#include <ResidueTypeFinder.hh>

Inheritance diagram for core::chemical::ResidueTypeFinder:

Public Member Functions
	ResidueTypeFinder (core::chemical::ResidueTypeSet const &residue_type_set)

	~ResidueTypeFinder () override

void	set_no_CCD_on_name3_match (bool setting)
	Don't consider CCD components if we already have a Rosetta type with the same three letter code, even if the two residue types have completely different chemical structure. Note we already have a mechanism (the exclude_pdb_component_list.txt file in the database) to exclude CCD components which chemically match the Rosetta type (and this exclusion is always on). More...

ResidueTypeCOP	get_representative_type (bool const metapatches=true) const
	Find a residue which matches all the requirement criteria. Typically this will be the "simplest" type that does so, though that's not guaranteed. Will ignore preferences/discouragements. More...

ResidueTypeCOPs	get_all_possible_residue_types (bool const allow_extra_variants=false) const
	Find all residues which match the requirement criteria Will apply preferences/discouragements. More...

ResidueTypeCOPs	get_possible_base_residue_types (bool const include_unpatchable=true, bool const apply_all_filters=false) const
	Find all base residue types which match the relevant requirement criteria. More...

ResidueTypeCOPs	get_possible_unpatchable_residue_types () const
	Find all unpatchable residue types which match the relevant requirement criteria. More...

ResidueTypeCOPs	get_possible_base_unpatchable_residue_types () const
	Get the unpatchable residue types where the any ResidueType with a non-self "base residue type" (as annotated in the ResidueType itself) filtered out. More...

ResidueTypeCOP	get_best_match_residue_type_for_atom_names (utility::vector1< std::string > const &atom_names)

ResidueTypeFinder &	aa (core::chemical::AA const &setting)

ResidueTypeFinder &	name1 (char const &setting)

ResidueTypeFinder &	name3 (std::string const &setting)

ResidueTypeFinder &	residue_base_name (std::string const &setting)

ResidueTypeFinder &	disable_metapatches ()
	Disable metapatches and do not consider them while patching. More...

bool	no_metapatches () const
	Have metapatched ResidueTypes been disabled (true)? Or are they to be considered (false)? More...

ResidueTypeFinder &	base_type (ResidueTypeCOP const &basetype)
	Allow a base type to be specified rigidly. Since any ResidueType's base type COP can now be accessed easily, this is a far more efficient way to prune the set of possible ResidueTypes. More...

ResidueTypeFinder &	interchangeability_group (std::string const &setting)

ResidueTypeFinder &	base_property (ResidueProperty const setting)

ResidueTypeFinder &	atom_names_soft (utility::vector1< std::string > const &setting)

ResidueTypeFinder &	variants_in_sets (utility::vector1< utility::vector1< VariantType > > const &setting)

ResidueTypeFinder &	variants (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
	Add a set of VariantTypes, all of which matching ResidueTypes MUST have. More...

ResidueTypeFinder &	variants (utility::vector1< std::string > const &setting)
	set function for variants More...

ResidueTypeFinder &	variants (utility::vector1< VariantType > const &std_variants, utility::vector1< std::string > const &custom_variants, bool const clear_existing=true)
	Specify a list of standard variant types (by enum) and custom variant types (by string). More...

ResidueTypeFinder &	disallow_variants (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
	Provide a list of VariantTypes that a matched ResidueType must NOT have. More...

ResidueTypeFinder &	variant_exceptions (utility::vector1< std::string > const &setting, bool const clear_existing=true)
	Variant exceptions are variants which are excluded from consideration during the `allow_extra_variants = false` filtering. More...

ResidueTypeFinder &	variant_exceptions (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
	Provide a list of VariantTypes that will be ignored when matching. More...

ResidueTypeFinder &	properties (utility::vector1< ResidueProperty > const &setting)

ResidueTypeFinder &	disallow_properties (utility::vector1< ResidueProperty > const &setting)

ResidueTypeFinder &	preferred_properties (utility::vector1< ResidueProperty > const &setting)

ResidueTypeFinder &	discouraged_properties (utility::vector1< ResidueProperty > const &setting)

ResidueTypeFinder &	patch_names (utility::vector1< std::string > const &setting)

ResidueTypeFinder &	connect_atoms (utility::vector1< std::string > const &setting)
	Attempt to find ResidueTypes with connection points on the given atoms. More...

ResidueTypeFinder &	ignore_atom_named_H (bool const setting)

ResidueTypeFinder &	check_nucleic_acid_virtual_phosphates (bool const setting)

Private Member Functions
void	apply_basic_filters (ResidueTypeCOPs &rsd_types) const

void	apply_filters_after_patches (ResidueTypeCOPs &rsd_types, bool const allow_extra_variants=false) const

ResidueTypeCOPs	apply_preferences_and_discouragements (ResidueTypeCOPs const &rsd_types) const

ResidueTypeCOPs	prioritize_rosetta_types_over_pdb_components (ResidueTypeCOPs const &rsd_types) const

void	initialize_relevant_pdb_components () const

utility::vector1< ResidueTypeCOP >	get_patched_types (utility::vector1< ResidueTypeCOP > const &rsd_types, bool const get_first_totally_ok_residue_type=false) const
	Attempt to apply patches to the residue types in rsd_types, returning the new types. (Existing residue types in rsd_types are not returned) get_first_totally_ok_residue_type is true, only the first residue type in the vector will be returned. This function will take care of multiply-patching the results. More...

utility::vector1< ResidueTypeCOP >	get_singly_metapatched_types (utility::vector1< ResidueTypeCOP > const &rsd_types, bool const get_first_totally_ok_residue_type=false) const
	Attempt to apply metapatches to the residue types in rsd_types, returning the new types. (Existing residue types in rsd_types are not returned) get_first_totally_ok_residue_type is true, only the first residue type in the vector will be returned. This function only gets types with a single metapatch applied. If the caller wants multiply-patched types, it's responsible for re-calling this function itself. More...

void	filter_by_name1 (ResidueTypeCOPs &rsd_types) const

void	filter_by_name3 (ResidueTypeCOPs &rsd_types, bool const keep_if_base_type_generates_aa) const

void	filter_by_aa (ResidueTypeCOPs &rsd_types) const

void	filter_by_residue_type_base_name (ResidueTypeCOPs &rsd_types) const

void	filter_by_interchangeability_group (ResidueTypeCOPs &rsd_types, bool const keep_if_base_type_generates_interchangeability_group) const

void	filter_by_base_property (ResidueTypeCOPs &base_rsd_types) const

void	filter_for_all_variant_sets (ResidueTypeCOPs &rsd_types) const

void	filter_variant_sets_have_all_candidate_variants (ResidueTypeCOPs &rsd_types) const

void	filter_all_variants_matched (ResidueTypeCOPs &rsd_types, bool const allow_extra_variants=false) const

void	filter_disallow_variants (ResidueTypeCOPs &rsd_types) const

void	filter_all_patch_names (ResidueTypeCOPs &rsd_types) const

void	filter_all_properties (ResidueTypeCOPs &rsd_types) const

void	filter_disallow_properties (ResidueTypeCOPs &rsd_types) const

void	filter_connections (ResidueTypeCOPs &rsd_types) const

void	filter_special_cases (ResidueTypeCOPs &rsd_types) const

bool	has_disallowed_variant (PatchCOP patch) const

bool	adds_any_variant (PatchCOP patch) const

bool	fixes_name3 (PatchCOP patch, ResidueTypeCOP rsd_type) const

bool	fixes_interchangeability_group (PatchCOP patch, ResidueTypeCOP rsd_type) const

bool	fixes_connects (PatchCOP patch, ResidueTypeCOP rsd_type) const

bool	adds_any_property (PatchCOP patch, ResidueTypeCOP rsd_type) const
	Returns true if this patch adds any of the properties that the ResidueTypeFinder is seeking. More...

bool	deletes_any_property (PatchCOP patch, ResidueTypeCOP rsd_type) const
	Returns true if this patch deletes any of the properties that the ResidueTypeFinder is seeking. More...

bool	deletes_any_variant (PatchCOP patch, ResidueTypeCOP rsd_type) const

bool	changes_to_wrong_aa (PatchCOP patch, ResidueTypeCOP rsd_type) const

bool	matches_any_patch_name (PatchCOP patch) const

bool	matches_any_atom_name (PatchCOP patch, ResidueTypeCOP rsd_type) const

ResidueTypeFinder &	variants (utility::vector1< VariantType > const &setting) const

Private Attributes
core::chemical::ResidueTypeSet const &	residue_type_set_

core::chemical::AA	aa_ = aa_none

char	name1_ = '?'

std::string	name3_ = ""

std::string	residue_type_base_name_ = ""

ResidueTypeCOP	base_type_ = nullptr

std::string	interchangeability_group_ = ""

utility::vector1< std::string >	atom_names_soft_

utility::vector1< utility::vector1< VariantType > >	variants_in_sets_

utility::vector1< std::string >	custom_variants_

utility::vector1< VariantType >	disallow_variants_

utility::vector1< VariantType >	variant_exceptions_

utility::vector1< ResidueProperty >	properties_

utility::vector1< ResidueProperty >	disallow_properties_

utility::vector1< ResidueProperty >	preferred_properties_

utility::vector1< ResidueProperty >	discouraged_properties_

utility::vector1< std::string >	patch_names_

utility::vector1< std::string >	connect_atoms_

ResidueProperty	base_property_ = NO_PROPERTY

bool	ignore_atom_named_H_ = false

bool	disallow_carboxyl_conjugation_at_glu_asp_

bool	check_nucleic_acid_virtual_phosphates_ = false

bool	no_metapatches_ = false
	Disable consideration of metapatched variants (relevant for speed). More...

bool	no_CCD_on_name3_match_ = false
	Don't consider CCD components if we already have a Rosetta type with the same three letter code. More...

Constructor & Destructor Documentation

◆ ResidueTypeFinder()

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

◆ ~ResidueTypeFinder()

core::chemical::ResidueTypeFinder::~ResidueTypeFinder ( )

overridedefault

Member Function Documentation

◆ aa()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::aa ( core::chemical::AA const & setting )

inline

References aa_.

Referenced by core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(), core::chemical::ResidueTypeSet::get_base_types_aa(), core::chemical::ResidueTypeSet::get_representative_type_aa(), core::conformation::get_residue_from_name1(), core::pose::get_rsd_type_from_aa(), and core::util::switch_to_residue_type_set().

◆ adds_any_property()

bool core::chemical::ResidueTypeFinder::adds_any_property	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

Returns true if this patch adds any of the properties that the ResidueTypeFinder is seeking.

ONLY works for canonical properties (not on-the-fly properties) at present. Modified on 24 Aug 2016 by VKM to remove string parsing.

References preferred_properties_, and properties_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ adds_any_variant()

bool core::chemical::ResidueTypeFinder::adds_any_variant ( PatchCOP patch ) const

private

References atom_names_soft_, check_nucleic_acid_virtual_phosphates_, custom_variants_, variant_exceptions_, variants_in_sets_, core::chemical::VIRTUAL_DNA_PHOSPHATE, and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ apply_basic_filters()

void core::chemical::ResidueTypeFinder::apply_basic_filters ( ResidueTypeCOPs & rsd_types ) const

private

References filter_by_aa(), filter_by_base_property(), filter_by_interchangeability_group(), filter_by_name1(), filter_by_name3(), filter_by_residue_type_base_name(), and core::chemical::TR().

Referenced by get_possible_base_residue_types(), and get_possible_unpatchable_residue_types().

◆ apply_filters_after_patches()

void core::chemical::ResidueTypeFinder::apply_filters_after_patches	(	ResidueTypeCOPs &	rsd_types,
		bool const	allow_extra_variants = `false`
	)		const

private

References filter_all_patch_names(), filter_all_properties(), filter_all_variants_matched(), filter_by_interchangeability_group(), filter_by_name3(), filter_connections(), filter_disallow_properties(), filter_disallow_variants(), filter_special_cases(), and core::chemical::TR().

Referenced by get_all_possible_residue_types(), get_patched_types(), get_possible_base_residue_types(), get_representative_type(), and get_singly_metapatched_types().

◆ apply_preferences_and_discouragements()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::apply_preferences_and_discouragements ( ResidueTypeCOPs const & rsd_types ) const

private

References discouraged_properties_, no_CCD_on_name3_match_, preferred_properties_, prioritize_rosetta_types_over_pdb_components(), and core::chemical::TR().

Referenced by get_all_possible_residue_types(), and get_possible_base_residue_types().

◆ atom_names_soft()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::atom_names_soft ( utility::vector1< std::string > const & setting )

inline

References atom_names_soft_.

◆ base_property()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::base_property ( ResidueProperty const setting )

inline

References base_property_.

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::pose::rna::mutate_position(), core::chemical::GlobalResidueTypeSet::place_adducts(), protocols::ligand_docking::GrowLigand::set_fragments(), and protocols::ligand_docking::LigandDesign::set_fragments().

◆ base_type()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::base_type ( ResidueTypeCOP const & basetype )

inline

Allow a base type to be specified rigidly. Since any ResidueType's base type COP can now be accessed easily, this is a far more efficient way to prune the set of possible ResidueTypes.

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

References base_type_.

Referenced by core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(), core::chemical::ResidueTypeSet::get_d_equivalent(), core::chemical::ResidueTypeSet::get_l_equivalent(), core::pack::palette::PackerPalette::get_residue_type_cop_with_variant_removed(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), and protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply().

◆ changes_to_wrong_aa()

bool core::chemical::ResidueTypeFinder::changes_to_wrong_aa	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

References aa_, and core::chemical::aa_none.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ check_nucleic_acid_virtual_phosphates()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates ( bool const setting )

inline

References check_nucleic_acid_virtual_phosphates_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ connect_atoms()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::connect_atoms ( utility::vector1< std::string > const & setting )

inline

Attempt to find ResidueTypes with connection points on the given atoms.

References connect_atoms_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types().

◆ deletes_any_property()

bool core::chemical::ResidueTypeFinder::deletes_any_property	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

Returns true if this patch deletes any of the properties that the ResidueTypeFinder is seeking.

ONLY works for canonical properties (not on-the-fly properties) at present. Modified on 25 Aug 2016 by VKM to remove string parsing.

References properties_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ deletes_any_variant()

bool core::chemical::ResidueTypeFinder::deletes_any_variant	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

References variants_in_sets_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ disable_metapatches()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::disable_metapatches ( )

inline

Disable metapatches and do not consider them while patching.

By default, metapatched ResidueTypes will be considered. This disables that.

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

References no_metapatches_.

Referenced by core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype().

◆ disallow_properties()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::disallow_properties ( utility::vector1< ResidueProperty > const & setting )

inline

References disallow_properties_.

◆ disallow_variants()

ResidueTypeFinder & core::chemical::ResidueTypeFinder::disallow_variants	(	utility::vector1< VariantType > const &	setting,
		bool const	clear_existing = `true`
	)

Provide a list of VariantTypes that a matched ResidueType must NOT have.

By default, this overwrites the existing list. To append to the existing list, set clear_existing to false.

Referenced by core::pack::palette::PackerPalette::get_residue_type_cop_with_variant_removed(), and core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ discouraged_properties()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::discouraged_properties ( utility::vector1< ResidueProperty > const & setting )

inline

References discouraged_properties_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ filter_all_patch_names()

void core::chemical::ResidueTypeFinder::filter_all_patch_names ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by apply_filters_after_patches().

◆ filter_all_properties()

void core::chemical::ResidueTypeFinder::filter_all_properties ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by apply_filters_after_patches().

◆ filter_all_variants_matched()

void core::chemical::ResidueTypeFinder::filter_all_variants_matched	(	ResidueTypeCOPs &	rsd_types,
		bool const	allow_extra_variants = `false`
	)		const

private

References filter_for_all_variant_sets(), filter_variant_sets_have_all_candidate_variants(), and core::chemical::TR().

Referenced by apply_filters_after_patches().

◆ filter_by_aa()

void core::chemical::ResidueTypeFinder::filter_by_aa ( ResidueTypeCOPs & rsd_types ) const

private

References aa_, core::chemical::aa_none, and core::chemical::TR().

Referenced by apply_basic_filters().

◆ filter_by_base_property()

void core::chemical::ResidueTypeFinder::filter_by_base_property ( ResidueTypeCOPs & base_rsd_types ) const

private

References base_property_, core::chemical::NO_PROPERTY, and core::chemical::TR().

Referenced by apply_basic_filters().

◆ filter_by_interchangeability_group()

void core::chemical::ResidueTypeFinder::filter_by_interchangeability_group	(	ResidueTypeCOPs &	rsd_types,
		bool const	keep_if_base_type_generates_interchangeability_group
	)		const

private

References interchangeability_group_, and core::chemical::TR().

Referenced by apply_basic_filters(), and apply_filters_after_patches().

◆ filter_by_name1()

void core::chemical::ResidueTypeFinder::filter_by_name1 ( ResidueTypeCOPs & rsd_types ) const

private

References name1_, and core::chemical::TR().

Referenced by apply_basic_filters().

◆ filter_by_name3()

void core::chemical::ResidueTypeFinder::filter_by_name3	(	ResidueTypeCOPs &	rsd_types,
		bool const	keep_if_base_type_generates_aa
	)		const

private

References name3_, and core::chemical::TR().

Referenced by apply_basic_filters(), and apply_filters_after_patches().

◆ filter_by_residue_type_base_name()

void core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name ( ResidueTypeCOPs & rsd_types ) const

private

References residue_type_base_name_, and core::chemical::TR().

Referenced by apply_basic_filters().

◆ filter_connections()

void core::chemical::ResidueTypeFinder::filter_connections ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by apply_filters_after_patches().

◆ filter_disallow_properties()

void core::chemical::ResidueTypeFinder::filter_disallow_properties ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by apply_filters_after_patches().

◆ filter_disallow_variants()

void core::chemical::ResidueTypeFinder::filter_disallow_variants ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by apply_filters_after_patches().

◆ filter_for_all_variant_sets()

void core::chemical::ResidueTypeFinder::filter_for_all_variant_sets ( ResidueTypeCOPs & rsd_types ) const

private

References custom_variants_.

Referenced by filter_all_variants_matched().

◆ filter_special_cases()

void core::chemical::ResidueTypeFinder::filter_special_cases ( ResidueTypeCOPs & rsd_types ) const

private

References core::chemical::FIVE_PRIME_PACKABLE_TRIPHOSPHATE, and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by apply_filters_after_patches().

◆ filter_variant_sets_have_all_candidate_variants()

void core::chemical::ResidueTypeFinder::filter_variant_sets_have_all_candidate_variants ( ResidueTypeCOPs & rsd_types ) const

private

Referenced by filter_all_variants_matched().

◆ fixes_connects()

bool core::chemical::ResidueTypeFinder::fixes_connects	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

Does the patch any desired property or any soft desired property

References connect_atoms_.

Referenced by get_patched_types().

◆ fixes_interchangeability_group()

bool core::chemical::ResidueTypeFinder::fixes_interchangeability_group	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

References core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(), interchangeability_group_, core::chemical::residue_type_base_name(), and residue_type_set_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ fixes_name3()

bool core::chemical::ResidueTypeFinder::fixes_name3	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

References core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3(), name3_, core::chemical::residue_type_base_name(), and residue_type_set_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ get_all_possible_residue_types()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_all_possible_residue_types ( bool const allow_extra_variants = false ) const

Find all residues which match the requirement criteria Will apply preferences/discouragements.

References apply_filters_after_patches(), apply_preferences_and_discouragements(), get_patched_types(), get_possible_base_residue_types(), get_possible_unpatchable_residue_types(), get_singly_metapatched_types(), no_metapatches(), and core::chemical::TR().

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(), core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(), core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(), core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(), get_best_match_residue_type_for_atom_names(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), core::chemical::GlobalResidueTypeSet::place_adducts(), protocols::ligand_docking::GrowLigand::set_fragments(), protocols::ligand_docking::LigandDesign::set_fragments(), and protocols::forge::components::VarLengthBuild::set_starting_non_canonical().

◆ get_best_match_residue_type_for_atom_names()

ResidueTypeCOP core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names ( utility::vector1< std::string > const & atom_names )

References atom_names_soft_, core::chemical::find_best_match(), get_all_possible_residue_types(), ignore_atom_named_H_, core::chemical::orbitals::strip_whitespace(), and core::chemical::TR().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ get_patched_types()

utility::vector1< ResidueTypeCOP > core::chemical::ResidueTypeFinder::get_patched_types	(	utility::vector1< ResidueTypeCOP > const &	rsd_types,
		bool const	get_first_totally_ok_residue_type = `false`
	)		const

private

Attempt to apply patches to the residue types in rsd_types, returning the new types. (Existing residue types in rsd_types are not returned) get_first_totally_ok_residue_type is true, only the first residue type in the vector will be returned. This function will take care of multiply-patching the results.

This does not call the filters on the returned types – that's for the caller to handle.

References adds_any_property(), adds_any_variant(), apply_filters_after_patches(), changes_to_wrong_aa(), deletes_any_property(), deletes_any_variant(), fixes_connects(), fixes_interchangeability_group(), fixes_name3(), has_disallowed_variant(), matches_any_atom_name(), matches_any_patch_name(), core::chemical::ResidueTypeSet::name_mapOP(), core::chemical::ResidueTypeSet::patches(), residue_type_set_, and core::chemical::TR().

Referenced by get_all_possible_residue_types(), and get_representative_type().

◆ get_possible_base_residue_types()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_possible_base_residue_types	(	bool const	include_unpatchable = `true`,
		bool const	apply_all_filters = `false`
	)		const

Find all base residue types which match the relevant requirement criteria.

References apply_basic_filters(), apply_filters_after_patches(), apply_preferences_and_discouragements(), core::chemical::ResidueTypeSet::base_residue_types(), base_type_, get_possible_base_unpatchable_residue_types(), initialize_relevant_pdb_components(), and residue_type_set_.

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), get_all_possible_residue_types(), core::chemical::ResidueTypeSet::get_base_types_aa(), core::chemical::ResidueTypeSet::get_base_types_name1(), core::chemical::ResidueTypeSet::get_base_types_name3(), and get_representative_type().

◆ get_possible_base_unpatchable_residue_types()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_possible_base_unpatchable_residue_types ( ) const

Get the unpatchable residue types where the any ResidueType with a non-self "base residue type" (as annotated in the ResidueType itself) filtered out.

References core::chemical::residue_type_base_name(), residue_type_set_, and core::chemical::ResidueTypeSet::unpatchable_residue_types().

Referenced by get_possible_base_residue_types().

◆ get_possible_unpatchable_residue_types()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_possible_unpatchable_residue_types ( ) const

Find all unpatchable residue types which match the relevant requirement criteria.

References apply_basic_filters(), residue_type_set_, and core::chemical::ResidueTypeSet::unpatchable_residue_types().

Referenced by get_all_possible_residue_types(), and get_representative_type().

◆ get_representative_type()

ResidueTypeCOP core::chemical::ResidueTypeFinder::get_representative_type ( bool const metapatches = true ) const

Find a residue which matches all the requirement criteria. Typically this will be the "simplest" type that does so, though that's not guaranteed. Will ignore preferences/discouragements.

References apply_filters_after_patches(), get_patched_types(), get_possible_base_residue_types(), get_possible_unpatchable_residue_types(), get_singly_metapatched_types(), and no_metapatches().

◆ get_singly_metapatched_types()

utility::vector1< ResidueTypeCOP > core::chemical::ResidueTypeFinder::get_singly_metapatched_types	(	utility::vector1< ResidueTypeCOP > const &	rsd_types,
		bool const	get_first_totally_ok_residue_type = `false`
	)		const

private

Attempt to apply metapatches to the residue types in rsd_types, returning the new types. (Existing residue types in rsd_types are not returned) get_first_totally_ok_residue_type is true, only the first residue type in the vector will be returned. This function only gets types with a single metapatch applied. If the caller wants multiply-patched types, it's responsible for re-calling this function itself.

This does not call the filters on the returned types – that's for the caller to handle.

References adds_any_property(), adds_any_variant(), apply_filters_after_patches(), changes_to_wrong_aa(), deletes_any_property(), deletes_any_variant(), fixes_interchangeability_group(), fixes_name3(), has_disallowed_variant(), matches_any_atom_name(), matches_any_patch_name(), core::chemical::ResidueTypeSet::metapatches(), core::chemical::ResidueTypeSet::name_mapOP(), no_metapatches(), and residue_type_set_.

Referenced by get_all_possible_residue_types(), and get_representative_type().

◆ has_disallowed_variant()

bool core::chemical::ResidueTypeFinder::has_disallowed_variant ( PatchCOP patch ) const

private

References disallow_variants_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ ignore_atom_named_H()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::ignore_atom_named_H ( bool const setting )

inline

References ignore_atom_named_H_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ initialize_relevant_pdb_components()

void core::chemical::ResidueTypeFinder::initialize_relevant_pdb_components ( ) const

private

References core::chemical::ResidueTypeSet::base_residue_types(), core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3(), name3_, core::chemical::ResidueTypeSet::name_mapOP(), no_CCD_on_name3_match_, core::chemical::residue_type_base_name(), and residue_type_set_.

Referenced by get_possible_base_residue_types().

◆ interchangeability_group()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::interchangeability_group ( std::string const & setting )

inline

References interchangeability_group_.

Referenced by core::chemical::ResidueTypeSet::has_interchangeability_group().

◆ matches_any_atom_name()

bool core::chemical::ResidueTypeFinder::matches_any_atom_name	(	PatchCOP	patch,
		ResidueTypeCOP	rsd_type
	)		const

private

References atom_names_soft_, core::chemical::orbitals::strip_whitespace(), and core::chemical::TR().

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ matches_any_patch_name()

bool core::chemical::ResidueTypeFinder::matches_any_patch_name ( PatchCOP patch ) const

private

References patch_names_.

Referenced by get_patched_types(), and get_singly_metapatched_types().

◆ name1()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::name1 ( char const & setting )

inline

References name1_.

Referenced by core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(), core::chemical::ResidueTypeSet::get_base_types_name1(), core::chemical::ResidueTypeSet::get_representative_type_name1(), and core::pose::rna::mutate_position().

◆ name3()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::name3 ( std::string const & setting )

inline

References name3_.

Referenced by protocols::farnesyl::InstallFarnesylMover::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::d_l_threeletter_codes_are_same_for_aa(), protocols::simple_moves::SimpleThreadingMover::determine_mutations_comma_separated(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(), core::chemical::ResidueTypeSet::get_base_types_name3(), core::chemical::ResidueTypeSet::get_representative_type_name3(), core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), core::pose::rna::mutate_position(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), protocols::forge::components::VarLengthBuild::set_starting_non_canonical(), and core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

◆ no_metapatches()

bool core::chemical::ResidueTypeFinder::no_metapatches ( ) const

inline

Have metapatched ResidueTypes been disabled (true)? Or are they to be considered (false)?

Author: Vikram K. Mulligan (vmullig.uw.edu).

References no_metapatches_.

Referenced by get_all_possible_residue_types(), get_representative_type(), and get_singly_metapatched_types().

◆ patch_names()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::patch_names ( utility::vector1< std::string > const & setting )

inline

References patch_names_.

Referenced by protocols::simple_moves::SimpleThreadingMover::determine_mutations_comma_separated(), and core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ preferred_properties()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::preferred_properties ( utility::vector1< ResidueProperty > const & setting )

inline

References preferred_properties_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type().

◆ prioritize_rosetta_types_over_pdb_components()

ResidueTypeCOPs core::chemical::ResidueTypeFinder::prioritize_rosetta_types_over_pdb_components ( ResidueTypeCOPs const & rsd_types ) const

private

References no_CCD_on_name3_match_.

Referenced by apply_preferences_and_discouragements().

◆ properties()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::properties ( utility::vector1< ResidueProperty > const & setting )

inline

References properties_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types().

◆ residue_base_name()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::residue_base_name ( std::string const & setting )

inline

References residue_type_base_name_.

Referenced by protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), protocols::simple_moves::SimpleThreadingMover::determine_mutations_comma_separated(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_nc_name_codes(), core::chemical::ResidueTypeSet::get_representative_type_base_name(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), and core::pose::Pose::virtual_to_real().

◆ set_no_CCD_on_name3_match()

void core::chemical::ResidueTypeFinder::set_no_CCD_on_name3_match ( bool setting )

inline

Don't consider CCD components if we already have a Rosetta type with the same three letter code, even if the two residue types have completely different chemical structure. Note we already have a mechanism (the exclude_pdb_component_list.txt file in the database) to exclude CCD components which chemically match the Rosetta type (and this exclusion is always on).

References no_CCD_on_name3_match_.

◆ variant_exceptions() [1/2]

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variant_exceptions	(	utility::vector1< std::string > const &	setting,
		bool const	clear_existing = `true`
	)

Variant exceptions are variants which are excluded from consideration during the allow_extra_variants = false filtering.

set function for variant exceptions

References core::chemical::NO_VARIANT.

Referenced by core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(), core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(), and core::chemical::GlobalResidueTypeSet::place_adducts().

◆ variant_exceptions() [2/2]

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variant_exceptions	(	utility::vector1< VariantType > const &	setting,
		bool const	clear_existing = `true`
	)

Provide a list of VariantTypes that will be ignored when matching.

By default, this overwritest the existing list. To append to the existing list, set clear_existing=false.

Note: Variant exceptions are variants which are excluded from consideration during the allow_extra_variants = false filtering

By default, this overwritest the existing list. To append to the existing list, set clear_existing=false.

◆ variants() [1/4]

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variants ( utility::vector1< std::string > const & setting )

set function for variants

actually updates variants_in_sets_.

References core::chemical::NO_VARIANT, and update_ResidueType_enum_files::variants.

◆ variants() [2/4]

ResidueTypeFinder& core::chemical::ResidueTypeFinder::variants ( utility::vector1< VariantType > const & setting ) const

private

◆ variants() [3/4]

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variants	(	utility::vector1< VariantType > const &	setting,
		bool const	clear_existing = `true`
	)

Add a set of VariantTypes, all of which matching ResidueTypes MUST have.

set function for variants

By default, clears old required VariantType list. To append to list, set clear_existing=false.

actually updates variants_in_sets_.

◆ variants() [4/4]

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variants	(	utility::vector1< VariantType > const &	std_variants,
		utility::vector1< std::string > const &	custom_variants,
		bool const	clear_existing = `true`
	)

Specify a list of standard variant types (by enum) and custom variant types (by string).

This is the most efficient way to handle variants, since it minimizes the string handling. Everything that can be handled by enum is handled by enum.

Parameters

[in]	std_variants	A vector of enums of standard variants that the ResidueTypeFinder should match.
[in]	custom_variants	A vector of strings of custom variant types that the ResidueTypeFinder should match. Note that standard types should NOT be included in this list. There is no check for this!
[in]	clear_existing	If true (default), the existing VariantType lists are cleared. If false, this just appends to those lists.

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

References update_ResidueType_enum_files::variants.

◆ variants_in_sets()

ResidueTypeFinder& core::chemical::ResidueTypeFinder::variants_in_sets ( utility::vector1< utility::vector1< VariantType > > const & setting )

inline

References variants_in_sets_.

Member Data Documentation

◆ aa_

core::chemical::AA core::chemical::ResidueTypeFinder::aa_ = aa_none

private

Referenced by aa(), changes_to_wrong_aa(), and filter_by_aa().

◆ atom_names_soft_

utility::vector1< std::string > core::chemical::ResidueTypeFinder::atom_names_soft_

private

Referenced by adds_any_variant(), atom_names_soft(), get_best_match_residue_type_for_atom_names(), and matches_any_atom_name().

◆ base_property_

ResidueProperty core::chemical::ResidueTypeFinder::base_property_ = NO_PROPERTY

private

Referenced by base_property(), and filter_by_base_property().

◆ base_type_

ResidueTypeCOP core::chemical::ResidueTypeFinder::base_type_ = nullptr

private

Referenced by base_type(), and get_possible_base_residue_types().

◆ check_nucleic_acid_virtual_phosphates_

bool core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates_ = false

private

Referenced by adds_any_variant(), and check_nucleic_acid_virtual_phosphates().

◆ connect_atoms_

utility::vector1< std::string > core::chemical::ResidueTypeFinder::connect_atoms_

private

Referenced by connect_atoms(), and fixes_connects().

◆ custom_variants_

utility::vector1< std::string > core::chemical::ResidueTypeFinder::custom_variants_

private

Referenced by adds_any_variant(), and filter_for_all_variant_sets().

◆ disallow_carboxyl_conjugation_at_glu_asp_

bool core::chemical::ResidueTypeFinder::disallow_carboxyl_conjugation_at_glu_asp_

private

◆ disallow_properties_

utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::disallow_properties_

private

Referenced by disallow_properties().

◆ disallow_variants_

utility::vector1< VariantType > core::chemical::ResidueTypeFinder::disallow_variants_

private

Referenced by has_disallowed_variant().

◆ discouraged_properties_

utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::discouraged_properties_

private

Referenced by apply_preferences_and_discouragements(), and discouraged_properties().

◆ ignore_atom_named_H_

bool core::chemical::ResidueTypeFinder::ignore_atom_named_H_ = false

private

Referenced by get_best_match_residue_type_for_atom_names(), and ignore_atom_named_H().

◆ interchangeability_group_

std::string core::chemical::ResidueTypeFinder::interchangeability_group_ = ""

private

Referenced by filter_by_interchangeability_group(), fixes_interchangeability_group(), and interchangeability_group().

◆ name1_

char core::chemical::ResidueTypeFinder::name1_ = '?'

private

Referenced by filter_by_name1(), and name1().

◆ name3_

std::string core::chemical::ResidueTypeFinder::name3_ = ""

private

Referenced by filter_by_name3(), fixes_name3(), initialize_relevant_pdb_components(), and name3().

◆ no_CCD_on_name3_match_

bool core::chemical::ResidueTypeFinder::no_CCD_on_name3_match_ = false

private

Don't consider CCD components if we already have a Rosetta type with the same three letter code.

Referenced by apply_preferences_and_discouragements(), initialize_relevant_pdb_components(), prioritize_rosetta_types_over_pdb_components(), and set_no_CCD_on_name3_match().

◆ no_metapatches_

bool core::chemical::ResidueTypeFinder::no_metapatches_ = false

private

Disable consideration of metapatched variants (relevant for speed).

False by default (considers metapatches); if true, metapatches are disabled.

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

Referenced by disable_metapatches(), and no_metapatches().

◆ patch_names_

utility::vector1< std::string > core::chemical::ResidueTypeFinder::patch_names_

private

Referenced by matches_any_patch_name(), and patch_names().

◆ preferred_properties_

utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::preferred_properties_

private

Referenced by adds_any_property(), apply_preferences_and_discouragements(), and preferred_properties().

◆ properties_

utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::properties_

private

Referenced by adds_any_property(), deletes_any_property(), and properties().

◆ residue_type_base_name_

std::string core::chemical::ResidueTypeFinder::residue_type_base_name_ = ""

private

Referenced by filter_by_residue_type_base_name(), and residue_base_name().

◆ residue_type_set_

core::chemical::ResidueTypeSet const& core::chemical::ResidueTypeFinder::residue_type_set_

private

Referenced by fixes_interchangeability_group(), fixes_name3(), get_patched_types(), get_possible_base_residue_types(), get_possible_base_unpatchable_residue_types(), get_possible_unpatchable_residue_types(), get_singly_metapatched_types(), and initialize_relevant_pdb_components().

◆ variant_exceptions_

utility::vector1< VariantType > core::chemical::ResidueTypeFinder::variant_exceptions_

private

Referenced by adds_any_variant().

◆ variants_in_sets_

utility::vector1< utility::vector1< VariantType > > core::chemical::ResidueTypeFinder::variants_in_sets_

private

Referenced by adds_any_variant(), deletes_any_variant(), and variants_in_sets().

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

src/core/chemical/ResidueTypeFinder.hh
src/core/chemical/ResidueTypeFinder.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ResidueTypeFinder()

◆ ~ResidueTypeFinder()

Member Function Documentation

◆ aa()

◆ adds_any_property()

◆ adds_any_variant()

◆ apply_basic_filters()

◆ apply_filters_after_patches()

◆ apply_preferences_and_discouragements()

◆ atom_names_soft()

◆ base_property()

◆ base_type()

◆ changes_to_wrong_aa()

◆ check_nucleic_acid_virtual_phosphates()

◆ connect_atoms()

◆ deletes_any_property()

◆ deletes_any_variant()

◆ disable_metapatches()

◆ disallow_properties()

◆ disallow_variants()

◆ discouraged_properties()

◆ filter_all_patch_names()

◆ filter_all_properties()

◆ filter_all_variants_matched()

◆ filter_by_aa()

◆ filter_by_base_property()

◆ filter_by_interchangeability_group()

◆ filter_by_name1()

◆ filter_by_name3()

◆ filter_by_residue_type_base_name()

◆ filter_connections()

◆ filter_disallow_properties()

◆ filter_disallow_variants()

◆ filter_for_all_variant_sets()

◆ filter_special_cases()

◆ filter_variant_sets_have_all_candidate_variants()

◆ fixes_connects()

◆ fixes_interchangeability_group()

◆ fixes_name3()

◆ get_all_possible_residue_types()

◆ get_best_match_residue_type_for_atom_names()

◆ get_patched_types()

◆ get_possible_base_residue_types()

◆ get_possible_base_unpatchable_residue_types()

◆ get_possible_unpatchable_residue_types()

◆ get_representative_type()

◆ get_singly_metapatched_types()

◆ has_disallowed_variant()

◆ ignore_atom_named_H()

◆ initialize_relevant_pdb_components()

◆ interchangeability_group()

◆ matches_any_atom_name()

◆ matches_any_patch_name()

◆ name1()

◆ name3()

◆ no_metapatches()

◆ patch_names()

◆ preferred_properties()

◆ prioritize_rosetta_types_over_pdb_components()

◆ properties()

◆ residue_base_name()

◆ set_no_CCD_on_name3_match()

◆ variant_exceptions() [1/2]

◆ variant_exceptions() [2/2]

◆ variants() [1/4]

◆ variants() [2/4]

◆ variants() [3/4]

◆ variants() [4/4]

◆ variants_in_sets()

Member Data Documentation

◆ aa_

◆ atom_names_soft_

◆ base_property_

◆ base_type_

◆ check_nucleic_acid_virtual_phosphates_

◆ connect_atoms_