A ResidueTypeSet which can be cached in the Pose. More...

#include <PoseResidueTypeSet.hh>

Inheritance diagram for core::chemical::PoseResidueTypeSet:

Public Member Functions
	PoseResidueTypeSet (TypeSetMode mode=INVALID_t)

	PoseResidueTypeSet (ResidueTypeSetCOP deflt_rts)

	PoseResidueTypeSet (PoseResidueTypeSet const &src)

virtual PoseResidueTypeSetOP	clone () const

void	default_rts (core::chemical::ResidueTypeSetCOP setting)
	Set the default fall-back ResidueTypeSet. More...

core::chemical::ResidueTypeSetCOP	default_rts () const
	What is the default fall-back ResidueTypesSet. More...

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

ResidueTypeCOP	get_l_equivalent (ResidueTypeCOP d_rsd) const override
	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...

ResidueTypeCOP	get_mirrored_type (ResidueTypeCOP original_rsd) const override
	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...

bool	generates_patched_residue_type_with_name3 (std::string const &base_residue_name, std::string const &name3) const override
	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 override
	Check if a base type (like "CYS") generates any types with a new interchangeability group (like "SCY" (via cys_acetylated)) More...

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

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

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

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

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

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

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

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

void	add_base_residue_type (MutableResidueTypeOP new_type) override
	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...

void	add_base_residue_type (std::string const &filename) override
	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...

void	read_files_for_base_residue_types (utility::vector1< std::string > const &filenames) override
	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...

void	add_unpatchable_residue_type (MutableResidueTypeOP new_type) override
	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...

void	add_unpatchable_residue_type (std::string const &filename) override
	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...

void	read_files_for_unpatchable_residue_types (utility::vector1< std::string > const &filenames) override
	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...

void	remove_base_residue_type (std::string const &name) override
	delete an base residue type from the set (Use with care) Currently will not remove any patched types Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. In any case, this is not a thread-safe function as it will invariably lead to race conditions if the RTS is shared between two threads. This method is only to be used on PoseResidueTypeSet objects (the GlobalResidueTypeSet class will exit if you call it), and these objects must not be shared between two threads. More...

void	remove_unpatchable_residue_type (std::string const &name) override
	delete an unpatchable residue type from the set (Use with care) Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. In any case, this is not a thread-safe function as it will invariably lead to race conditions if the RTS is shared between two threads. This method is only to be used on PoseResidueTypeSet objects (the GlobalResidueTypeSet class will exit if you call it), and these objects must not be shared between two threads. More...

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

void	set_merge_behavior_manager (MergeBehaviorManagerCOP mbm) override

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)

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...

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

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

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

ResidueTypeCOP	generate_residue_type_write_locked (std::string const &name_in) const override
	Generate the ResidueType from either/both of the local RTS and the default RTS. More...

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...

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	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...

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...

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

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 Attributes
core::chemical::ResidueTypeSetCOP	default_rts_

std::map< std::string, utility::vector1< PatchCOP > >	all_patch_map_
	patches indexed by name Includes both the patches from this map and the default_rts_ patches. More...

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

Detailed Description

A ResidueTypeSet which can be cached in the Pose.

Constructor & Destructor Documentation

core::chemical::PoseResidueTypeSet::PoseResidueTypeSet ( TypeSetMode mode = INVALID_t )

References default_rts(), and core::chemical::INVALID_t.

core::chemical::PoseResidueTypeSet::PoseResidueTypeSet ( ResidueTypeSetCOP deflt_rts )

References default_rts().

core::chemical::PoseResidueTypeSet::PoseResidueTypeSet ( PoseResidueTypeSet const & src )

default

Member Function Documentation

void core::chemical::PoseResidueTypeSet::add_base_residue_type ( MutableResidueTypeOP new_type )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::add_base_residue_type ( std::string const & filename )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::add_metapatch ( MetapatchCOP p )

overrideprotectedvirtual

Add a metapatch object to the RTS.

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::add_metapatch(), and all_metapatch_map_.

void core::chemical::PoseResidueTypeSet::add_patch ( PatchCOP p )

overrideprotectedvirtual

Add a patch object to the RTS.

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::add_patch(), and all_patch_map_.

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

overridevirtual

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type ( MutableResidueTypeOP new_type )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type ( std::string const & filename )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

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

inline

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

Referenced by atom_type_set(), and default_rts().

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

References core::chemical::ResidueTypeSet::atom_type_set(), atom_type_set(), and core::chemical::TR().

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

overridevirtual

the residues with no patches applied

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::base_residue_types(), and default_rts_.

PoseResidueTypeSetOP core::chemical::PoseResidueTypeSet::clone ( ) const

virtual

void core::chemical::PoseResidueTypeSet::default_rts ( core::chemical::ResidueTypeSetCOP setting )

Set the default fall-back ResidueTypeSet.

References all_metapatch_map_, all_patch_map_, atom_type_set(), core::chemical::ResidueTypeSet::cache_object(), default_rts_, element_set(), core::chemical::ResidueTypeSet::metapatches(), mm_atom_type_set(), orbital_type_set(), and core::chemical::ResidueTypeSet::patches().

core::chemical::ResidueTypeSetCOP core::chemical::PoseResidueTypeSet::default_rts ( ) const

What is the default fall-back ResidueTypesSet.

References default_rts_.

Referenced by PoseResidueTypeSet().

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

inline

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

Referenced by default_rts(), and element_set().

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

References core::chemical::ResidueTypeSet::element_set(), element_set(), and core::chemical::TR().

ResidueTypeCOP core::chemical::PoseResidueTypeSet::generate_residue_type_write_locked ( std::string const & name_in ) const

overrideprotectedvirtual

Generate the ResidueType from either/both of the local RTS and the default RTS.

Assumes that we already have a write lock to the cache object for this RTS (but not for the default RTS).

Reimplemented from core::chemical::ResidueTypeSet.

References core::chemical::ResidueTypeSet::apply_patch(), core::chemical::ResidueTypeSet::cache_object(), default_rts_, core::chemical::ResidueTypeSet::figure_out_last_patch_from_name(), core::chemical::ResidueType::make(), metapatch_map(), core::chemical::ResidueTypeSet::metapatch_map(), patch_map(), and core::chemical::ResidueTypeSet::patch_map().

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

overridevirtual

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

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_, and core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group().

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

overridevirtual

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

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_, and core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3().

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

overridevirtual

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

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

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not a D-residue. Preserves variant types. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Note: Works for L-amino acids and L-peptoids (peptoids with chiral "L" sidechains").

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

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

Note: Works for L-amino acids and L-peptoids (peptoids with chiral "L" sidechains").

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

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_.

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

overridevirtual

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.

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

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

Note: Works for D-amino acids and D-peptoids (peptoids with chiral "D" sidechains").

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

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_.

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

overridevirtual

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.

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.

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_.

bool core::chemical::PoseResidueTypeSet::has_metapatch ( std::string const & name ) const

overridevirtual

Do we have this metapatch?

Reimplemented from core::chemical::ResidueTypeSet.

References all_metapatch_map_.

bool core::chemical::PoseResidueTypeSet::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.

Implements core::chemical::ResidueTypeSet.

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

MetapatchCOP core::chemical::PoseResidueTypeSet::metapatch ( std::string const & name ) const

overridevirtual

Reimplemented from core::chemical::ResidueTypeSet.

References all_metapatch_map_.

std::map< std::string, MetapatchCOP > const& core::chemical::PoseResidueTypeSet::metapatch_map ( ) const

inlineoverridevirtual

the metapatches, index by name.

Reimplemented from core::chemical::ResidueTypeSet.

References all_metapatch_map_.

Referenced by generate_residue_type_write_locked().

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

overridevirtual

the metapatches

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_, and core::chemical::ResidueTypeSet::metapatches().

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

inline

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

Referenced by default_rts(), and mm_atom_type_set().

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

References core::chemical::ResidueTypeSet::mm_atom_type_set(), mm_atom_type_set(), and core::chemical::TR().

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

inline

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

Referenced by default_rts(), and orbital_type_set().

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

References core::chemical::ResidueTypeSet::orbital_type_set(), orbital_type_set(), and core::chemical::TR().

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

inlineoverridevirtual

the patches, index by name.

Reimplemented from core::chemical::ResidueTypeSet.

References all_patch_map_.

Referenced by generate_residue_type_write_locked().

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

overridevirtual

the patches

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_, and core::chemical::ResidueTypeSet::patches().

void core::chemical::PoseResidueTypeSet::read_files_for_base_residue_types ( utility::vector1< std::string > const & filenames )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::read_files_for_unpatchable_residue_types ( utility::vector1< std::string > const & filenames )

overridevirtual

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.

Reimplemented from core::chemical::ResidueTypeSet.

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

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

overridevirtual

delete an base residue type from the set (Use with care) Currently will not remove any patched types Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. In any case, this is not a thread-safe function as it will invariably lead to race conditions if the RTS is shared between two threads. This method is only to be used on PoseResidueTypeSet objects (the GlobalResidueTypeSet class will exit if you call it), and these objects must not be shared between two threads.

Reimplemented from core::chemical::ResidueTypeSet.

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

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

overridevirtual

delete an unpatchable residue type from the set (Use with care) Note: creates write lock on RTSC and must not be invoked in the generate_residue_type_write_locked call chain. In any case, this is not a thread-safe function as it will invariably lead to race conditions if the RTS is shared between two threads. This method is only to be used on PoseResidueTypeSet objects (the GlobalResidueTypeSet class will exit if you call it), and these objects must not be shared between two threads.

Reimplemented from core::chemical::ResidueTypeSet.

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

void core::chemical::PoseResidueTypeSet::set_merge_behavior_manager ( MergeBehaviorManagerCOP mbm )

overridevirtual

Reimplemented from core::chemical::ResidueTypeSet.

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

ResidueTypeCOPs core::chemical::PoseResidueTypeSet::unpatchable_residue_types ( ) const

overridevirtual

the residues with no patches applied

Reimplemented from core::chemical::ResidueTypeSet.

References default_rts_, and core::chemical::ResidueTypeSet::unpatchable_residue_types().

Member Data Documentation

std::map< std::string, MetapatchCOP > core::chemical::PoseResidueTypeSet::all_metapatch_map_

private

Referenced by add_metapatch(), default_rts(), has_metapatch(), metapatch(), and metapatch_map().

std::map< std::string, utility::vector1< PatchCOP > > core::chemical::PoseResidueTypeSet::all_patch_map_

private

patches indexed by name Includes both the patches from this map and the default_rts_ patches.

Referenced by add_patch(), default_rts(), and patch_map().

core::chemical::ResidueTypeSetCOP core::chemical::PoseResidueTypeSet::default_rts_

private

Referenced by base_residue_types(), default_rts(), generate_residue_type_write_locked(), generates_patched_residue_type_with_interchangeability_group(), generates_patched_residue_type_with_name3(), get_d_equivalent(), get_l_equivalent(), get_mirrored_type(), metapatches(), patches(), and unpatchable_residue_types().

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

src/core/chemical/PoseResidueTypeSet.hh
src/core/chemical/PoseResidueTypeSet.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation