core::chemical::ResidueTypeFinder Class Reference

#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
ResidueTypeCOPs	apply_basic_filters (ResidueTypeCOPs rsd_types) const
ResidueTypeCOPs	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 >	apply_patches_recursively (utility::vector1< ResidueTypeCOP > const &rsd_types, Size const patch_number, bool const get_first_totally_ok_residue_type=false) const
	Instantiates ResidueType (and gets exponentially slower), based on the number of desired features that a patch might offer: More...
utility::vector1< ResidueTypeCOP >	apply_metapatches_recursively (utility::vector1< ResidueTypeCOP > const &rsd_types, Size const metapatch_number, bool const get_first_totally_ok_residue_type=false) const
ResidueTypeCOPs	filter_by_name1 (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_by_name3 (ResidueTypeCOPs const &rsd_types, bool const keep_if_base_type_generates_aa) const
ResidueTypeCOPs	filter_by_aa (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_by_residue_type_base_name (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_by_interchangeability_group (ResidueTypeCOPs const &rsd_types, bool const keep_if_base_type_generates_interchangeability_group) const
ResidueTypeCOPs	filter_by_base_property (ResidueTypeCOPs const &base_rsd_types) const
ResidueTypeCOPs	check_candidate_has_all_variant_sets (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	check_variant_sets_have_all_candidate_variants (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_all_variants_matched (ResidueTypeCOPs const &rsd_types, bool const allow_extra_variants=false) const
ResidueTypeCOPs	filter_disallow_variants (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_all_patch_names (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_all_properties (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_disallow_properties (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_connections (ResidueTypeCOPs const &rsd_types) const
ResidueTypeCOPs	filter_special_cases (ResidueTypeCOPs const &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

core::chemical::ResidueTypeFinder::ResidueTypeFinder

(

core::chemical::ResidueTypeSet const &

residue_type_set

)

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

overridedefault

Member Function Documentation

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().

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 apply_metapatches_recursively(), and apply_patches_recursively().

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 apply_metapatches_recursively(), and apply_patches_recursively().

ResidueTypeCOPs 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().

ResidueTypeCOPs 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 apply_metapatches_recursively(), apply_patches_recursively(), get_all_possible_residue_types(), get_possible_base_residue_types(), and get_representative_type().

vector1< ResidueTypeCOP > core::chemical::ResidueTypeFinder::apply_metapatches_recursively ( utility::vector1< ResidueTypeCOP > const &  rsd_types, Size const  metapatch_number, bool const  get_first_totally_ok_residue_type = false  ) const

private

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().

vector1< ResidueTypeCOP > core::chemical::ResidueTypeFinder::apply_patches_recursively ( utility::vector1< ResidueTypeCOP > const &  rsd_types, Size const  patch_number, bool const  get_first_totally_ok_residue_type = false  ) const

private

Instantiates ResidueType (and gets exponentially slower), based on the number of desired features that a patch might offer:

(1) xyz_atom_names Does patch introduce this atom via ADD_ATOM? (2) variants Does patch introduce this VariantType through its TYPES? (3) properties Does patch introduce this ResidueProperty through ADD_PROPERTY? (4) patch_names Used for carbohydrate branching –> look explicitly for name.

This function will take less time and memory if the lists above are short.

So you can be smart about tuning performance – for example, if you are looking for "->2)-branch" carbohydrates, set that through patch_names; and do not also look for BRANCH_POINT under properties (which is also a property of patches applied to amino acids).

           -- rhiju, 2015

This function made extensive use of string parsing, which is very inefficient, particularly in a recursive context. Cleaned up considerably by V. Mulligan on 18 Aug 2016.

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().

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().

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

inline

References atom_names_soft_.

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

inline

References base_property_.

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), core::chemical::GlobalResidueTypeSet::place_adducts(), protocols::ligand_docking::LigandDesign::set_fragments(), and protocols::ligand_docking::GrowLigand::set_fragments().

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().

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

private

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

Referenced by apply_metapatches_recursively(), and apply_patches_recursively().

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

private

References custom_variants_, variant_exceptions_, and variants_in_sets_.

Referenced by filter_all_variants_matched().

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().

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

private

References custom_variants_, variant_exceptions_, and variants_in_sets_.

Referenced by filter_all_variants_matched().

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().

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 apply_metapatches_recursively(), and apply_patches_recursively().

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

private

References variants_in_sets_.

Referenced by apply_metapatches_recursively(), and apply_patches_recursively().

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().

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

inline

References disallow_properties_.

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.

References disallow_variants_.

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

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().

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

private

References patch_names_, core::chemical::residue_type_all_patches_name(), and core::chemical::TR().

Referenced by apply_filters_after_patches().

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

private

References core::chemical::ResidueProperties::get_string_from_property(), properties_, and core::chemical::TR().

Referenced by apply_filters_after_patches().

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

private

References check_candidate_has_all_variant_sets(), check_variant_sets_have_all_candidate_variants(), and core::chemical::TR().

Referenced by apply_filters_after_patches().

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

private

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

Referenced by apply_basic_filters().

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

private

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

Referenced by apply_basic_filters().

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

private

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

Referenced by apply_basic_filters(), and apply_filters_after_patches().

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

private

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

Referenced by apply_basic_filters().

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

private

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

Referenced by apply_basic_filters(), and apply_filters_after_patches().

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

private

References protocols::vip::base_name(), core::chemical::residue_type_base_name(), residue_type_base_name_, and core::chemical::TR().

Referenced by apply_basic_filters().

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

private

References connect_atoms_.

Referenced by apply_filters_after_patches().

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

private

References disallow_properties_, core::chemical::ResidueProperties::get_string_from_property(), and core::chemical::TR().

Referenced by apply_filters_after_patches().

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

private

References disallow_variants_, core::chemical::ResidueProperties::get_string_from_variant(), and core::chemical::TR().

Referenced by apply_filters_after_patches().

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

private

References aa_, core::chemical::aa_h2o, atom_names_soft_, check_nucleic_acid_virtual_phosphates_, core::chemical::FIVE_PRIME_PACKABLE_TRIPHOSPHATE, name1_, core::chemical::TR(), core::chemical::VIRTUAL_DNA_PHOSPHATE, and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by apply_filters_after_patches().

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 apply_patches_recursively().

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 apply_metapatches_recursively(), and apply_patches_recursively().

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 apply_metapatches_recursively(), and apply_patches_recursively().

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_metapatches_recursively(), apply_patches_recursively(), apply_preferences_and_discouragements(), get_possible_base_residue_types(), get_possible_unpatchable_residue_types(), no_metapatches(), and core::chemical::TR().

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), 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(), 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(), core::chemical::GlobalResidueTypeSet::place_adducts(), protocols::ligand_docking::LigandDesign::set_fragments(), protocols::ligand_docking::GrowLigand::set_fragments(), and protocols::forge::components::VarLengthBuild::set_starting_non_canonical().

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().

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().

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().

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().

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(), apply_metapatches_recursively(), apply_patches_recursively(), get_possible_base_residue_types(), get_possible_unpatchable_residue_types(), and no_metapatches().

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), core::io::pose_from_sfr::PoseFromSFRBuilder::d_l_threeletter_codes_are_same_for_aa(), core::chemical::ResidueTypeSet::get_d_equivalent(), core::chemical::ResidueTypeSet::get_l_equivalent(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_nc_name_codes(), core::chemical::ResidueTypeSet::get_representative_type_aa(), core::chemical::ResidueTypeSet::get_representative_type_base_name(), core::chemical::ResidueTypeSet::get_representative_type_name1(), core::chemical::ResidueTypeSet::get_representative_type_name3(), core::conformation::get_residue_from_name1(), 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(), core::pose::get_rsd_type_from_aa(), core::chemical::ResidueTypeSet::has_interchangeability_group(), core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), core::pose::rna::mutate_position(), protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::setup(), core::util::switch_to_residue_type_set(), and core::pose::Pose::virtual_to_real().

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

private

References disallow_variants_.

Referenced by apply_metapatches_recursively(), and apply_patches_recursively().

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().

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().

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

inline

References interchangeability_group_.

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

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 apply_metapatches_recursively(), and apply_patches_recursively().

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

private

References patch_names_.

Referenced by apply_metapatches_recursively(), and apply_patches_recursively().

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().

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

inline

References name3_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::d_l_threeletter_codes_are_same_for_aa(), 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(), protocols::forge::components::VarLengthBuild::set_starting_non_canonical(), and core::io::pose_from_sfr::PoseFromSFRBuilder::setup().

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 (vmulliguw.edu).

References no_metapatches_.

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

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

inline

References patch_names_.

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

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().

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().

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

inline

References properties_.

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

inline

References residue_type_base_name_.

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), 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(), and core::pose::Pose::virtual_to_real().

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_.

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::ResidueProperties::get_variant_from_string(), core::chemical::NO_VARIANT, and variant_exceptions_.

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().

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.

References variant_exceptions_.

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_.

References variants_in_sets_.

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), 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(), core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(), core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(), core::chemical::ResidueTypeSet::get_d_equivalent(), core::chemical::ResidueTypeSet::get_l_equivalent(), core::chemical::ResidueTypeSet::get_representative_type_aa(), core::chemical::ResidueTypeSet::get_representative_type_name1(), core::chemical::ResidueTypeSet::get_representative_type_name3(), core::conformation::get_residue_from_name1(), 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::pose::get_rsd_type_from_aa(), core::pose::rna::mutate_position(), protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply(), variants(), and core::pose::Pose::virtual_to_real().

ResidueTypeFinder & core::chemical::ResidueTypeFinder::variants

(

utility::vector1< std::string > const &

setting

)

set function for variants

actually updates variants_in_sets_.

References custom_variants_, core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::NO_VARIANT, and variants().

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 custom_variants_, and variants().

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

private

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

inline

References variants_in_sets_.

Member Data Documentation

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

private

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

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

private

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

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

private

Referenced by base_property(), and filter_by_base_property().

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

private

Referenced by base_type(), and get_possible_base_residue_types().

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

private

Referenced by adds_any_variant(), check_nucleic_acid_virtual_phosphates(), and filter_special_cases().

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

private

Referenced by connect_atoms(), filter_connections(), and fixes_connects().

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

private

Referenced by adds_any_variant(), check_candidate_has_all_variant_sets(), check_variant_sets_have_all_candidate_variants(), and variants().

bool core::chemical::ResidueTypeFinder::disallow_carboxyl_conjugation_at_glu_asp_

private

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

private

Referenced by disallow_properties(), and filter_disallow_properties().

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

private

Referenced by disallow_variants(), filter_disallow_variants(), and has_disallowed_variant().

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

private

Referenced by apply_preferences_and_discouragements(), and discouraged_properties().

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().

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

private

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

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

private

Referenced by filter_by_name1(), filter_special_cases(), and name1().

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

private

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

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().

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().

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

private

Referenced by filter_all_patch_names(), matches_any_patch_name(), and patch_names().

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

private

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

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

private

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

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

private

Referenced by filter_by_residue_type_base_name(), and residue_base_name().

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

private

Referenced by apply_metapatches_recursively(), apply_patches_recursively(), filter_by_interchangeability_group(), filter_by_name3(), fixes_interchangeability_group(), fixes_name3(), get_possible_base_residue_types(), get_possible_base_unpatchable_residue_types(), get_possible_unpatchable_residue_types(), and initialize_relevant_pdb_components().

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

private

Referenced by adds_any_variant(), check_candidate_has_all_variant_sets(), check_variant_sets_have_all_candidate_variants(), and variant_exceptions().

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

private

Referenced by adds_any_variant(), check_candidate_has_all_variant_sets(), check_variant_sets_have_all_candidate_variants(), deletes_any_variant(), variants(), 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