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core::chemical::GlobalResidueTypeSet Class Reference

A collection of ResidueType defined. More...

#include <GlobalResidueTypeSet.hh>

Inheritance diagram for core::chemical::GlobalResidueTypeSet:
Inheritance graph
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Public Member Functions

 GlobalResidueTypeSet ()=delete
 default c-tor More...
 
 GlobalResidueTypeSet (std::string const &name, std::string const &directory)
 constructor from directory More...
 
virtual ~GlobalResidueTypeSet ()
 
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...
 
 ~ResidueTypeSet ()
 
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 &)
 
ResidueTypeSetoperator= (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 
)
core::chemical::GlobalResidueTypeSet::~GlobalResidueTypeSet ( )
virtualdefault
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
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
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
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
void core::chemical::GlobalResidueTypeSet::init_restypes_from_database ( )
private
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
void core::chemical::GlobalResidueTypeSet::load_residue_types_from_sql_database ( )
private
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
std::string const& core::chemical::GlobalResidueTypeSet::pdb_components_directory ( ) const
inlineprivate
void core::chemical::GlobalResidueTypeSet::pdb_components_overrides ( utility::vector1< std::string > const &  setting)
inlineprivate
utility::vector1< std::string > const& core::chemical::GlobalResidueTypeSet::pdb_components_overrides ( ) const
inlineprivate
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.

Member Data Documentation

const std::string core::chemical::GlobalResidueTypeSet::database_directory_
private

the database directory of the generating files —> allows to use cached dunbrack libs

Referenced by database_directory(), init_patches_from_database(), and init_restypes_from_database().

std::set< std::string > core::chemical::GlobalResidueTypeSet::exclude_pdb_component_ids_
private

Which components shouldn't be loaded from the components file.

Referenced by init_restypes_from_commandline(), lazy_load_base_type_already_write_locked(), and load_exclude_pdb_component_ids().

std::string core::chemical::GlobalResidueTypeSet::name_
private

What does the ChemicalManager call this GlobalResidueTypeSet?

Referenced by name().

std::string core::chemical::GlobalResidueTypeSet::pdb_components_directory_
private

data for lazy loading of PDB components

Referenced by load_pdb_component(), and pdb_components_directory().

utility::vector1< std::string > core::chemical::GlobalResidueTypeSet::pdb_components_overrides_
private

data for lazy loading of PDB components

Referenced by load_pdb_component(), and pdb_components_overrides().


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