A collection of ResidueType defined. More...

#include <ResidueTypeSet.hh>

Inheritance diagram for core::chemical::ResidueTypeSet:

Public Types
typedef std::list< AA > ::const_iterator	AAsIter

typedef std::map< std::string, ResidueTypeCOP > ::const_iterator	const_residue_iterator

Public Member Functions
	ResidueTypeSet ()
	default c-tor More...

	ResidueTypeSet (std::string const &name, std::string const &directory)
	constructor from directory More...

virtual	~ResidueTypeSet ()

void	init (std::vector< std::string > const &extra_res_param_files=std::vector< std::string >(), std::vector< std::string > const &extra_patch_files=std::vector< std::string >())

ResidueTypeSetCOP	get_self_ptr () const
	self pointers More...

ResidueTypeSetOP	get_self_ptr ()

ResidueTypeSetCAP	get_self_weak_ptr () const

std::string const &	name () const
	name of the residue type set More...

AtomTypeSetCOP	atom_type_set () const

ElementSetCOP	element_set () const

MMAtomTypeSetCOP	mm_atom_type_set () const

orbitals::OrbitalTypeSetCOP	orbital_type_set () const

void	atom_type_set (AtomTypeSetCOP atom_types)

void	element_set (ElementSetCOP elements)

void	mm_atom_type_set (MMAtomTypeSetCOP mm_atom_types)

void	orbital_type_set (orbitals::OrbitalTypeSetCOP orbital_types)

void	add_custom_residue_type (ResidueTypeOP new_type)
	adds a new residue type to the set, one that CANNOT be generated from a base_residue_type and patches More...

void	add_custom_residue_type (std::string const &filename)
	adds a new residue type to the set, one that CANNOT be generated from a base_residue_type and patches More...

void	apply_patches (utility::vector1< std::string > const &patch_filenames, utility::vector1< std::string > const &metapatch_filenames)
	delete a custom residue type from the set (Use with care) More...

void	remove_custom_residue_type (std::string const &name)
	delete a custom residue type from the set (Use with care) More...

void	read_files_for_custom_residue_types (utility::vector1< std::string > const &filenames)
	adds new residue types, ones that CANNOT be generated from a base_residue_type and patches More...

void	remove_base_residue_type_DO_NOT_USE (std::string const &name)
	delete a custom residue type from the set (Use with extreme care) More...

virtual ResidueType const &	name_map (std::string const &name) const
	query ResidueType by its unique residue id. More...

ResidueTypeCOP	name_mapOP (std::string const &name) const
	Get ResidueType by exact name, returning COP Will return null pointer for no matches. More...

ResidueTypeCOP	get_representative_type_aa (AA aa, utility::vector1< std::string > const &variants) const
	Get the base ResidueType with the given aa type and variants. More...

ResidueTypeCOP	get_representative_type_aa (AA aa) const

ResidueTypeCOP	get_representative_type_name1 (char name1, utility::vector1< std::string > const &variants) const
	Get the base ResidueType with the given name1 and variants. More...

ResidueTypeCOP	get_representative_type_name1 (char name1) const

ResidueTypeCOP	get_representative_type_name3 (std::string const &name3, utility::vector1< std::string > const &variants) const
	Get the base ResidueType with the given name3 and variants. More...

ResidueTypeCOP	get_representative_type_name3 (std::string const &name3) const

ResidueTypeCOPs	get_base_types_aa (AA aa) const
	Gets all non-patched types with the given aa type. More...

ResidueTypeCOPs	get_base_types_name1 (char name1) const
	Get all non-patched ResidueTypes with the given name1. More...

ResidueTypeCOPs	get_base_types_name3 (std::string const &name3) const
	Get all non-patched ResidueTypes with the given name3. More...

ResidueTypeCOP	get_d_equivalent (ResidueTypeCOP l_rsd) const
	Given a D-residue, get its L-equivalent. More...

ResidueTypeCOP	get_l_equivalent (ResidueTypeCOP d_rsd) const
	Given an L-residue, get its D-equivalent. More...

ResidueTypeCOP	get_mirrored_type (ResidueTypeCOP original_rsd) const
	Given a residue, get its mirror-image type. More...

bool	generates_patched_residue_type_with_name3 (std::string const &base_residue_name, std::string const &name3) const
	Check if a base type (like "SER") generates any types with another name3 (like "SEP") More...

bool	generates_patched_residue_type_with_interchangeability_group (std::string const &base_residue_name, std::string const &interchangeability_group) const
	Check if a base type (like "CYS") generates any types with a new interchangeability group (like "SCY" (via cys_acetylated)) More...

ResidueTypeCOPs	get_all_types_with_variants_aa (AA aa, utility::vector1< std::string > const &variants) const
	Gets all types with the given aa type and variants. More...

ResidueTypeCOPs	get_all_types_with_variants_aa (AA aa, utility::vector1< std::string > const &variants, utility::vector1< VariantType > const &exceptions) const
	Gets all types with the given aa type and variants, making exceptions for some variants. More...

ResidueTypeCOPs	get_all_types_with_variants_name1 (char name1, utility::vector1< std::string > const &variants) const
	Get all non-patched ResidueTypes with the given name1. More...

ResidueTypeCOPs	get_all_types_with_variants_name3 (std::string const &name3, utility::vector1< std::string > const &variants) const
	Get all non-patched ResidueTypes with the given name3. More...

bool	has_name (std::string const &name) const
	query if a ResidueType of the unique residue id (name) is present. More...

bool	has_name3 (std::string const &name3) const
	query if any ResidueTypes in the set have a "name3" tat matches the input name3 More...

bool	has_interchangeability_group (std::string const &name) const
	Does this ResidueTypeSet have ResidueTypes with the given interchangeability group? More...

ResidueType const &	get_residue_type_with_variant_added (ResidueType const &init_rsd, VariantType const new_type) const
	Query a variant ResidueType by its base ResidueType and VariantType. More...

ResidueType const &	get_residue_type_with_variant_removed (ResidueType const &init_rsd, VariantType const old_type) const
	return the residuetype we get from variant rsd type after removing the desired variant type More...

std::string const &	database_directory () const
	accessor for database_directory More...

MergeBehaviorManager const &	merge_behavior_manager () const
	accessor for merge behavior manager More...

ResidueTypeCOPs	base_residue_types () const
	the residues with no patches applied More...

ResidueTypeCOPs	custom_residue_types () const
	the residues with no patches applied More...

utility::vector1< PatchCOP > const &	patches () const
	the patches More...

utility::vector1< MetapatchCOP > const &	metapatches () const
	the metapatches More...

std::map< std::string, utility::vector1< PatchCOP > > const &	patch_map () const
	the patches, index by name. More...

MetapatchCOP	metapatch (std::string name) const

Private Member Functions
void	read_list_of_residues (std::string const &list_filename)
	read a list of residue types More...

void	read_files (utility::vector1< std::string > const &filenames)

void	update_info_on_name3_and_interchangeability_group (ResidueTypeCOPs base_residue_types)

void	generate_all_residue_types ()

bool	generate_residue_type (std::string const &rsd_name) const

void	figure_out_last_patch_from_name (std::string const &rsd_name, std::string &rsd_name_base, std::string &patch_name) const

bool	update_base_residue_types_if_replaced (ResidueTypeCOP rsd_type, ResidueTypeCOP rsd_type_new)
	helper function used during replacing residue types after, e.g., orbitals. More...

void	load_shadowed_ids (std::string const &directory, std::string const &file="shadow_list.txt")
	From a file, read which IDs shouldn't be loaded from the components. More...

bool	lazy_load_base_type (std::string const &rsd_base_name) const
	Attempt to lazily load the given residue type from data. More...

ResidueTypeOP	load_pdb_component (std::string const &pdb_id) const
	Load a residue type from the components dictionary. More...

	ResidueTypeSet (ResidueTypeSet const &)

ResidueTypeSet const &	operator= (ResidueTypeSet const &)

Private Attributes
std::string	name_
	What does the ChemicalManager call this ResidueTypeSet? More...

AtomTypeSetCOP	atom_types_

ElementSetCOP	elements_

MMAtomTypeSetCOP	mm_atom_types_

orbitals::OrbitalTypeSetCOP	orbital_types_

ResidueTypeCOPs	base_residue_types_
	residue types with no patches applied, read in from database. More...

std::map< std::string, std::set< std::string > >	name3_generated_by_base_residue_name_
	information on residue types whose name3's can be changed by patches. More...

std::map< std::string, std::set< std::string > >	interchangeability_group_generated_by_base_residue_name_
	interchangeability groups that appear upon patch application. More...

ResidueTypeCOPs	custom_residue_types_
	new residue types added at runtime with, e.g., custom variants. More...

const std::string	database_directory_
	the database directory of the generating files —> allows to use cached dunbrack libs More...

MergeBehaviorManagerCOP	merge_behavior_manager_

utility::vector1< PatchCOP >	patches_
	the patches More...

utility::vector1< MetapatchCOP >	metapatches_

std::map< std::string, utility::vector1< PatchCOP > >	patch_map_
	patches indexed by name More...

std::map< std::string, MetapatchCOP >	metapatch_map_

std::set< std::string >	shadowed_ids_
	Which components shouldn't be loaded from the components file. More...

std::string	pdb_components_filename_
	data for lazy loading of PDB components More...

ResidueTypeSetCacheOP	cache_
	all cached residue_type information including generated residue_types, name3_map, etc. By making the following an OP (instead of COP) the cache effectively becomes mutable even when in a const ResidueTypeSet. More...

std::map< ResidueTypeCOP, ResidueTypeCOP >	l_to_d_mapping_
	A list of L-chirality base types with an equivalent D-chirality base type. More...

std::map< ResidueTypeCOP, ResidueTypeCOP >	d_to_l_mapping_
	A list of D-chirality base types with an equivalent L-chirality base type. More...

Detailed Description

A collection of ResidueType defined.

One thing that is not nailed down is whether a single ResidueSet can have ResidueType's with different AtomTypeSets. I've left open this possibility currently although there isnt any code for this yet (PB-07/07)

Member Typedef Documentation

typedef std::list< AA >::const_iterator core::chemical::ResidueTypeSet::AAsIter

typedef std::map< std::string, ResidueTypeCOP >::const_iterator core::chemical::ResidueTypeSet::const_residue_iterator

Constructor & Destructor Documentation

core::chemical::ResidueTypeSet::ResidueTypeSet ( )

default c-tor

core::chemical::ResidueTypeSet::ResidueTypeSet	(	std::string const &	name,
		std::string const &	directory
	)

constructor from directory

c-tor from directory

References load_shadowed_ids().

core::chemical::ResidueTypeSet::~ResidueTypeSet ( )

virtual

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

private

Member Function Documentation

void core::chemical::ResidueTypeSet::add_custom_residue_type ( ResidueTypeOP new_type )

adds a new residue type to the set, one that CANNOT be generated from a base_residue_type and patches

References core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), cache_, custom_residue_types_, and get_self_weak_ptr().

Referenced by add_custom_residue_type(), protocols::ligand_docking::AddHydrogen::apply(), core::chemical::create_adduct_combinations(), and read_files_for_custom_residue_types().

void core::chemical::ResidueTypeSet::add_custom_residue_type ( std::string const & filename )

adds a new residue type to the set, one that CANNOT be generated from a base_residue_type and patches

References add_custom_residue_type(), atom_types_, elements_, get_self_weak_ptr(), mm_atom_types_, orbital_types_, and core::chemical::read_topology_file().

void core::chemical::ResidueTypeSet::apply_patches	(	utility::vector1< std::string > const &	patch_filenames,
		utility::vector1< std::string > const &	metapatch_filenames
	)

delete a custom residue type from the set (Use with care)

References base_residue_types_, cache_, d_to_l_mapping_, core::chemical::ResidueType::finalized(), l_to_d_mapping_, metapatch_map_, metapatches_, core::chemical::ResidueType::name(), name_, patch_map_, patches_, update_base_residue_types_if_replaced(), and update_info_on_name3_and_interchangeability_group().

Referenced by init().

AtomTypeSetCOP core::chemical::ResidueTypeSet::atom_type_set ( ) const

inline

References atom_types_.

void core::chemical::ResidueTypeSet::atom_type_set ( AtomTypeSetCOP atom_types )

inline

References atom_types_.

ResidueTypeCOPs core::chemical::ResidueTypeSet::base_residue_types ( ) const

inline

the residues with no patches applied

References base_residue_types_.

Referenced by core::chemical::ResidueTypeFinder::get_possible_base_residue_types(), and core::chemical::place_adducts().

ResidueTypeCOPs core::chemical::ResidueTypeSet::custom_residue_types ( ) const

inline

the residues with no patches applied

References custom_residue_types_.

Referenced by core::chemical::ResidueTypeFinder::get_possible_base_custom_residue_types(), and core::chemical::ResidueTypeFinder::get_possible_custom_residue_types().

std::string const & core::chemical::ResidueTypeSet::database_directory ( ) const

accessor for database_directory

References database_directory_.

ElementSetCOP core::chemical::ResidueTypeSet::element_set ( ) const

inline

References elements_.

void core::chemical::ResidueTypeSet::element_set ( ElementSetCOP elements )

inline

References elements_.

void core::chemical::ResidueTypeSet::figure_out_last_patch_from_name	(	std::string const &	rsd_name,
		std::string &	rsd_name_base,
		std::string &	patch_name
	)		const

private

References has_name(), and core::chemical::PATCH_LINKER.

Referenced by generate_residue_type().

void core::chemical::ResidueTypeSet::generate_all_residue_types ( )

private

bool core::chemical::ResidueTypeSet::generate_residue_type ( std::string const & rsd_name ) const

private

Instantiates ResidueType

References core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), cache_, figure_out_last_patch_from_name(), core::chemical::ResidueType::finalized(), core::chemical::ResidueType::get_base_type_cop(), core::chemical::ResidueType::get_self_ptr(), lazy_load_base_type(), metapatch_map_, name_mapOP(), patch_map_, and patches().

Referenced by has_name(), and name_mapOP().

bool core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group	(	std::string const &	base_residue_name,
		std::string const &	interchangeability_group
	)		const

Check if a base type (like "CYS") generates any types with a new interchangeability group (like "SCY" (via cys_acetylated))

References interchangeability_group_generated_by_base_residue_name_.

Referenced by core::chemical::ResidueTypeFinder::filter_by_interchangeability_group(), and core::chemical::ResidueTypeFinder::fixes_interchangeability_group().

bool core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3	(	std::string const &	base_residue_name,
		std::string const &	name3
	)		const

Check if a base type (like "SER") generates any types with another name3 (like "SEP")

References name3_generated_by_base_residue_name_.

Referenced by core::chemical::ResidueTypeFinder::filter_by_name3(), and core::chemical::ResidueTypeFinder::fixes_name3().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_all_types_with_variants_aa	(	AA	aa,
		utility::vector1< std::string > const &	variants
	)		const

Gets all types with the given aa type and variants.

The number of variants must match exactly. Variants can be custom variants. (It's assumed that the passed VariantTypeList contains no duplicates.)

The number of variants must match exactly. (It's assumed that the passed VariantTypeList contains no duplicates.)

References cache_.

Referenced by core::pack::task::ResidueLevelTask_::reset().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_all_types_with_variants_aa	(	AA	aa,
		utility::vector1< std::string > const &	variants,
		utility::vector1< VariantType > const &	exceptions
	)		const

Gets all types with the given aa type and variants, making exceptions for some variants.

The number of variants must match exactly. Variants can be custom variants, but exceptions must be standard types, listed in VariantType.hh. (It's assumed that the passed VariantTypeList contains no duplicates.)

References cache_.

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_all_types_with_variants_name1	(	char	name1,
		utility::vector1< std::string > const &	variants
	)		const

Get all non-patched ResidueTypes with the given name1.

Gets all types with the given name1 and variants.

The number of variants must match exactly. (It's assumed that the passed VariantTypeList contains no duplicates.)

Get all non-patched ResidueTypes with the given name1

The number of variants must match exactly. (It's assumed that the passed VariantTypeList contains no duplicates.)

References core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeFinder::name1(), and core::chemical::ResidueTypeFinder::variants().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_all_types_with_variants_name3	(	std::string const &	name3,
		utility::vector1< std::string > const &	variants
	)		const

Get all non-patched ResidueTypes with the given name3.

Gets all types with the given name3 and variants.

The number of variants must match exactly. (It's assumed that the passed VariantTypeList contains no duplicates.)

References core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeFinder::name3(), and core::chemical::ResidueTypeFinder::variants().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_base_types_aa ( AA aa ) const

Gets all non-patched types with the given aa type.

References core::chemical::ResidueTypeFinder::aa(), and core::chemical::ResidueTypeFinder::get_possible_base_residue_types().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_base_types_name1 ( char name1 ) const

Get all non-patched ResidueTypes with the given name1.

References core::chemical::ResidueTypeFinder::get_possible_base_residue_types(), and core::chemical::ResidueTypeFinder::name1().

ResidueTypeCOPs core::chemical::ResidueTypeSet::get_base_types_name3 ( std::string const & name3 ) const

Get all non-patched ResidueTypes with the given name3.

References core::chemical::ResidueTypeFinder::get_possible_base_residue_types(), and core::chemical::ResidueTypeFinder::name3().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_d_equivalent ( ResidueTypeCOP l_rsd ) const

Given a D-residue, get its L-equivalent.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not a D-residue. Preserves variant types.

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

References core::chemical::ResidueTypeFinder::base_type(), core::chemical::ResidueTypeFinder::get_representative_type(), l_to_d_mapping_, and core::chemical::ResidueTypeFinder::variants().

Referenced by get_mirrored_type().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_l_equivalent ( ResidueTypeCOP d_rsd ) const

Given an L-residue, get its D-equivalent.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not an L-residue. Preserves variant types.

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

References core::chemical::ResidueTypeFinder::base_type(), d_to_l_mapping_, core::chemical::ResidueTypeFinder::get_representative_type(), and core::chemical::ResidueTypeFinder::variants().

Referenced by get_mirrored_type().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_mirrored_type ( ResidueTypeCOP original_rsd ) const

Given a residue, get its mirror-image type.

Returns the same residue if this is an ACHIRAL type (e.g. gly), the D-equivalent for an L-residue, the L-equivalent of a D-residue, or NULL if this is an L-residue with no D-equivalent (or a D- with no L-equivalent). Preserves variant types.

References get_d_equivalent(), and get_l_equivalent().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_aa	(	AA	aa,
		utility::vector1< std::string > const &	variants
	)		const

Get the base ResidueType with the given aa type and variants.

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn't availible.

Returns 0 if one does not exist.

References core::chemical::ResidueTypeFinder::aa(), core::chemical::ResidueTypeFinder::get_representative_type(), and core::chemical::ResidueTypeFinder::variants().

Referenced by get_representative_type_aa(), and core::fragment::make_pose_from_sequence_().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_aa ( AA aa ) const

References get_representative_type_aa(), and update_ResidueType_enum_files::variants.

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_name1	(	char	name1,
		utility::vector1< std::string > const &	variants
	)		const

Get the base ResidueType with the given name1 and variants.

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn't availible.

Returns 0 if one does not exist.

References core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeFinder::name1(), and core::chemical::ResidueTypeFinder::variants().

Referenced by get_representative_type_name1().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_name1 ( char name1 ) const

References get_representative_type_name1(), and update_ResidueType_enum_files::variants.

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_name3	(	std::string const &	name3,
		utility::vector1< std::string > const &	variants
	)		const

Get the base ResidueType with the given name3 and variants.

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn't availible.

Returns 0 if one does not exist.

References core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueTypeFinder::name3(), and core::chemical::ResidueTypeFinder::variants().

Referenced by get_representative_type_name3(), and has_name3().

ResidueTypeCOP core::chemical::ResidueTypeSet::get_representative_type_name3 ( std::string const & name3 ) const

References get_representative_type_name3(), and update_ResidueType_enum_files::variants.

ResidueType const & core::chemical::ResidueTypeSet::get_residue_type_with_variant_added	(	ResidueType const &	init_rsd,
		VariantType const	new_type
	)		const

Query a variant ResidueType by its base ResidueType and VariantType.

Return the first match with both base ResidueType id and variant_type name. Abort if there is no match.

Note: Currently, this will not work for variant types defined as alternate base residues (i.e., different .params files).

Remarks: TODO: This should be refactored to make better use of the new ResidueProperties system. ~Labonte

References protocols::vip::base_name(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueProperties::get_string_from_variant(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name(), core::chemical::ResidueType::properties(), core::chemical::ResidueTypeFinder::residue_base_name(), core::chemical::residue_type_base_name(), and core::chemical::ResidueTypeFinder::variants().

Referenced by protocols::environment::add_variant(), core::pose::make_pose_from_saccharide_sequence(), and core::pose::residue_types_from_saccharide_sequence().

ResidueType const & core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed	(	ResidueType const &	init_rsd,
		VariantType const	old_type
	)		const

return the residuetype we get from variant rsd type after removing the desired variant type

Note: Currently, this will not work for variant types defined as alternate base residues (i.e., different .params files).

Remarks: TODO: This should be refactored to make better use of the new ResidueProperties system. ~Labonte

References protocols::vip::base_name(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueTypeFinder::get_representative_type(), core::chemical::ResidueProperties::get_string_from_variant(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name(), core::chemical::ResidueType::properties(), core::chemical::ResidueTypeFinder::residue_base_name(), core::chemical::residue_type_base_name(), and core::chemical::ResidueTypeFinder::variants().

Referenced by core::pose::make_pose_from_saccharide_sequence(), core::pack::task::ResidueLevelTask_::reset(), and protocols::environment::rm_variant().

ResidueTypeSetCOP core::chemical::ResidueTypeSet::get_self_ptr ( ) const

inline

self pointers

Referenced by core::import_pose::build_pose_as_is(), core::io::pdb::build_pose_from_pdb_as_is(), and core::io::pose_from_pose().

ResidueTypeSetOP core::chemical::ResidueTypeSet::get_self_ptr ( )

inline

ResidueTypeSetCAP core::chemical::ResidueTypeSet::get_self_weak_ptr ( ) const

inline

Referenced by add_custom_residue_type(), init(), lazy_load_base_type(), and read_files().

bool core::chemical::ResidueTypeSet::has_interchangeability_group ( std::string const & name ) const

Does this ResidueTypeSet have ResidueTypes with the given interchangeability group?

References core::chemical::ResidueTypeFinder::get_representative_type(), and core::chemical::ResidueTypeFinder::interchangeability_group().

bool core::chemical::ResidueTypeSet::has_name ( std::string const & name ) const

query if a ResidueType of the unique residue id (name) is present.

checks if name exists.

actually instantiates the residue type if it does not exist.

References generate_residue_type().

Referenced by protocols::simple_filters::ResidueCountFilter::add_residue_type_by_name(), figure_out_last_patch_from_name(), and protocols::ligand_docking::generate_unique_name().

bool core::chemical::ResidueTypeSet::has_name3 ( std::string const & name3 ) const

query if any ResidueTypes in the set have a "name3" tat matches the input name3

any residue types with this name3?

References get_representative_type_name3().

void core::chemical::ResidueTypeSet::init	(	std::vector< std::string > const &	extra_res_param_files = `std::vector< std::string >()`,
		std::vector< std::string > const &	extra_patch_files = `std::vector< std::string >()`
	)

References apply_patches(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), atom_types_, base_residue_types_, cache_, database_directory_, elements_, protocols::stepwise::modeler::rna::file_exists(), protocols::abinitio::filename(), get_self_weak_ptr(), mm_atom_types_, name_, orbital_types_, pdb_components_filename_, core::chemical::place_adducts(), core::chemical::read_topology_file(), core::chemical::tr(), and update_base_residue_types_if_replaced().

bool core::chemical::ResidueTypeSet::lazy_load_base_type ( std::string const & rsd_base_name ) const

private

Attempt to lazily load the given residue type from data.

References cache_, get_self_weak_ptr(), load_pdb_component(), shadowed_ids_, and core::chemical::tr().

Referenced by generate_residue_type().

ResidueTypeOP core::chemical::ResidueTypeSet::load_pdb_component ( std::string const & pdb_id ) const

private

Load a residue type from the components dictionary.

References core::chemical::sdf::convert_to_ResidueType(), core::chemical::mmCIF::mmCIFParser::parse(), pdb_components_filename_, and core::chemical::tr().

Referenced by lazy_load_base_type().

void core::chemical::ResidueTypeSet::load_shadowed_ids	(	std::string const &	directory,
		std::string const &	file = `"shadow_list.txt"`
	)

private

From a file, read which IDs shouldn't be loaded from the components.

References name(), shadowed_ids_, and core::chemical::tr().

Referenced by ResidueTypeSet().

MergeBehaviorManager const & core::chemical::ResidueTypeSet::merge_behavior_manager ( ) const

accessor for merge behavior manager

References merge_behavior_manager_.

MetapatchCOP core::chemical::ResidueTypeSet::metapatch ( std::string name ) const

inline

References metapatch_map_.

utility::vector1< MetapatchCOP > const& core::chemical::ResidueTypeSet::metapatches ( ) const

inline

the metapatches

References metapatches_.

Referenced by core::chemical::ResidueTypeFinder::apply_metapatches_recursively().

MMAtomTypeSetCOP core::chemical::ResidueTypeSet::mm_atom_type_set ( ) const

inline

References mm_atom_types_.

void core::chemical::ResidueTypeSet::mm_atom_type_set ( MMAtomTypeSetCOP mm_atom_types )

inline

References mm_atom_types_.

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

inline

name of the residue type set

References name_.

Referenced by core::import_pose::build_pose_as_is2(), load_shadowed_ids(), name_mapOP(), and core::import_pose::pose_from_file().

ResidueType const & core::chemical::ResidueTypeSet::name_map ( std::string const & name_in ) const

virtual

query ResidueType by its unique residue id.

since residue id is unique, it only returns one residue type or exit without match.

References name_mapOP().

Referenced by core::chemical::ResidueTypeFinder::apply_metapatches_recursively(), core::chemical::ResidueTypeFinder::apply_patches_recursively(), protocols::magnesium::get_useful_HOH_coords(), protocols::motifs::Motif::Motif(), core::pose::residue_types_from_saccharide_sequence(), and core::pose::residue_types_from_sequence().

ResidueTypeCOP core::chemical::ResidueTypeSet::name_mapOP ( std::string const & name_in ) const

Get ResidueType by exact name, returning COP Will return null pointer for no matches.

MOST RESIDUE TYPES WILL BE GENERATED THROUGH THIS FUNCTION.

References cache_, core::chemical::fixup_patches(), generate_residue_type(), and name().

Referenced by generate_residue_type(), core::chemical::ResidueTypeFinder::get_possible_base_residue_types(), and name_map().

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

private

orbitals::OrbitalTypeSetCOP core::chemical::ResidueTypeSet::orbital_type_set ( ) const

inline

References orbital_types_.

void core::chemical::ResidueTypeSet::orbital_type_set ( orbitals::OrbitalTypeSetCOP orbital_types )

inline

References orbital_types_.

std::map< std::string, utility::vector1< PatchCOP > > const& core::chemical::ResidueTypeSet::patch_map ( ) const

inline

the patches, index by name.

References patch_map_.

utility::vector1< PatchCOP > const& core::chemical::ResidueTypeSet::patches ( ) const

inline

the patches

References patches_.

Referenced by core::chemical::ResidueTypeFinder::apply_patches_recursively(), and generate_residue_type().

void core::chemical::ResidueTypeSet::read_files ( utility::vector1< std::string > const & filenames )

private

References atom_types_, base_residue_types_, elements_, get_self_weak_ptr(), mm_atom_types_, orbital_types_, and core::chemical::read_topology_file().

Referenced by read_list_of_residues().

void core::chemical::ResidueTypeSet::read_files_for_custom_residue_types ( utility::vector1< std::string > const & filenames )

adds new residue types, ones that CANNOT be generated from a base_residue_type and patches

References add_custom_residue_type().

void core::chemical::ResidueTypeSet::read_list_of_residues ( std::string const & list_filename )

private

read a list of residue types

the file contains a list of names of residue type parameter files stored in the database path

References read_files().

void core::chemical::ResidueTypeSet::remove_base_residue_type_DO_NOT_USE ( std::string const & name )

delete a custom residue type from the set (Use with extreme care)

References base_residue_types_, and cache_.

void core::chemical::ResidueTypeSet::remove_custom_residue_type ( std::string const & name )

delete a custom residue type from the set (Use with care)

References cache_, and custom_residue_types_.

bool core::chemical::ResidueTypeSet::update_base_residue_types_if_replaced	(	ResidueTypeCOP	rsd_type,
		ResidueTypeCOP	rsd_type_new
	)

private

helper function used during replacing residue types after, e.g., orbitals.

helper function used during replacing residue types after, e.g., orbitals. Could possibly expand to update all maps.

References base_residue_types_.

Referenced by apply_patches(), and init().

void core::chemical::ResidueTypeSet::update_info_on_name3_and_interchangeability_group ( ResidueTypeCOPs base_residue_types )

private

following assumes that all new name3 and interchangeability groups for residue types can be discovered by applying patches to base residue types – i.e. on the 'first patch'. Probably should set up a runtime_assert in ResidueTypeFinder to check this assumption.

References interchangeability_group_generated_by_base_residue_name_, core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), name3_generated_by_base_residue_name_, and patches_.

Referenced by apply_patches().

Member Data Documentation

AtomTypeSetCOP core::chemical::ResidueTypeSet::atom_types_

private

Referenced by add_custom_residue_type(), atom_type_set(), init(), and read_files().

ResidueTypeCOPs core::chemical::ResidueTypeSet::base_residue_types_

private

residue types with no patches applied, read in from database.

Referenced by apply_patches(), base_residue_types(), init(), read_files(), remove_base_residue_type_DO_NOT_USE(), and update_base_residue_types_if_replaced().

ResidueTypeSetCacheOP core::chemical::ResidueTypeSet::cache_

private

all cached residue_type information including generated residue_types, name3_map, etc. By making the following an OP (instead of COP) the cache effectively becomes mutable even when in a const ResidueTypeSet.

Referenced by add_custom_residue_type(), apply_patches(), generate_residue_type(), get_all_types_with_variants_aa(), init(), lazy_load_base_type(), name_mapOP(), remove_base_residue_type_DO_NOT_USE(), and remove_custom_residue_type().