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...

Atom &	atom (Size const atom_index)

Atom const &	atom (Size const atom_index) const

Atom &	atom (VD const vd)

Atom const &	atom (VD const vd) const

Atom &	atom (std::string const &atom_name)

Atom const &	atom (std::string const &atom_name) const

Orbital const &	orbital (Size const orbital_index) const

Orbital const &	orbital (std::string const &orbital_name) const

Bond &	bond (ED const ed)

Bond const &	bond (ED const ed) 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
	Get the chemical atom_type index number for this atom by its index number in this residue. 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

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...

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...

Size	atom_base (Size const atomno) const
	get index of an atom's base atom More...

Size	abase2 (Size const atomno) const
	get index of an atom's second base atom More...

std::string const &	atom_name (Size const index) const
	get atom name by index 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 VD More...

VD	vd_from_name (std::string const &name) const
	get the vertex descriptor from the name of the atom. More...

VD	vd_from_index (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	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...

VD const &	get_vertex (Size atomno) const

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...

ResidueConnection &	residue_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...

void	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 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	set_atom_type (std::string const &atom_name, 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)
	add a bond between atom1 and atom2, if bond type is not specified, default to SingleBond More...

void	add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel)

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...

void	nbr_atom (std::string const &atom_name)
	set nbr_atom used to define residue-level neighbors More...

Size	nbr_atom () const
	get nbr_atom 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_backbone_heavyatom (std::string const &name)
	set an atom as backbone heavy atom More...

void	debug_dump_icoor ()
	Dump out atomnames and icoor values. More...

AtomICoor const &	icoor (Size 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 (Size const &index, 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	assign_neighbor_atom ()

void	assign_internal_coordinates ()

void	calculate_icoor (std::string const &child, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)
	calculate AtomICoor for an atom and set it More...

void	set_ideal_xyz (std::string const &atm, Vector const &xyz_in)

void	set_ideal_xyz (Size index, Vector const &xyz_in)

void	set_shadowing_atom (std::string const &atom, std::string const &atom_being_shadowed)

void	retype_atoms (ElementMap const &emap, bool preserve=false)
	Reassign Rosetta atom types based on the current heuristics. emap is a map of VD->element strings. If an atom is not present in the element map, attempt to get the element string from the current type (it's an error if it doesn't have one.) If preserve is true, only retype those atoms which have an atom_type_index of zero. More...

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, 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 > dihedral_samples, utility::vector1< Real > extra_samples)

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	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 ResidueConnection Doesn't set the ideal geometry – maybe it should? More...

utility::vector1< std::string > const &	properties () const
	acess specified properties More...

void	add_property (std::string const &property)
	add properties More...

void	add_numeric_property (std::string const &tag, core::Real value)
	add a numeric property More...

void	add_string_property (std::string const &tag, std::string value)
	add a string property More...

void	delete_property (std::string const &property)
	delete properties More...

void	add_actcoord_atom (std::string const &atom)
	add an atom to the list for calculating actcoord center 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_carbohydrate () const
	is carbohydrate? More...

bool	is_lipid () const
	is lipid? More...

bool	is_ligand () const

bool	is_metal () const
	Returns true if this residue type is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES. More...

bool	is_metalbinding () const
	Returns true if this residue 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. 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 (Size const &atomno) const
	Check if atom is virtual. More...

bool	is_virtual_residue () const
	Check if residue is 'VIRTUAL_RESIDUE'. More...

bool	is_adduct () const
	is an adduct-modified residue? More...

void	set_adduct_flag (bool adduct_in)

bool	has_property (std::string const &property) const
	Generic property access – SLOW!!!!! More...

core::Real	get_numeric_property (std::string const &tag) const
	get a numeric property More...

std::string	get_string_property (std::string const &tag) const
	get a numeric property More...

bool	has_variant_type (VariantType const &variant_type) const
	Generic variant access – SLOW!!!!! More...

utility::vector1< VariantType > const &	variant_types () const
	get all the variant types for this ResidueType More...

bool	variants_match (ResidueType const &other) const
	Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property. More...

bool	nonadduct_variants_match (ResidueType const &other) const
	similar to variants_match(), but allows different adduct-modified states More...

void	add_variant_type (VariantType const &variant_type)
	add one more variant type to this ResidueType More...

void	aa (std::string const &type)
	set our aa-type (could be "UNK") 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	set_mol_data (sdf::MolData const &mol_data)
	set the MolData object More...

sdf::MolData	get_mol_data () const

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...

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...

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...

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) 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_

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...

void	assign_internal_coordinates (std::string const &current_atom)
	@ recursive function to assign internal coordinates More...

Private Attributes
AtomTypeSetCAP	atom_types_

ElementSetCAP	elements_

MMAtomTypeSetCAP	mm_atom_types_

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_types_

orbitals::OrbitalTypeSetCAP	orbital_types_

RingConformerSetOP	conformer_set_

ResidueTypeSetCAP	residue_type_set_

ResidueGraph	graph_

std::map< VD, Size >	vd_to_index_

std::map< VD, VD >	atom_base_

std::map< VD, VD >	abase2_

utility::vector1< Orbital >	orbitals_

Size	nheavyatoms_

Size	n_hbond_acceptors_

Size	n_hbond_donors_

Size	n_orbitals_

Size	n_backbone_heavyatoms_

Size	first_sidechain_hydrogen_

Size	ndihe_

Size	nbonds_

utility::vector1< AtomIndices >	bonded_neighbor_

utility::vector1 < utility::vector1< BondName > >	bonded_neighbor_type_

std::map< VD, utility::vector1 < VD > >	cut_bond_neighbor_

utility::vector1< Size >	attached_H_begin_

utility::vector1< Size >	attached_H_end_

utility::vector1< VD >	parents_

std::map< VD, AtomICoor >	icoor_

utility::vector1 < dihedral_atom_set >	dihedral_atom_sets_

utility::vector1 < utility::vector1< Size > >	dihedrals_for_atom_

utility::vector1 < bondangle_atom_set >	bondangle_atom_sets_

utility::vector1 < utility::vector1< Size > >	bondangles_for_atom_

std::map< VD, VD >	atom_shadowed_

utility::vector1< Size >	last_controlling_chi_

utility::vector1< AtomIndices >	atoms_last_controlled_by_chi_

AtomIndices	atoms_with_orb_index_

AtomIndices	Haro_index_

AtomIndices	Hpol_index_

AtomIndices	accpt_pos_

AtomIndices	Hpos_polar_

AtomIndices	Hpos_apolar_

AtomIndices	accpt_pos_sc_

AtomIndices	Hpos_polar_sc_

AtomIndices	all_bb_atoms_

AtomIndices	all_sc_atoms_

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< VD >	mainchain_atoms_
	indices of all mainchain atoms More...

utility::vector1< VD >	actcoord_atoms_
	indices of action coordinate centers More...

utility::vector1 < utility::vector1< VD > >	chi_atoms_

utility::vector1< bool >	is_proton_chi_

utility::vector1< Size >	proton_chis_

utility::vector1< Size >	chi_2_proton_chi_

utility::vector1 < utility::vector1< Real > >	proton_chi_samples_

utility::vector1 < utility::vector1< Real > >	proton_chi_extra_samples_

utility::vector1 < utility::vector1< VD > >	nu_atoms_

utility::vector1 < utility::vector1< int > >	path_distance_

std::map< std::string, VD >	atom_name_to_vd_

VDs	ordered_atoms_

std::map< std::string, int >	orbitals_index_

utility::vector1 < utility::vector1< std::pair < Real, Real > > >	chi_rotamers_

std::string	rotamer_library_name_

bool	use_ncaa_rotlib_

std::string	ncaa_rotlib_path_

Size	ncaa_rotlib_n_rots_

utility::vector1< Size >	ncaa_rotlib_n_bins_per_rot_

utility::vector1< std::string >	properties_

bool	is_polymer_

bool	is_protein_

bool	is_alpha_aa_

bool	is_beta_aa_

bool	is_l_aa_

bool	is_d_aa_

bool	is_charged_

bool	is_polar_

bool	has_sc_orbitals_

bool	is_aromatic_

bool	is_cyclic_

bool	is_DNA_

bool	is_RNA_

bool	is_NA_

bool	is_carbohydrate_

bool	is_lipid_

bool	is_ligand_

bool	is_metal_

bool	is_metalbinding_

bool	is_surface_

bool	is_terminus_

bool	is_lower_terminus_

bool	is_upper_terminus_

bool	is_branch_lower_terminus_

bool	is_phosphonate_

bool	is_phosphonate_upper_

bool	is_acetylated_nterminus_

bool	is_methylated_cterminus_

bool	is_coarse_

bool	is_adduct_

utility::vector1< VariantType >	variant_types_

std::map< std::string, core::Real >	numeric_properties_

std::map< std::string, std::string >	string_properties_

AA	aa_

AA	rotamer_aa_

AA	backbone_aa_

std::string	name_

std::string	name3_

char	name1_

std::string	interchangeability_group_

VD	nbr_atom_

Real	nbr_radius_

bool	force_nbr_atom_orient_

Real	mass_

Size	n_actcoord_atoms_

sdf::MolData	mol_data_

utility::vector1 < ResidueConnection >	residue_connections_
	Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections. More...

utility::vector1 < utility::vector1< Size > >	atom_2_residue_connection_map_

utility::vector1 < utility::vector1 < two_atom_set > >	atoms_within_one_bond_of_a_residue_connection_
	For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More...

utility::vector1 < utility::vector1< std::pair < Size, Size > > >	within1bonds_sets_for_atom_
	For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. More...

utility::vector1 < utility::vector1 < three_atom_set > >	atoms_within_two_bonds_of_a_residue_connection_
	For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. More...

utility::vector1 < utility::vector1< std::pair < Size, Size > > >	within2bonds_sets_for_atom_
	For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. More...

Size	lower_connect_id_
	Polymer lower connections. More...

Size	upper_connect_id_
	Polymer upper connections. More...

Size	n_non_polymeric_residue_connections_

Size	n_polymeric_residue_connections_

utility::vector1< VD >	force_bb_
	a list of atom indices to be deleted More...

core::chemical::rna::RNA_ResidueTypeOP	rna_residue_type_

core::chemical::carbohydrates::CarbohydrateInfoOP	carbohydrate_info_

std::list< utility::vector1< ED > >	rings_and_their_edges_

utility::vector1< Size >	atom_base_indices_

utility::vector1< Size >	abase2_indices_

utility::vector1< AtomIndices >	chi_atoms_indices_

utility::vector1< AtomIndices >	nu_atoms_indices_

AtomIndices	mainchain_atoms_indices_

Size	nbr_atom_indices_

AtomIndices	actcoord_atoms_indices_

utility::vector1< AtomIndices >	cut_bond_neighbor_indices_

utility::vector1< Size >	atom_shadowed_indices_

bool	finalized_
	status More...

utility::vector1< Adduct >	defined_adducts_

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. Several lines of code must be modified to get them to work, all found in ResidueType.cc.

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 ( 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

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

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

inline

References defined_adducts_.

void 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

Note: this does not set xyz coordinates for the added atom

References atom(), atom_2_residue_connection_map_, atom_base_, core::chemical::AtomType::atom_has_orbital(), atom_name(), atom_name_to_vd_, atom_types_, bonded_neighbor_, bonded_neighbor_type_, elements_, finalized_, graph_, icoor_, core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_haro(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), core::chemical::AtomType::is_virtual(), mass_, mm_atom_types_, n_hbond_acceptors_, n_hbond_donors_, ordered_atoms_, parents_, core::chemical::strip_whitespace(), core::chemical::tr, type, and vd_to_index_.

Referenced by core::chemical::AddAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_atom().

void core::chemical::ResidueType::add_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 SingleBond

add a bond between atom1 and atom2 and add a BondType object referencing the bond (default bond type of SingleBond) update bonded_neighbor_ and resize it as necessary

References core::chemical::SingleBond.

Referenced by core::util::add_covalent_linkage_helper(), core::chemical::AddBond::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_bond().

void core::chemical::ResidueType::add_bond	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		BondName	bondLabel
	)

add a bond between atom1 and atom2 and add a BondType object referencing the bond using the specified bondName

References atom_index(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, has(), nbonds_, target, and utility_exit_with_message.

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

Referenced by add_chi(), core::chemical::AddChi::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi().

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_, has(), 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 numeric_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_, n_orbitals_, 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 )

add properties

add a property to this residue update boolean property member data accordingly

References finalized_, has_sc_orbitals_, is_acetylated_nterminus_, is_alpha_aa_, is_aromatic_, is_beta_aa_, is_branch_lower_terminus_, is_carbohydrate_, is_charged_, is_coarse_, is_cyclic_, is_d_aa_, is_DNA_, is_l_aa_, is_ligand_, is_lipid_, is_lower_terminus_, is_metal_, is_metalbinding_, is_methylated_cterminus_, is_NA_, is_phosphonate_, is_phosphonate_upper_, is_polar_, is_polymer_, is_protein_, is_RNA_, is_surface_, is_terminus_, is_upper_terminus_, properties_, core::chemical::carbohydrates::CarbohydrateInfo::sugar_properties(), and core::chemical::tr.

Referenced by core::chemical::AddProperty::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_properties().

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

add a ResidueConnection 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 string_properties_.

void core::chemical::ResidueType::add_variant_type ( VariantType const & variant_type )

inline

add one more variant type to this ResidueType

References has_variant_type(), and variant_types_.

Referenced by core::util::add_covalent_linkage_helper(), and core::chemical::ResidueDatabaseIO::read_residue_type_variant().

AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const

inline

Indices of all backbone atoms, hydrogens and heavyatoms.

References all_bb_atoms_.

Referenced by core::conformation::Residue::all_bb_atoms(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::sasa::get_sc_bb_sasa(), and core::scoring::sasa::get_sc_bb_sasa_per_res().

AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const

inline

Indices of all sidechain atoms, hydrogens and heavyatoms.

References all_sc_atoms_.

Referenced by core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::sasa::get_sc_bb_sasa(), core::scoring::sasa::get_sc_bb_sasa_per_res(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().

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 ( )

References atom_name(), core::chemical::ICoorAtomID::atomno(), icoor(), nbr_atom(), set_icoor(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), and core::chemical::AtomICoor::stub_atom3().

Referenced by assign_internal_coordinates().

void core::chemical::ResidueType::assign_internal_coordinates ( std::string const & current_atom )

private

@ recursive function to assign internal coordinates

References assign_internal_coordinates(), atom_index(), atom_name(), core::chemical::ICoorAtomID::atomno(), bonded_neighbor(), calculate_icoor(), icoor(), nbr_atom(), parents_, core::io::serialization::size(), core::chemical::AtomICoor::stub_atom2(), and vd_to_index_.

void core::chemical::ResidueType::assign_neighbor_atom ( )

References atom_is_hydrogen(), center(), numeric::xyzVector< class >::distance(), core::kinematics::distance(), graph_, name(), and nbr_atom().

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

References atom_index(), graph_, and ordered_atoms_.

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

References atom_index(), graph_, and ordered_atoms_.

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

References graph_.

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

References graph_.

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_.

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

get index of an atom's base atom

References atom_base_indices_, ordered_atoms_, and PyAssert.

Referenced by core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::atom_base(), core::util::auto_setup_all_metal_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), note_chi_controls_atom(), select_orient_atoms(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), update_derived_data(), update_last_controlling_chi(), and core::chemical::ResidueTypeKinWriter::write_restype().

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.

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

get atom index by VD

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

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

inline

is a backbone atom (heavy or hydrogen)?

References finalized_, first_sidechain_hydrogen_, n_backbone_heavyatoms_, natoms(), and nheavyatoms_.

Referenced by core::conformation::Residue::atom_is_backbone(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Residue::place(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::constraints::requires_CB_mapping(), select_orient_atoms(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::setup_water_builders_for_residue_type(), and core::scoring::orbitals::surrogate_atom_for_orbital().

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

References finalized_, graph_, and ordered_atoms_.

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

VIterPair core::chemical::ResidueType::atom_iterators ( ) const

inline

References graph_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

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(), assign_internal_coordinates(), atom(), core::conformation::Residue::atom_name(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), debug_dump_icoor(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::chemical::rna::get_rna_base_centroid(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::rna::RNA_TorsionPotential::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::conformation::print_node(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::mm::score_atom_centrally(), core::scoring::methods::MMBondAngleEnergy::score_atom_centrally(), set_atom_type(), 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(), and core::chemical::write_topology_file().

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

access by reference the atomset for which this residue is constructed

References atom_types_.

Referenced by core::io::pdb::FileData::append_residue(), core::conformation::Residue::atom_type_set(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), and core::scoring::methods::LKB_ResidueInfo::setup_atom_weights().

AtomTypeSetCAP core::chemical::ResidueType::atom_type_set_ptr ( ) const

inline

access by const pointer the atomset for which this residue is constructed

References atom_types_.

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_scoring(), core::scoring::etable::CoarseEtableEnergy::setup_for_scoring_(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), and core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_().

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

References atoms_with_orb_index_.

Referenced by core::conformation::Residue::atoms_with_orb_index(), core::conformation::Residue::Residue(), and core::conformation::Residue::update_orbital_coords().

utility::vector1< two_atom_set > const& core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection ( Size resconn ) const

inline

Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.

References atoms_within_one_bond_of_a_residue_connection_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().

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

index number of the first attached Hydrogen on an atom

References atom(), and attached_H_begin_.

Referenced by core::coarse::Translator::add_atom(), core::conformation::Residue::attached_H_begin(), and core::scoring::orbitals::surrogate_atom_for_orbital().

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::backbone_aa ( std::string const & type )

inline

AA to use for backbone scoring.

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

Referenced by core::conformation::Residue::backbone_aa(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv().

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

References base_restype_name_.

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

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

inline

References base_restype_name_.

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

References graph_.

Referenced by core::chemical::find_bonds_in_rings(), and generate_atom_indices().

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

References graph_.

EIterPair core::chemical::ResidueType::bond_iterators ( ) const

inline

References graph_.

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

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

References bondangle_atom_sets_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), and core::scoring::mm::MMBondAngleResidueTypeParam::init().

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

indices of the bonded neighbors for an atom

References bonded_neighbor_.

Referenced by core::util::add_covalent_linkage_helper(), core::conformation::Residue::apply_transform_downstream(), assign_internal_coordinates(), core::conformation::Residue::bonded_neighbor(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), nbrs(), core::conformation::Residue::nbrs(), note_chi_controls_atom(), number_bonded_heavyatoms(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), select_orient_atoms(), core::scoring::orbitals::surrogate_atom_for_orbital(), update_derived_data(), update_last_controlling_chi(), and core::chemical::ResidueTypeKinWriter::write_restype().

AdjacentIterPair core::chemical::ResidueType::bonded_neighbor_iterators ( VD const & atom ) const

References graph_.

utility::vector1< BondName > const & core::chemical::ResidueType::bonded_neighbor_types ( Size const atomno ) const

References bonded_neighbor_type_.

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

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

inline

indices of the orbitals bonded to an atom

References graph_, and ordered_atoms_.

Referenced by core::conformation::Residue::bonded_orbitals(), generate_atom_indices(), core::conformation::Residue::Residue(), ResidueType(), and core::conformation::Residue::update_orbital_coords().

void core::chemical::ResidueType::calculate_icoor	(	std::string const &	child,
		std::string const &	stub_atom1,
		std::string const &	stub_atom2,
		std::string const &	stub_atom3
	)

calculate AtomICoor for an atom and set it

References atom(), atom_index(), numeric::xyzVector< class >::distance(), core::kinematics::distance(), core::chemical::Atom::ideal_xyz(), numeric::NumericTraits< class >::pi(), set_icoor(), and core::chemical::tr.

Referenced by assign_internal_coordinates().

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

References chi_2_proton_chi_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi().

AtomIndices const& core::chemical::ResidueType::chi_atoms ( Size const chino ) const

inline

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

References chi_atoms_indices_.

Referenced by core::conformation::Residue::chi_atoms(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::conformation::Residue::Residue(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

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

all rotamers bins (mean, std) for a given chi angle

References chi_rotamers_.

Referenced by core::conformation::Residue::chi_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), and core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer().

ResidueTypeOP core::chemical::ResidueType::clone ( ) const

make a copy

References ResidueType().

Referenced by core::util::add_covalent_linkage_helper(), core::chemical::PatchCase::apply(), core::scoring::automorphic_rmsd(), and core::scoring::FACTSRsdTypeInfo::initialize_parameters().

AtomIndices const& core::chemical::ResidueType::cut_bond_neighbor ( Size const atomno ) const

inline

indices of the bonded neighbors for an atom

References cut_bond_neighbor_indices_.

Referenced by core::conformation::Residue::cut_bond_neighbor(), and core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond().

void core::chemical::ResidueType::debug_dump_icoor ( )

Dump out atomnames and icoor values.

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

utility::vector1< Adduct > const& core::chemical::ResidueType::defined_adducts ( ) const

inline

get the adducts defined for this residue

References defined_adducts_.

Referenced by core::chemical::apply_adducts_to_residue(), core::chemical::ResidueTypeSet::create_adduct_combinations(), core::chemical::error_check_requested_adducts(), and core::chemical::ResidueTypeSet::place_adducts().

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_property ( std::string const & property )

delete properties

delete a property to this residue update boolean property member data accordingly

References finalized_, has_sc_orbitals_, is_acetylated_nterminus_, is_alpha_aa_, is_aromatic_, is_beta_aa_, is_branch_lower_terminus_, is_carbohydrate_, is_charged_, is_coarse_, is_cyclic_, is_d_aa_, is_DNA_, is_l_aa_, is_ligand_, is_lipid_, is_lower_terminus_, is_metal_, is_metalbinding_, is_methylated_cterminus_, is_phosphonate_, is_phosphonate_upper_, is_polar_, is_polymer_, is_protein_, is_RNA_, is_surface_, is_terminus_, is_upper_terminus_, properties_, and core::chemical::tr.

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().

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::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

index of the first sidechain atom (heavy or hydrogen)

References n_backbone_heavyatoms_, natoms(), and nheavyatoms_.

Referenced by core::coarse::Translator::add_remaining_sidechain(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::conformation::Residue::first_sidechain_atom(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), and select_orient_atoms().

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.

References actcoord_atoms_, actcoord_atoms_indices_, atom_2_residue_connection_map_, 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, j, 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().

sdf::MolData core::chemical::ResidueType::get_mol_data ( ) const

inline

References mol_data_.

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_NCAARotamerLibrary().

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_NCAARotamerLibrary().

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

inline

get a numeric property

References name3_, and numeric_properties_.

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

inline

get a numeric property

References name3_, and string_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().

VD const& core::chemical::ResidueType::get_vertex ( Size atomno ) const

inline

References ordered_atoms_.

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

ResidueGraph const& core::chemical::ResidueType::graph ( ) const

inline

Constant access to the underlying graph.

References graph_.

Referenced by acceptor_atoms(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::convert_residuetype_to_light_graph(), core::chemical::find_bonds_in_rings(), core::chemical::get_bond(), core::chemical::get_connecting_atoms(), heavy_atom_with_hydrogens(), and heavy_atom_with_polar_hydrogens().

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_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::AddAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), 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::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), 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::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::is_disulfide_bond(), core::pose::named_atom_id_to_atom_id(), core::conformation::Residue::place(), 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::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_backbone_heavyatom(), core::scoring::setup_matching_atoms_with_given_names(), and core::coarse::Translator::Translator().

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

inline

Generic property access – SLOW!!!!!

References properties_.

Referenced by core::conformation::Residue::has_property(), core::pack::task::operation::ResidueHasProperty::operator()(), and core::chemical::Selector_PROPERTY::operator[]().

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

inline

does this residue have sidechain orbitals?

References has_sc_orbitals_.

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

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

inline

Generic variant access – SLOW!!!!!

References variant_types_.

Referenced by core::util::add_covalent_linkage_helper(), add_variant_type(), core::io::pdb::build_pose_as_is1(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::get_root_atomno(), core::conformation::Residue::has_variant_type(), core::pose::rna::is_cutpoint_open(), is_virtual_residue(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_sequence(), nonadduct_variants_match(), core::chemical::Selector_VARIANT_TYPE::operator[](), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::pose::residue_types_from_sequence(), and variants_match().

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

References finalized_, graph_, and ordered_atoms_.

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

bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size atomno ) const

inline

References finalized_, graph_, and ordered_atoms_.

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

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

References Hpos_polar_sc_.

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

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

AtomICoord of an atom.

References icoor_, and ordered_atoms_.

Referenced by assign_internal_coordinates(), core::conformation::Residue::icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), and core::chemical::write_topology_file().

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(), and core::chemical::AppendInterchangeabilityGroup_String::apply().

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

inline

is acetylated n terminus

References is_acetylated_nterminus_.

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

inline

is an adduct-modified residue?

References is_adduct_.

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

inline

is this an alpha amino acid?

References is_alpha_aa_.

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

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

inline

is aromatic?

References is_aromatic_.

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

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

inline

is this a beta amino acid?

References is_beta_aa_.

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

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

inline

is lower terminus of a branch?

References is_branch_lower_terminus_.

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

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

inline

is carbohydrate?

References is_carbohydrate_.

Referenced by core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), and core::chemical::Selector_UPPER_POSITION::operator[]().

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

inline

is charged?

References is_charged_.

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

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

inline

is coarse?

References is_coarse_.

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

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

inline

is cyclic?

References is_cyclic_.

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

inline

is this a d-amino acid?

References is_d_aa_.

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

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

inline

is DNA?

References is_DNA_.

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

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

inline

is this an l-amino acid?

References is_l_aa_.

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

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

inline

References is_ligand_.

Referenced by core::util::add_covalent_linkage_helper(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::is_ligand(), and core::chemical::write_topology_file().

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

inline

is lipid?

References is_lipid_.

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

inline

is lower terminus?

References is_lower_terminus_.

Referenced by core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_lower_terminus(), core::pose::make_pose_from_sequence(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), and core::chemical::write_topology_file().

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

inline

Returns 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 is_metal_.

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

inline

Returns 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 is_metalbinding_.

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

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

inline

is methylated c terminus

References is_methylated_cterminus_.

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

inline

is Nucleic Acid?

References is_NA_.

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

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

inline

is polar?

References is_polar_.

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

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

inline

is polymer?

References is_polymer_.

Referenced by core::io::pdb::build_pose_as_is1(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_polymer_bonded(), core::io::serialization::read_binary(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::pose::residue_types_from_sequence(), and core::chemical::write_topology_file().

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

inline

is protein?

References is_protein_.

Referenced by add_actcoord_atom(), atom_index(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::dfire::DFIRE_Energy::defines_residue_pair_energy(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::scoring::cryst::fix_bfactorsMissing(), core::scoring::methods::get_restag(), core::util::ABEGOManager::get_symbols(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::pose::remove_nonprotein_residues(), core::pose::set_ss_from_phipsi(), core::pose::transfer_phi_psi(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_proton_chi ( Size const chino ) const

inline

number of proton chis

References proton_chis_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), and core::chemical::write_topology_file().

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

inline

is RNA?

References is_RNA_.

Referenced by core::pose::rna::correctly_add_cutpoint_variants(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::conformation::Residue::is_RNA(), core::scoring::rna::StackElecEnergy::is_rna_base(), and core::chemical::write_topology_file().

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

inline

is surface? (e.g. enamel)

References is_surface_.

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

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

inline

is terminus?

References is_terminus_.

Referenced by core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::conformation::Residue::is_terminus(), core::scoring::methods::GoapEnergy::setup_for_scoring(), and core::chemical::write_topology_file().

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

inline

is upper terminus?

References is_upper_terminus_.

Referenced by core::io::pdb::build_pose_as_is1(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_upper_terminus(), core::pose::make_pose_from_sequence(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), and core::chemical::write_topology_file().

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 has_variant_type().

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

References is_polymer_, lower_connect_id_, and residue_connections_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::lower_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

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

index number of the atom which connects to the lower connection

References is_polymer_, lower_connect_id_, residue_connections_, and vd_to_index_.

Referenced by core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::chemical::ICoorAtomID::xyz().

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

inline

References lower_connect_id_.

Referenced by core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::conformation::Residue::has_lower_connect(), and core::conformation::Residue::is_polymer_bonded().

Size core::chemical::ResidueType::mainchain_atom ( Size const atm ) const

inline

index of mainchain atom

References mainchain_atoms_indices_.

Referenced by core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), and core::conformation::Residue::mainchain_atom().

AtomIndices const& core::chemical::ResidueType::mainchain_atoms ( ) const

inline

indices of all mainchain atoms

References mainchain_atoms_indices_.

Referenced by core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), core::conformation::Residue::Residue(), and core::chemical::ResidueTypeKinWriter::write_restype().

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

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

References graph_, mm_atom_types_, and ordered_atoms_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init(), print_bondangles(), print_dihedrals(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

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

References n_non_polymeric_residue_connections_.

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

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

inline

number of orbitals

References n_orbitals_.

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

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

inline

References n_polymeric_residue_connections_.

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

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

inline

number of proton chis

References proton_chis_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), and core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().

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

number of ResidueConnections, counting polymeric residue connections

References residue_connections_.

Size core::chemical::ResidueType::n_residue_connections_for_atom ( Size const atomid ) const

inline

How many inter-residue chemical bonds does a particular atom form?

References atom_2_residue_connection_map_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().

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)

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_.

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

get our 1letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name3 string.

References name1_.

Referenced by core::chemical::SetIO_String::apply(), core::pose::full_model_info::check_full_model_info_OK(), core::conformation::is_disulfide_bond(), core::conformation::Residue::name1(), core::chemical::Selector_NAME1::operator[](), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::chemical::ResidueTypeKinWriter::write_kin_header(), and core::chemical::write_topology_file().

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(), core::scoring::automorphic_rmsd(), 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::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), 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::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(), vd_from_name(), 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

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

number of atoms

References graph_.

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

inline

number of bonds

References nbonds_.

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

set nbr_atom used to define residue-level neighbors

References atom_index(), nbr_atom_, nbr_atom_indices_, and ordered_atoms_.

Referenced by core::chemical::SetNbrAtom::apply(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

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

inline

get nbr_atom used to define residue-level neighbors

References nbr_atom_indices_.

Referenced by assign_internal_coordinates(), assign_neighbor_atom(), and select_orient_atoms().

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

inline

set nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

Referenced by core::chemical::SetNbrRadius::apply(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), core::scoring::Energies::update_neighbor_links(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

Real core::chemical::ResidueType::nbr_radius ( ) const

inline

get nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

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

inline

indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)

References bonded_neighbor().

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::chemical::get_residue_path_distances(), note_chi_controls_atom(), select_orient_atoms(), core::scoring::orbitals::surrogate_atom_for_orbital(), and core::chemical::write_topology_file().

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

inline

number of chi angles

References chi_atoms_.

Referenced by add_chi(), add_chi_rotamer_to_last_chi(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::conformation::Residue::nchi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::conformation::Residue::Residue(), set_proton_chi(), update_last_controlling_chi(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

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 ndihe_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_energy().

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

References orbital_index(), and orbitals_.

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

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

inline

number of heavy atoms

References nheavyatoms_.

Referenced by core::coarse::Translator::add_all_remaining(), core::coarse::Translator::add_remaining_sidechain(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), core::scoring::methods::LKB_ResidueInfo::initialize(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::place(), select_orient_atoms(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), and core::scoring::methods::LKB_ResidueInfo::setup_atom_weights().

bool core::chemical::ResidueType::nonadduct_variants_match ( ResidueType const & other ) const

similar to variants_match(), but allows different adduct-modified states

References core::chemical::ADDUCT, has_variant_type(), and variant_types_.

Referenced by core::pack::task::ResidueLevelTask_::ResidueLevelTask_().

void core::chemical::ResidueType::nondefault ( bool in )

inline

References nondefault_.

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

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

get number of intraresidue bond angles

References bondangle_atom_sets_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), and core::scoring::mm::MMBondAngleResidueTypeParam::init().

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

References orbital_index(), and orbitals_.

Referenced by core::conformation::Residue::orbital_name(), core::conformation::Residue::Residue(), and core::conformation::Residue::set_orbital_xyz().

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

get orbital index by name

References name3(), orbitals_index_, and utility_exit_with_message.

Referenced by new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), and set_orbital_icoor_id().

orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type ( int const orbital_index ) const

References orbital_index(), orbital_types_, and orbitals_.

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

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

path distance (number of bonds separated) between a pair of atoms

References path_distance_.

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), and core::conformation::Residue::path_distance().

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, backbone_aa_, is_alpha_aa_, is_beta_aa_, is_d_aa_, is_l_aa_, is_metal(), is_metalbinding(), is_virtual(), metal_binding_atoms_, nheavyatoms_, 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

print intraresidue bond angles to standard out

References atom_type(), bondangle_atom_sets_, graph_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), and core::chemical::tr.

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

References atom_type(), dihedral_atom_sets_, graph_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), ndihe_, and core::chemical::tr.

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

print chemical-bond path distances to standard out

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

utility::vector1< std::string > const & core::chemical::ResidueType::properties ( ) const

acess specified properties

get all specified properties for this residue type

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

References proton_chi_extra_samples_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().

utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_samples ( Size proton_chi ) const

inline

References proton_chi_samples_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().

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::report_adducts ( )

References add(), core::chemical::Adduct::adduct_name(), core::chemical::Adduct::atom_name(), defined_adducts_, name3(), and core::chemical::tr.

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

inline

require actcoord?

References is_aromatic_, is_polar_, is_protein_, and n_actcoord_atoms_.

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

Size core::chemical::ResidueType::residue_connect_atom_index ( Size const resconn_id ) const

References residue_connections_, and vd_to_index_.

Referenced by core::conformation::Residue::residue_connect_atom_index(), and core::chemical::ICoorAtomID::xyz().

ResidueConnection const & core::chemical::ResidueType::residue_connection ( Size const i ) const

get a ResidueConection

References residue_connections_.

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

Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom.

References atom_2_residue_connection_map_, and core::io::serialization::size().

Referenced by core::conformation::Residue::copy_residue_connections(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), and core::conformation::Conformation::fix_disulfides().

bool core::chemical::ResidueType::residue_connection_is_polymeric ( Size const resconn_id ) const

inline

References lower_connect_id_, and upper_connect_id_.

utility::vector1< Size > const& core::chemical::ResidueType::residue_connections_for_atom ( Size const atomid ) const

inline

References atom_2_residue_connection_map_.

Referenced by core::conformation::Residue::copy_residue_connections(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().

ResidueTypeSet const & core::chemical::ResidueType::residue_type_set ( ) const

References residue_type_set_, and utility_exit_with_message.

Referenced by core::pack::dunbrack::RotamerLibrary::add_residue_library(), 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::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_residue_typeset(), core::conformation::Residue::residue_type_set(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), and core::io::serialization::write_binary().

void core::chemical::ResidueType::residue_type_set ( ResidueTypeSetCAP set_in )

set the residue type set of origin.

References residue_type_set_.

void core::chemical::ResidueType::retype_atoms	(	ElementMap const &	emap,
		bool	preserve = `false`
	)

Reassign Rosetta atom types based on the current heuristics. emap is a map of VD->element strings. If an atom is not present in the element map, attempt to get the element string from the current type (it's an error if it doesn't have one.) If preserve is true, only retype those atoms which have an atom_type_index of zero.

The logic here comes from molfile_to_params.py Which is itself based on Rosetta++ ligand_ns.cc set_rosetta_atom_types(), and has been validated against the Meiler and Baker 2006 cross docking test set assignments

I'm not saying the logic is good, but it's the logic we're using.

This function assumes that:

All bonds and atoms exist.
Bond types (bond_name) are correctly set
The element symbols are either provided in emap, or are available through the currently set types.

References core::chemical::AromaticBond, core::chemical::Atom::atom_type_index(), atom_types_, core::chemical::DoubleBond, graph_, core::chemical::retype_get_element(), core::chemical::retype_is_aromatic(), core::chemical::retype_is_virtual(), core::chemical::SingleBond, smallest_ring_size(), core::scoring::hbonds::t, core::chemical::TripleBond, core::chemical::UnknownBond, and utility_exit_with_message.

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

References rings_and_their_edges_.

core::chemical::rna::RNA_ResidueType const & core::chemical::ResidueType::RNA_type ( ) const

References rna_residue_type_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), and core::conformation::Residue::RNA_type().

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_.

Referenced by core::pack::dunbrack::RotamerLibrary::get_rsd_library(), and core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded().

AA const& core::chemical::ResidueType::rotamer_aa ( ) const

inline

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

void core::chemical::ResidueType::select_orient_atoms	(	Size &	center,
		Size &	nbr1,
		Size &	nbr2
	)		const

Selects three atoms for orienting this residue type.

References atom_base(), atom_index(), atom_is_backbone(), bonded_neighbor(), first_sidechain_atom(), force_nbr_atom_orient(), j, name(), natoms(), nbr_atom(), nbrs(), nheavyatoms(), core::io::serialization::size(), and utility_exit_with_message.

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

void core::chemical::ResidueType::set_adduct_flag ( bool adduct_in )

inline

References is_adduct_.

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_base_, atom_name_to_vd_, cut_bond_neighbor_, finalized_, graph_, has(), and utility_exit_with_message.

Referenced by core::util::add_covalent_linkage_helper(), and core::chemical::ResidueDatabaseIO::read_residue_type_icoor().

void core::chemical::ResidueType::set_atom_type	(	std::string const &	atom_name,
		std::string const &	atom_type_name
	)

set atom type

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

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
	)

set gasteiger atom type

References atom_name(), atom_name_to_vd_, core::chemical::Atom::gasteiger_atom_type(), core::chemical::ChemicalManager::gasteiger_atom_type_set(), gasteiger_atom_types_, core::chemical::ChemicalManager::get_instance(), and graph_.

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`
	)

set AtomICoor for an atom

Referenced by core::util::add_covalent_linkage_helper(), core::chemical::AddConnect::apply(), core::chemical::SetICoor::apply(), assign_internal_coordinates(), calculate_icoor(), and core::chemical::ResidueDatabaseIO::read_residue_type_icoor().

void core::chemical::ResidueType::set_icoor	(	Size const &	index,
		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

void core::chemical::ResidueType::set_ideal_xyz	(	std::string const &	atm,
		Vector const &	xyz_in
	)

References atom_index().

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

void core::chemical::ResidueType::set_ideal_xyz	(	Size	index,
		Vector const &	xyz_in
	)

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

void core::chemical::ResidueType::set_lower_connect_atom ( std::string const & atm_name )

set the atom which connects to the lower connection

References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, ordered_atoms_, residue_connections_, core::chemical::tr, update_residue_connection_mapping(), and upper_connect_id_.

Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().

void core::chemical::ResidueType::set_mainchain_atoms ( AtomIndices const & mainchain )

set indices of all mainchain atoms

References mainchain_atoms_, and ordered_atoms_.

Referenced by core::chemical::PrependMainchainAtom::apply(), and core::chemical::AppendMainchainAtom::apply().

void core::chemical::ResidueType::set_mm_atom_type	(	std::string const &	atom_name,
		std::string const &	mm_atom_type_name
	)

set mm atom type

References atom_name(), atom_name_to_vd_, graph_, core::chemical::Atom::mm_atom_type_index(), and mm_atom_types_.

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

void core::chemical::ResidueType::set_mol_data ( sdf::MolData const & mol_data )

inline

set the MolData object

References mol_data_.

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_, s1, and s2.

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

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().

void core::chemical::ResidueType::set_RotamerLibraryName ( std::string const & filename )

References rotamer_library_name_.

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

void core::chemical::ResidueType::set_shadowing_atom	(	std::string const &	atom,
		std::string const &	atom_being_shadowed
	)

References atom_index(), and atom_shadowed_.

void core::chemical::ResidueType::set_upper_connect_atom ( std::string const & atm_name )

set the atom which connects to the upper connection

References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, ordered_atoms_, residue_connections_, core::chemical::tr, update_residue_connection_mapping(), and upper_connect_id_.

Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().

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::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.

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 ) const

Generate string representation of ResidueType for debugging purposes.

Author: Labonte

References all_bb_atoms_, all_sc_atoms_, atom_name(), carbohydrate_info_, is_carbohydrate_, mainchain_atoms_indices_, name1_, name3_, name_, and properties_.

Referenced by core::chemical::operator<<(), and core::conformation::Residue::show().

void core::chemical::ResidueType::show_all_atom_names ( std::ostream & out ) const

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

Referenced by atom_index(), and vd_from_name().

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 retype_atoms().

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

update actcoord

update actcoord average geometrical center of the set of actcoord_atoms_

References core::conformation::Residue::actcoord(), actcoord_atoms_, core::conformation::Residue::atoms(), n_actcoord_atoms_, vd_to_index_, and numeric::xyzVector< class >::zero().

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

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, including
, Hbond donor and acceptors, path_distance etc.

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(), carbohydrate_info_, conformer_set_, 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_, core::chemical::Atom::is_acceptor(), is_carbohydrate_, is_cyclic_, core::chemical::Atom::is_haro(), core::chemical::Atom::is_hydrogen(), core::chemical::Atom::is_polar_hydrogen(), is_RNA_, core::chemical::Atom::is_virtual(), j, last_controlling_chi_, n_backbone_heavyatoms_, natoms(), ndihe_, nheavyatoms_, nu_atoms_indices_, ordered_atoms_, path_distance_, path_distances(), residue_connections_, 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

References atom_2_residue_connection_map_, natoms(), residue_connections_, and vd_to_index_.

Referenced by add_residue_connection(), generate_atom_indices(), set_lower_connect_atom(), and set_upper_connect_atom().

ResidueConnection const & core::chemical::ResidueType::upper_connect ( ) const

References is_polymer_, residue_connections_, and upper_connect_id_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::upper_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

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

index number of the atom which connects to the upper connection

References is_polymer_, residue_connections_, upper_connect_id_, and vd_to_index_.

Referenced by core::chemical::ICoorAtomID::atom_id(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ICoorAtomID::xyz().

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

inline

References upper_connect_id_.

Referenced by core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::conformation::Residue::has_upper_connect(), and core::conformation::Residue::is_polymer_bonded().

utility::vector1< VariantType > const& core::chemical::ResidueType::variant_types ( ) const

inline

get all the variant types for this ResidueType

References variant_types_.

Referenced by core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::chemical::ResidueSelector::match_variants(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::chemical::Selector_NO_VARIANTS::operator[](), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), and core::pose::residue_types_from_sequence().

bool core::chemical::ResidueType::variants_match ( ResidueType const & other ) const

Does this residue have exactly the same set of properties as residue other? phil – this code does not look correct to me should probably be other.has_variant_type not other.has_property.

References core::chemical::DEPROTONATED, has_variant_type(), basic::options::option, basic::options::OptionKeys::pH::pH_mode, core::chemical::PROTONATED, user, and variant_types_.

Referenced by core::pack::task::ResidueLevelTask_::ResidueLevelTask_().

VD core::chemical::ResidueType::vd_from_index ( Size const & atomno ) const

Get the vertex descriptor from the atom index.

References ordered_atoms_.

VD core::chemical::ResidueType::vd_from_name ( std::string const & name ) const

get the vertex descriptor from the name of the atom.

References atom_name_to_vd_, name3(), show_all_atom_names(), and core::chemical::tr.

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

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

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

private

Referenced by update_derived_data().

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

private

Referenced by abase2(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_

private

Referenced by accpt_pos(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_sc_

private

Referenced by accpt_pos_sc(), and update_derived_data().

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

private

indices of action coordinate centers

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

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

AtomIndices core::chemical::ResidueType::actcoord_atoms_indices_

private

Referenced by actcoord_atoms(), and generate_atom_indices().

AtomIndices core::chemical::ResidueType::all_bb_atoms_

private

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

AtomIndices core::chemical::ResidueType::all_sc_atoms_

private

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

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::atom_2_residue_connection_map_

private

Referenced by add_atom(), atom_forms_residue_connection(), generate_atom_indices(), n_residue_connections_for_atom(), residue_connection_id_for_atom(), residue_connections_for_atom(), and update_residue_connection_mapping().

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

private

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

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

private

Referenced by atom_base(), and generate_atom_indices().

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

private

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

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

private

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

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

private

Referenced by atom_being_shadowed(), and generate_atom_indices().

AtomTypeSetCAP core::chemical::ResidueType::atom_types_

private

Referenced by acceptor_atoms(), add_atom(), 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(), retype_atoms(), and set_atom_type().

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

private

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

AtomIndices core::chemical::ResidueType::atoms_with_orb_index_

private

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.

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.

Referenced by atoms_within_two_bonds_of_a_residue_connection(), and update_derived_data().

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

private

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

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

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

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

private

Referenced by bondangles_for_atom(), and update_derived_data().

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

private

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

utility::vector1<utility::vector1<BondName> > core::chemical::ResidueType::bonded_neighbor_type_

private

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

core::chemical::carbohydrates::CarbohydrateInfoOP core::chemical::ResidueType::carbohydrate_info_

private

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

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

private

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

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

private

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

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

private

Referenced by chi_atoms(), and generate_atom_indices().

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

private

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

RingConformerSetOP core::chemical::ResidueType::conformer_set_

private

Referenced by ring_conformer_set(), and update_derived_data().

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

private

Referenced by add_cut_bond(), generate_atom_indices(), ResidueType(), and set_atom_base().

utility::vector1< AtomIndices > core::chemical::ResidueType::cut_bond_neighbor_indices_

private

Referenced by cut_bond_neighbor(), and generate_atom_indices().

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

private

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

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

private

Referenced by dihedral(), print_dihedrals(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::dihedrals_for_atom_

private

Referenced by dihedrals_for_atom(), and update_derived_data().

ElementSetCAP core::chemical::ResidueType::elements_

private

Referenced by add_atom(), and element_set().

bool core::chemical::ResidueType::finalized_

private

Size core::chemical::ResidueType::first_sidechain_hydrogen_

private

Referenced by atom_is_backbone(), first_sidechain_hydrogen(), and update_derived_data().

utility::vector1<VD> core::chemical::ResidueType::force_bb_

private

a list of atom indices to be deleted

in the next call to finalize(), used in delete_atom which is called during patching atom indices forced to be considered backbone

Referenced by ResidueType(), set_backbone_heavyatom(), and setup_atom_ordering().

bool core::chemical::ResidueType::force_nbr_atom_orient_

private

Referenced by force_nbr_atom_orient().

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueType::gasteiger_atom_types_

private

Referenced by set_gasteiger_atom_type(), and set_gasteiger_typeset().

ResidueGraph core::chemical::ResidueType::graph_

private

Referenced by acceptor_atoms(), add_atom(), add_bond(), add_orbital_bond(), apolar_hydrogens(), aromatic_atoms(), assign_neighbor_atom(), atom(), atom_index(), atom_is_polar_hydrogen(), atom_iterators(), atom_name(), atom_type(), bond(), bond_iterators(), bonded_neighbor_iterators(), bonded_orbitals(), delete_atom(), gasteiger_atom_type(), generate_atom_indices(), graph(), heavy_atom_with_hydrogens(), heavy_atom_with_polar_hydrogens(), heavy_atoms(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), hydrogens(), mm_atom_type(), natoms(), nbonds(), polar_hydrogens(), print_bondangles(), print_dihedrals(), print_pretty_path_distances(), ResidueType(), retype_atoms(), set_atom_base(), set_atom_type(), set_gasteiger_atom_type(), set_ideal_xyz(), set_mm_atom_type(), setup_atom_ordering(), show_all_atom_names(), smallest_ring_size(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Haro_index_

private

Referenced by Haro_index(), and update_derived_data().

bool core::chemical::ResidueType::has_sc_orbitals_

private

Referenced by add_property(), delete_property(), and has_sc_orbitals().

AtomIndices core::chemical::ResidueType::Hpol_index_

private

Referenced by Hpol_index(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_apolar_

private

Referenced by Hpos_apolar(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_

private

Referenced by Hpos_polar(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_sc_

private

Referenced by Hpos_polar_sc(), and update_derived_data().

std::map< VD, AtomICoor > core::chemical::ResidueType::icoor_

private

Referenced by add_atom(), generate_atom_indices(), icoor(), and ResidueType().

std::string core::chemical::ResidueType::interchangeability_group_

private

Referenced by interchangeability_group().

bool core::chemical::ResidueType::is_acetylated_nterminus_

private

Referenced by add_property(), delete_property(), and is_acetylated_nterminus().

bool core::chemical::ResidueType::is_adduct_

private

Referenced by is_adduct(), and set_adduct_flag().

bool core::chemical::ResidueType::is_alpha_aa_

private

Referenced by add_property(), delete_property(), is_alpha_aa(), and perform_checks().

bool core::chemical::ResidueType::is_aromatic_

private

Referenced by add_property(), delete_property(), is_aromatic(), and requires_actcoord().

bool core::chemical::ResidueType::is_beta_aa_

private

Referenced by add_property(), delete_property(), is_beta_aa(), and perform_checks().

bool core::chemical::ResidueType::is_branch_lower_terminus_

private

Referenced by add_property(), delete_property(), and is_branch_lower_terminus().

bool core::chemical::ResidueType::is_carbohydrate_

private

Referenced by add_property(), delete_property(), is_carbohydrate(), show(), and update_derived_data().

bool core::chemical::ResidueType::is_charged_

private

Referenced by add_property(), delete_property(), and is_charged().

bool core::chemical::ResidueType::is_coarse_

private

Referenced by add_property(), delete_property(), and is_coarse().

bool core::chemical::ResidueType::is_cyclic_

private

Referenced by add_property(), delete_property(), is_cyclic(), and update_derived_data().

bool core::chemical::ResidueType::is_d_aa_

private

Referenced by add_property(), delete_property(), is_d_aa(), and perform_checks().

bool core::chemical::ResidueType::is_DNA_

private

Referenced by add_property(), delete_property(), and is_DNA().

bool core::chemical::ResidueType::is_l_aa_

private

Referenced by add_property(), delete_property(), is_l_aa(), and perform_checks().

bool core::chemical::ResidueType::is_ligand_

private

Referenced by add_property(), delete_property(), and is_ligand().

bool core::chemical::ResidueType::is_lipid_

private

Referenced by add_property(), delete_property(), and is_lipid().

bool core::chemical::ResidueType::is_lower_terminus_

private

Referenced by add_property(), delete_property(), and is_lower_terminus().

bool core::chemical::ResidueType::is_metal_

private

Referenced by add_property(), delete_property(), and is_metal().

bool core::chemical::ResidueType::is_metalbinding_

private

Referenced by add_property(), delete_property(), and is_metalbinding().

bool core::chemical::ResidueType::is_methylated_cterminus_

private

Referenced by add_property(), delete_property(), and is_methylated_cterminus().

bool core::chemical::ResidueType::is_NA_

private

Referenced by add_property(), and is_NA().

bool core::chemical::ResidueType::is_phosphonate_

private

Referenced by add_property(), and delete_property().

bool core::chemical::ResidueType::is_phosphonate_upper_

private

Referenced by add_property(), and delete_property().

bool core::chemical::ResidueType::is_polar_

private

Referenced by add_property(), delete_property(), is_polar(), and requires_actcoord().

bool core::chemical::ResidueType::is_polymer_

private

Referenced by add_property(), delete_property(), is_polymer(), lower_connect(), lower_connect_atom(), upper_connect(), and upper_connect_atom().

bool core::chemical::ResidueType::is_protein_

private

Referenced by add_property(), delete_property(), is_protein(), and requires_actcoord().

utility::vector1< bool > core::chemical::ResidueType::is_proton_chi_

private

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

bool core::chemical::ResidueType::is_RNA_

private

Referenced by add_property(), delete_property(), is_RNA(), and update_derived_data().

bool core::chemical::ResidueType::is_surface_

private

Referenced by add_property(), delete_property(), and is_surface().

bool core::chemical::ResidueType::is_terminus_

private

Referenced by add_property(), delete_property(), and is_terminus().

bool core::chemical::ResidueType::is_upper_terminus_

private

Referenced by add_property(), delete_property(), and is_upper_terminus().

utility::vector1< Size > core::chemical::ResidueType::last_controlling_chi_

private

Referenced by last_controlling_chi(), note_chi_controls_atom(), update_derived_data(), and update_last_controlling_chi().

Size core::chemical::ResidueType::lower_connect_id_

private

Polymer lower connections.

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by lower_connect(), lower_connect_atom(), lower_connect_id(), residue_connection_is_polymeric(), set_lower_connect_atom(), and set_upper_connect_atom().

utility::vector1<VD> core::chemical::ResidueType::mainchain_atoms_

private

indices of all mainchain atoms

mainchain_atoms are those atoms on a path from polymer lower_connect to upper_connect. For protein, this will be N, CA and C.

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

AtomIndices core::chemical::ResidueType::mainchain_atoms_indices_

private

Referenced by generate_atom_indices(), mainchain_atom(), mainchain_atoms(), and show().

Real core::chemical::ResidueType::mass_

private

Referenced by add_atom(), and mass().

utility::vector1< std::string > core::chemical::ResidueType::metal_binding_atoms_

private

Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types.

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

Referenced by add_metalbinding_atom(), get_metal_binding_atoms(), and perform_checks().

MMAtomTypeSetCAP core::chemical::ResidueType::mm_atom_types_

private

Referenced by add_atom(), mm_atom_type(), and set_mm_atom_type().

sdf::MolData core::chemical::ResidueType::mol_data_

private

Referenced by get_mol_data(), and set_mol_data().

Size core::chemical::ResidueType::n_actcoord_atoms_

private

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

Size core::chemical::ResidueType::n_backbone_heavyatoms_

private

Referenced by atom_is_backbone(), first_sidechain_atom(), last_backbone_atom(), setup_atom_ordering(), and update_derived_data().

Size core::chemical::ResidueType::n_hbond_acceptors_

private

Referenced by add_atom(), and n_hbond_acceptors().

Size core::chemical::ResidueType::n_hbond_donors_

private

Referenced by add_atom(), and n_hbond_donors().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections_

private

Referenced by add_residue_connection(), and n_non_polymeric_residue_connections().

Size core::chemical::ResidueType::n_orbitals_

private

Referenced by add_orbital(), and n_orbitals().

Size core::chemical::ResidueType::n_polymeric_residue_connections_

private

Referenced by n_polymeric_residue_connections(), set_lower_connect_atom(), and set_upper_connect_atom().

char core::chemical::ResidueType::name1_

private

Referenced by name1(), and show().

std::string core::chemical::ResidueType::name3_

private

Referenced by get_numeric_property(), get_string_property(), name3(), and show().

std::string core::chemical::ResidueType::name_

private

Referenced by add_actcoord_atom(), name(), and show().

Size core::chemical::ResidueType::nbonds_

private

Referenced by add_bond(), and nbonds().

VD core::chemical::ResidueType::nbr_atom_

private

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

Size core::chemical::ResidueType::nbr_atom_indices_

private

Referenced by generate_atom_indices(), and nbr_atom().

Real core::chemical::ResidueType::nbr_radius_

private

Referenced by nbr_radius().

utility::vector1< Size > core::chemical::ResidueType::ncaa_rotlib_n_bins_per_rot_

private

Referenced by get_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_bin_per_rot().

Size core::chemical::ResidueType::ncaa_rotlib_n_rots_

private

Referenced by set_ncaa_rotlib_n_bin_per_rot(), and set_ncaa_rotlib_n_rotameric_bins().

std::string core::chemical::ResidueType::ncaa_rotlib_path_

private

Referenced by get_ncaa_rotlib_path(), and set_ncaa_rotlib_path().

Size core::chemical::ResidueType::ndihe_

private

Referenced by ndihe(), print_dihedrals(), and update_derived_data().

Size core::chemical::ResidueType::nheavyatoms_

private

Referenced by atom_is_backbone(), atom_is_hydrogen(), first_sidechain_atom(), nheavyatoms(), perform_checks(), setup_atom_ordering(), and update_derived_data().

bool core::chemical::ResidueType::nondefault_

private

Referenced by nondefault().

utility::vector1<utility::vector1<VD> > core::chemical::ResidueType::nu_atoms_

private

Referenced by add_nu(), generate_atom_indices(), n_nus(), and ResidueType().

utility::vector1<AtomIndices> core::chemical::ResidueType::nu_atoms_indices_

private

Referenced by generate_atom_indices(), nu_atoms(), and update_derived_data().

std::map<std::string,core::Real> core::chemical::ResidueType::numeric_properties_

private

Referenced by add_numeric_property(), and get_numeric_property().

orbitals::OrbitalTypeSetCAP core::chemical::ResidueType::orbital_types_

private

Referenced by add_orbital(), and orbital_type().

utility::vector1< Orbital > core::chemical::ResidueType::orbitals_

private

Referenced by add_orbital(), generate_atom_indices(), new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), ResidueType(), and set_orbital_icoor_id().

std::map< std::string, int > core::chemical::ResidueType::orbitals_index_

private

Referenced by add_orbital(), add_orbital_bond(), has_orbital(), and orbital_index().

VDs core::chemical::ResidueType::ordered_atoms_

private

utility::vector1<VD> core::chemical::ResidueType::parents_

private

Referenced by add_atom(), and assign_internal_coordinates().

utility::vector1< utility::vector1< int > > core::chemical::ResidueType::path_distance_

private

Referenced by path_distance(), path_distances(), print_pretty_path_distances(), and update_derived_data().

utility::vector1< std::string > core::chemical::ResidueType::properties_

private

Referenced by add_property(), delete_property(), has_property(), properties(), and show().

utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_extra_samples_

private

Referenced by proton_chi_extra_samples(), and set_proton_chi().

utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_samples_

private

Referenced by proton_chi_samples(), and set_proton_chi().

utility::vector1< Size > core::chemical::ResidueType::proton_chis_

private

Referenced by is_proton_chi(), n_proton_chi(), proton_chi_2_chi(), and set_proton_chi().

utility::vector1< ResidueConnection > core::chemical::ResidueType::residue_connections_

private

Vector of inter-residue connections expected for this residuetype NOW includes the polymer connections, as well as disulf-type connections.

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom; Much of the code assumes at most one residue connection per atom. The pseudobond code has been partially written to handle cases where multiple connections to a single atom can exist, but much of the standard residue connection code assumes a simple correspondence between atoms and residue connections. That code will have to be updated to support single-atom "backbones."

Referenced by add_residue_connection(), generate_atom_indices(), lower_connect(), lower_connect_atom(), n_residue_connections(), residue_connect_atom_index(), residue_connection(), ResidueType(), set_lower_connect_atom(), set_upper_connect_atom(), update_derived_data(), update_residue_connection_mapping(), upper_connect(), and upper_connect_atom().

ResidueTypeSetCAP core::chemical::ResidueType::residue_type_set_

private

Referenced by residue_type_set().

std::list<utility::vector1< ED > > core::chemical::ResidueType::rings_and_their_edges_

private

Referenced by ResidueType(), and rings().

core::chemical::rna::RNA_ResidueTypeOP core::chemical::ResidueType::rna_residue_type_

private

Referenced by RNA_type(), and update_derived_data().

AA core::chemical::ResidueType::rotamer_aa_

private

Referenced by rotamer_aa().

std::string core::chemical::ResidueType::rotamer_library_name_

private

Referenced by get_RotamerLibraryName(), and set_RotamerLibraryName().

bool core::chemical::ResidueType::serialized_

mutable

std::map<std::string,std::string> core::chemical::ResidueType::string_properties_

private

Referenced by add_string_property(), and get_string_property().

Size core::chemical::ResidueType::upper_connect_id_

private

Polymer upper connections.

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by residue_connection_is_polymeric(), set_lower_connect_atom(), set_upper_connect_atom(), upper_connect(), upper_connect_atom(), and upper_connect_id().

bool core::chemical::ResidueType::use_ncaa_rotlib_

private

Referenced by get_use_ncaa_rotlib(), and set_use_ncaa_rotlib().

utility::vector1< VariantType > core::chemical::ResidueType::variant_types_

private

Referenced by add_variant_type(), has_variant_type(), nonadduct_variants_match(), variant_types(), and variants_match().

std::map<VD, Size> core::chemical::ResidueType::vd_to_index_

private

Referenced by add_atom(), assign_internal_coordinates(), generate_atom_indices(), lower_connect_atom(), residue_connect_atom_index(), ResidueType(), update_actcoord(), update_derived_data(), update_residue_connection_mapping(), and upper_connect_atom().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within1bonds_sets_for_atom_

private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array.

Referenced by update_derived_data(), and within1bonds_sets_for_atom().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within2bonds_sets_for_atom_

private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array.

Referenced by update_derived_data(), and within2bonds_sets_for_atom().

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

symlinks/rosetta/src/core/chemical/ResidueType.hh
symlinks/rosetta/src/core/chemical/ResidueType.cc

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

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