A collection of ResidueType defined. More...

#include <GlobalResidueTypeSet.hh>

Inheritance diagram for core::chemical::GlobalResidueTypeSet:

Public Member Functions
	GlobalResidueTypeSet ()=delete
	default c-tor More...

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

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

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

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

Public Member Functions inherited from core::chemical::ResidueTypeSet
	ResidueTypeSet (TypeSetMode mode=INVALID_t)
	default c-tor More...

ResidueTypeSetCOP	get_self_ptr () const

ResidueTypeSetCAP	get_self_weak_ptr () const

AtomTypeSetCOP	atom_type_set () const

ElementSetCOP	element_set () const

MMAtomTypeSetCOP	mm_atom_type_set () const

orbitals::OrbitalTypeSetCOP	orbital_type_set () const

TypeSetMode	mode () const
	The type of the ResidueTypeSet. More...

virtual ResidueType const &	name_map (std::string const &name) const
	query ResidueType by its unique residue id. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

virtual ResidueTypeCOP	name_mapOP (std::string const &name) const
	Get ResidueType by exact name, returning COP. Will return null pointer for no matches. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

virtual bool	has_name (std::string const &name) const
	query if a ResidueType of the unique residue id (name) is present. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

bool	has_name3 (std::string const &name3) const
	query if any ResidueTypes in the set have a "name3" that matches the input name3 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

bool	has_interchangeability_group (std::string const &name) const
	Does this ResidueTypeSet have ResidueTypes with the given interchangeability group? Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. 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

ResidueTypeCOP	get_representative_type_base_name (std::string const &base_name) const

ResidueTypeCOPs	get_base_types_aa (AA aa) const
	Gets all non-patched types with the given aa type Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

ResidueTypeCOPs	get_base_types_name1 (char name1) const
	Get all non-patched ResidueTypes with the given name1 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

ResidueTypeCOPs	get_base_types_name3 (std::string const &name3) const
	Get all non-patched ResidueTypes with the given name3 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

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

virtual ResidueTypeCOP	get_l_equivalent (ResidueTypeCOP d_rsd) const
	Given an L-residue, get its D-equivalent. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

virtual ResidueTypeCOP	get_mirrored_type (ResidueTypeCOP original_rsd) const
	Given a residue, get its mirror-image type. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

virtual 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") Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

virtual 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)) Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. 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 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. 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 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. 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 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

ResidueType const &	get_residue_type_with_variant_added (ResidueType const &init_rsd, std::string const &new_type) const

ResidueType const &	get_residue_type_with_custom_variant_added (ResidueType const &init_rsd, std::string const &new_type) const

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 Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache. More...

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

virtual ResidueTypeCOPs	base_residue_types () const
	The list of ResidueTypes that don't have any patches, but can be patched. More...

virtual ResidueTypeCOPs	unpatchable_residue_types () const
	The list of ResidueTypes which shouldn't get patches applied to them. More...

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

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

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

virtual std::map< std::string, MetapatchCOP > const &	metapatch_map () const
	the metapatches, index by name. More...

virtual bool	has_metapatch (std::string const &name) const
	Do we have this metapatch? More...

virtual MetapatchCOP	metapatch (std::string const &name) const

ResidueTypeCOPs	get_all_types_with_variants_by_basetype (ResidueTypeCOP base_type, utility::vector1< VariantType > const &variants, utility::vector1< std::string > const &variant_strings, utility::vector1< VariantType > const &exceptions, bool const no_metapatches) const
	Given a base residue type, desired variants, and undesired variants, retrieve a list of cached ResidueTypeCOPs. If not cached, generate the data and cache them. More...

Protected Member Functions
bool	lazy_load_base_type_already_write_locked (std::string const &rsd_base_name) const override
	Attempt to lazily load the given residue type from data. More...

void	remove_base_residue_type (std::string const &name) override
	delete an unpatchable residue type from the set. This should never be called in a GlobalResidueTypeSet - it's here just to match the base class interface. More...

void	remove_unpatchable_residue_type (std::string const &name) override
	delete an unpatchable residue type from the set. This should never be called in a GlobalResidueTypeSet - it's here just to match the base class interface. More...

Protected Member Functions inherited from core::chemical::ResidueTypeSet
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	prep_restype (MutableResidueTypeOP new_type) const
	Centralize the steps for preparing the ResidueType for addition to the RTS (e.g. if there's any additional modifications that need to get done.) More...

virtual void	add_base_residue_type (MutableResidueTypeOP new_type)
	adds a new base residue type to the set, one that isn't patched, but can be. (Needs a modifiable type so that it can call prep_restype() on it.) Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	force_add_base_residue_type_already_write_locked (MutableResidueTypeOP new_type) const
	Force the addition of a new residue type despite a const context. More...

virtual void	add_base_residue_type (std::string const &filename)
	adds a new residue type to the set, one that can be patched Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	read_files_for_base_residue_types (utility::vector1< std::string > const &filenames)
	adds new residue types, ones that can be patched Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	add_unpatchable_residue_type (MutableResidueTypeOP new_type)
	adds a new residue type to the set, one that CANNOT be generated from a base_residue_type and patches, and shouldn't have patches applied (Needs a modifiable type so that it can call prep_restype() on it.) Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	add_unpatchable_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, and shouldn't have patches applied Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	read_files_for_unpatchable_residue_types (utility::vector1< std::string > const &filenames)
	adds new residue types, ones that CANNOT be generated from a base_residue_type and patches, and shouldn't have patches applied Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. More...

virtual void	add_patch (PatchCOP p)
	Add a patch object to the RTS. More...

virtual void	add_metapatch (MetapatchCOP p)
	Add a metapatch object to the RTS. More...

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. Does not lock the RTSC, but does modify the RTS and should not be used outside of construction in a multi-threaded context More...

void	mode (TypeSetMode setting)

ResidueTypeSetCacheOP	cache_object () const
	The alterable cache object. More...

virtual ResidueTypeCOP	generate_residue_type (std::string const &rsd_name) const
	Template method invoked by the base class to be overridden by the derived class when a not-yet-generated ResidueType is requested by name. The function returns the COP of the ResidueType if it can be generated, and a nullptr if it cannot. More...

MutableResidueTypeCOP	apply_patch (ResidueTypeCOP const &rsd_base_ptr, std::string const &patch_name, std::map< std::string, utility::vector1< PatchCOP > > const &patch_mapping, std::map< std::string, MetapatchCOP > const &metapach_mapping) const
	Static method which will apply a given patch to a given ResidueType If the patch cannot be applies, it will return nullptr. More...

virtual ResidueTypeCOP	name_mapOP_write_locked (std::string const &name) const
	Template method to return a residue type with the given name, updating the ResidueTypeSetCache as needed – meant to be overridden by the derived ResidueTypeSet. Note that this method must only be called by a function that has obtained a write lock or a function that itself requires a write lock to call it. The derived class's version of this method must not attempt to call any function that would itself try to obtain a read- or write lock on the ResidueTypeSetCache. More...

virtual bool	has_name_write_locked (std::string const &name) const
	Template method to return whether a residue type with a given name is creatable or has already been created; meant to be overridden by the derived ResidueTypeSet. Note that this should only be invoked after a write lock has been obtained on the ResidueTypeSetCache (e.g. inside functions within the generate_residue_type call chain); and that the derived class's version of this function must assume a write lock has already been obtained when it is invoked. Therefore, it must not attempt to call any function that would itself try and obtain a read or write lock. More...

virtual ResidueTypeCOP	generate_residue_type_write_locked (std::string const &rsd_name) const
	Template method to recursively determine whether or not the requested residue type exists / can be created in this ResidueTypeSet – meant to be overridden by the derived ResidueTypeSet. More...

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

virtual void	add_patches (utility::vector1< std::string > const &patch_filenames, utility::vector1< std::string > const &metapatch_filenames)

virtual void	set_merge_behavior_manager (MergeBehaviorManagerCOP mbm)

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...

	ResidueTypeSet (ResidueTypeSet const &)

ResidueTypeSet &	operator= (ResidueTypeSet const &)=delete

Private Member Functions
void	init_restypes_from_database ()
	Read in params files from the given Rosetta database directory. More...

void	init_restypes_from_commandline ()
	Read in the extra resdiue types specified with command line options. More...

utility::vector1< std::string >	params_files_from_commandline () const
	Provide a list of params files based on commandline options, appropriate for the current RTS mode. More...

utility::vector1 < MutableResidueTypeOP >	extra_nonparam_restypes_from_commandline () const
	Load various non-param files from commandline. These will be loaded as full atom types - it's the responsibility of the caller to convert. More...

void	load_residue_types_from_sql_database ()
	Load residue types from the command line-specified SQL database. More...

void	init_patches_from_database ()
	Read in patch and metapatch files from the given Rosetta database directory. More...

void	init_patches_from_commandline ()
	Read in the extra patches specified with command line options. More...

void	deal_with_patch_special_cases ()
	Deal with some special cases in patching. More...

void	place_adducts ()
	apply patches to base ResidueType to generate variant ResidueTyes More...

void	name (std::string const &setting)

void	pdb_components_overrides (utility::vector1< std::string > const &setting)

utility::vector1< std::string > const &	pdb_components_overrides () const

void	pdb_components_directory (std::string const &setting)

std::string const &	pdb_components_directory () const

void	generate_all_residue_types ()

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

void	attempt_readin (std::string const &db_filename, std::string const &pdb_id, MutableResidueTypeOP &new_rsd_type, bool &found_file) const
	Worker that actually takes care of file access for load_pdb_component. More...

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

	GlobalResidueTypeSet (GlobalResidueTypeSet const &)=delete

GlobalResidueTypeSet const &	operator= (GlobalResidueTypeSet const &)=delete

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

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

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

utility::vector1< std::string >	pdb_components_overrides_
	data for lazy loading of PDB components More...

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

Detailed Description

A collection of ResidueType defined.

Constructor & Destructor Documentation

core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet ( )

delete

default c-tor

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

constructor from directory

c-tor from directory

References core::chemical::ResidueTypeSet::base_residue_types(), deal_with_patch_special_cases(), init_patches_from_commandline(), init_patches_from_database(), init_restypes_from_commandline(), init_restypes_from_database(), load_exclude_pdb_component_ids(), name(), pdb_components_directory(), pdb_components_overrides(), place_adducts(), core::chemical::ResidueTypeSet::set_merge_behavior_manager(), core::chemical::TR(), and core::chemical::ResidueTypeSet::unpatchable_residue_types().

core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet ( GlobalResidueTypeSet const & )

privatedelete

Member Function Documentation

void core::chemical::GlobalResidueTypeSet::attempt_readin	(	std::string const &	db_filename,
		std::string const &	pdb_id,
		MutableResidueTypeOP &	new_rsd_type,
		bool &	found_file
	)		const

private

Worker that actually takes care of file access for load_pdb_component.

References core::chemical::CENTROID_t, core::chemical::sdf::convert_to_ResidueType(), core::chemical::FULL_ATOM_t, core::chemical::make_centroid(), core::chemical::ResidueTypeSet::mode(), core::chemical::mmCIF::mmCIFParser::parse(), and core::chemical::TR().

Referenced by load_pdb_component().

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

inline

accessor for database_directory

References database_directory_.

void core::chemical::GlobalResidueTypeSet::deal_with_patch_special_cases ( )

private

Deal with some special cases in patching.

Replacing residue types and D_AAs

References core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::base_residue_types(), core::chemical::ResidueTypeSet::cache_object(), core::chemical::ResidueTypeSet::d_to_l_mapping(), core::chemical::ResidueTypeSet::l_to_d_mapping(), core::chemical::ResidueType::make(), core::chemical::ResidueTypeSet::name_mapOP(), core::chemical::ResidueTypeSet::patches(), and core::chemical::ResidueTypeSet::update_base_residue_types_if_replaced().

Referenced by GlobalResidueTypeSet().

utility::vector1< MutableResidueTypeOP > core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline ( ) const

private

Load various non-param files from commandline. These will be loaded as full atom types - it's the responsibility of the caller to convert.

References core::chemical::sdf::convert_to_ResidueTypes(), protocols::abinitio::filename(), core::chemical::mmCIF::mmCIFParser::parse(), core::chemical::sdf::MolFileIOReader::parse_file(), and core::chemical::TR().

Referenced by init_restypes_from_commandline().

void core::chemical::GlobalResidueTypeSet::generate_all_residue_types ( )

private

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

overridevirtual

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.)

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::get_all_types_with_variants_aa().

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

overridevirtual

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.)

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::get_all_types_with_variants_aa().

void core::chemical::GlobalResidueTypeSet::init_patches_from_commandline ( )

private

Read in the extra patches specified with command line options.

References core::chemical::ResidueTypeSet::add_patches(), core::chemical::CENTROID_t, core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeSet::mode(), and core::chemical::TR().

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::init_patches_from_database ( )

private

Read in patch and metapatch files from the given Rosetta database directory.

References core::chemical::ResidueTypeSet::add_patches(), database_directory_, name(), and core::chemical::TR().

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline ( )

private

Read in the extra resdiue types specified with command line options.

References core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::atom_type_set(), core::chemical::CENTROID_t, core::chemical::ResidueTypeSet::element_set(), exclude_pdb_component_ids_, extra_nonparam_restypes_from_commandline(), protocols::abinitio::filename(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeSet::has_name(), load_residue_types_from_sql_database(), core::chemical::make_centroid(), core::chemical::ResidueTypeSet::mm_atom_type_set(), core::chemical::ResidueTypeSet::mode(), core::chemical::ResidueTypeSet::orbital_type_set(), params_files_from_commandline(), core::chemical::read_topology_file(), and core::chemical::TR().

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::init_restypes_from_database ( )

private

Read in params files from the given Rosetta database directory.

References core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::atom_type_set(), database_directory_, core::chemical::ResidueTypeSet::element_set(), protocols::abinitio::filename(), core::chemical::ResidueTypeSet::mm_atom_type_set(), core::chemical::ResidueTypeSet::mode(), core::chemical::ResidueTypeSet::orbital_type_set(), core::chemical::read_topology_file(), core::chemical::TR(), and core::chemical::type_set_mode_from_string().

Referenced by GlobalResidueTypeSet().

bool core::chemical::GlobalResidueTypeSet::lazy_load_base_type_already_write_locked ( std::string const & rsd_base_name ) const

overrideprotectedvirtual

Attempt to lazily load the given residue type from data.

Note that the base class has already created a write lock on the cache object when this function is called. This function must not call any functions of the parent that attempts to create a write or a read lock, or this function will deadlock.

Implements core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::cache_object(), exclude_pdb_component_ids_, core::chemical::ResidueTypeSet::force_add_base_residue_type_already_write_locked(), load_pdb_component(), and core::chemical::TR().

void core::chemical::GlobalResidueTypeSet::load_exclude_pdb_component_ids	(	std::string const &	directory,
		std::string const &	file = `"exclude_pdb_component_list.txt"`
	)

private

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

References exclude_pdb_component_ids_, name(), and core::chemical::TR().

Referenced by GlobalResidueTypeSet().

MutableResidueTypeOP core::chemical::GlobalResidueTypeSet::load_pdb_component ( std::string const & pdb_id ) const

private

Load a residue type from the components dictionary.

References attempt_readin(), core::chemical::ResidueTypeSet::cache_object(), pdb_components_directory_, pdb_components_overrides_, and core::chemical::TR().

Referenced by lazy_load_base_type_already_write_locked().

void core::chemical::GlobalResidueTypeSet::load_residue_types_from_sql_database ( )

private

Load residue types from the command line-specified SQL database.

References core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::atom_type_set(), core::chemical::ResidueTypeSet::element_set(), core::chemical::FULL_ATOM_t, core::chemical::ResidueDatabaseIO::get_all_residues_in_database(), core::chemical::ResidueTypeSet::mm_atom_type_set(), core::chemical::ResidueTypeSet::mode(), core::chemical::ResidueTypeSet::orbital_type_set(), core::chemical::ResidueDatabaseIO::read_residuetype_from_database(), and core::chemical::TR().

Referenced by init_restypes_from_commandline().

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

inline

name of the residue type set (may be empty)

The difference between a ResidueTypeSet name and a ResidueTypeSet category is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same category. The type specifies what compatibility class (full atom, centroid) the ResidueTypeSet has. Generally speaking, the name should only be used when interacting with the user.

References name_.

Referenced by GlobalResidueTypeSet(), init_patches_from_database(), and load_exclude_pdb_component_ids().

void core::chemical::GlobalResidueTypeSet::name ( std::string const & setting )

inlineprivate

References name_.

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

privatedelete

utility::vector1< std::string > core::chemical::GlobalResidueTypeSet::params_files_from_commandline ( ) const

private

Provide a list of params files based on commandline options, appropriate for the current RTS mode.

References core::chemical::CENTROID_t, core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeSet::mode(), protocols::hybridization::path, and core::chemical::TR().

Referenced by init_restypes_from_commandline().

void core::chemical::GlobalResidueTypeSet::pdb_components_directory ( std::string const & setting )

inlineprivate

References pdb_components_directory_.

std::string const& core::chemical::GlobalResidueTypeSet::pdb_components_directory ( ) const

inlineprivate

References pdb_components_directory_.

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::pdb_components_overrides ( utility::vector1< std::string > const & setting )

inlineprivate

References pdb_components_overrides_.

utility::vector1< std::string > const& core::chemical::GlobalResidueTypeSet::pdb_components_overrides ( ) const

inlineprivate

References pdb_components_overrides_.

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::place_adducts ( )

private

apply patches to base ResidueType to generate variant ResidueTyes

Generation of new residue types augmented by adduct atoms

Note: This is almost perfectly consistent with on_the_fly residue type sets. Why not just make adducts a patch? Then it will all work together nicely. Just need to have the -adduct string (add_map) turned into a PatchSelector – rhiju

References core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), core::chemical::ADDUCT_VARIANT, core::chemical::ResidueTypeFinder::base_property(), core::chemical::ResidueTypeSet::base_residue_types(), core::chemical::create_adduct_combinations(), core::chemical::DNA, core::chemical::error_check_requested_adducts(), core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::parse_adduct_string(), core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::ResidueTypeFinder::variant_exceptions().

Referenced by GlobalResidueTypeSet().

void core::chemical::GlobalResidueTypeSet::remove_base_residue_type ( std::string const & name )

overrideprotectedvirtual

delete an unpatchable residue type from the set. This should never be called in a GlobalResidueTypeSet - it's here just to match the base class interface.

Reimplemented from core::chemical::ResidueTypeSet.

void core::chemical::GlobalResidueTypeSet::remove_unpatchable_residue_type ( std::string const & name )

overrideprotectedvirtual

delete an unpatchable residue type from the set. This should never be called in a GlobalResidueTypeSet - it's here just to match the base class interface.

Reimplemented from core::chemical::ResidueTypeSet.