::chemical::ResidueType::set_shadowing_atom ( std::string const &  atom,
std::string const &  atom_being_shadowed 
)
void core::chemical::ResidueType::set_upper_connect_atom ( std::string const &  atm_name)
void core::chemical::ResidueType::set_use_ncaa_rotlib ( bool  flag)
inline

Sets whether we are using a NCAA rotlib for the residue type.

References use_ncaa_rotlib_.

Referenced by core::chemical::NCAARotLibPath::apply().

void core::chemical::ResidueType::set_use_peptoid_rotlib ( bool  flag)
inline

Sets whether we are using a peptoid rotlib for the residue type.

References use_peptoid_rotlib_.

void core::chemical::ResidueType::setup_atom_ordering ( )
private

set up atom ordering map old2new, called by finalize()

Because some new heavy atoms are added and removed by patching we need to reorder the atoms. The atoms are reordered with the backbone atoms coming first, sidechain atoms second, and finaly hydrogens last.

The graph is iterated over, where bb atoms are defined by the force_bb_ map. If a hydrogen is encountered, it is pushed into the hydrogen vector. If the backbone is not found in the force_bb_ map, then the atom is a side chain atom, if not a hydrogen.

During this process, the attached_H_end and attached_H_begin vectors are filled out.

In order to keep the bb hydrogen atoms first in the hydrogen vector, only the heavy sidechain atoms are assigned to the sidechain vector while bb hydorgens atoms are pushed into the hydrogen vectors.

After the bb and sidechain vectors are assigned, the sidechains are iterated over and their hydrogens are pushed into the hydrogen vector.

Finally, the ordered_atoms_ vector is filled out with the bb atoms, sidechain, and hydrogen atoms.

Derived data set in this method: ordered_atoms_ - (Reset from graph.) n_backbone_heavyatoms_ nheavyatoms_ attached_H_begin_ attached_H_end_

References attached_H_begin_, attached_H_end_, force_bb_, graph_, hydrogens(), n_backbone_heavyatoms_, nheavyatoms_, ordered_atoms_, and target.

Referenced by finalize().

void core::chemical::ResidueType::show ( std::ostream &  output = std::cout,
bool  output_atomic_details = false 
) const
void core::chemical::ResidueType::show_all_atom_names ( std::ostream &  out) const

References graph_, and core::chemical::Atom::name().

Referenced by atom_index(), and atom_vertex().

core::Size core::chemical::ResidueType::smallest_ring_size ( VD const &  atom,
core::Size const &  max_size = 999999 
) const

A graph-based function to determine the size of the smallest ring that involves a given atom.

References graph_, and utility::graph::smallest_ring_size().

Referenced by core::chemical::rosetta_retype_fullatom().

void core::chemical::ResidueType::update_actcoord ( conformation::Residue rot) const
void core::chemical::ResidueType::update_derived_data ( )
private

update derived data in ResidueType, called by finalize()

update derived data in ResidueType, called by finalize() after primary data have been reordered, update derived data accordingly.

Derived data updated by this method: first_sidechain_hydrogen_ accpt_pos_ accpt_pos_sc_ Haro_index_ Hpol_index_ atoms_with_orb_index_ Hpos_polar_ Hpos_apolar_ Hpos_polar_sc_ all_bb_atoms_ all_sc_atoms_ abase2_ path_distance_ dihedral_atom_sets_ dihedrals_for_atom_ bondangle_atom_sets_ bondangles_for_atom_ atoms_within_one_bond_of_a_residue_connection_ within1bonds_sets_for_atom_ atoms_within_two_bonds_of_a_residue_connection_ within2bonds_sets_for_atom_ last_controlling_chi_ atoms_last_controlled_by_chi_

Atom.heavyatom_has_polar_hydrogens_ - for all atoms.

rna_residue_type_ – Will be reset based on other ResidueType data carbohydrate_info_ – Will be reset based on other ResidueType data

References abase2_, abase2_indices_, accpt_pos_, accpt_pos_sc_, all_bb_atoms_, all_sc_atoms_, atom(), atom_base(), atoms_last_controlled_by_chi_, atoms_with_orb_index_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, attached_H_begin_, attached_H_end_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor(), core::chemical::CARBOHYDRATE, carbohydrate_info_, conformer_set_, core::chemical::CYCLIC, dihedral_atom_sets_, dihedrals_for_atom_, first_sidechain_hydrogen_, core::chemical::get_residue_path_distances(), graph_, Haro_index_, core::chemical::Atom::has_orbitals(), Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, improper_dihedral_atom_sets_, improper_dihedrals_for_atom_, core::chemical::Atom::is_acceptor(), core::chemical::Atom::is_haro(), core::chemical::Atom::is_hydrogen(), core::chemical::Atom::is_polar_hydrogen(), core::chemical::Atom::is_virtual(), last_controlling_chi_, n_backbone_heavyatoms_, natoms(), nheavyatoms_, nu_atoms_indices_, ordered_atoms_, path_distance_, path_distances(), properties_, residue_connections_, core::chemical::RNA, rna_residue_type_, update_last_controlling_chi(), utility_exit_with_message, vd_to_index_, within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.

Referenced by finalize().

void core::chemical::ResidueType::update_last_controlling_chi ( )
private

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.

References atom_base(), atoms_last_controlled_by_chi_, bonded_neighbor(), chi_atoms(), last_controlling_chi_, natoms(), nchi(), and note_chi_controls_atom().

Referenced by update_derived_data().

void core::chemical::ResidueType::update_residue_connection_mapping ( )
private
ResidueConnection const & core::chemical::ResidueType::upper_connect ( ) const
Size core::chemical::ResidueType::upper_connect_atom ( ) const
Size core::chemical::ResidueType::upper_connect_id ( ) const
inline
utility::vector1< VariantType > const & core::chemical::ResidueType::variant_types ( ) const
bool core::chemical::ResidueType::variants_match ( ResidueType const &  other) const
utility::vector1< std::pair< Size, Size > > const& core::chemical::ResidueType::within1bonds_sets_for_atom ( Size  atomid) const
inline

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().

utility::vector1< std::pair< Size, Size > > core::chemical::ResidueType::within2bonds_sets_for_atom ( Size  atomid) const
inline

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().

Member Data Documentation

AA core::chemical::ResidueType::aa_
private

standard rosetta aa-type for knowledge-based potentials, may be aa_unk – Primary

Referenced by aa(), backbone_aa(), and rotamer_aa().

std::map<VD, VD> core::chemical::ResidueType::abase2_
private

The base of the atom base – Derived.

Referenced by update_derived_data().

utility::vector1<Size> core::chemical::ResidueType::abase2_indices_
private

Index version of abase2_ – Derived.

Referenced by abase2(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_
private

indices of Hbond acceptor positions – Derived

Referenced by accpt_pos(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_sc_
private

indices of Hbond acceptor positions that are part of the sidechain – Derived must be a subset of the atoms listed in the accpt_pos_ array

Referenced by accpt_pos_sc(), and update_derived_data().

utility::vector1< VD > core::chemical::ResidueType::actcoord_atoms_
private

indices of action coordinate centers – Primary

the geometric center of the atoms listed defined the residue's "action coordinate"

Referenced by add_actcoord_atom(), generate_atom_indices(), requires_actcoord(), ResidueType(), and update_actcoord().

AtomIndices core::chemical::ResidueType::actcoord_atoms_indices_
private

Index version of actcoord_atoms_ – Derived.

Referenced by actcoord_atoms(), and generate_atom_indices().

AtomIndices core::chemical::ResidueType::all_bb_atoms_
private

Indices of all backbone atoms, hydrogens and heavyatoms – Derived.

Referenced by all_bb_atoms(), show(), and update_derived_data().

AtomIndices core::chemical::ResidueType::all_sc_atoms_
private

Indices of all sidechain atoms, hydrogens and heavyatoms – Derived.

Referenced by all_sc_atoms(), show(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::atom_2_residue_connection_map_
private
std::map< std::string, std::string > core::chemical::ResidueType::atom_aliases_
private

A mapping of alias atom names to canonical atom names – Primary Will be added to atom_name_to_vd_ during finalization.

Referenced by add_atom_alias(), delete_atom_alias(), generate_atom_indices(), and ResidueType().

std::map<VD, VD> core::chemical::ResidueType::atom_base_
private

The atom "one up" in the atom tree. – Derived, valid during Mutable. Updated in set_icoor. (also set_atom_base - TODO: Fix redundancy issue.

Referenced by add_atom(), atom_base(), generate_atom_indices(), ResidueType(), and set_atom_base().

utility::vector1<Size> core::chemical::ResidueType::atom_base_indices_
private

Index version of atom_base_ – Derived.

Referenced by atom_base(), and generate_atom_indices().

std::map< std::string, VD > core::chemical::ResidueType::atom_name_to_vd_
private

atom index lookup by atom name string – Derived, valid during Mutable, with caveats

Note that during the Mutable stage not all atoms will necessarily have names or unique names. This map will merely map those which do,

Referenced by add_atom(), add_bond(), add_cut_bond(), add_orbital_bond(), atom(), atom_index(), atom_vertex(), generate_atom_indices(), has(), ResidueType(), set_atom_base(), set_atom_type(), set_backbone_heavyatom(), set_gasteiger_atom_type(), and set_mm_atom_type().

std::map<VD, VD> core::chemical::ResidueType::atom_shadowed_
private

Data to describe virtual atoms that should shadow other atoms for the sake of keeping intraresidue cycles closed when working with an atom tree, e.g. NV shadows N on proline. For each atom, the following vector lists the index of the atom it is shadowing. – Primary.

Referenced by generate_atom_indices(), ResidueType(), and set_shadowing_atom().

utility::vector1< Size > core::chemical::ResidueType::atom_shadowed_indices_
private

Index version of atom_shadowed_ – Derived.

Referenced by atom_being_shadowed(), and generate_atom_indices().

AtomTypeSetCAP core::chemical::ResidueType::atom_types_
private

The type set for Rosetta Atom types. – Primary used to define the set of allowed atomtypes for this residue and their properties Needs to be non-null by the time finalize() is called.

ResidueType Data Organization

These notes apply to ResidueType and associated subsidiary types. (Atom, Bond, AtomICoor, ICoorAtomID ...)

Data stored here is in one of two classes. Primary and Derived:

  • Primary data cannot be deduced from any of the other data in the ResidueType
  • Derived data can be deduced from Primary data, and is stored separately mainly for access efficiency reasons.

A ResidueType also has three stages of its existence:

  • Mutable - In this stage only the Primary data and selected Derived data are valid. All other Derived data may be in an inconsistent state with itself or the Primary data. If you're creating or modifying residue types, you'll be in this stage.
  • Finalized - In this stage the all Derived data is self consistent with primary data. To go from Building to Finalized, call the finalize() method. You can go back to the Building stage by calling a function which modifies the ResidueType.
  • Fixed - A conceptual stage at this point. The ResidueType is completely finished. Only Fixed ResidueTypes should be placed into ResidueTypeSets and be used to construct Residues. Do not call any modification methods on Fixed ResidueTypes. There may be programatic enforcement of this in the future.

Documentation requirements:

Data: All data stored in ResidueType should be annotated with it's Primary/Derived state. For derived data, it should also annotate whether it's valid during the Mutable stage. (If not mentioned it's valid during mutability, it should be assumed it's not.)

Methods: Methods which return/use derived data should note whether it's valid during the Mutable stage. Non-const methods should mention if they're meant to be called during the Mutable stage. (Such methods can be called from the Finalized stage, but will turn the ResidueType into a mutable one.

N.B. For typical ResidueType usage pretty much all of the levels/category distinctions can be ignored. For a constant, finalized ResidueType such as one gets as a COP from a ResidueTypeSet or a Residue, all data and methods which are allowed are valid.

Referenced by acceptor_atoms(), apolar_hydrogens(), aromatic_atoms(), atom_type(), atom_type_set(), atom_type_set_ptr(), heavy_atom_with_hydrogens(), heavy_atom_with_polar_hydrogens(), heavy_atoms(), hydrogens(), polar_hydrogens(), and set_atom_type().

utility::vector1< AtomIndices > core::chemical::ResidueType::atoms_last_controlled_by_chi_
private

for chi i, the list of atoms last controlled by i – Derived E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1

Referenced by atoms_last_controlled_by_chi(), update_derived_data(), and update_last_controlling_chi().

AtomIndices core::chemical::ResidueType::atoms_with_orb_index_
private

indices of atoms with orbitals – Derived

Referenced by atoms_with_orb_index(), and update_derived_data().

utility::vector1< utility::vector1< two_atom_set > > core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection_
private

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. – Derived.

Referenced by atoms_within_one_bond_of_a_residue_connection(), and update_derived_data().

utility::vector1< utility::vector1< three_atom_set > > core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection_
private

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. – Derived.

Referenced by atoms_within_two_bonds_of_a_residue_connection(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_begin_
private

indices of each heavyatom's first attached hydrogen – Derived.

Referenced by attached_H_begin(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_end_
private

indices of each heavyatom's last attached hydrogen – Derived.

Referenced by attached_H_end(), number_bonded_hydrogens(), setup_atom_ordering(), and update_derived_data().

AA core::chemical::ResidueType::backbone_aa_
private

Referenced by backbone_aa(), and perform_checks().

std::string core::chemical::ResidueType::base_restype_name_
private

Referenced by base_restype_name().

utility::vector1< bondangle_atom_set > core::chemical::ResidueType::bondangle_atom_sets_
private

vector of sets of atoms that make up bond angles in the residue – Derived

Referenced by bondangle(), num_bondangles(), print_bondangles(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::bondangles_for_atom_
private

??? – Derived

Referenced by bondangles_for_atom(), and update_derived_data().

utility::vector1< AtomIndices > core::chemical::ResidueType::bonded_neighbor_
private

indices of the atoms psuedo bonded atoms. Used in orbital code – Derived

Referenced by add_atom(), add_bond(), bonded_neighbor(), and generate_atom_indices().

utility::vector1<utility::vector1<BondName> > core::chemical::ResidueType::bonded_neighbor_type_
private
core::chemical::carbohydrates::CarbohydrateInfoOP core::chemical::ResidueType::carbohydrate_info_
private

A container for residue properties unique to carbohydrates. – Derived, can be null.

Referenced by carbohydrate_info(), show(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::chi_2_proton_chi_
private

A "map" of chi indices to proteon_chi indices – Derived, valid during Mutable.

Referenced by add_chi(), autodetermine_chi_bonds(), chi_2_proton_chi(), redefine_chi(), and set_proton_chi().

utility::vector1<utility::vector1<VD> > core::chemical::ResidueType::chi_atoms_
private

the four atoms to build each chi angle – Primary.

Referenced by add_chi(), autodetermine_chi_bonds(), chi_atom_vds(), generate_atom_indices(), nchi(), redefine_chi(), and ResidueType().

utility::vector1< AtomIndices > core::chemical::ResidueType::chi_atoms_indices_
private

Index version of chi_atoms_ – Derived.

Referenced by chi_atoms(), and generate_atom_indices().

utility::vector1< utility::vector1< std::pair< Real, Real > > > core::chemical::ResidueType::chi_rotamers_
private

Additional non-Dunbrack rotamer bins – Primary.

pair<Real,Real> ==> mean,sdev for each chi angle i and rotamer j: chi_rotamers_[i][j]

Referenced by add_chi(), add_chi_rotamer(), autodetermine_chi_bonds(), and chi_rotamers().

RingConformerSetOP core::chemical::ResidueType::conformer_set_
private

The set of all possible ring conformers – Derived, can be null.

Referenced by ring_conformer_set(), and update_derived_data().

std::map<VD, utility::vector1<VD> > core::chemical::ResidueType::cut_bond_neighbor_
private
utility::vector1< AtomIndices > core::chemical::ResidueType::cut_bond_neighbor_indices_
private

Index version of cut_bond_neighbor_ – Primary - will be converted to derived (from Bond.cut_bond())

Referenced by cut_bond_neighbor(), and generate_atom_indices().

utility::vector1< Adduct > core::chemical::ResidueType::defined_adducts_
private

Adducts defined for this residue – Primary.

Referenced by add_adduct(), defined_adducts(), and report_adducts().

utility::vector1< dihedral_atom_set > core::chemical::ResidueType::dihedral_atom_sets_
private

Data for the mm potentials. – Derived 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(), ndihe(), print_dihedrals(), and update_derived_data().