A collection of ResidueType defined. More...

#include <ResidueTypeSet.hh>

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...

AtomTypeSetCAP	atom_type_set () const

ElementSetCAP	element_set () const

MMAtomTypeSetCAP	mm_atom_type_set () const

orbitals::OrbitalTypeSetCAP	orbital_type_set () const

void	atom_type_set (AtomTypeSetCAP atom_types)

void	element_set (ElementSetCAP elements)

void	mm_atom_type_set (MMAtomTypeSetCAP mm_atom_types)

void	orbital_type_set (orbitals::OrbitalTypeSetCAP orbital_types)

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

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

void	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	add_residue_type (std::string const &filename)

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 &	interchangeability_group_map (std::string const &name) const
	query ResidueTypes by their interchangeability-group name 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...

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

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

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...

AtomTypeSetCAP	atom_types_

ElementSetCAP	elements_

MMAtomTypeSetCAP	mm_atom_types_

orbitals::OrbitalTypeSetCAP	orbital_types_

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 >	interchangeability_group_map_
	map between ResidueType's interchangeability group string and a vector of ResidueTypeCOPs 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)

Member Typedef Documentation

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

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

Constructor & Destructor Documentation

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

default c-tor

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

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

virtual

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

private

Member Function Documentation

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

query ResidueTypes by their AA enum type

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

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

References aas_defined_.

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

end of aas_defined_ list

References aas_defined_.

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

adds a new residue type to the set

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

Referenced by core::util::add_covalent_linkage_helper(), and add_residue_type().

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

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

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

private

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

Referenced by add_residue_type(), and update_residue_maps().

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

inline

References name_map_.

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

inline

References name_map_.

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

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().

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

inline

References atom_types_.

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

inline

References atom_types_, and runtime_assert.

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

private

clear residue maps

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.

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

References database_directory_.

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

inline

References elements_.

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

inline

References elements_, and runtime_assert.

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)

References core::chemical::ResidueType::has_variant_type(), match, core::chemical::ResidueType::name(), name_map_, core::chemical::residue_type_base_name(), residue_types_, utility_exit_with_message, 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)

References core::chemical::ResidueType::has_variant_type(), match, core::chemical::ResidueType::name(), name_map_, core::chemical::residue_type_base_name(), residue_types_, utility_exit_with_message, and core::chemical::ResidueType::variant_types().

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

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

References name_map_.

Referenced by core::util::add_covalent_linkage_helper(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), remove_residue_type(), and remove_residue_type_from_maps().

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

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

References name3_map_.

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

query ResidueTypes by their interchangeability-group name

References empty_residue_list_, and interchangeability_group_map_.

Referenced by core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), and core::pack::task::NC::residue_action().

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

inline

References mm_atom_types_.

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

inline

References mm_atom_types_, and runtime_assert.

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

inline

name of the residue type set

References name_.

Referenced by core::util::add_covalent_linkage_helper(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::import_pose::build_pose(), core::import_pose::build_pose_as_is2(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::io::pdb::fixup_rinfo_based_on_residue_type_set(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_residue_typeset(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdbstring(), core::import_pose::poses_from_pdbs(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), and core::io::serialization::write_binary().

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

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.

References empty_residue_list_, and name3_map_.

Referenced by core::util::add_covalent_linkage_helper(), and core::io::pdb::build_pose_as_is1().

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

query ResidueType by its unique residue id.

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

References name_map_, and utility_exit_with_message.

Referenced by core::util::add_covalent_linkage_helper(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), 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().

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

private

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

inline

References orbital_types_.

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

inline

References orbital_types_, and runtime_assert.

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

apply patches to base ResidueType to generate variant ResidueTyes

Generation of new residue types augmented by adduct atoms

References create_adduct_combinations(), core::chemical::ResidueType::defined_adducts(), core::chemical::error_check_requested_adducts(), option, core::chemical::parse_adduct_string(), residue_types(), residue_types_, utility::options::StringVectorOption::size(), and update_residue_maps().

Referenced by ResidueTypeSet().

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

References atom_types_, elements_, mm_atom_types_, orbital_types_, 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 )

read a list of residue types

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

References basic::database::full_name(), getline(), and read_files().

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

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

References has_name(), nonconst_name_map_, remove_residue_type_from_maps(), residue_types_, and utility_exit_with_message.

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

private

References aa_map_, core::chemical::aa_unk, aas_defined_, has_name(), interchangeability_group_map_, name3_map_, name_map_, nonconst_name_map_, residue_types_, and residue_types_const_.

Referenced by remove_residue_type().

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

inline

alternate access to all residuetypes as vector

References residue_types_const_.

Referenced by place_adducts(), and core::chemical::ResidueSelector::select().

void core::chemical::ResidueTypeSet::select_residues	(	ResidueSelector const &	selector,
		ResidueTypeCOPs &	matches
	)		const

select a set of ResidueTypes give certain criteria

selection done by ResidueSelector class

References residue_types_.

void core::chemical::ResidueTypeSet::update_residue_maps ( )

private

update residue maps

check that residue id map should be unique, sort the aas_defined list and make its membe unique

References aas_defined_, add_residue_type_to_maps(), clear_residue_maps(), residue_types_, and residue_types_const_.

Referenced by apply_patches(), place_adducts(), read_files(), and ResidueTypeSet().

Member Data Documentation

std::map< AA, ResidueTypeCOPs > core::chemical::ResidueTypeSet::aa_map_

private

map to ResidueType pointers by AA enum

Referenced by aa_map(), add_residue_type_to_maps(), clear_residue_maps(), and remove_residue_type_from_maps().

std::list< AA > core::chemical::ResidueTypeSet::aas_defined_

private

list of AA types defined

Referenced by aas_defined_begin(), aas_defined_end(), add_residue_type(), add_residue_type_to_maps(), clear_residue_maps(), remove_residue_type_from_maps(), and update_residue_maps().

AtomTypeSetCAP core::chemical::ResidueTypeSet::atom_types_

private

Referenced by add_residue_type(), atom_type_set(), read_files(), and ResidueTypeSet().

const std::string core::chemical::ResidueTypeSet::database_directory_

private

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

Referenced by database_directory().

ElementSetCAP core::chemical::ResidueTypeSet::elements_

private

Referenced by add_residue_type(), element_set(), read_files(), and ResidueTypeSet().

ResidueTypeCOPs core::chemical::ResidueTypeSet::empty_residue_list_

private

null list of residues when query fails

Referenced by aa_map(), interchangeability_group_map(), and name3_map().

std::map< std::string, ResidueTypeCOPs > core::chemical::ResidueTypeSet::interchangeability_group_map_

private

map between ResidueType's interchangeability group string and a vector of ResidueTypeCOPs

Referenced by add_residue_type_to_maps(), interchangeability_group_map(), and remove_residue_type_from_maps().

MMAtomTypeSetCAP core::chemical::ResidueTypeSet::mm_atom_types_

private

Referenced by add_residue_type(), mm_atom_type_set(), read_files(), and ResidueTypeSet().

std::map< std::string, ResidueTypeCOPs > core::chemical::ResidueTypeSet::name3_map_

private

map to ResidueType pointers by 3-letter string name

Referenced by add_residue_type_to_maps(), clear_residue_maps(), has_name3(), name3_map(), and remove_residue_type_from_maps().

std::string core::chemical::ResidueTypeSet::name_

private

What does the ChemicalManager call this ResidueTypeSet?

Referenced by name().

std::map< std::string, ResidueTypeCOP > core::chemical::ResidueTypeSet::name_map_

private

map to ResidueType pointers by unique residue id

Referenced by add_residue_type_to_maps(), all_residues_begin(), all_residues_end(), clear_residue_maps(), get_residue_type_with_variant_added(), get_residue_type_with_variant_removed(), has_name(), name_map(), and remove_residue_type_from_maps().

std::map< std::string, ResidueTypeOP > core::chemical::ResidueTypeSet::nonconst_name_map_

private

map to ResidueType pointers by unique residue id, for nonconst access

Referenced by add_residue_type_to_maps(), clear_residue_maps(), remove_residue_type(), and remove_residue_type_from_maps().

orbitals::OrbitalTypeSetCAP core::chemical::ResidueTypeSet::orbital_types_

private

Referenced by add_residue_type(), orbital_type_set(), read_files(), and ResidueTypeSet().

ResidueTypeOPs core::chemical::ResidueTypeSet::residue_types_

private

the residues

Referenced by add_residue_type(), apply_patches(), create_adduct_combinations(), get_residue_type_with_variant_added(), get_residue_type_with_variant_removed(), place_adducts(), read_files(), remove_residue_type(), remove_residue_type_from_maps(), ResidueTypeSet(), select_residues(), and update_residue_maps().

ResidueTypeCOPs core::chemical::ResidueTypeSet::residue_types_const_

private

for handing out

Referenced by add_residue_type_to_maps(), clear_residue_maps(), remove_residue_type_from_maps(), residue_types(), and update_residue_maps().

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

symlinks/rosetta/src/core/chemical/ResidueTypeSet.hh
symlinks/rosetta/src/core/chemical/ResidueTypeSet.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation