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core::chemical::ResidueTypeFinder Class Reference

#include <ResidueTypeFinder.hh>

Inheritance diagram for core::chemical::ResidueTypeFinder:
Inheritance graph
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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)
 
ResidueTypeFinderaa (core::chemical::AA const &setting)
 
ResidueTypeFindername1 (char const &setting)
 
ResidueTypeFindername3 (std::string const &setting)
 
ResidueTypeFinderresidue_base_name (std::string const &setting)
 
ResidueTypeFinderdisable_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...
 
ResidueTypeFinderbase_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...
 
ResidueTypeFinderinterchangeability_group (std::string const &setting)
 
ResidueTypeFinderbase_property (ResidueProperty const setting)
 
ResidueTypeFinderatom_names_soft (utility::vector1< std::string > const &setting)
 
ResidueTypeFindervariants_in_sets (utility::vector1< utility::vector1< VariantType > > const &setting)
 
ResidueTypeFindervariants (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
 Add a set of VariantTypes, all of which matching ResidueTypes MUST have. More...
 
ResidueTypeFindervariants (utility::vector1< std::string > const &setting)
 set function for variants More...
 
ResidueTypeFindervariants (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...
 
ResidueTypeFinderdisallow_variants (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
 Provide a list of VariantTypes that a matched ResidueType must NOT have. More...
 
ResidueTypeFindervariant_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...
 
ResidueTypeFindervariant_exceptions (utility::vector1< VariantType > const &setting, bool const clear_existing=true)
 Provide a list of VariantTypes that will be ignored when matching. More...
 
ResidueTypeFinderproperties (utility::vector1< ResidueProperty > const &setting)
 
ResidueTypeFinderdisallow_properties (utility::vector1< ResidueProperty > const &setting)
 
ResidueTypeFinderpreferred_properties (utility::vector1< ResidueProperty > const &setting)
 
ResidueTypeFinderdiscouraged_properties (utility::vector1< ResidueProperty > const &setting)
 
ResidueTypeFinderpatch_names (utility::vector1< std::string > const &setting)
 
ResidueTypeFinderconnect_atoms (utility::vector1< std::string > const &setting)
 Attempt to find ResidueTypes with connection points on the given atoms. More...
 
ResidueTypeFinderignore_atom_named_H (bool const setting)
 
ResidueTypeFindercheck_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< ResidueTypeCOPapply_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< ResidueTypeCOPapply_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
 
ResidueTypeFindervariants (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< VariantTypedisallow_variants_
 
utility::vector1< VariantTypevariant_exceptions_
 
utility::vector1< ResiduePropertyproperties_
 
utility::vector1< ResiduePropertydisallow_properties_
 
utility::vector1< ResiduePropertypreferred_properties_
 
utility::vector1< ResiduePropertydiscouraged_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
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
ResidueTypeCOPs core::chemical::ResidueTypeFinder::apply_basic_filters ( ResidueTypeCOPs  rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::apply_filters_after_patches ( ResidueTypeCOPs  rsd_types,
bool const  allow_extra_variants = false 
) const
private
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
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
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
ResidueTypeFinder& core::chemical::ResidueTypeFinder::base_type ( ResidueTypeCOP const &  basetype)
inline
bool core::chemical::ResidueTypeFinder::changes_to_wrong_aa ( PatchCOP  patch,
ResidueTypeCOP  rsd_type 
) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::check_candidate_has_all_variant_sets ( ResidueTypeCOPs const &  rsd_types) const
private
ResidueTypeFinder& core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates ( bool const  setting)
inline
ResidueTypeCOPs core::chemical::ResidueTypeFinder::check_variant_sets_have_all_candidate_variants ( ResidueTypeCOPs const &  rsd_types) const
private
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
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
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_all_patch_names ( ResidueTypeCOPs const &  rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_all_properties ( ResidueTypeCOPs const &  rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_all_variants_matched ( ResidueTypeCOPs const &  rsd_types,
bool const  allow_extra_variants = false 
) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_by_aa ( ResidueTypeCOPs const &  rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_by_base_property ( ResidueTypeCOPs const &  base_rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_by_interchangeability_group ( ResidueTypeCOPs const &  rsd_types,
bool const  keep_if_base_type_generates_interchangeability_group 
) const
private
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
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name ( ResidueTypeCOPs const &  rsd_types) const
private
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
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_disallow_variants ( ResidueTypeCOPs const &  rsd_types) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::filter_special_cases ( ResidueTypeCOPs const &  rsd_types) const
private
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
bool core::chemical::ResidueTypeFinder::fixes_name3 ( PatchCOP  patch,
ResidueTypeCOP  rsd_type 
) const
private
ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_all_possible_residue_types ( bool const  allow_extra_variants = false) const
ResidueTypeCOP core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names ( utility::vector1< std::string > const &  atom_names)
ResidueTypeCOPs core::chemical::ResidueTypeFinder::get_possible_base_residue_types ( bool const  include_unpatchable = true,
bool const  apply_all_filters = false 
) const
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::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
ResidueTypeFinder& core::chemical::ResidueTypeFinder::ignore_atom_named_H ( bool const  setting)
inline
void core::chemical::ResidueTypeFinder::initialize_relevant_pdb_components ( ) const
private
ResidueTypeFinder& core::chemical::ResidueTypeFinder::interchangeability_group ( std::string const &  setting)
inline
bool core::chemical::ResidueTypeFinder::matches_any_atom_name ( PatchCOP  patch,
ResidueTypeCOP  rsd_type 
) const
private
bool core::chemical::ResidueTypeFinder::matches_any_patch_name ( PatchCOP  patch) const
private
ResidueTypeFinder& core::chemical::ResidueTypeFinder::name1 ( char const &  setting)
inline
ResidueTypeFinder& core::chemical::ResidueTypeFinder::name3 ( std::string const &  setting)
inline
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
ResidueTypeFinder& core::chemical::ResidueTypeFinder::preferred_properties ( utility::vector1< ResidueProperty > const &  setting)
inline
ResidueTypeCOPs core::chemical::ResidueTypeFinder::prioritize_rosetta_types_over_pdb_components ( ResidueTypeCOPs const &  rsd_types) const
private
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
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 
)
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_variantsA vector of enums of standard variants that the ResidueTypeFinder should match.
[in]custom_variantsA 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_existingIf 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
utility::vector1< std::string > core::chemical::ResidueTypeFinder::atom_names_soft_
private
ResidueProperty core::chemical::ResidueTypeFinder::base_property_ = NO_PROPERTY
private
ResidueTypeCOP core::chemical::ResidueTypeFinder::base_type_ = nullptr
private
bool core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates_ = false
private
utility::vector1< std::string > core::chemical::ResidueTypeFinder::connect_atoms_
private
utility::vector1< std::string > core::chemical::ResidueTypeFinder::custom_variants_
private
bool core::chemical::ResidueTypeFinder::disallow_carboxyl_conjugation_at_glu_asp_
private
utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::disallow_properties_
private
utility::vector1< VariantType > core::chemical::ResidueTypeFinder::disallow_variants_
private
utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::discouraged_properties_
private
bool core::chemical::ResidueTypeFinder::ignore_atom_named_H_ = false
private
std::string core::chemical::ResidueTypeFinder::interchangeability_group_ = ""
private
char core::chemical::ResidueTypeFinder::name1_ = '?'
private
std::string core::chemical::ResidueTypeFinder::name3_ = ""
private
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
utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::preferred_properties_
private
utility::vector1< ResidueProperty > core::chemical::ResidueTypeFinder::properties_
private
std::string core::chemical::ResidueTypeFinder::residue_type_base_name_ = ""
private
core::chemical::ResidueTypeSet const& core::chemical::ResidueTypeFinder::residue_type_set_
private
utility::vector1< VariantType > core::chemical::ResidueTypeFinder::variant_exceptions_
private
utility::vector1< utility::vector1< VariantType > > core::chemical::ResidueTypeFinder::variants_in_sets_
private

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