A collection of ResidueType defined. More...

#include <ResidueTypeSet.hh>

Inheritance diagram for core::chemical::ResidueTypeSet:

Collaboration 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, 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 >())
	constructor from directory More...

virtual	~ResidueTypeSet ()

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

void	read_list_of_residues (std::string const &list_filename, AtomTypeSetCAP atom_types, ElementSetCAP elements, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types)
	read a list of residue types More...

void	read_files (utility::vector1< std::string > const &filenames, AtomTypeSetCAP atom_types, ElementSetCAP elements, MMAtomTypeSetCAP mm_atom_types, orbitals::OrbitalTypeSetCAP orbital_types)

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

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

void	add_residue_type (ResidueTypeOP new_type)
	adds a new residue type to the set More...

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

void	create_adduct_combinations (ResidueType const &rsd, std::map< std::string, int > ref_map, std::map< std::string, int > count_map, utility::vector1< bool > add_mask, utility::vector1< Adduct >::const_iterator work_iter)
	Create correct combinations of adducts for a residue type. More...

ResidueTypeCOPs const &	name3_map (std::string const &name) const
	query ResidueTypes by their 3-letter name More...

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

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

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

bool	has_name3 (std::string const &name3) const
	query if a ResidueType of a certain 3letter name is present. 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...

ResidueTypeCOPs const &	aa_map (AA const &aa) const
	query ResidueTypes by their AA enum type More...

void	select_residues (ResidueSelector const &selector, ResidueTypeCOPs &matches) const
	select a set of ResidueTypes give certain criteria More...

std::list< AA >::const_iterator	aas_defined_begin () const
	beginning of aas_defined_ list More...

std::list< AA >::const_iterator	aas_defined_end () const
	end of aas_defined_ list More...

const_residue_iterator	all_residues_begin () const

const_residue_iterator	all_residues_end () const

ResidueTypeCOPs const &	residue_types () const
	alternate access to all residuetypes as vector More...

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

Private Member Functions
void	clear_residue_maps ()
	clear residue maps More...

void	update_residue_maps ()
	update residue maps More...

void	add_residue_type_to_maps (ResidueTypeOP rsd)

void	remove_residue_type_from_maps (ResidueTypeOP rsd)

	ResidueTypeSet (ResidueTypeSet const &)

ResidueTypeSet const &	operator= (ResidueTypeSet const &)

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

ResidueTypeOPs	residue_types_
	the residues More...

ResidueTypeCOPs	residue_types_const_
	for handing out More...

ResidueTypeCOPs	empty_residue_list_
	null list of residues when query fails More...

std::map< AA, ResidueTypeCOPs >	aa_map_
	map to ResidueType pointers by AA enum More...

std::map< std::string, ResidueTypeCOPs >	name3_map_
	map to ResidueType pointers by 3-letter string name More...

std::map< std::string, ResidueTypeCOP >	name_map_
	map to ResidueType pointers by unique residue id More...

std::map< std::string, ResidueTypeOP >	nonconst_name_map_
	map to ResidueType pointers by unique residue id, for nonconst access More...

std::list< AA >	aas_defined_
	list of AA types defined More...

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

Definition at line 74 of file ResidueTypeSet.hh.

Member Typedef Documentation

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

Definition at line 77 of file ResidueTypeSet.hh.

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

Definition at line 78 of file ResidueTypeSet.hh.

Constructor & Destructor Documentation

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

default c-tor

Definition at line 263 of file ResidueTypeSet.cc.

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

constructor from directory

c-tor from directory

Definition at line 84 of file ResidueTypeSet.cc.

References apply_patches(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::chemical::ChemicalManager::atom_type_set(), core::chemical::ChemicalManager::element_set(), protocols::abinitio::filename(), core::chemical::ChemicalManager::get_instance(), core::chemical::ChemicalManager::mm_atom_type_set(), core::chemical::ChemicalManager::orbital_type_set(), place_adducts(), core::chemical::read_topology_file(), residue_types_, and update_residue_maps().

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

virtual

Definition at line 266 of file ResidueTypeSet.cc.

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

private

Member Function Documentation

ResidueTypeCOPs const& core::chemical::ResidueTypeSet::aa_map ( AA const & aa) const

inline

query ResidueTypes by their AA enum type

similar to name3_map, return all matched residue types or an empty list.

Definition at line 232 of file ResidueTypeSet.hh.

References aa_map_, and empty_residue_list_.

Referenced by core::coarse::CoarseEtable::dump_oldstyle_type_table(), core::fragment::make_pose_from_sequence_(), and core::pose::residue_types_from_sequence().

std::list< AA >::const_iterator core::chemical::ResidueTypeSet::aas_defined_begin ( ) const

beginning of aas_defined_ list

Definition at line 516 of file ResidueTypeSet.cc.

References aas_defined_.

std::list< AA >::const_iterator core::chemical::ResidueTypeSet::aas_defined_end ( ) const

end of aas_defined_ list

Definition at line 522 of file ResidueTypeSet.cc.

References aas_defined_.

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

adds a new residue type to the set

Definition at line 673 of file ResidueTypeSet.cc.

References aas_defined_, add_residue_type_to_maps(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), and residue_types_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), and protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job().

void core::chemical::ResidueTypeSet::add_residue_type_to_maps ( ResidueTypeOP rsd)

private

Definition at line 436 of file ResidueTypeSet.cc.

References aa_map_, core::chemical::aa_unk, aas_defined_, name3_map_, name_map_, nonconst_name_map_, and residue_types_const_.

Referenced by add_residue_type(), and update_residue_maps().

const_residue_iterator core::chemical::ResidueTypeSet::all_residues_begin ( ) const

inline

Definition at line 256 of file ResidueTypeSet.hh.

References name_map_.

const_residue_iterator core::chemical::ResidueTypeSet::all_residues_end ( ) const

inline

Definition at line 262 of file ResidueTypeSet.hh.

References name_map_.

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

Definition at line 370 of file ResidueTypeSet.cc.

References core::chemical::Patch::applies_to(), core::chemical::Patch::apply(), core::chemical::Patch::read_file(), core::chemical::Patch::replaces(), residue_types_, and update_residue_maps().

Referenced by ResidueTypeSet().

void core::chemical::ResidueTypeSet::clear_residue_maps ( )

private

clear residue maps

Definition at line 402 of file ResidueTypeSet.cc.

References aa_map_, aas_defined_, name3_map_, name_map_, nonconst_name_map_, and residue_types_const_.

Referenced by update_residue_maps().

void core::chemical::ResidueTypeSet::create_adduct_combinations	(	ResidueType const &	rsd,
		std::map< std::string, int >	ref_map,
		std::map< std::string, int >	count_map,
		utility::vector1< bool >	add_mask,
		utility::vector1< Adduct >::const_iterator	work_iter
	)

Create correct combinations of adducts for a residue type.

Definition at line 702 of file ResidueTypeSet.cc.

References core::chemical::apply_adducts_to_residue(), core::chemical::ResidueType::defined_adducts(), and residue_types_.

Referenced by place_adducts().

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

inline

accessor for database_directory

Definition at line 276 of file ResidueTypeSet.hh.

References database_directory_.

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

Note: currently, this will not work for variant types defined as alternate base residues (ie different params files)

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 (ie different params files)

Definition at line 550 of file ResidueTypeSet.cc.

References protocols::vip::base_name(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name(), name_map_, core::chemical::residue_type_base_name(), residue_types_, and core::chemical::ResidueType::variant_types().

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 (ie different params files)

Definition at line 587 of file ResidueTypeSet.cc.

References protocols::vip::base_name(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name(), name_map_, core::chemical::residue_type_base_name(), residue_types_, and core::chemical::ResidueType::variant_types().

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

inline

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

Definition at line 199 of file ResidueTypeSet.hh.

References name_map_.

Referenced by protocols::simple_filters::ResidueCountFilter::add_residue_type_by_name(), protocols::ligand_docking::generate_unique_name(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), remove_residue_type(), remove_residue_type_from_maps(), and core::pack::task::NC::residue_action().

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

inline

query if a ResidueType of a certain 3letter name is present.

Definition at line 206 of file ResidueTypeSet.hh.

References name3_map_.

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

inline

name of the residue type set

Definition at line 98 of file ResidueTypeSet.hh.

References name_.

Referenced by core::pack::dunbrack::RotamerLibrary::add_residue_library(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::forge::components::VarLengthBuild::apply(), core::import_pose::build_pose_as_is2(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_residue_typeset(), core::import_pose::pose_from_pdb(), protocols::comparative_modeling::rebuild_loops_until_closed(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), and core::io::serialization::write_binary().

ResidueTypeCOPs const& core::chemical::ResidueTypeSet::name3_map ( std::string const & name) const

inline

query ResidueTypes by their 3-letter name

3-letter name is not unique to each ResidueType for example, 3-letter name "HIS" matches both his tautomers, HIS and HIS_D. Return an empty list if no match is found.

Definition at line 160 of file ResidueTypeSet.hh.

References empty_residue_list_, and name3_map_.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), core::io::pdb::build_pose_as_is1(), and protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing().

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

inline

query ResidueType by its unique residue id.

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

Definition at line 174 of file ResidueTypeSet.hh.

References name_map_.

Referenced by protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::relax::add_virtual_residue_to_cterm(), protocols::kinmatch::alapose(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), protocols::relax::coordinate_constrain_selection(), protocols::forge::build::BuildManager::modify(), protocols::motifs::Motif::Motif(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::pose::residue_types_from_saccharide_sequence(), and core::pose::residue_types_from_sequence().

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

inline

query ResidueType by its unique residue id.

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

Definition at line 187 of file ResidueTypeSet.hh.

References nonconst_name_map_.

Referenced by remove_residue_type().

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

private

void core::chemical::ResidueTypeSet::place_adducts ( )

apply patches to base ResidueType to generate variant ResidueTyes

Generation of new residue types augmented by adduct atoms

Definition at line 626 of file ResidueTypeSet.cc.

References create_adduct_combinations(), core::chemical::ResidueType::defined_adducts(), core::chemical::error_check_requested_adducts(), core::chemical::parse_adduct_string(), residue_types(), residue_types_, and update_residue_maps().

Referenced by ResidueTypeSet().

void core::chemical::ResidueTypeSet::read_files	(	utility::vector1< std::string > const &	filenames,
		AtomTypeSetCAP	atom_types,
		ElementSetCAP	elements,
		MMAtomTypeSetCAP	mm_atom_types,
		orbitals::OrbitalTypeSetCAP	orbital_types
	)

Definition at line 300 of file ResidueTypeSet.cc.

References core::chemical::read_topology_file(), residue_types_, and update_residue_maps().

Referenced by read_list_of_residues().

void core::chemical::ResidueTypeSet::read_list_of_residues	(	std::string const &	list_filename,
		AtomTypeSetCAP	atom_types,
		ElementSetCAP	elements,
		MMAtomTypeSetCAP	mm_atom_types,
		orbitals::OrbitalTypeSetCAP	orbital_types
	)