A class for defining a type of residue, modifiable version. More...

#include <MutableResidueType.hh>

Inheritance diagram for core::chemical::MutableResidueType:

Public Member Functions
	MutableResidueType (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)
	constructor More...

	MutableResidueType (MutableResidueType const &residue_type)
	Make a copy of a MutableResidueType. More...

	MutableResidueType (ResidueType const &residue_type)
	Make a modifiable residue type from a standard one. More...

MutableResidueTypeOP	clone () const
	make a copy More...

MutableResidueTypeOP	placeholder_clone () const
	make a copy More...

	MutableResidueType (MutableResidueType &&residue_type)=default
	Move constructor, for rule of 5. More...

	~MutableResidueType () override
	destructor, for rule of 5 More...

MutableResidueType &	operator= (MutableResidueType const &src)
	Copies <src> into the MutableResidueType. More...

MutableResidueType &	operator= (MutableResidueType &&)=default
	Move assignment, for rule of 5. More...

Size	natoms () const override
	number of atoms Note: Don't use this to iterate over atoms – use the vector returned by all_atoms() instead. More...

Size	nheavyatoms () const override
	number of heavy atoms More...

Size	nbonds () const override
	number of bonds More...

Size	nbonds (VD atom) const
	number of bonds for given atom More...

Size	n_virtual_atoms () const override
	Counts the number of virtual atoms and returns the count. More...

ResidueGraph const &	graph () const
	Constant access to the underlying graph. More...

VIterPair	atom_iterators () const

EIterPair	bond_iterators () const

OutEdgeIterPair	bond_iterators (VD const &atom) const

utility::vector1< VD > const &	all_atoms () const
	Convenience function for iterating over all the atoms e.g. `for ( VA atm: restype->all_atoms() ) {` More...

Atom &	atom (VD const atom_vd)

Atom const &	atom (VD const atom_vd) const

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

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

bool	has (std::string const &atom_name) const override
	is this atom present in this residue? More...

bool	has (VD const vd) const
	is this vertex descriptor present in this residue? More...

std::string const &	atom_name (VD const vd) const
	get atom name by vertex descriptor IMPORTANT NOTE: Atoms don't necessarily have names! More...

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

Size	atom_index (VD const &vd) const
	Get an integer value for the atom (the index for all_atoms()) More...

AtomType const &	atom_type (VD const vd) const
	Get the chemical atom_type for this atom. More...

Bond &	bond (ED const ed)

Bond const &	bond (ED const ed) const

Bond &	bond (VD vd1, VD vd2)

Bond const &	bond (VD vd1, VD vd2) const

Bond &	bond (std::string const &atom1, std::string const &atom2)

Bond const &	bond (std::string const &atom1, std::string const &atom2) const

bool	atoms_are_bonded (std::string const &atom1, std::string const &atom2) const

AdjacentIterPair	bonded_neighbor_iterators (VD const &atom) const

utility::vector1< VD >	bonded_neighbors (VD const &atom) const
	Get the atoms bonded to the specified atom. More...

Size	number_bonded_hydrogens (VD atomvd) const
	indicates how many proton bonded neighbors an atom has More...

utility::vector1< VD >	bonded_hydrogens (VD const &atom) const
	Get the atoms bonded to the specified atom, if they're annotated as hydrogens. More...

Size	number_bonded_heavyatoms (VD atomvd) const
	indicates how many heavyatom bonded neighbors an atom has, graph version More...

utility::vector1< VD >	bonded_heavyatoms (VD const &atom) const
	Get the atoms bonded to the specified atom, if they're annotated as heavyatoms. More...

Size	nchi () const
	number of chi 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...

bool	chi_valid (Size const chino) const
	Will return if the chi is currently valid. More...

Size	n_nus () const
	Return number of nu (internal ring) angles. More...

Size	n_rings () const
	Return the number of rings in this residue. More...

VDs const &	chi_atom_vds (Size const chino) const
	VDs of the atoms which are used to define a given chi angle (chino) More...

utility::vector1< Real > const &	proton_chi_samples_for_chi (Size chino) const
	The proton chi samples Important - this takes the full chi numbering (not proton chi numbering) More...

utility::vector1< Real > const &	proton_chi_extra_samples_for_chi (Size chino) const
	The proton chi extra samples Important - this takes the full chi numbering (not proton chi numbering) More...

utility::vector1< std::pair < Real, Real > > const &	chi_rotamers (Size const chino) const
	all rotamers bins (mean, std) for a given chi angle More...

utility::vector1< VD > const &	nu_atoms (core::uint const nu_index) const

utility::vector1< VD > const &	ring_atoms (core::uint const ring_num) const

core::chemical::rings::RingSaturationType	ring_saturation_type (uint const ring_num) const
	Return the saturation level of this residue's nth cycle. More...

utility::vector1< std::string > const &	low_ring_conformers (core::uint const ring_num) const
	Low-energy ring conformers for the given ring. More...

std::string const &	lowest_ring_conformer (core::uint const ring_num) const
	Lowest-energy ring conformer for the given ring. More...

Size	n_possible_residue_connections () const
	number of ResidueConnections, counting polymeric residue connections More...

MutableResidueConnection const &	residue_connection (Size const i) const
	Get a ResidueConection. More...

MutableResidueConnection &	residue_connection (Size const i)
	Get a ResidueConection. More...

VD	residue_connect_atom (Size const resconn_id) const

Size	n_residue_connections_for_atom (VD const atomid) const

Size	add_residue_connection (std::string const &atom_name)
	add a non-polymeric ResidueConnection More...

void	delete_residue_connection (VD atm)
	Remove all connections (both polymeric and otherwise) for an atom. More...

Size	n_polymeric_residue_connections () const
	The number of polymeric residue connections. More...

bool	residue_connection_is_polymeric (Size const resconn_id) const

MutableResidueConnection const &	lower_connect () const

Size	lower_connect_id () const

VD	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...

MutableResidueConnection const &	upper_connect () const

Size	upper_connect_id () const

VD	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...

void	add_metapatch_connect (std::string const &atom)

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

void	nbr_atom (VD vertex)
	set nbr_atom used to define residue-level neighbors More...

VD	nbr_vertex () const
	get VD used to define residue-level neighbors More...

void	nbr_radius (Real const radius)
	set nbr_radius_ used to define residue-level neighbors More...

Real	nbr_radius () const
	get nbr_radius_ used to define residue-level neighbors More...

void	set_backbone_heavyatom (std::string const &name)
	set an atom as backbone heavy atom More...

bool	is_backbone_heavyatom (VD atom) const

utility::vector1< VD > const &	mainchain_atoms () const
	indices of all mainchain atoms More...

void	set_mainchain_atoms (utility::vector1< VD > const &mainchain)
	set indices of all mainchain atoms TODO Should we make sure that mainchain atoms are also backbones? More...

utility::vector1< VD >	actcoord_atoms () const
	get descriptors for atoms used to define actcoord More...

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

void	delete_actcoord_atom (std::string const &atom_name)
	Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used) More...

void	add_atom_alias (std::string const &rosetta_atom, std::string const &alias)
	Add an alias name for an atom. More...

void	add_canonical_atom_alias (std::string const &rosetta_atom, std::string const &alias)
	store canonical to alias mapping More...

void	delete_atom_alias (std::string const &alias, bool error=true)
	Remove a given alias name for an atom. More...

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

std::map< VD, VD > const &	shadow_atoms () const

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	delete_metalbinding_atom (std::string const &atom_name)
	Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used) More...

bool	is_base_type () const override
	Is this ResidueType a base type? More...

ResidueTypeCOP	get_base_type_cop () const override
	Get a pointer to this ResidueType's base ResidueType. More...

void	reset_base_type_cop ()
	Reset the base type COP to be null. This implies that this ResidueTypeBase is a base type. More...

void	set_base_type_cop (ResidueTypeCOP new_base_type)
	Set the base type COP. This implies that this ResidueTypeBase is NOT a base type. More...

VD	add_atom (std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge)
	add an atom into this residue Will return the vertex descriptor of the added atom. More...

VD	add_atom (std::string const &atom_name="")
	add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom. More...

VD	add_atom (Atom const &atom, MutableICoorRecord const &icoor)

void	delete_atom (std::string const &name)
	Remove the atom from the ResidueType. More...

void	delete_atom (VD atom)
	Remove the atom from the ResidueType. More...

void	rename_atom (VD atom, std::string const &name)
	Rename the atom, updating the ResidueType-internal data mapping. More...

void	set_atom_type (std::string const &name, std::string const &atom_type_name)
	set atom type More...

void	set_atom_type (VD atom, std::string const &atom_type_name)

void	set_gasteiger_atom_type (std::string const &atom_name, std::string const &gasteiger_atom_type_name)
	set gasteiger atom type More...

void	set_gasteiger_atom_type (VD atom, std::string const &gasteiger_atom_type_name)
	set gasteiger atom type More...

void	delete_child_proton (std::string const &atom)

void	add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond)
	add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...

void	add_bond (VD atom1, VD atom2, BondName bondLabel=SingleBond)
	add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...

void	delete_bond (VD atom1, VD atom2)
	Delete a bond between the two atoms. More...

void	change_bond_type (std::string const &atom_name1, std::string const &atom_name2, BondName const new_bond_label)
	Change the bond type of the given bond from one type to another. More...

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	reset_bond_distance_to_atom (std::string const &atm, core::Distance const d)
	Reset the bond distance to an atom whose internal coordinates have already been set. More...

VD	root_atom () const
	get root_atom used as the base of the icoor tree. More...

MutableICoorRecordCOP	icoor (VD const atm) const
	MutableICoorRecord 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 MutableICoorRecord for an atom More...

void	set_icoor (VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false)
	set MutableICoorRecord for an atom, vertex descriptor version More...

void	set_icoor (VD 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 MutableICoorRecord for an atom, vertex descriptor version More...

void	clear_icoor ()

VD	atom_base (VD const atm) const
	The atom base is the distance atom the atom is bonded to. If the specified atom doesn't have valid ICOOR record yet, this function will return a null vertex. More...

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

void	set_ideal_xyz (VD atm, Vector const &xyz_in)

void	add_chi (Size const chino, VD atom1, VD atom2, VD atom3, VD atom4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (VD atom1, VD atom2, VD atom3, VD atom4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	Add a chi (side-chain) angle defined by four atoms to the end of the list of chis. More...

void	redefine_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	redefine a chi angle based on four atoms More...

void	set_proton_chi (Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples)
	Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior. More...

void	add_chi_rotamer (Size const chino, Real const mean, Real const sdev)
	Add a rotamer bin for a given chi. More...

void	add_chi_rotamer_to_last_chi (core::Angle const mean, core::Angle const sdev)
	Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this MutableResidueType. More...

void	clear_chi_rotamers (core::uint const chi_no)
	Delete all of the chi rotamer bins from the specified chi for this MutableResidueType. More...

void	delete_terminal_chi ()
	delete terminal chi angle More...

void	delete_chi (Size const chino)
	Deletes a given chi, potentially renumbering the remaining 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	delete_nu (core::uint const nu_index)
	Deletes a given nu, potentially renumbering the remaining nus. More...

void	add_ring (core::uint const ring_num, utility::vector1< std::string > const &ring_atoms, core::chemical::rings::RingSaturationType const saturation_type=core::chemical::rings::ALIPHATIC)
	Add a ring definition. More...

void	set_lowest_energy_ring_conformer (core::uint const ring_num, std::string const &conformer)
	Set this cyclic residue's lowest-energy ring conformer for the nth ring by IUPAC name. More...

void	set_low_energy_ring_conformers (core::uint const ring_num, utility::vector1< std::string > const &conformers)
	Set this cyclic residue's low-energy ring conformers for the nth ring by IUPAC name. More...

void	delete_ring (core::uint const ring_num)
	Deletes a given ring, potentially renumbering the remaining ring. More...

void	clear_orbitals ()
	clear orbitals 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...

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...

void	show (std::ostream &output=std::cout, bool output_atomic_details=false) const override
	Generate string representation of MutableResidueType for debugging purposes. More...

void	dump_vd_info () const

void	show_all_atom_names (std::ostream &out) const override

void	assign_neighbor_atom ()
	Figure out what the "center" atom of the residue is from current coordinates. More...

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

void	assign_internal_coordinates (core::chemical::VD new_root)
	Function to assign internal coordinates from bonding patterns Note that it currently does not work well with polymers. More...

void	fill_ideal_xyz_from_icoor ()
	Assign ideal_xyz coordinates from icoor records. More...

void	autodetermine_chi_bonds (core::Size max_proton_chi_samples=500)
	Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all. More...

bool	validate_residue_type () const
	Run checks on this MutableResidueType, checking to make sure it's okay. Return true on success and false on failure (Intended usage is within something like a debug_assert()) More...

std::map< std::string, VD > const &	get_atom_name_to_vd_map () const
	Get access to the atom_name-to-vd map. Provided only for MutableResidueType->ResidueType conversion. More...

void	update_atom_type_set (AtomTypeSetCOP setting)
	Change which atom type set this MutableResidueType points to WARNING - While this tries to switch over the atom types, it will null out any that don't have exact name correspondences. You NEED to go through and manually reset the types on all atoms. Exposed for black-magic use only. More...

Public Member Functions inherited from core::chemical::ResidueTypeBase
TypeSetMode	mode () const

AtomTypeSet const &	atom_type_set () const
	access by reference the atomset for which this residue is constructed More...

AtomTypeSetCOP	atom_type_set_ptr () const
	access by const pointer the atomset for which this residue is constructed More...

ElementSet const &	element_set () const
	access by reference the element set for which this residue is constructed More...

ElementSetCOP	element_set_ptr () const
	access by const pointer the element set for which this residue is constructed More...

MMAtomTypeSetCOP	mm_atom_types_ptr () const

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_typeset () const

void	set_gasteiger_atom_typeset (gasteiger::GasteigerAtomTypeSetCOP setting)

orbitals::OrbitalTypeSetCOP	orbital_types_ptr () const
	Get the MM atom_type for this atom by its index number in this residue. More...

void	set_orbital_typeset (orbitals::OrbitalTypeSetCOP setting)

bool	has_orbital_types () const
	Does this residue type define orbital types? More...

signed long int	net_formal_charge () const
	Get the nominal net formal charge on this residue type. More...

void	net_formal_charge (signed long int charge_in)
	Set the nominal net formal charge on this residue type. More...

utility::vector1< std::string > const &	get_metal_binding_atoms () const

std::string const &	get_disulfide_atom_name () const
	Gets disulfide atom name. More...

void	set_disulfide_atom_name (std::string const &n)
	Sets disulfide atom name. More...

std::map< std::string, std::string > const &	atom_aliases () const
	returns atom aliases More...

std::string const &	atom_alias (std::string const &name) const
	returns atom alias More...

std::map< std::string, std::string > const &	canonical_atom_aliases () const
	returns atom aliases More...

std::string const &	canonical_atom_alias (std::string const &name) const
	returns atom alias More...

Orbital const &	orbital (Size const orbital_index) const

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

orbitals::OrbitalType const &	orbital_type (Size const orbital_index) const

Size	n_orbitals () const
	number of orbitals More...

bool	has_orbital (std::string const &orbital_name) const
	is this orbital present in this residue? More...

core::Size	orbital_index (std::string const &name) const
	get orbital index by name More...

ResidueProperties const &	properties () const
	Access the collection of properties for this ResidueTypeBase. More...

void	set_properties (ResiduePropertiesOP properties)
	Set the collection of properties for this ResidueTypeBase. More...

void	add_property (std::string const &property)
	Add a property to this ResidueTypeBase. More...

void	add_property (core::chemical::ResidueProperty const property)
	Add a property to this ResidueType, by properties enum. More...

void	set_adduct_flag (bool adduct_in)

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

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

void	delete_property (std::string const &property)
	Delete a property of this ResidueType. More...

void	delete_property (core::chemical::ResidueProperty const property)
	Delete a property of this ResidueType, by properties enum. More...

void	set_metapatched ()
	Set that this is a metapatched ResidueType. More...

bool	is_metapatched () const
	Get whether this is a metapatched ResidueType. More...

bool	is_polymer () const
	is polymer? More...

bool	is_protein () const
	is protein? More...

bool	is_DNA () const
	is DNA? More...

bool	is_RNA () const
	is RNA? More...

bool	is_d_aa () const
	is this a d-amino acid? More...

bool	is_l_aa () const
	is this an l-amino acid? More...

bool	is_d_rna () const
	is this a d-RNA? More...

bool	is_l_rna () const
	is this an l-RNA? More...

bool	is_peptoid () const
	is peptoid? More...

bool	is_r_peptoid () const
	Is this a peptoid with a chiral side-chain with "R" chirality? More...

bool	is_s_peptoid () const
	Is this a peptoid with a chiral side-chain with "S" chirality? More...

bool	is_achiral_backbone () const
	is this an achiral backbone? More...

bool	is_achiral_sidechain () const
	Does this have an achiral sidechain? More...

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

bool	has_property (ResidueProperty const property) const
	Generic property access, by ResidueProperty. More...

core::Real	get_numeric_property (std::string const &tag) const
	Get a numeric property, if it exists. More...

std::string	get_string_property (std::string const &tag) const
	Get a string property, if it exists. More...

void	add_variant_type (VariantType const variant_type)
	Add a variant type to this ResidueTypeBase. More...

void	add_variant_type (std::string const &variant_type)
	Add a variant type to this ResidueTypeBase by string. More...

void	remove_variant_type (VariantType const variant_type)
	Remove a variant type to this ResidueTypeBase. More...

void	remove_variant_type (std::string const &variant_type)
	Remove a variant type to this ResidueTypeBase by string. More...

bool	has_variant_type (VariantType const variant_type) const
	Generic variant access. More...

bool	has_variant_type (std::string const &variant_type) const
	Generic variant access by string. More...

void	enable_custom_variant_types ()
	Turn on the ability to create VariantTypes "on-the-fly". More...

utility::vector1< std::string >	variant_types () const
	get all the variant types for this ResidueTypeBase More...

utility::vector1< VariantType >	variant_type_enums () const
	Get a vector of VariantType enums for this ResidueTypeBase. More...

utility::vector1< std::string > const &	custom_variant_types () const
	Get a list of custom VariantType strings for this ResidueTypeBase (by const reference). More...

void	aa (AA const &type)
	set our aa-type (could be "UNK") More...

void	aa (std::string const &type)
	set our aa-type (could be "UNK") More...

void	backbone_aa (std::string const &type)
	AA to use for backbone scoring. More...

void	backbone_aa (core::chemical::AA const type)
	Set AA to use for backbone scoring directly (without string conversion). More...

void	base_analogue (std::string const &type)
	NA to use for base-specific generalization (can be more forgiving than na_analogue for new NA backbones) More...

void	na_analogue (std::string const &type)
	NA to use for fragment sampling and some scoring purposes. More...

std::string const &	base_name () const
	Get this ResidueTypeBase's base name (shared with other residue types with the same base type). More...

std::string const &	name () const
	get our (unique) residue name More...

void	base_name (std::string const &base_name_in)
	Set this ResidueTypeBase's base name (shared with other residue types with the same base type). More...

void	name (std::string const &name_in)
	set our (unique) residue name More...

std::string const &	name3 () const
	get our 3letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...

void	name3 (std::string const &name_in)
	set our 3letter code More...

char	name1 () const
	get our 1letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name3 string. More...

void	name1 (char const code)
	set our 1letter code More...

std::string	interchangeability_group () const
	get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag. More...

void	interchangeability_group (std::string const &setting)
	set our interchangeability-group id More...

void	remap_pdb_atom_names (bool rename)
	Turn on geometry-based atom renaming when loading this residue type from PDB files. More...

bool	remap_pdb_atom_names () const
	Are we using geometry-based atom renaming when loading this residue type from PDB. More...

AA const &	aa () const
	our traditional residue type, if any More...

AA const &	backbone_aa () const
	Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More...

AA const &	base_analogue () const
	Returns the nucleic acid type to be used for base features. More...

AA const &	na_analogue () const
	Returns the nucleic acid type to be used for fragment sampling/scoring. More...

void	rotamer_library_specification (rotamers::RotamerLibrarySpecificationOP)

rotamers::RotamerLibrarySpecificationCOP	rotamer_library_specification () const

rotamers::RotamerLibrarySpecificationOP	rotamer_library_specification_nonconst ()
	Nonconst access to the RotamerLibrarySpecification. More...

void	strip_rotamer_library_specification ()
	Remove any rotamer library specifications attached to this ResidueTypeBase. More...

bool	force_nbr_atom_orient () const
	dihedral methods More...

void	force_nbr_atom_orient (bool force_orient)
	Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...

std::string const &	get_rama_prepro_mainchain_torsion_potential_name (bool const pre_proline_position) const
	Get the key name for the mainchain torsion potential used by the RamaPrePro score term. More...

bool	mainchain_potentials_match (ResidueTypeBase const &other) const
	Do the rama_prepro mainchain torsion potentials of this residue match another? More...

void	set_rama_prepro_mainchain_torsion_potential_name (std::string const &name_in, bool const pre_proline_position)
	Set the key name for the mainchain torsion potential used by the RamaPrePro score term. More...

std::string const &	get_rama_prepro_map_file_name (bool const pre_proline_position) const
	Get the file name for the mainchain torsion potential used by the RamaPrePro score term. More...

void	set_rama_prepro_map_file_name (std::string const &filename_in, bool const pre_proline_position)
	Set the file name for the mainchain torsion potential used by the RamaPrePro score term. More...

bool	defines_custom_rama_prepro_map (bool const pre_proline_position) const
	Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueTypeBase (which is presumably different from that of the base type). More...

void	reset_mainchain_torsion_potential_names ()
	Set the names of the mainchain torsion potential maps to use to "". More...

utility::vector1< Adduct > const &	defined_adducts () const
	get the adducts defined for this residue More...

void	add_adduct (Adduct &adduct_in)

void	report_adducts () const

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

Private Member Functions
	MutableResidueType ()

void	update_icoors_after_connection_deletion (core::Size const conn_id_deleted)
	After deleting a connection, update the icoors of any atoms dependent on HIGHER-numbered connections. More...

void	copy_atom_info (ResidueType const &source)
	Copy over the atom information from the ResidueType. Used for the conversion constructor. More...

void	copy_other_info (ResidueType const &source)
	Fill in various other information which is being copied over from the ResidueType Used for the conversion constructor. More...

Private Attributes
ResidueGraph	graph_
	The Atoms and Bonds of the MutableResidueType, stored as Nodes and Edges. More...

std::map< std::string, VD >	atom_name_to_vd_
	atom index lookup by atom name string More...

VDs	ordered_atoms_
	The atoms in order. This is primarily to keep track of the order which that atoms have been added, for consistency. Unlike the main ResidueType class, there is no guarantees regarding property ordering of atoms. More...

ResidueTypeCOP	base_type_cop_
	Const-access owning pointer to the base residue type. More...

VD	root_atom_ = MutableResidueType::null_vertex

VD	nbr_atom_ = MutableResidueType::null_vertex
	atom used for calculating residue-level neighbors More...

Real	nbr_radius_ = 0
	radius cutoff to define neighbors More...

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

utility::vector1< VD >	mainchain_atoms_
	Verticies of all mainchain atoms. More...

utility::vector1 < MutableChiRecordOP >	chis_

utility::vector1 < utility::vector1< VD > >	nu_atoms_
	VDs of four atoms to build each nu angle. More...

utility::vector1 < utility::vector1< VD > >	ring_atoms_
	VDs of all ring atoms, not counting virtual atoms. More...

utility::vector1 < core::chemical::rings::RingSaturationType >	ring_saturation_types_
	The saturation type of each ring in this residue. More...

utility::vector1 < utility::vector1 < std::string > >	low_ring_conformers_
	Low-energy ring conformers for each ring. More...

utility::vector1< std::string >	lowest_ring_conformer_
	Lowest-energy ring conformer for each ring. More...

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

Size	lower_connect_id_ = 0
	Polymer lower connections Updated in set_lower_connect_atom() More...

Size	upper_connect_id_ = 0
	Polymer upper connections Updated in set_upper_connect_atom() More...

Additional Inherited Members
Protected Member Functions inherited from core::chemical::ResidueTypeBase
	ResidueTypeBase ()

	ResidueTypeBase (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)
	constructor More...

	ResidueTypeBase (ResidueTypeBase const &)=default

ResidueTypeBase &	operator= (ResidueTypeBase const &)=default
	Copies <src> into the ResidueTypeBase. More...

void	atom_type_set (AtomTypeSetCOP setting)

utility::vector1< std::string > &	metal_binding_atoms ()

std::map< std::string, std::string > &	atom_aliases ()
	returns atom aliases More...

std::map< std::string, std::string > &	canonical_atom_aliases ()
	returns atom aliases More...

utility::vector1< Orbital > &	get_orbitals ()

std::map< std::string, int > &	get_orbitals_index ()

AA const &	backbone_aa_raw () const

AA const &	base_analogue_raw () const

AA const &	na_analogue_raw () const

Detailed Description

A class for defining a type of residue, modifiable version.

This class contains the "chemical" information for residues. A MutableResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. MutableResidueTypes are normally generated through .params files, which are read from the database chemical/residue_types. However, there are several other ways of generating this class, and the MutableResidueTypes can even be modified during the run (hence their name).

The MutableResidueType differs from a plain ResidueType in that it's constructed to be modifiable. It's also not intented to be used itself (aside from ResidueType modification). Instead, the typical usage is to convert a MutableResidueType into a plain ResidueType.

Another MutableResidueType/ResidueType distinction is that in a MutableResidueType the atom information is encoded in a molecular graph which should make it easier to add/remove/modify atoms. These atoms are referred to primarily by their "vertex desciptor" in the graph, which should be invariant to insertion/deletion/etc. While MutableResidueType does has a minimal sense of atom indexing, this is not the primary way to identify atoms, and will not be robust to addition/deletion of atoms.

To actually use a MutableResidueType for a simulation, you need to create a plain ResidueType from it. At this point all of the derived data will be calculated and converted to a more efficient struct-of-arrays format.

Constructor & Destructor Documentation

core::chemical::MutableResidueType::MutableResidueType ( )

privatedefault

Referenced by clone(), and placeholder_clone().

core::chemical::MutableResidueType::MutableResidueType	(	AtomTypeSetCOP	atom_types,
		ElementSetCOP	element_types,
		MMAtomTypeSetCOP	mm_atom_types,
		orbitals::OrbitalTypeSetCOP	orbital_types
	)

constructor

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

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

Make a copy of a MutableResidueType.

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

explicit

Make a modifiable residue type from a standard one.

References copy_atom_info(), copy_other_info(), and validate_residue_type().

core::chemical::MutableResidueType::MutableResidueType ( MutableResidueType && residue_type )

default

Move constructor, for rule of 5.

core::chemical::MutableResidueType::~MutableResidueType ( )

overridedefault

destructor, for rule of 5

Member Function Documentation

utility::vector1< VD > core::chemical::MutableResidueType::actcoord_atoms ( ) const

get descriptors for atoms used to define actcoord

References all_atoms(), and graph_.

Referenced by core::chemical::ResidueType::copy_other_info().

void core::chemical::MutableResidueType::add_actcoord_atom ( std::string const & atm )

add an atom to the list for calculating actcoord center

References atom(), core::chemical::Atom::is_actcoord(), core::chemical::ResidueTypeBase::name(), and core::chemical::TR().

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

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

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

References atom(), atom_name(), atom_name_to_vd_, graph_, core::chemical::ResidueTypeBase::name(), ordered_atoms_, and set_atom_type().

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

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

References atom_name(), atom_name_to_vd_, graph_, core::chemical::ResidueTypeBase::name(), ordered_atoms_, and core::chemical::regenerate_graph_vertex_index().

VD core::chemical::MutableResidueType::add_atom	(	Atom const &	atom,
		MutableICoorRecord const &	icoor
	)

References atom_name(), atom_name_to_vd_, graph_, core::chemical::Atom::name(), core::chemical::ResidueTypeBase::name(), ordered_atoms_, and core::chemical::regenerate_graph_vertex_index().

void core::chemical::MutableResidueType::add_atom_alias	(	std::string const &	rosetta_atom,
		std::string const &	alias
	)

Add an alias name for an atom.

References core::chemical::ResidueTypeBase::atom_aliases(), has(), and core::chemical::ResidueTypeBase::name().

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

void core::chemical::MutableResidueType::add_bond	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		BondName	bondLabel = `SingleBond`
	)

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

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

References atom_vertex(), and has().

void core::chemical::MutableResidueType::add_bond	(	VD	atom1,
		VD	atom2,
		BondName	bondLabel = `SingleBond`
	)

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

References atom_name(), graph_, has(), and core::chemical::ResidueTypeBase::name().

void core::chemical::MutableResidueType::add_canonical_atom_alias	(	std::string const &	rosetta_atom,
		std::string const &	alias
	)

store canonical to alias mapping

store map of canonical name to atom alias

References core::chemical::ResidueTypeBase::canonical_atom_aliases().

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

void core::chemical::MutableResidueType::add_chi	(	Size const	chino,
		VD	atom1,
		VD	atom2,
		VD	atom3,
		VD	atom4
	)

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

References chis_, has(), core::chemical::ResidueTypeBase::name(), and core::chemical::TR().

Referenced by add_chi(), core::chemical::AddChi::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), autodetermine_chi_bonds(), core::chemical::ResidueDatabaseIO::read_residue_type_chi(), and redefine_chi().

void core::chemical::MutableResidueType::add_chi	(	VD	atom1,
		VD	atom2,
		VD	atom3,
		VD	atom4
	)

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

References add_chi(), and nchi().

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

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

References add_chi(), and atom_vertex().

void core::chemical::MutableResidueType::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 MutableResidueTypes 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::MutableResidueType::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 chis_.

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

void core::chemical::MutableResidueType::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 MutableResidueType.

This method is needed for combinatorial patching of MutableResidueTypes 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::MutableResidueType::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.

References atom_vertex(), graph_, and has().

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

void core::chemical::MutableResidueType::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); Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu) TODO Should this be an annotation on the Atom?

References has(), core::chemical::ResidueTypeBase::metal_binding_atoms(), and core::chemical::ResidueTypeBase::name3().

void core::chemical::MutableResidueType::add_metapatch_connect ( std::string const & atom )

References add_residue_connection(), core::chemical::ResidueTypeBase::add_variant_type(), atom_vertex(), bonded_hydrogens(), core::chemical::ResidueTypeBase::enable_custom_variant_types(), has(), core::chemical::ResidueTypeBase::has_variant_type(), icoor(), core::chemical::ResidueTypeBase::name(), set_icoor(), and core::id::to_string().

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

void core::chemical::MutableResidueType::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_vertex(), has(), and nu_atoms_.

void core::chemical::MutableResidueType::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 coordinates for the added orbital but sets the index of the orbital and maps it to the type of orbital.

References core::chemical::ResidueTypeBase::get_orbitals(), core::chemical::ResidueTypeBase::get_orbitals_index(), core::chemical::ResidueTypeBase::n_orbitals(), and core::chemical::ResidueTypeBase::orbital_types_ptr().

void core::chemical::MutableResidueType::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_name_to_vd_, atom_vertex(), graph_, has(), core::chemical::ResidueTypeBase::has_orbital(), and core::chemical::ResidueTypeBase::orbital_index().

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

add a non-polymeric ResidueConnection

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

References atom_vertex(), and residue_connections_.

Referenced by add_metapatch_connect(), core::chemical::AddConnect::apply(), and core::chemical::AddConnectAndTrackingVirt::apply().

void core::chemical::MutableResidueType::add_ring	(	core::uint const	ring_num,
		utility::vector1< std::string > const &	ring_atoms,
		core::chemical::rings::RingSaturationType const	saturation_type = `core::chemical::rings::ALIPHATIC`
	)

Add a ring definition.

References atom_vertex(), has(), low_ring_conformers_, lowest_ring_conformer_, ring_atoms_, and ring_saturation_types_.

utility::vector1< VD > const& core::chemical::MutableResidueType::all_atoms ( ) const

inline

Convenience function for iterating over all the atoms e.g. for ( VA atm: restype->all_atoms() ) {

References ordered_atoms_.

void core::chemical::MutableResidueType::assign_internal_coordinates ( )

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

References has(), nbr_atom_, null_vertex, ordered_atoms_, and root_atom_.

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

Function to assign internal coordinates from bonding patterns Note that it currently does not work well with polymers.

References graph_, n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), null_vertex, core::chemical::reroot_restype(), root_atom_, and core::chemical::TR().

void core::chemical::MutableResidueType::assign_neighbor_atom ( )

Figure out what the "center" atom of the residue is from current coordinates.

Assumes that all the ideal_xyz values have been set

References core::conformation::membrane::center, core::kinematics::distance(), graph_, core::chemical::ResidueTypeBase::name(), nbr_atom(), null_vertex, ordered_atoms_, and protocols::analysis::total.

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

References graph_, and has().

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

References graph_, and has().

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

References atom_name(), atom_name_to_vd_, and graph_.

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

References atom_name_to_vd_, and graph_.

VD core::chemical::MutableResidueType::atom_base ( VD const atm ) const

The atom base is the distance atom the atom is bonded to. If the specified atom doesn't have valid ICOOR record yet, this function will return a null vertex.

get vd of an atom's base atom

References atom(), atom_vertex(), has(), core::chemical::Atom::icoor(), icoor(), core::chemical::ResidueTypeBase::name(), natoms(), and null_vertex.

Referenced by core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::find_chi_bonds(), core::chemical::reroot_restype(), and core::chemical::walk_back_to_find_usable_base().

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

Get an integer value for the atom (the index for all_atoms())

This is provided purely for a convenience in matching up external vector entries Use all_atoms() directly for normal iteration over atoms Will return 0 if the vd isn't in the MutableResidueType.

References ordered_atoms_.

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

inline

References graph_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::AtomRefMapping< VD, core::Size >::AtomRefMapping(), core::chemical::calculate_rigid_matrix(), core::chemical::clean_up_dangling_connect(), and core::chemical::find_nbr_dist().

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

get atom name by vertex descriptor IMPORTANT NOTE: Atoms don't necessarily have names!

Get atom name by vertex descriptor.

References graph_, has(), and protocols::antibody::unknown.

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

Get the chemical atom_type for this atom.

References core::chemical::ResidueTypeBase::atom_type_set(), graph_, has(), and ordered_atoms_.

Referenced by core::chemical::sdf::MolWriter::compose_atoms(), and core::chemical::sdf::MolWriter::compose_typeinfo().

VD core::chemical::MutableResidueType::atom_vertex ( std::string const & name ) const

get the vertex descriptor from the name of the atom.

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

bool core::chemical::MutableResidueType::atoms_are_bonded	(	std::string const &	atom1,
		std::string const &	atom2
	)		const

References atom_vertex(), and graph_.

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

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

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

References add_chi(), core::chemical::annotate_backbone(), atom(), atom_name(), atom_vertex(), chis_, core::chemical::find_chi_bonds(), core::chemical::rna::first_base_atom(), core::chemical::element::H, has(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::is_sp2_proton_chi(), core::chemical::ResidueTypeBase::name(), nchi(), set_proton_chi(), and core::chemical::TR().

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

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

References graph_.

Referenced by core::chemical::annotate_backbone(), bond(), core::chemical::complex_ring_detection(), core::chemical::sdf::MolWriter::compose_bonds(), copy_atom_info(), core::chemical::ResidueType::copy_atom_info(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::find_bonds_in_rings(), core::chemical::find_chi_bonds(), core::chemical::is_sp2_proton_chi(), core::chemical::rdkit::RestypeToRDMol::Mol(), and core::chemical::quick_ring_detection().

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

References graph_.

Bond & core::chemical::MutableResidueType::bond	(	VD	vd1,
		VD	vd2
	)

References atom_name(), graph_, and core::chemical::ResidueTypeBase::name().

Bond const & core::chemical::MutableResidueType::bond	(	VD	vd1,
		VD	vd2
	)		const

References atom_name(), graph_, and core::chemical::ResidueTypeBase::name().

Bond & core::chemical::MutableResidueType::bond	(	std::string const &	atom1,
		std::string const &	atom2
	)

References atom_vertex(), and bond().

Bond const & core::chemical::MutableResidueType::bond	(	std::string const &	atom1,
		std::string const &	atom2
	)		const

References atom_vertex(), and bond().

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

inline

References graph_.

Referenced by core::chemical::find_chi_bonds(), and core::chemical::is_sp2_proton_chi().

OutEdgeIterPair core::chemical::MutableResidueType::bond_iterators ( VD const & atom ) const

inline

References graph_.

utility::vector1< VD > core::chemical::MutableResidueType::bonded_heavyatoms ( VD const & atom ) const

Get the atoms bonded to the specified atom, if they're annotated as heavyatoms.

This is recalculated each time the function is called.

References atom(), graph_, and core::chemical::Atom::is_hydrogen().

Referenced by number_bonded_heavyatoms().

utility::vector1< VD > core::chemical::MutableResidueType::bonded_hydrogens ( VD const & atom ) const

Get the atoms bonded to the specified atom, if they're annotated as hydrogens.

This is recalculated each time the function is called.

References atom(), graph_, and core::chemical::Atom::is_hydrogen().

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

References graph_.

Referenced by core::chemical::find_nbr_dist(), core::chemical::RigidDistanceVisitor::is_nub(), and core::chemical::walk_back_to_find_usable_base().

utility::vector1< VD > core::chemical::MutableResidueType::bonded_neighbors ( VD const & atom ) const

Get the atoms bonded to the specified atom.

This is recalculated each time the function is called.

References graph_.

Referenced by core::chemical::annotate_backbone(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_bonds(), and core::chemical::ResidueType::copy_atom_info().

void core::chemical::MutableResidueType::change_bond_type	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		BondName const	new_bond_label
	)

Change the bond type of the given bond from one type to another.

Acts like a bond deletion + bond add, rather than a change.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_vertex(), graph_, has(), and core::chemical::ResidueTypeBase::name().

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

VDs const& core::chemical::MutableResidueType::chi_atom_vds ( Size const chino ) const

inline

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

References chis_.

Referenced by core::chemical::annotate_backbone(), core::chemical::ResidueType::copy_other_info(), delete_child_proton(), core::chemical::is_sp2_proton_chi(), core::chemical::print_chis(), and core::chemical::reroot_restype().

utility::vector1< std::pair< Real, Real > > const& core::chemical::MutableResidueType::chi_rotamers ( Size const chino ) const

inline

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

References chis_.

Referenced by core::chemical::ResidueType::copy_other_info().

bool core::chemical::MutableResidueType::chi_valid ( Size const chino ) const

Will return if the chi is currently valid.

References chis_, and has().

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

void core::chemical::MutableResidueType::clear_chi_rotamers ( core::uint const chi_no )

Delete all of the chi rotamer bins from the specified chi for this MutableResidueType.

This method is useful if one has redefined a chi within a patch file such that the old rotamer bins need to be regenerated.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References chis_.

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

void core::chemical::MutableResidueType::clear_icoor ( )

References atom(), core::chemical::Atom::icoor(), null_vertex, ordered_atoms_, and root_atom_.

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

void core::chemical::MutableResidueType::clear_orbitals ( )

clear orbitals

References core::chemical::ResidueTypeBase::get_orbitals(), core::chemical::ResidueTypeBase::get_orbitals_index(), graph_, and ordered_atoms_.

MutableResidueTypeOP core::chemical::MutableResidueType::clone ( ) const

make a copy

References MutableResidueType().

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

void core::chemical::MutableResidueType::copy_atom_info ( ResidueType const & source )

private

Copy over the atom information from the ResidueType. Used for the conversion constructor.

The ordered_atoms_ vector matches the ResidueType order, so we don't need an old-to-new.

Referenced by MutableResidueType().

void core::chemical::MutableResidueType::copy_other_info ( ResidueType const & source )

private

Fill in various other information which is being copied over from the ResidueType Used for the conversion constructor.

The ordered_atoms_ vector matches the ResidueType order, so we don't need an old-to-new.

Referenced by MutableResidueType().

void core::chemical::MutableResidueType::delete_actcoord_atom ( std::string const & atom_name )

Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used)

Author: Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu)

References atom(), has(), core::chemical::Atom::is_actcoord(), and core::chemical::ResidueTypeBase::name3().

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

void core::chemical::MutableResidueType::delete_atom ( std::string const & name )

Remove the atom from the ResidueType.

References atom_vertex(), and has().

void core::chemical::MutableResidueType::delete_atom ( VD atom )

Remove the atom from the ResidueType.

References atom_name_to_vd_, atom_shadowed_, chis_, protocols::sparta::contains(), delete_nu(), delete_residue_connection(), delete_ring(), graph_, has(), mainchain_atoms_, core::chemical::ResidueTypeBase::name(), nbr_atom_, nu_atoms_, null_vertex, ordered_atoms_, ring_atoms_, root_atom_, and core::chemical::TR().

void core::chemical::MutableResidueType::delete_atom_alias	(	std::string const &	alias,
		bool	error = `true`
	)

Remove a given alias name for an atom.

If error is true, raise error if the alias can't be found

References core::chemical::ResidueTypeBase::atom_aliases().

void core::chemical::MutableResidueType::delete_bond	(	VD	atom1,
		VD	atom2
	)

Delete a bond between the two atoms.

Note that this might leave dangling atoms.

References graph_.

void core::chemical::MutableResidueType::delete_chi ( core::Size const chino )

Deletes a given chi, potentially renumbering the remaining chis.

References chis_, core::chemical::ResidueTypeBase::name(), and core::chemical::TR().

Referenced by delete_child_proton().

void core::chemical::MutableResidueType::delete_child_proton ( std::string const & atom )

References core::chemical::ResidueTypeBase::add_variant_type(), atom_name(), atom_vertex(), bonded_hydrogens(), chi_atom_vds(), chis_, delete_atom(), delete_chi(), core::chemical::ResidueTypeBase::enable_custom_variant_types(), core::chemical::ResidueTypeBase::has_variant_type(), icoor(), core::chemical::ResidueTypeBase::name(), nchi(), set_proton_chi(), core::id::to_string(), and core::chemical::TR().

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

void core::chemical::MutableResidueType::delete_metalbinding_atom ( std::string const & atom_name )

Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used)

Author: Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu); Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu) TODO Should this be an annotation on the Atom?

References core::sequence::end, has(), core::chemical::ResidueTypeBase::metal_binding_atoms(), and core::chemical::ResidueTypeBase::name3().

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

void core::chemical::MutableResidueType::delete_nu ( core::uint const nu_index )

Deletes a given nu, potentially renumbering the remaining nus.

References core::chemical::ResidueTypeBase::name(), nu_atoms_, and core::chemical::TR().

Referenced by delete_atom().

void core::chemical::MutableResidueType::delete_residue_connection ( VD atm )

Remove all connections (both polymeric and otherwise) for an atom.

References lower_connect_id_, residue_connections_, update_icoors_after_connection_deletion(), and upper_connect_id_.

Referenced by delete_atom().

void core::chemical::MutableResidueType::delete_ring ( core::uint const ring_num )

Deletes a given ring, potentially renumbering the remaining ring.

References low_ring_conformers_, lowest_ring_conformer_, core::chemical::ResidueTypeBase::name(), ring_atoms_, ring_saturation_types_, and core::chemical::TR().

Referenced by delete_atom().

void core::chemical::MutableResidueType::delete_terminal_chi ( )

delete terminal chi angle

Author: Andrew M. Watkins (April 2015)

References chis_.

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

void core::chemical::MutableResidueType::dump_vd_info ( ) const

References atom_name(), graph_, has(), core::chemical::ResidueTypeBase::name(), ordered_atoms_, and core::chemical::TR().

void core::chemical::MutableResidueType::fill_ideal_xyz_from_icoor ( )

Assign ideal_xyz coordinates from icoor records.

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

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

std::map< std::string, VD > const& core::chemical::MutableResidueType::get_atom_name_to_vd_map ( ) const

inline

Get access to the atom_name-to-vd map. Provided only for MutableResidueType->ResidueType conversion.

References atom_name_to_vd_.

Referenced by core::chemical::ResidueType::copy_other_info().

ResidueTypeCOP core::chemical::MutableResidueType::get_base_type_cop ( ) const

overridevirtual

Get a pointer to this ResidueType's base ResidueType.

Returns NULL if base_type_cop_ is NULL. (Difference from ResidueType behavior!)

Implements core::chemical::ResidueTypeBase.

References base_type_cop_.

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

inline

Constant access to the underlying graph.

References graph_.

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

inlineoverridevirtual

is this atom present in this residue?

Implements core::chemical::ResidueTypeBase.

References atom_name_to_vd_.

bool core::chemical::MutableResidueType::has ( VD const vd ) const

inline

is this vertex descriptor present in this residue?

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

MutableICoorRecordCOP core::chemical::MutableResidueType::icoor ( VD const atm ) const

MutableICoorRecord of an atom.

AtomICoord of an atom.

References graph_, and has().

bool core::chemical::MutableResidueType::is_backbone_heavyatom ( VD atom ) const

References atom(), and graph_.

Referenced by core::chemical::VirtualizeSidechain::apply(), and core::chemical::ResidueType::setup_atom_ordering().

bool core::chemical::MutableResidueType::is_base_type ( ) const

overridevirtual

Is this ResidueType a base type?

Is this ResidueTypeBase a base type?

Checks the base_type_cop_ pointer. If it's null, this is assumed to be a base type.

Implements core::chemical::ResidueTypeBase.

References base_type_cop_.

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

inline

number of proton chis

References chis_.

Referenced by core::chemical::ResidueType::copy_other_info(), and core::chemical::print_chis().

utility::vector1< std::string > const& core::chemical::MutableResidueType::low_ring_conformers ( core::uint const ring_num ) const

inline

Low-energy ring conformers for the given ring.

References low_ring_conformers_.

Referenced by core::chemical::ResidueType::copy_other_info().

MutableResidueConnection const & core::chemical::MutableResidueType::lower_connect ( ) const

References lower_connect_id_, and residue_connections_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::MutableICoorRecord::build_xyz(), core::chemical::has_assigned_coords(), and core::chemical::MutableICoorRecord::xyz().

VD core::chemical::MutableResidueType::lower_connect_atom ( ) const

index number of the atom which connects to the lower connection

References lower_connect_id_, and residue_connections_.

Referenced by core::chemical::annotate_backbone(), and core::chemical::mainchain_path().

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

inline

References lower_connect_id_.

Referenced by core::chemical::annotate_backbone(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::MutableICoorRecord::buildable(), core::chemical::clean_up_dangling_connect(), core::chemical::ResidueType::copy_other_info(), and core::chemical::mainchain_path().

std::string const& core::chemical::MutableResidueType::lowest_ring_conformer ( core::uint const ring_num ) const

inline

Lowest-energy ring conformer for the given ring.

References lowest_ring_conformer_.

Referenced by core::chemical::ResidueType::copy_other_info().

utility::vector1< VD > const& core::chemical::MutableResidueType::mainchain_atoms ( ) const

inline

indices of all mainchain atoms

References mainchain_atoms_.

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

Size core::chemical::MutableResidueType::n_nus ( ) const

inline

Return number of nu (internal ring) angles.

References nu_atoms_.

Referenced by core::chemical::ResidueType::copy_other_info().

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

inline

The number of polymeric residue connections.

References lower_connect_id_, and upper_connect_id_.

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), and core::chemical::ResidueType::copy_other_info().

Size core::chemical::MutableResidueType::n_possible_residue_connections ( ) const

number of ResidueConnections, counting polymeric residue connections

References residue_connections_.

Referenced by assign_internal_coordinates(), core::chemical::MutableICoorRecord::buildable(), core::chemical::ResidueType::copy_other_info(), core::chemical::expand_icoor_atom_name(), and core::chemical::make_centroid().

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

number of proton chis

References chis_.

Referenced by core::chemical::ResidueType::copy_other_info().

Size core::chemical::MutableResidueType::n_residue_connections_for_atom ( VD const atomid ) const

References residue_connections_.

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

Size core::chemical::MutableResidueType::n_rings ( ) const

inline

Return the number of rings in this residue.

References ring_atoms_.

Referenced by core::chemical::ResidueType::copy_other_info().

Size core::chemical::MutableResidueType::n_virtual_atoms ( ) const

overridevirtual

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

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

The virtual count is not stored in the residue type. This count is performed on the fly, and can hurt performance if repeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

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

Implements core::chemical::ResidueTypeBase.

References core::chemical::ResidueTypeBase::atom_type_set(), graph_, natoms(), and ordered_atoms_.

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

Size core::chemical::MutableResidueType::natoms ( ) const

inlineoverridevirtual

number of atoms Note: Don't use this to iterate over atoms – use the vector returned by all_atoms() instead.

Implements core::chemical::ResidueTypeBase.

References graph_.

Referenced by core::chemical::ChiralFlipAtoms::apply(), atom_base(), core::chemical::sdf::MolWriter::compose_ctab(), core::chemical::sdf::MolWriter::compose_metadata(), core::chemical::ResidueType::copy_other_info(), core::chemical::fill_ideal_xyz_from_icoor(), core::chemical::find_nbr_dist(), n_virtual_atoms(), core::chemical::reroot_restype(), and validate_residue_type().

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

inlineoverridevirtual

number of bonds

Implements core::chemical::ResidueTypeBase.

References graph_.

Referenced by core::chemical::sdf::MolWriter::compose_ctab(), and core::chemical::sdf::MolWriter::compose_metadata().

Size core::chemical::MutableResidueType::nbonds ( VD atom ) const

inline

number of bonds for given atom

References graph_.

void core::chemical::MutableResidueType::nbr_atom ( std::string const & atom_name )

inline

set nbr_atom used to define residue-level neighbors

References atom_vertex(), and nbr_atom_.

Referenced by core::chemical::SetNbrAtom::apply(), assign_neighbor_atom(), core::chemical::ResidueDatabaseIO::read_residue_type(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::MutableResidueType::nbr_atom ( VD vertex )

inline

set nbr_atom used to define residue-level neighbors

References nbr_atom_.

void core::chemical::MutableResidueType::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::chemical::sdf::MolWriter::compose_nbr_atom(), core::chemical::ResidueType::copy_other_info(), core::chemical::ResidueDatabaseIO::read_residue_type(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

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

inline

get nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

VD core::chemical::MutableResidueType::nbr_vertex ( ) const

inline

get VD used to define residue-level neighbors

References nbr_atom_.

Referenced by core::chemical::sdf::MolWriter::compose_nbr_atom(), and core::chemical::ResidueType::copy_other_info().

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

inline

number of chi angles

References chis_.

Referenced by add_chi(), add_chi_rotamer_to_last_chi(), core::chemical::annotate_backbone(), core::chemical::DeleteTerminalChi::apply(), core::chemical::ClearChiRotamers::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), autodetermine_chi_bonds(), core::chemical::ResidueType::copy_other_info(), delete_child_proton(), core::chemical::print_chis(), and core::chemical::reroot_restype().

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

overridevirtual

number of heavy atoms

Implements core::chemical::ResidueTypeBase.

References atom(), and ordered_atoms_.

utility::vector1< VD > const& core::chemical::MutableResidueType::nu_atoms ( core::uint const nu_index ) const

inline

References nu_atoms_.

Referenced by core::chemical::ResidueType::copy_other_info().

Size core::chemical::MutableResidueType::number_bonded_heavyatoms ( VD atomvd ) const

indicates how many heavyatom bonded neighbors an atom has, graph version

References bonded_heavyatoms().

Size core::chemical::MutableResidueType::number_bonded_hydrogens ( VD atomvd ) const

indicates how many proton bonded neighbors an atom has

References bonded_hydrogens().

MutableResidueType & core::chemical::MutableResidueType::operator= ( MutableResidueType const & residue_type )

Copies <src> into the MutableResidueType.

This needs to be explicit, as we're copying over VDs.

References atom_name_to_vd_, atom_shadowed_, chis_, graph_, low_ring_conformers_, lower_connect_id_, lowest_ring_conformer_, mainchain_atoms_, nbr_atom_, nbr_radius_, nu_atoms_, null_vertex, core::chemical::ResidueTypeBase::operator=(), ordered_atoms_, core::scoring::pair, core::chemical::remap_vect(), residue_connections_, ring_atoms_, ring_saturation_types_, root_atom_, and upper_connect_id_.

MutableResidueType& core::chemical::MutableResidueType::operator= ( MutableResidueType && )

default

Move assignment, for rule of 5.

MutableResidueTypeOP core::chemical::MutableResidueType::placeholder_clone ( ) const

make a copy

make a copy, but only with all the stuff needed by patch selectors needs to be filled.

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

utility::vector1< Real > const& core::chemical::MutableResidueType::proton_chi_extra_samples_for_chi ( Size chino ) const

inline

The proton chi extra samples Important - this takes the full chi numbering (not proton chi numbering)

References chis_.

Referenced by core::chemical::ResidueType::copy_other_info().

utility::vector1< Real > const& core::chemical::MutableResidueType::proton_chi_samples_for_chi ( Size chino ) const

inline

The proton chi samples Important - this takes the full chi numbering (not proton chi numbering)

References chis_.

Referenced by core::chemical::ResidueType::copy_other_info().

void core::chemical::MutableResidueType::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 add_chi(), atom_vertex(), and has().

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

void core::chemical::MutableResidueType::rename_atom	(	VD	atom,
		std::string const &	name
	)

Rename the atom, updating the ResidueType-internal data mapping.

References atom_name(), atom_name_to_vd_, graph_, and has().

Referenced by core::chemical::RenameAtom::apply(), core::chemical::rename_atoms(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::MutableResidueType::reset_base_type_cop ( )

Reset the base type COP to be null. This implies that this ResidueTypeBase is a base type.

References base_type_cop_.

void core::chemical::MutableResidueType::reset_bond_distance_to_atom	(	std::string const &	atm,
		core::Distance const	d
	)

Reset the bond distance to an atom whose internal coordinates have already been set.

Looks up the internal coordinates to build the given atom and then resets the bond distance, updating the xyz coordinates afterward.
One cannot currently reset the bond distance of residue connections using this method.

Parameters

<atm>	the string name of the atom
<d>	the new bond distance in angstroms

Note: This method is primarily useful for patch operations, which may need to change the hybridization of an atom and thus the bond length from the atom to which it is attached.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_vertex(), icoor(), and set_icoor().

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

VD core::chemical::MutableResidueType::residue_connect_atom ( Size const resconn_id ) const

References residue_connections_.

MutableResidueConnection const & core::chemical::MutableResidueType::residue_connection ( Size const i ) const

Get a ResidueConection.

References residue_connections_.

Referenced by core::chemical::MutableICoorRecord::build_xyz(), core::chemical::ResidueType::copy_other_info(), core::chemical::has_assigned_coords(), and core::chemical::MutableICoorRecord::xyz().

MutableResidueConnection & core::chemical::MutableResidueType::residue_connection ( Size const i )

Get a ResidueConection.

References residue_connections_.

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

inline

References lower_connect_id_, and upper_connect_id_.

utility::vector1< VD > const& core::chemical::MutableResidueType::ring_atoms ( core::uint const ring_num ) const

inline

References ring_atoms_.

Referenced by core::chemical::ResidueType::copy_other_info().

core::chemical::rings::RingSaturationType core::chemical::MutableResidueType::ring_saturation_type ( uint const ring_num ) const

inline

Return the saturation level of this residue's nth cycle.

References ring_saturation_types_.

Referenced by core::chemical::ResidueType::copy_other_info().

VD core::chemical::MutableResidueType::root_atom ( ) const

inline

get root_atom used as the base of the icoor tree.

References root_atom_.

Referenced by core::chemical::ResidueType::copy_other_info(), core::chemical::find_chi_bonds(), core::chemical::formatted_icoord_tree(), and core::chemical::walk_back_to_find_usable_base().

void core::chemical::MutableResidueType::set_atom_type	(	std::string const &	name,
		std::string const &	atom_type_name
	)

inline

set atom type

References atom_vertex().

Referenced by add_atom(), core::chemical::SetAtomType::apply(), core::chemical::SetAllAtomsRepulsive::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::VirtualizeAll::apply(), core::chemical::VirtualizeSidechain::apply(), core::chemical::real_to_virtual(), core::chemical::rosetta_retype_fullatom(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and update_atom_type_set().

void core::chemical::MutableResidueType::set_atom_type	(	VD	atom,
		std::string const &	atom_type_name
	)

Set atom type, correctly updating internal state.

Note: This method also sets/updates the atom's element and the residue's mass.

References core::pose::motif::a(), atom(), atom_name(), core::chemical::Atom::atom_type_index(), core::chemical::AtomTypeSet::atom_type_index(), core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::ElementSet::element_index(), core::chemical::ResidueTypeBase::element_set(), core::chemical::ResidueTypeBase::element_set_ptr(), core::chemical::Atom::element_type(), graph_, has(), core::chemical::Atom::is_virtual(), core::chemical::AtomType::is_virtual(), and core::chemical::TR().

void core::chemical::MutableResidueType::set_backbone_heavyatom ( std::string const & name )

set an atom as backbone heavy atom

When converted to a plain ResidueType, backbone atoms will be placed first. This is differenct from the mainchain atoms below, as the mainchain is a subset of the backbone

References atom_name_to_vd_, graph_, has(), and core::chemical::ResidueTypeBase::name().

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

void core::chemical::MutableResidueType::set_base_type_cop ( ResidueTypeCOP new_base_type )

Set the base type COP. This implies that this ResidueTypeBase is NOT a base type.

References base_type_cop_.

void core::chemical::MutableResidueType::set_gasteiger_atom_type	(	std::string const &	atom_name,
		std::string const &	gasteiger_atom_type_name
	)

set gasteiger atom type

References atom_vertex().

void core::chemical::MutableResidueType::set_gasteiger_atom_type	(	VD	atom,
		std::string const &	gasteiger_atom_type_name
	)

set gasteiger atom type

References core::pose::motif::a(), atom(), core::chemical::Atom::gasteiger_atom_type(), core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), graph_, and core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset().

void core::chemical::MutableResidueType::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 MutableICoorRecord for an atom

phi and theta are in radians

set AtomICoor for an atom

will update the xyz coords as well if desired, useful inside a patching operation where new atoms are being added.

References atom_vertex(), core::chemical::CONNECT, core::chemical::get_connection_number(), has(), core::chemical::INTERNAL, lower_connect_id_, core::chemical::POLYMER_LOWER, core::chemical::POLYMER_UPPER, residue_connections_, core::chemical::string_to_icoord_type(), and upper_connect_id_.

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

set MutableICoorRecord for an atom, vertex descriptor version

phi and theta are in radians

References atom_name(), has(), and set_icoor().

void core::chemical::MutableResidueType::set_icoor	(	VD 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 MutableICoorRecord for an atom, vertex descriptor version

phi and theta are in radians

References atom(), atom_name(), atom_vertex(), has(), core::chemical::Atom::icoor(), null_vertex, root_atom_, set_ideal_xyz(), and core::chemical::TR().

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

References atom_vertex().

Referenced by core::chemical::fill_ideal_xyz_from_icoor(), and set_icoor().

void core::chemical::MutableResidueType::set_ideal_xyz	(	VD	atm,
		Vector const &	xyz_in
	)

References core::pose::motif::a(), graph_, has(), and core::chemical::Atom::ideal_xyz().

void core::chemical::MutableResidueType::set_low_energy_ring_conformers	(	core::uint const	ring_num,
		utility::vector1< std::string > const &	conformers
	)

Set this cyclic residue's low-energy ring conformers for the nth ring by IUPAC name.

References low_ring_conformers_.

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

set the atom which connects to the lower connection

References atom_vertex(), lower_connect_id_, residue_connections_, core::chemical::TR(), update_icoors_after_connection_deletion(), and upper_connect_id_.

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

void core::chemical::MutableResidueType::set_lowest_energy_ring_conformer	(	core::uint const	ring_num,
		std::string const &	conformer
	)

Set this cyclic residue's lowest-energy ring conformer for the nth ring by IUPAC name.

References lowest_ring_conformer_.

void core::chemical::MutableResidueType::set_mainchain_atoms ( utility::vector1< VD > const & mainchain )

inline

set indices of all mainchain atoms TODO Should we make sure that mainchain atoms are also backbones?

References mainchain_atoms_.

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

void core::chemical::MutableResidueType::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 core::chemical::ResidueTypeBase::get_orbitals(), and core::chemical::ResidueTypeBase::orbital_index().

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

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

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

References chis_.

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

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

References atom_shadowed_, and atom_vertex().

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

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

set the atom which connects to the upper connection

References atom_vertex(), lower_connect_id_, residue_connections_, core::chemical::TR(), update_icoors_after_connection_deletion(), and upper_connect_id_.

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

std::map< VD, VD > const& core::chemical::MutableResidueType::shadow_atoms ( ) const

inline

References atom_shadowed_.

Referenced by core::chemical::ResidueType::copy_other_info().

void core::chemical::MutableResidueType::show	(	std::ostream &	output = `std::cout`,
		bool	output_atomic_details = `false`
	)		const

overridevirtual

Generate string representation of MutableResidueType for debugging purposes.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Implements core::chemical::ResidueTypeBase.

References all_atoms(), atom(), atom_name(), core::chemical::ResidueTypeBase::base_name(), graph_, mainchain_atoms_, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueTypeBase::properties(), ring_atoms_, core::chemical::ResidueProperties::show(), and core::chemical::Atom::show().

Referenced by core::chemical::operator<<().

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

overridevirtual

Implements core::chemical::ResidueTypeBase.

References core::pose::motif::a(), graph_, core::chemical::Atom::name(), and ordered_atoms_.

Referenced by atom_vertex().

void core::chemical::MutableResidueType::update_atom_type_set ( AtomTypeSetCOP setting )

Change which atom type set this MutableResidueType points to WARNING - While this tries to switch over the atom types, it will null out any that don't have exact name correspondences. You NEED to go through and manually reset the types on all atoms. Exposed for black-magic use only.

References core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::ResidueTypeBase::atom_type_set_ptr(), graph_, core::chemical::ResidueTypeBase::name(), ordered_atoms_, and set_atom_type().

void core::chemical::MutableResidueType::update_icoors_after_connection_deletion ( core::Size const conn_id_deleted )

private

After deleting a connection, update the icoors of any atoms dependent on HIGHER-numbered connections.

Will not attempt to adjust any ICOOR referencing a delete UPPER/LOWER

References core::chemical::CONNECT, core::chemical::correct_conn(), core::chemical::get_connection_number(), graph_, and ordered_atoms_.

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

MutableResidueConnection const & core::chemical::MutableResidueType::upper_connect ( ) const

References residue_connections_, and upper_connect_id_.

Referenced by core::chemical::MutableICoorRecord::build_xyz(), core::chemical::has_assigned_coords(), and core::chemical::MutableICoorRecord::xyz().

VD core::chemical::MutableResidueType::upper_connect_atom ( ) const

index number of the atom which connects to the upper connection

References residue_connections_, and upper_connect_id_.

Referenced by core::chemical::annotate_backbone(), core::chemical::mainchain_path(), and core::chemical::Selector_UPPER_ATOM::operator[]().

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

inline

References upper_connect_id_.

Referenced by core::chemical::annotate_backbone(), core::chemical::MutableICoorRecord::buildable(), core::chemical::clean_up_dangling_connect(), core::chemical::ResidueType::copy_other_info(), core::chemical::mainchain_path(), and core::chemical::Selector_UPPER_ATOM::operator[]().

bool core::chemical::MutableResidueType::validate_residue_type ( ) const

Run checks on this MutableResidueType, checking to make sure it's okay. Return true on success and false on failure (Intended usage is within something like a debug_assert())

References atom(), chis_, has(), icoor(), core::chemical::Atom::name(), core::chemical::ResidueTypeBase::name(), natoms(), ordered_atoms_, and core::chemical::TR().

Referenced by MutableResidueType(), and core::chemical::ResidueType::ResidueType().

Member Data Documentation

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

private

atom index lookup by atom name string

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

Referenced by add_atom(), add_orbital_bond(), atom(), atom_vertex(), delete_atom(), get_atom_name_to_vd_map(), has(), operator=(), rename_atom(), and set_backbone_heavyatom().

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

private

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

Referenced by copy_atom_info(), delete_atom(), operator=(), set_shadowing_atom(), and shadow_atoms().

ResidueTypeCOP core::chemical::MutableResidueType::base_type_cop_

private

Const-access owning pointer to the base residue type.

NULL if this MutableResidueType doesn't have a base type.

Referenced by copy_other_info(), get_base_type_cop(), is_base_type(), reset_base_type_cop(), and set_base_type_cop().

utility::vector1< MutableChiRecordOP > core::chemical::MutableResidueType::chis_

private

ResidueGraph core::chemical::MutableResidueType::graph_

private

The Atoms and Bonds of the MutableResidueType, stored as Nodes and Edges.

Referenced by actcoord_atoms(), add_atom(), add_bond(), add_cut_bond(), add_orbital_bond(), assign_internal_coordinates(), assign_neighbor_atom(), atom(), atom_iterators(), atom_name(), atom_type(), atoms_are_bonded(), bond(), bond_iterators(), bonded_heavyatoms(), bonded_hydrogens(), bonded_neighbor_iterators(), bonded_neighbors(), change_bond_type(), clear_orbitals(), copy_atom_info(), copy_other_info(), delete_atom(), delete_bond(), dump_vd_info(), fill_ideal_xyz_from_icoor(), graph(), has(), icoor(), is_backbone_heavyatom(), n_virtual_atoms(), natoms(), nbonds(), operator=(), rename_atom(), set_atom_type(), set_backbone_heavyatom(), set_gasteiger_atom_type(), set_ideal_xyz(), show(), show_all_atom_names(), update_atom_type_set(), and update_icoors_after_connection_deletion().

utility::vector1< utility::vector1< std::string > > core::chemical::MutableResidueType::low_ring_conformers_

private

Low-energy ring conformers for each ring.

used for setting up the RingConformerSets

Referenced by add_ring(), copy_other_info(), delete_ring(), low_ring_conformers(), operator=(), and set_low_energy_ring_conformers().

Size core::chemical::MutableResidueType::lower_connect_id_ = 0

private

Polymer lower connections Updated in set_lower_connect_atom()

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

Referenced by copy_other_info(), delete_residue_connection(), lower_connect(), lower_connect_atom(), lower_connect_id(), n_polymeric_residue_connections(), operator=(), residue_connection_is_polymeric(), set_icoor(), set_lower_connect_atom(), and set_upper_connect_atom().

utility::vector1< std::string > core::chemical::MutableResidueType::lowest_ring_conformer_

private

Lowest-energy ring conformer for each ring.

used for setting up the RingConformerSets

Referenced by add_ring(), copy_other_info(), delete_ring(), lowest_ring_conformer(), operator=(), and set_lowest_energy_ring_conformer().

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

private

Verticies 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 copy_other_info(), delete_atom(), mainchain_atoms(), operator=(), set_mainchain_atoms(), and show().

VD core::chemical::MutableResidueType::nbr_atom_ = MutableResidueType::null_vertex

private

atom used for calculating residue-level neighbors

Referenced by assign_internal_coordinates(), copy_other_info(), delete_atom(), nbr_atom(), nbr_vertex(), and operator=().

Real core::chemical::MutableResidueType::nbr_radius_ = 0

private

radius cutoff to define neighbors

Should be the maximum distance from the nbr_atom_ to any heavy atom in any valid rotamer.

Referenced by copy_other_info(), nbr_radius(), and operator=().

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

private

VDs of four atoms to build each nu angle.

Referenced by add_nu(), copy_other_info(), delete_atom(), delete_nu(), n_nus(), nu_atoms(), and operator=().

VD const core::chemical::MutableResidueType::null_vertex = boost::graph_traits<ResidueGraph>::null_vertex()

static

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), assign_internal_coordinates(), assign_neighbor_atom(), core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom(), core::chemical::orbitals::AssignOrbitals::assign_sp2_orbitals_to_one_bonded_atom(), core::chemical::orbitals::AssignOrbitals::assign_sp2_sp_orbitals_to_one_bonded_atom(), atom_base(), clear_icoor(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), delete_atom(), core::chemical::find_nbr_dist(), core::chemical::formatted_icoord_tree(), core::chemical::rdkit::RDMolToRestype::generate_restype(), operator=(), and set_icoor().

VDs core::chemical::MutableResidueType::ordered_atoms_

private

The atoms in order. This is primarily to keep track of the order which that atoms have been added, for consistency. Unlike the main ResidueType class, there is no guarantees regarding property ordering of atoms.

Referenced by add_atom(), all_atoms(), assign_internal_coordinates(), assign_neighbor_atom(), atom_index(), atom_type(), clear_icoor(), clear_orbitals(), copy_atom_info(), copy_other_info(), delete_atom(), dump_vd_info(), n_virtual_atoms(), nheavyatoms(), operator=(), show_all_atom_names(), update_atom_type_set(), update_icoors_after_connection_deletion(), and validate_residue_type().

utility::vector1< MutableResidueConnection > core::chemical::MutableResidueType::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(), copy_other_info(), delete_residue_connection(), lower_connect(), lower_connect_atom(), n_possible_residue_connections(), n_residue_connections_for_atom(), operator=(), residue_connect_atom(), residue_connection(), set_icoor(), set_lower_connect_atom(), set_upper_connect_atom(), upper_connect(), and upper_connect_atom().