A base class for definiting types of residues. More...

#include <ResidueTypeBase.hh>

Inheritance diagram for core::chemical::ResidueTypeBase:

[legend]

Public Member Functions
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...

virtual Size	natoms () const =0
	number of atoms More...

virtual Size	nheavyatoms () const =0
	number of heavy atoms More...

virtual Size	nbonds () const =0
	number of bonds More...

virtual Size	n_virtual_atoms () const =0
	Counts the number of virtual atoms and returns the count. More...

virtual bool	has (std::string const &atom_name) const =0
	is this atom present in this residue? 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...

virtual void	show_all_atom_names (std::ostream &out) const =0

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...

virtual bool	is_base_type () const =0
	Is this ResidueTypeBase a base type? More...

virtual ResidueTypeCOP	get_base_type_cop () const =0
	Get a pointer to this ResidueTypeBase's base ResidueTypeBase. 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...

virtual void	show (std::ostream &output=std::cout, bool output_atomic_details=false) const =0
	Generate string representation of ResidueTypeBase for debugging purposes. More...

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

void	add_adduct (Adduct &adduct_in)

void	report_adducts () const

Protected Member Functions
	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< OrbitalOP > &	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

Private Attributes
TypeSetMode	mode_ = INVALID_t
	The TypeSet mode for this ResidueTypeBase. More...

AtomTypeSetCOP	atom_types_
	The type set for Rosetta Atom types. Required to be non-null for standard ResidueTypes. More...

ElementSetCOP	elements_
	The set for element objects. – can be null. More...

MMAtomTypeSetCOP	mm_atom_types_
	The set for MMAtomTypes. – can be null. More...

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_types_
	The set for GasteigerAtomTypes. – can be null. More...

orbitals::OrbitalTypeSetCOP	orbital_types_
	The set for OrbitalTypes. – can be null. More...

AA	aa_ = aa_unk
	standard rosetta aa-type for knowledge-based potentials, may be aa_unk More...

AA	backbone_aa_ = aa_unk

AA	na_analogue_ = aa_unp

AA	base_analogue_ = aa_unp

std::string	base_name_
	Residue id for the base type (i.e. sans variants). More...

std::string	name_
	Residue id – Should be unique within a ResidueTypeSet. More...

std::string	name3_
	PDB-file id, need not be unique NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...

char	name1_ = ' '
	one-letter code, also not necessarily unique More...

std::string	interchangeability_group_
	interchangeability group lets a ResidueTypeBase claim to be functionally interchangeable with any other ResidueTypeBase in the same group. This is used by the packer to decide which ResidueTypeBase from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueTypeBase and build rotamers for it. More...

std::string	rama_prepro_mainchain_torsion_potential_name_
	The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...

std::string	rama_prepro_mainchain_torsion_potential_name_beforeproline_
	The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...

std::string	rama_prepro_map_file_name_
	The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...

std::string	rama_prepro_map_file_name_beforeproline_
	The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...

signed long int	net_formal_charge_ = 0
	What is the total formal charge of the ResidueType? (Note that this may be different from the sum of the formal charges on each atom.) More...

bool	force_nbr_atom_orient_ = false

bool	remap_pdb_atom_names_ = false
	Should we attempt to rename atoms for this residue type when we read in PDB files? More...

utility::pointer::DeepCopyOP< ResidueProperties >	properties_
	Residue properties as defined in the residue topology (.params) files. More...

bool	is_metapatched_ = false
	Is this ResidueType the product of metapatching? More...

utility::pointer::DeepCopyOP< rotamers::RotamerLibrarySpecification >	rotamer_library_specification_
	How to construct a rotamer library for this ResidueTypeBase. More...

utility::vector1< std::string >	metal_binding_atoms_
	Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types. More...

std::string	disulfide_atom_name_ = "NONE"
	Name of the disulfide-forming atom, if any. More...

std::map< std::string, std::string >	atom_aliases_
	A mapping of alias atom names to canonical atom names Will be added to atom_name_to_vd_ during finalization. More...

std::map< std::string, std::string >	canonical_atom_aliases_
	A map of canonical atom names to atom aliases (white space included) More...

utility::vector1< Adduct >	defined_adducts_
	Adducts defined for this residue. More...

utility::deep_copy_vector1< OrbitalOP >	orbitals_
	The orbitals on the ResidueTypeBase, if any. More...

std::map< std::string, int >	orbitals_index_
	index lookup for orbitals based on atom name Updated in add_orbital() More...

Detailed Description

A base class for definiting types of residues.

This class is a base class for the "chemical" information for residues in Rosetta. It's a base class for two different classes. ResidueType, which is the main class used by Rosetta, but which is a fixed-content type, and MutableResidueType, which is a modifiable class. The two type also differ also in how Atoms information is represented. The atom information in MutableResidueType is represented in a molecular graph, which is more convenient for modification, with atoms referenced primarily by "vertex descriptor" in the graph. The atom information in ResidueType is in a struct-of-arrays format, which allows better optimization, with atoms in a defined order. There are also differences in guarantees for each class. ResidueType has certain atom ordering guarantees which MutableResidueType lacks.

To accomodate the two different classes, this base class only stores the common, (non-atom dependent) information, along with some convenient accessors.

See the documentation of each class for more information.

A note on things which belong in this class: Only include things which are atom-independent, and are "primary" information. (Things which can/should be derived from atoms or other info should be placed in the plain ResidueType class, and updated on MutableResidueType -> ResidueType conversion. You can also include (as a virtual method) functions needed for PatchSelector function, but any atom indexing/references should be name-based.

Constructor & Destructor Documentation

◆ ResidueTypeBase() [1/3]

core::chemical::ResidueTypeBase::ResidueTypeBase ( )

protecteddefault

◆ ResidueTypeBase() [2/3]

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

protected

constructor

We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc. This is protected as we don't want to instantiate a plain ResidueType directly.

References atom_types_, and mode_.

◆ ResidueTypeBase() [3/3]

core::chemical::ResidueTypeBase::ResidueTypeBase ( ResidueTypeBase const & )

protecteddefault

Member Function Documentation

◆ aa() [1/3]

AA const& core::chemical::ResidueTypeBase::aa ( ) const

inline

our traditional residue type, if any

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

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

References aa_.

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

◆ aa() [2/3]

void core::chemical::ResidueTypeBase::aa ( AA const & type )

inline

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

References aa_.

◆ aa() [3/3]

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

inline

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

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

◆ add_adduct()

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

inline

References defined_adducts_.

◆ add_numeric_property()

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

Add a numeric property.

References properties_.

◆ add_property() [1/2]

void core::chemical::ResidueTypeBase::add_property ( core::chemical::ResidueProperty const property )

◆ add_property() [2/2]

void core::chemical::ResidueTypeBase::add_property ( std::string const & property )

Add a property to this ResidueTypeBase.

References core::chemical::ResidueProperties::get_property_from_string(), and core::chemical::NO_PROPERTY.

Referenced by core::chemical::AddProperty::apply(), core::chemical::ResidueDatabaseIO::read_residue_type_properties(), core::chemical::real_to_virtual(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and core::chemical::setup_patch_atomic_charge_reassignments_from_commandline().

◆ add_string_property()

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

Add a string property.

References properties_.

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

◆ add_variant_type() [1/2]

void core::chemical::ResidueTypeBase::add_variant_type ( std::string const & variant_type )

Add a variant type to this ResidueTypeBase by string.

References properties_.

◆ add_variant_type() [2/2]

void core::chemical::ResidueTypeBase::add_variant_type ( VariantType const variant_type )

Add a variant type to this ResidueTypeBase.

References properties_.

Referenced by core::chemical::MutableResidueType::add_metapatch_connect(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::MutableResidueType::delete_child_proton(), and core::chemical::ResidueDatabaseIO::read_residue_type_variant().

◆ atom_alias()

std::string const& core::chemical::ResidueTypeBase::atom_alias ( std::string const & name ) const

inline

returns atom alias

References atom_aliases_, and name().

◆ atom_aliases() [1/2]

std::map< std::string, std::string >& core::chemical::ResidueTypeBase::atom_aliases ( )

inlineprotected

returns atom aliases

References atom_aliases_.

◆ atom_aliases() [2/2]

std::map< std::string, std::string > const& core::chemical::ResidueTypeBase::atom_aliases ( ) const

inline

returns atom aliases

References atom_aliases_.

Referenced by core::chemical::MutableResidueType::add_atom_alias(), core::chemical::ResidueType::copy_other_info(), core::chemical::MutableResidueType::delete_atom_alias(), and core::chemical::write_topology_file().

◆ atom_type_set() [1/2]

AtomTypeSet const& core::chemical::ResidueTypeBase::atom_type_set ( ) const

inline

access by reference the atomset for which this residue is constructed

References atom_types_.

◆ atom_type_set() [2/2]

void core::chemical::ResidueTypeBase::atom_type_set ( AtomTypeSetCOP setting )

protected

References atom_types_, and mode_.

◆ atom_type_set_ptr()

AtomTypeSetCOP core::chemical::ResidueTypeBase::atom_type_set_ptr ( ) const

inline

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

References atom_types_.

◆ backbone_aa() [1/3]

AA const& core::chemical::ResidueTypeBase::backbone_aa ( ) const

inline

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

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

◆ backbone_aa() [2/3]

void core::chemical::ResidueTypeBase::backbone_aa ( core::chemical::AA const type )

inline

Set AA to use for backbone scoring directly (without string conversion).

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References backbone_aa_.

◆ backbone_aa() [3/3]

void core::chemical::ResidueTypeBase::backbone_aa ( std::string const & type )

inline

AA to use for backbone scoring.

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

Referenced by core::chemical::ChiralFlipNaming::apply(), core::conformation::Residue::backbone_aa(), core::scoring::ResidueExclParams::create_excl_info(), core::energy_methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::energy_methods::GenericBondedEnergy::eval_intrares_derivatives(), core::energy_methods::GenericBondedEnergy::eval_intrares_energy(), and core::chemical::write_topology_file().

◆ backbone_aa_raw()

AA const& core::chemical::ResidueTypeBase::backbone_aa_raw ( ) const

inlineprotected

References backbone_aa_.

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

◆ base_analogue() [1/2]

AA const& core::chemical::ResidueTypeBase::base_analogue ( ) const

inline

Returns the nucleic acid type to be used for base features.

References aa_, core::chemical::aa_unp, and base_analogue_.

◆ base_analogue() [2/2]

void core::chemical::ResidueTypeBase::base_analogue ( std::string const & type )

inline

NA to use for base-specific generalization (can be more forgiving than na_analogue for new NA backbones)

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

Referenced by core::chemical::rna::get_base_pair_atoms(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::constraints::BasePairConstraint::read_def(), core::energy_methods::ReferenceEnergy::residue_energy(), and core::chemical::write_topology_file().

◆ base_analogue_raw()

AA const& core::chemical::ResidueTypeBase::base_analogue_raw ( ) const

inlineprotected

References base_analogue_.

◆ base_name() [1/2]

std::string const& core::chemical::ResidueTypeBase::base_name ( ) const

inline

Get this ResidueTypeBase's base name (shared with other residue types with the same base type).

References base_name_.

◆ base_name() [2/2]

void core::chemical::ResidueTypeBase::base_name ( std::string const & base_name_in )

inline

Set this ResidueTypeBase's base name (shared with other residue types with the same base type).

References base_name_.

◆ canonical_atom_alias()

std::string const& core::chemical::ResidueTypeBase::canonical_atom_alias ( std::string const & name ) const

inline

returns atom alias

References canonical_atom_aliases_, and name().

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record().

◆ canonical_atom_aliases() [1/2]

std::map< std::string, std::string >& core::chemical::ResidueTypeBase::canonical_atom_aliases ( )

inlineprotected

returns atom aliases

References canonical_atom_aliases_.

◆ canonical_atom_aliases() [2/2]

std::map< std::string, std::string > const& core::chemical::ResidueTypeBase::canonical_atom_aliases ( ) const

inline

returns atom aliases

References canonical_atom_aliases_.

Referenced by core::chemical::MutableResidueType::add_canonical_atom_alias(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), and core::scoring::cryst::PhenixInterface::stealBfactorsFromFile().

◆ custom_variant_types()

utility::vector1< std::string > const & core::chemical::ResidueTypeBase::custom_variant_types ( ) const

Get a list of custom VariantType strings for this ResidueTypeBase (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

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

References properties_.

Referenced by protocols::cyclic_peptide::RamaMutationSelector::apply(), and core::pack::palette::PackerPalette::get_types_on_residue().

◆ defined_adducts()

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

inline

get the adducts defined for this residue

References defined_adducts_.

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

◆ defines_custom_rama_prepro_map()

bool core::chemical::ResidueTypeBase::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).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

References is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

◆ delete_property() [1/2]

void core::chemical::ResidueTypeBase::delete_property ( core::chemical::ResidueProperty const property )

Delete a property of this ResidueType, by properties enum.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

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

◆ delete_property() [2/2]

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

Delete a property of this ResidueType.

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

References properties_.

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

◆ element_set()

ElementSet const& core::chemical::ResidueTypeBase::element_set ( ) const

inline

access by reference the element set for which this residue is constructed

References elements_.

Referenced by core::chemical::MutableResidueType::set_atom_type().

◆ element_set_ptr()

ElementSetCOP core::chemical::ResidueTypeBase::element_set_ptr ( ) const

inline

access by const pointer the element set for which this residue is constructed

References elements_.

Referenced by core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::MutableResidueType::placeholder_clone(), and core::chemical::MutableResidueType::set_atom_type().

◆ enable_custom_variant_types()

void core::chemical::ResidueTypeBase::enable_custom_variant_types ( )

Turn on the ability to create VariantTypes "on-the-fly".

"Custom" VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

References properties_.

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

◆ force_nbr_atom_orient() [1/2]

bool core::chemical::ResidueTypeBase::force_nbr_atom_orient ( ) const

inline

dihedral methods

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

References force_nbr_atom_orient_.

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

◆ force_nbr_atom_orient() [2/2]

void core::chemical::ResidueTypeBase::force_nbr_atom_orient ( bool force_orient )

inline

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

References force_nbr_atom_orient_.

◆ gasteiger_atom_typeset()

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueTypeBase::gasteiger_atom_typeset ( ) const

References gasteiger_atom_types_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::ResidueType::copy_atom_info(), core::chemical::ResidueType::gasteiger_atom_type(), core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::MutableResidueType::set_gasteiger_atom_type(), and core::chemical::ResidueType::show().

◆ get_base_type_cop()

virtual ResidueTypeCOP core::chemical::ResidueTypeBase::get_base_type_cop ( ) const

pure virtual

Get a pointer to this ResidueTypeBase's base ResidueTypeBase.

NOTE: Behavior when is_base_type() == true varies by subclass!

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), and get_rama_prepro_map_file_name().

◆ get_disulfide_atom_name()

std::string const& core::chemical::ResidueTypeBase::get_disulfide_atom_name ( ) const

inline

Gets disulfide atom name.

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

References disulfide_atom_name_.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_closebond_logic_thioether_lariat(), core::conformation::Conformation::add_disulfide_bond(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::energy_methods::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::get_disulf_partner(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), and core::chemical::write_topology_file().

◆ get_metal_binding_atoms()

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

inline

References metal_binding_atoms_.

◆ get_numeric_property()

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

Get a numeric property, if it exists.

References name3_, and properties_.

Referenced by protocols::simple_moves::AddJobPairData::apply(), and protocols::qsar::scoring_grid::LigandPropertyScore::score().

◆ get_orbitals()

utility::vector1< OrbitalOP >& core::chemical::ResidueTypeBase::get_orbitals ( )

inlineprotected

References orbitals_.

Referenced by core::chemical::MutableResidueType::add_orbital(), core::chemical::MutableResidueType::clear_orbitals(), and core::chemical::MutableResidueType::set_orbital_icoor_id().

◆ get_orbitals_index()

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

inlineprotected

References orbitals_index_.

Referenced by core::chemical::MutableResidueType::add_orbital(), and core::chemical::MutableResidueType::clear_orbitals().

◆ get_rama_prepro_mainchain_torsion_potential_name()

std::string const & core::chemical::ResidueTypeBase::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.

Get the key name for the mainchain torsion potential.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Note: Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_mainchain_torsion_potential_name_, and rama_prepro_mainchain_torsion_potential_name_beforeproline_.

Referenced by core::chemical::ResidueType::update_derived_data(), and core::chemical::write_topology_file().

◆ get_rama_prepro_map_file_name()

std::string const & core::chemical::ResidueTypeBase::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.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Note: Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

Referenced by core::scoring::ResidueExclParams::create_excl_info(), core::chemical::ResidueType::update_derived_data(), and core::chemical::write_topology_file().

◆ get_string_property()

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

Get a string property, if it exists.

References name3_, and properties_.

Referenced by protocols::simple_moves::AddJobPairData::apply().

◆ has()

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

pure virtual

is this atom present in this residue?

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

References name().

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

◆ has_orbital()

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

inline

is this orbital present in this residue?

References orbitals_index_.

Referenced by core::chemical::MutableResidueType::add_orbital_bond().

◆ has_orbital_types()

bool core::chemical::ResidueTypeBase::has_orbital_types ( ) const

inline

Does this residue type define orbital types?

References orbital_types_.

◆ has_property() [1/2]

bool core::chemical::ResidueTypeBase::has_property ( ResidueProperty const property ) const

Generic property access, by ResidueProperty.

References properties_.

◆ has_property() [2/2]

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

Generic property access.

References properties_.

◆ has_variant_type() [1/2]

bool core::chemical::ResidueTypeBase::has_variant_type ( std::string const & variant_type ) const

Generic variant access by string.

References properties_.

◆ has_variant_type() [2/2]

bool core::chemical::ResidueTypeBase::has_variant_type ( VariantType const variant_type ) const

Generic variant access.

References properties_.

◆ interchangeability_group() [1/2]

std::string core::chemical::ResidueTypeBase::interchangeability_group ( ) const

inline

get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. 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.

References interchangeability_group_.

Referenced by core::chemical::SetInterchangeabilityGroup_String::apply(), core::chemical::ChiralFlipNaming::apply(), core::chemical::sdf::MolWriter::compose_naming(), core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::MutableResidueType::placeholder_clone(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and core::chemical::write_topology_file().

◆ interchangeability_group() [2/2]

void core::chemical::ResidueTypeBase::interchangeability_group ( std::string const & setting )

inline

set our interchangeability-group id

References interchangeability_group_.

◆ is_achiral_backbone()

bool core::chemical::ResidueTypeBase::is_achiral_backbone ( ) const

inline

is this an achiral backbone?

References core::chemical::ACHIRAL_BACKBONE, core::chemical::ResidueProperties::has_property(), and properties().

Referenced by core::energy_methods::RamachandranEnergy::residue_energy().

◆ is_achiral_sidechain()

bool core::chemical::ResidueTypeBase::is_achiral_sidechain ( ) const

inline

Does this have an achiral sidechain?

Includes gly and aib, and most (but not all) peptoids.

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

References core::chemical::ACHIRAL_SIDECHAIN, core::chemical::ResidueProperties::has_property(), and properties().

◆ is_base_type()

virtual bool core::chemical::ResidueTypeBase::is_base_type ( ) const

pure virtual

Is this ResidueTypeBase a base type?

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_mainchain_torsion_potential_name(), and get_rama_prepro_map_file_name().

◆ is_d_aa()

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

inline

is this a d-amino acid?

References core::chemical::D_AA, core::chemical::ResidueProperties::has_property(), and properties().

Referenced by protocols::denovo_design::movers::FastDesign::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), core::fragment::IndependentBBTorsionSRFD::apply(), protocols::simple_filters::ResidueChiralityFilter::compute(), protocols::denovo_design::construct_poly_ala_pose(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::energy_methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::pack::dunbrack::MainchainTorsionReporter::get_dof(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::chemical::ResidueType::is_mirrored_type(), core::energy_methods::ProClosureEnergy::measure_chi4(), protocols::denovo_design::DisulfidizeMover::mixed_disulfide(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy(), and core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide().

◆ is_d_rna()

bool core::chemical::ResidueTypeBase::is_d_rna ( ) const

inline

is this a d-RNA?

References core::chemical::D_RNA, core::chemical::ResidueProperties::has_property(), and properties().

Referenced by core::chemical::ChiralFlipAtoms::apply(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), and core::conformation::Residue::is_d_rna().

◆ is_DNA()

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

inline

is DNA?

References core::chemical::DNA, core::chemical::ResidueProperties::has_property(), and properties().

◆ is_l_aa()

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

inline

is this an l-amino acid?

References core::chemical::ResidueProperties::has_property(), core::chemical::L_AA, and properties().

Referenced by protocols::denovo_design::movers::FastDesign::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), core::chemical::ChiralFlipAtoms::apply(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(), core::scoring::bin_transitions::BinTransitionData::has_property(), and core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy().

◆ is_l_rna()

bool core::chemical::ResidueTypeBase::is_l_rna ( ) const

inline

is this an l-RNA?

References core::chemical::ResidueProperties::has_property(), core::chemical::L_RNA, and properties().

Referenced by core::conformation::Residue::is_l_rna(), and core::chemical::ResidueType::is_mirrored_type().

◆ is_metapatched()

bool core::chemical::ResidueTypeBase::is_metapatched ( ) const

inline

Get whether this is a metapatched ResidueType.

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

References is_metapatched_.

◆ is_peptoid()

bool core::chemical::ResidueTypeBase::is_peptoid ( ) const

inline

is peptoid?

References core::chemical::ResidueProperties::has_property(), core::chemical::PEPTOID, and properties().

◆ is_polymer()

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

inline

is polymer?

References core::chemical::ResidueProperties::has_property(), core::chemical::POLYMER, and properties().

◆ is_protein()

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

inline

is protein?

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::PROTEIN.

◆ is_r_peptoid()

bool core::chemical::ResidueTypeBase::is_r_peptoid ( ) const

inline

Is this a peptoid with a chiral side-chain with "R" chirality?

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

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::R_PEPTOID.

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

◆ is_RNA()

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

inline

is RNA?

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::RNA.

◆ is_s_peptoid()

bool core::chemical::ResidueTypeBase::is_s_peptoid ( ) const

inline

Is this a peptoid with a chiral side-chain with "S" chirality?

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

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::S_PEPTOID.

Referenced by core::chemical::ChiralFlipNaming::apply(), and core::chemical::ChiralFlipAtoms::apply().

◆ mainchain_potentials_match()

bool core::chemical::ResidueTypeBase::mainchain_potentials_match ( ResidueTypeBase const & other ) const

Do the rama_prepro mainchain torsion potentials of this residue match another?

References rama_prepro_mainchain_torsion_potential_name_, rama_prepro_mainchain_torsion_potential_name_beforeproline_, rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

◆ metal_binding_atoms()

utility::vector1< std::string >& core::chemical::ResidueTypeBase::metal_binding_atoms ( )

inlineprotected

References metal_binding_atoms_.

Referenced by core::chemical::MutableResidueType::add_metalbinding_atom(), and core::chemical::MutableResidueType::delete_metalbinding_atom().

◆ mm_atom_types_ptr()

MMAtomTypeSetCOP core::chemical::ResidueTypeBase::mm_atom_types_ptr ( ) const

inline

References mm_atom_types_.

Referenced by core::chemical::ResidueType::copy_atom_info(), core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::ResidueType::mm_atom_type(), core::chemical::ResidueType::mm_name(), and core::chemical::MutableResidueType::placeholder_clone().

◆ mode()

TypeSetMode core::chemical::ResidueTypeBase::mode ( ) const

inline

References mode_.

Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::util::add_covalent_linkage_helper(), core::pose::add_custom_variant_type_to_pose_residue(), core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose(), core::conformation::add_variant_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::kinmatch::alapose(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::chemistries::PatchChemistry::apply(), protocols::cyclic_peptide::FlipChiralityMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pose::rna::assert_phosphate_nomenclature_matches_mini(), core::pack::dunbrack::cenrot::CenRotDunEnergy::atoms_with_dof_derivatives(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), core::conformation::change_cys_state(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::util::generate_replacement_restype(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pose::carbohydrates::glycosylate_pose(), core::pose::toolbox::AtomID_Mapper::initialize(), protocols::magnesium::instantiate_water_at_octahedral_vertex(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::environment::ProtectedConformation::match_variants(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), core::pose::rna::mutate_position(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::conformation::remove_variant_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), protocols::metal_interface::RemoveMetalConnectionsMover::remove_variant_types_from_res(), protocols::features::RotamerFeatures::report_features(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::energy_methods::HybridVDW_Energy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResPairDistEnergy::residue_pair_energy(), core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), core::util::switch_to_centroid_rot_set(), core::util::switch_to_residue_type_set(), core::pose::carbohydrates::tautomerize_anomer(), core::pose::Pose::virtual_to_real(), and core::io::serialization::write_binary().

◆ n_orbitals()

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

number of orbitals

References orbitals_.

Referenced by core::chemical::MutableResidueType::add_orbital(), and core::conformation::Residue::n_orbitals().

◆ n_virtual_atoms()

virtual Size core::chemical::ResidueTypeBase::n_virtual_atoms ( ) const

pure virtual

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)

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ na_analogue() [1/2]

AA const& core::chemical::ResidueTypeBase::na_analogue ( ) const

inline

Returns the nucleic acid type to be used for fragment sampling/scoring.

References aa_, core::chemical::aa_unp, and na_analogue_.

◆ na_analogue() [2/2]

void core::chemical::ResidueTypeBase::na_analogue ( std::string const & type )

inline

NA to use for fragment sampling and some scoring purposes.

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

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks(), core::fragment::rna::analyze_for_homology(), core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::rna::get_bin(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::energy_methods::get_restag(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::get_rna_motifs(), core::chemical::rna::get_watson_crick_base_pair_atoms(), core::conformation::Residue::na_analogue(), core::import_pose::libraries::one_letter_from_rt(), core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment(), core::scoring::rna::rna_residue_type_to_num(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), and core::chemical::write_topology_file().

◆ na_analogue_raw()

AA const& core::chemical::ResidueTypeBase::na_analogue_raw ( ) const

inlineprotected

References na_analogue_.

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

◆ name() [1/2]

std::string const& core::chemical::ResidueTypeBase::name ( ) const

inline

get our (unique) residue name

References name_.

◆ name() [2/2]

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

inline

set our (unique) residue name

References name_, and properties_.

◆ name1() [1/2]

char core::chemical::ResidueTypeBase::name1 ( ) const

inline

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

References name1_.

◆ name1() [2/2]

void core::chemical::ResidueTypeBase::name1 ( char const code )

inline

set our 1letter code

References name1_.

◆ name3() [1/2]

std::string const& core::chemical::ResidueTypeBase::name3 ( ) const

inline

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.

If you need three characters, the PDB convention is to right pad.

References name3_.

◆ name3() [2/2]

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

inline

set our 3letter code

References name3_.

◆ natoms()

virtual Size core::chemical::ResidueTypeBase::natoms ( ) const

pure virtual

number of atoms

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ nbonds()

virtual Size core::chemical::ResidueTypeBase::nbonds ( ) const

pure virtual

number of bonds

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ net_formal_charge() [1/2]

signed long int core::chemical::ResidueTypeBase::net_formal_charge ( ) const

inline

Get the nominal net formal charge on this residue type.

This may not match the sum of the formal charges on the atoms

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

References net_formal_charge_.

Referenced by core::chemical::SetNetFormalCharge::apply(), core::chemical::VirtualizeAll::apply(), core::energy_methods::NetChargeEnergy::calculate_energy(), and core::chemical::write_topology_file().

◆ net_formal_charge() [2/2]

void core::chemical::ResidueTypeBase::net_formal_charge ( signed long int charge_in )

inline

Set the nominal net formal charge on this residue type.

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

References net_formal_charge_.

◆ nheavyatoms()

virtual Size core::chemical::ResidueTypeBase::nheavyatoms ( ) const

pure virtual

number of heavy atoms

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ operator=()

ResidueTypeBase& core::chemical::ResidueTypeBase::operator= ( ResidueTypeBase const & )

protecteddefault

Copies <src> into the ResidueTypeBase.

Referenced by core::chemical::MutableResidueType::operator=().

◆ orbital() [1/2]

Orbital const & core::chemical::ResidueTypeBase::orbital ( Size const orbital_index ) const

References orbital_index(), and orbitals_.

Referenced by core::conformation::Residue::assign_orbitals(), core::chemical::ResidueType::new_orbital_icoor_data(), core::chemical::ResidueType::orbital_icoor_data(), core::conformation::Residue::orbital_name(), core::chemical::MutableResidueType::set_orbital_icoor_id(), and core::conformation::Residue::set_orbital_xyz().

◆ orbital() [2/2]

Orbital const & core::chemical::ResidueTypeBase::orbital ( std::string const & orbital_name ) const

References orbital_index(), and orbitals_.

◆ orbital_index()

core::Size core::chemical::ResidueTypeBase::orbital_index ( std::string const & name ) const

get orbital index by name

References name(), name3(), and orbitals_index_.

Referenced by core::chemical::MutableResidueType::add_orbital_bond(), core::chemical::ResidueType::new_orbital_icoor_data(), orbital(), core::chemical::ResidueType::orbital_icoor_data(), orbital_type(), and core::chemical::MutableResidueType::set_orbital_icoor_id().

◆ orbital_type()

orbitals::OrbitalType const & core::chemical::ResidueTypeBase::orbital_type ( Size const orbital_index ) const

References orbital_index(), orbital_types_, and orbitals_.

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

◆ orbital_types_ptr()

orbitals::OrbitalTypeSetCOP core::chemical::ResidueTypeBase::orbital_types_ptr ( ) const

inline

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

References orbital_types_.

Referenced by core::chemical::MutableResidueType::add_orbital(), core::chemical::rdkit::RDMolToRestype::generate_restype(), and core::chemical::MutableResidueType::placeholder_clone().

◆ properties()

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

inline

Access the collection of properties for this ResidueTypeBase.

References properties_.

◆ remap_pdb_atom_names() [1/2]

bool core::chemical::ResidueTypeBase::remap_pdb_atom_names ( ) const

inline

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

References remap_pdb_atom_names_.

◆ remap_pdb_atom_names() [2/2]

void core::chemical::ResidueTypeBase::remap_pdb_atom_names ( bool rename )

inline

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

References remap_pdb_atom_names_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), core::chemical::rename_atoms(), and core::chemical::write_topology_file().

◆ remove_variant_type() [1/2]

void core::chemical::ResidueTypeBase::remove_variant_type ( std::string const & variant_type )

Remove a variant type to this ResidueTypeBase by string.

References properties_.

◆ remove_variant_type() [2/2]

void core::chemical::ResidueTypeBase::remove_variant_type ( VariantType const variant_type )

Remove a variant type to this ResidueTypeBase.

References properties_.

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

◆ report_adducts()

void core::chemical::ResidueTypeBase::report_adducts ( ) const

References protocols::mean_field::add(), defined_adducts_, name3(), and core::chemical::TR().

◆ reset_mainchain_torsion_potential_names()

void core::chemical::ResidueTypeBase::reset_mainchain_torsion_potential_names ( )

Set the names of the mainchain torsion potential maps to use to "".

Also resets the mainchain torsion potential filename strings.

References rama_prepro_mainchain_torsion_potential_name_, rama_prepro_mainchain_torsion_potential_name_beforeproline_, rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

◆ rotamer_library_specification() [1/2]

rotamers::RotamerLibrarySpecificationCOP core::chemical::ResidueTypeBase::rotamer_library_specification ( ) const

References rotamer_library_specification_.

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

◆ rotamer_library_specification() [2/2]

void core::chemical::ResidueTypeBase::rotamer_library_specification ( rotamers::RotamerLibrarySpecificationOP rotlibspec )

References rotamer_library_specification_.

Referenced by core::chemical::RemoveRotamerSpecifications::apply(), core::chemical::NCAARotLibPath::apply(), core::chemical::NCAARotLibBBTorsions::apply(), core::pack::dunbrack::PeptideTorsionReporter::bb_torsion_index_for_rsd(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::create(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::rotamers::StoredRotamerLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_cachetag(), core::pack::dunbrack::RotamerLibraryScratchSpace::get_scratch_index(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::features::RotamerFeatures::report_features(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::pack::rotamers::SingleResidueRotamerLibraryFactory::type_for_residuetype(), and core::chemical::write_topology_file().

◆ rotamer_library_specification_nonconst()

rotamers::RotamerLibrarySpecificationOP core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst ( )

Nonconst access to the RotamerLibrarySpecification.

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

References rotamer_library_specification_.

Referenced by core::chemical::NCAARotLibNumRotamerBins::apply(), and core::chemical::ResidueType::update_ncaa_rotamer_library_specification_if_present().

◆ set_adduct_flag()

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

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

◆ set_disulfide_atom_name()

void core::chemical::ResidueTypeBase::set_disulfide_atom_name ( std::string const & n )

inline

Sets disulfide atom name.

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

References disulfide_atom_name_.

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

◆ set_gasteiger_atom_typeset()

void core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset ( gasteiger::GasteigerAtomTypeSetCOP setting )

References gasteiger_atom_types_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), and core::chemical::MutableResidueType::set_gasteiger_atom_type().

◆ set_metapatched()

void core::chemical::ResidueTypeBase::set_metapatched ( )

inline

Set that this is a metapatched ResidueType.

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

References is_metapatched_.

◆ set_orbital_typeset()

void core::chemical::ResidueTypeBase::set_orbital_typeset ( orbitals::OrbitalTypeSetCOP setting )

inline

References orbital_types_.

◆ set_properties()

void core::chemical::ResidueTypeBase::set_properties ( ResiduePropertiesOP properties )

Set the collection of properties for this ResidueTypeBase.

References properties(), and properties_.

◆ set_rama_prepro_mainchain_torsion_potential_name()

void core::chemical::ResidueTypeBase::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.

Set the key name for the mainchain torsion potential.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Note: Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

References rama_prepro_mainchain_torsion_potential_name_, and rama_prepro_mainchain_torsion_potential_name_beforeproline_.

Referenced by core::chemical::RamaPreproResname::apply(), and core::chemical::ResidueType::update_derived_data().

◆ set_rama_prepro_map_file_name()

void core::chemical::ResidueTypeBase::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.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Note: Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

References rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

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

◆ show()

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

pure virtual

Generate string representation of ResidueTypeBase for debugging purposes.

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ show_all_atom_names()

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

pure virtual

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

◆ strip_rotamer_library_specification()

void core::chemical::ResidueTypeBase::strip_rotamer_library_specification ( )

Remove any rotamer library specifications attached to this ResidueTypeBase.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

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

References rotamer_library_specification_.

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

◆ variant_type_enums()

utility::vector1< VariantType > core::chemical::ResidueTypeBase::variant_type_enums ( ) const

Get a vector of VariantType enums for this ResidueTypeBase.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

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

References properties_.

Referenced by protocols::cyclic_peptide::RamaMutationSelector::apply(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), and core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added().

◆ variant_types()

utility::vector1< std::string > core::chemical::ResidueTypeBase::variant_types ( ) const

get all the variant types for this ResidueTypeBase

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants. – rhiju (merging roccomoretti/restypeset_fiddle)

References properties_.

Referenced by protocols::loops::apply_sequence_mapping(), protocols::motifs::make_base_pair_mutation(), core::pose::rna::mutate_position(), core::util::switch_to_residue_type_set(), and core::chemical::write_topology_file().

Member Data Documentation

◆ aa_

AA core::chemical::ResidueTypeBase::aa_ = aa_unk

private

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

Referenced by aa(), backbone_aa(), base_analogue(), and na_analogue().

◆ atom_aliases_

std::map< std::string, std::string > core::chemical::ResidueTypeBase::atom_aliases_

private

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

Referenced by atom_alias(), and atom_aliases().

◆ atom_types_

AtomTypeSetCOP core::chemical::ResidueTypeBase::atom_types_

private

The type set for Rosetta Atom types. Required to be non-null for standard ResidueTypes.

Referenced by atom_type_set(), atom_type_set_ptr(), and ResidueTypeBase().

◆ backbone_aa_

AA core::chemical::ResidueTypeBase::backbone_aa_ = aa_unk

private

Referenced by backbone_aa(), and backbone_aa_raw().

◆ base_analogue_

AA core::chemical::ResidueTypeBase::base_analogue_ = aa_unp

private

Referenced by base_analogue(), and base_analogue_raw().

◆ base_name_

std::string core::chemical::ResidueTypeBase::base_name_

private

Residue id for the base type (i.e. sans variants).

Does not accumulate VariantType names (e.g. "ALA").

Referenced by base_name().

◆ canonical_atom_aliases_

std::map< std::string, std::string > core::chemical::ResidueTypeBase::canonical_atom_aliases_

private

A map of canonical atom names to atom aliases (white space included)

Referenced by canonical_atom_alias(), and canonical_atom_aliases().

◆ defined_adducts_

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

private

Adducts defined for this residue.

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

◆ disulfide_atom_name_

std::string core::chemical::ResidueTypeBase::disulfide_atom_name_ = "NONE"

private

Name of the disulfide-forming atom, if any.

Referenced by get_disulfide_atom_name(), and set_disulfide_atom_name().

◆ elements_

ElementSetCOP core::chemical::ResidueTypeBase::elements_

private

The set for element objects. – can be null.

Referenced by element_set(), and element_set_ptr().

◆ force_nbr_atom_orient_

bool core::chemical::ResidueTypeBase::force_nbr_atom_orient_ = false

private

Controls which atoms are selected by "select_orient_atoms", used to overlay residues during packing.

Referenced by force_nbr_atom_orient().

◆ gasteiger_atom_types_

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueTypeBase::gasteiger_atom_types_

private

The set for GasteigerAtomTypes. – can be null.

Referenced by gasteiger_atom_typeset(), and set_gasteiger_atom_typeset().

◆ interchangeability_group_

std::string core::chemical::ResidueTypeBase::interchangeability_group_

private

interchangeability group lets a ResidueTypeBase claim to be functionally interchangeable with any other ResidueTypeBase in the same group. This is used by the packer to decide which ResidueTypeBase from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueTypeBase and build rotamers for it.

Referenced by interchangeability_group().

◆ is_metapatched_

bool core::chemical::ResidueTypeBase::is_metapatched_ = false

private

Is this ResidueType the product of metapatching?

False by default; true if and only if a metapatch contributed to this ResidueType.

Referenced by is_metapatched(), and set_metapatched().

◆ metal_binding_atoms_

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

private

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

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

Referenced by get_metal_binding_atoms(), and metal_binding_atoms().

◆ mm_atom_types_

MMAtomTypeSetCOP core::chemical::ResidueTypeBase::mm_atom_types_

private

The set for MMAtomTypes. – can be null.

Referenced by mm_atom_types_ptr().

◆ mode_

TypeSetMode core::chemical::ResidueTypeBase::mode_ = INVALID_t

private

The TypeSet mode for this ResidueTypeBase.

Referenced by atom_type_set(), mode(), and ResidueTypeBase().

◆ na_analogue_

AA core::chemical::ResidueTypeBase::na_analogue_ = aa_unp

private

Referenced by na_analogue(), and na_analogue_raw().

◆ name1_

char core::chemical::ResidueTypeBase::name1_ = ' '

private

one-letter code, also not necessarily unique

Referenced by name1().

◆ name3_

std::string core::chemical::ResidueTypeBase::name3_

private

PDB-file id, need not be unique NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters.

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

◆ name_

std::string core::chemical::ResidueTypeBase::name_

private

Residue id – Should be unique within a ResidueTypeSet.

Accumulates VariantType names (e.g. "ALA:NtermProteinFull").

Referenced by name().

◆ net_formal_charge_

signed long int core::chemical::ResidueTypeBase::net_formal_charge_ = 0

private

What is the total formal charge of the ResidueType? (Note that this may be different from the sum of the formal charges on each atom.)

Referenced by net_formal_charge().

◆ orbital_types_

orbitals::OrbitalTypeSetCOP core::chemical::ResidueTypeBase::orbital_types_

private

The set for OrbitalTypes. – can be null.

Referenced by has_orbital_types(), orbital_type(), orbital_types_ptr(), and set_orbital_typeset().

◆ orbitals_

utility::deep_copy_vector1< OrbitalOP > core::chemical::ResidueTypeBase::orbitals_

private

The orbitals on the ResidueTypeBase, if any.

Referenced by get_orbitals(), n_orbitals(), orbital(), and orbital_type().

◆ orbitals_index_

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

private

index lookup for orbitals based on atom name Updated in add_orbital()

Referenced by get_orbitals_index(), has_orbital(), and orbital_index().

◆ properties_

utility::pointer::DeepCopyOP< ResidueProperties > core::chemical::ResidueTypeBase::properties_

private

Residue properties as defined in the residue topology (.params) files.

Referenced by add_numeric_property(), add_property(), add_string_property(), add_variant_type(), custom_variant_types(), delete_property(), enable_custom_variant_types(), get_numeric_property(), get_string_property(), has_property(), has_variant_type(), name(), properties(), remove_variant_type(), set_adduct_flag(), set_properties(), variant_type_enums(), and variant_types().

◆ rama_prepro_mainchain_torsion_potential_name_

std::string core::chemical::ResidueTypeBase::rama_prepro_mainchain_torsion_potential_name_

private

The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's mainchain torsion potential is used.

Note: This one is for maps used if this residue is not immediately before a proline.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_mainchain_torsion_potential_name().

◆ rama_prepro_mainchain_torsion_potential_name_beforeproline_

std::string core::chemical::ResidueTypeBase::rama_prepro_mainchain_torsion_potential_name_beforeproline_

private

The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's mainchain torsion potential is used.

Note: This one is for maps used if this residue occurs before a proline.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_mainchain_torsion_potential_name().

◆ rama_prepro_map_file_name_

std::string core::chemical::ResidueTypeBase::rama_prepro_map_file_name_

private

The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's file is used. If that's blank too, then this ResidueTypeBase isn't scored by RamaPrePro.

Note: This one is for maps used if this residue is not immediately before a proline.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_map_file_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_map_file_name().

◆ rama_prepro_map_file_name_beforeproline_

std::string core::chemical::ResidueTypeBase::rama_prepro_map_file_name_beforeproline_

private

The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's file is used. If that's blank too, then this ResidueTypeBase isn't scored by RamaPrePro.

Note: This one is for maps used if this residue occurs before a proline.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_map_file_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_map_file_name().

◆ remap_pdb_atom_names_

bool core::chemical::ResidueTypeBase::remap_pdb_atom_names_ = false

private

Should we attempt to rename atoms for this residue type when we read in PDB files?

Referenced by remap_pdb_atom_names().

◆ rotamer_library_specification_

utility::pointer::DeepCopyOP< rotamers::RotamerLibrarySpecification > core::chemical::ResidueTypeBase::rotamer_library_specification_

private

How to construct a rotamer library for this ResidueTypeBase.

Referenced by rotamer_library_specification(), rotamer_library_specification_nonconst(), and strip_rotamer_library_specification().

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

src/core/chemical/ResidueTypeBase.hh
src/core/chemical/ResidueTypeBase.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ResidueTypeBase() [1/3]

◆ ResidueTypeBase() [2/3]

◆ ResidueTypeBase() [3/3]

Member Function Documentation

◆ aa() [1/3]

◆ aa() [2/3]

◆ aa() [3/3]

◆ add_adduct()

◆ add_numeric_property()

◆ add_property() [1/2]

◆ add_property() [2/2]

◆ add_string_property()

◆ add_variant_type() [1/2]

◆ add_variant_type() [2/2]

◆ atom_alias()

◆ atom_aliases() [1/2]

◆ atom_aliases() [2/2]

◆ atom_type_set() [1/2]

◆ atom_type_set() [2/2]

◆ atom_type_set_ptr()

◆ backbone_aa() [1/3]

◆ backbone_aa() [2/3]

◆ backbone_aa() [3/3]

◆ backbone_aa_raw()

◆ base_analogue() [1/2]

◆ base_analogue() [2/2]

◆ base_analogue_raw()

◆ base_name() [1/2]

◆ base_name() [2/2]

◆ canonical_atom_alias()

◆ canonical_atom_aliases() [1/2]

◆ canonical_atom_aliases() [2/2]

◆ custom_variant_types()

◆ defined_adducts()

◆ defines_custom_rama_prepro_map()

◆ delete_property() [1/2]

◆ delete_property() [2/2]

◆ element_set()

◆ element_set_ptr()

◆ enable_custom_variant_types()

◆ force_nbr_atom_orient() [1/2]

◆ force_nbr_atom_orient() [2/2]

◆ gasteiger_atom_typeset()

◆ get_base_type_cop()

◆ get_disulfide_atom_name()

◆ get_metal_binding_atoms()

◆ get_numeric_property()

◆ get_orbitals()

◆ get_orbitals_index()

◆ get_rama_prepro_mainchain_torsion_potential_name()

◆ get_rama_prepro_map_file_name()

◆ get_string_property()

◆ has()

◆ has_orbital()

◆ has_orbital_types()

◆ has_property() [1/2]

◆ has_property() [2/2]

◆ has_variant_type() [1/2]

◆ has_variant_type() [2/2]

◆ interchangeability_group() [1/2]

◆ interchangeability_group() [2/2]

◆ is_achiral_backbone()

◆ is_achiral_sidechain()

◆ is_base_type()

◆ is_d_aa()

◆ is_d_rna()

◆ is_DNA()

◆ is_l_aa()

◆ is_l_rna()

◆ is_metapatched()

◆ is_peptoid()

◆ is_polymer()

◆ is_protein()

◆ is_r_peptoid()

◆ is_RNA()