a class managing different sets of atom_type_set and residue_type_set More...

#include <ChemicalManager.hh>

Public Member Functions
AtomTypeSetCAP	atom_type_set (std::string const &tag)
	query atom_type_set by a name tag More...

ElementSetCAP	element_set (std::string const &tag)
	query atom_type_set by a name tag More...

IdealBondLengthSetCAP	ideal_bond_length_set (std::string const &tag)
	query ideal_bond_lengths More...

MMAtomTypeSetCAP	mm_atom_type_set (std::string const &tag)
	query mm_atom_type_set by a name tag More...

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_type_set (std::string const &tag="default")
	query gasteiger_atom_type_set by a name tag More...

orbitals::OrbitalTypeSetCAP	orbital_type_set (std::string const &tag)
	query orbital_type_set by a name tag More...

ResidueTypeSetCAP	residue_type_set (std::string tag)
	query residue_type_set by a name tag More...

ResidueTypeSet &	nonconst_residue_type_set (std::string const &tag)
	query residue_type_set by a name tag More...

Static Public Member Functions
static ChemicalManager *	get_instance ()
	static function to get the instance of ( pointer to) this singleton class More...

Private Types
typedef std::map< std::string, AtomTypeSetOP >	AtomTypeSets

typedef std::map< std::string, ElementSetOP >	ElementSets

typedef std::map< std::string, IdealBondLengthSetOP >	IdealBondLengthSets

typedef std::map< std::string, orbitals::OrbitalTypeSetOP >	OrbitalTypeSets

typedef std::map< std::string, MMAtomTypeSetOP >	MMAtomTypeSets

typedef std::map< std::string, gasteiger::GasteigerAtomTypeSetOP >	GasteigerAtomTypeSets

typedef std::map< std::string, ResidueTypeSetOP >	ResidueTypeSets

Private Member Functions
	ChemicalManager ()
	private constructor More...

AtomTypeSetOP	create_atom_type_set (std::string const &tag) const
	Go and create an atom type set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

ElementSetOP	create_element_set (std::string const &tag) const
	Go and create an element type set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

orbitals::OrbitalTypeSetOP	create_orbital_type_set (std::string const &tag) const
	Go and create an orbital type set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

MMAtomTypeSetOP	create_mm_atom_type_set (std::string const &tag) const
	Go and create an mm atom type set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

ResidueTypeSetOP	create_residue_type_set (std::string const &tag) const
	Go and create a residue type set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

IdealBondLengthSetOP	create_ideal_bond_length_set (std::string const &tag) const
	Go and create an ideal bond length set. Should be called only after it's been determined safe (and neccessary) to construct it. More...

Static Private Member Functions
static ChemicalManager *	create_singleton_instance ()
	private singleton creation function to be used with utility::thread::threadsafe_singleton More...

Private Attributes
AtomTypeSets	atom_type_sets_
	lookup map for querying atom_type_set by name tag More...

ElementSets	element_sets_
	lookup map for querying element_type_set by name tag More...

OrbitalTypeSets	orbital_type_sets_
	lookup map for querying orbital_type_set by name tag. More...

MMAtomTypeSets	mm_atom_type_sets_
	lookup map for querying mm_atom_type_set by name tag More...

GasteigerAtomTypeSets	gasteiger_atom_type_sets_
	lookup map for querying gasteiger_atom_type_set by name tag More...

ResidueTypeSets	residue_type_sets_
	lookup map for querying residue_type_set by name tag More...

IdealBondLengthSets	ideal_bond_length_sets_
	lookup map for the set of ideal bond lengths More...

Detailed Description

a class managing different sets of atom_type_set and residue_type_set

make it as a singleton class so that atom_type_set and residue_type_set are only input and initialized once. They can be later retrieved by querying this class.

Member Typedef Documentation

typedef std::map< std::string, AtomTypeSetOP > core::chemical::ChemicalManager::AtomTypeSets

private

typedef std::map< std::string, ElementSetOP > core::chemical::ChemicalManager::ElementSets

private

typedef std::map< std::string, gasteiger::GasteigerAtomTypeSetOP > core::chemical::ChemicalManager::GasteigerAtomTypeSets

private

typedef std::map< std::string, IdealBondLengthSetOP> core::chemical::ChemicalManager::IdealBondLengthSets

private

typedef std::map< std::string, MMAtomTypeSetOP > core::chemical::ChemicalManager::MMAtomTypeSets

private

typedef std::map< std::string, orbitals::OrbitalTypeSetOP > core::chemical::ChemicalManager::OrbitalTypeSets

private

typedef std::map< std::string, ResidueTypeSetOP > core::chemical::ChemicalManager::ResidueTypeSets

private

Constructor & Destructor Documentation

core::chemical::ChemicalManager::ChemicalManager ( )

private

private constructor

private constructor to guarantee the singleton

Referenced by create_singleton_instance().

Member Function Documentation

AtomTypeSetCAP core::chemical::ChemicalManager::atom_type_set ( std::string const & tag )

query atom_type_set by a name tag

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References atom_type_sets_, and create_atom_type_set().

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::sdf::convert_to_ResidueType(), create_residue_type_set(), core::chemical::ResidueLoader::create_resource(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::chemical::IdealBondLengthSet::get_bond_length(), core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential(), and core::chemical::ResidueTypeSet::ResidueTypeSet().

AtomTypeSetOP core::chemical::ChemicalManager::create_atom_type_set ( std::string const & tag ) const

private

Go and create an atom type set. Should be called only after it's been determined safe (and neccessary) to construct it.

Actually go and create an AtomTypeSet

References core::chemical::add_atom_type_set_parameters_from_command_line(), basic::database::full_name(), and core::chemical::modify_atom_properties_from_command_line().

Referenced by atom_type_set().

ElementSetOP core::chemical::ChemicalManager::create_element_set ( std::string const & tag ) const

private

Go and create an element type set. Should be called only after it's been determined safe (and neccessary) to construct it.

References filename(), and basic::database::full_name().

Referenced by element_set().

IdealBondLengthSetOP core::chemical::ChemicalManager::create_ideal_bond_length_set ( std::string const & tag ) const

private

Go and create an ideal bond length set. Should be called only after it's been determined safe (and neccessary) to construct it.

References filename(), and basic::database::full_name().

Referenced by ideal_bond_length_set().

MMAtomTypeSetOP core::chemical::ChemicalManager::create_mm_atom_type_set ( std::string const & tag ) const

private

Go and create an mm atom type set. Should be called only after it's been determined safe (and neccessary) to construct it.

References filename(), and basic::database::full_name().

Referenced by mm_atom_type_set().

orbitals::OrbitalTypeSetOP core::chemical::ChemicalManager::create_orbital_type_set ( std::string const & tag ) const

private

Go and create an orbital type set. Should be called only after it's been determined safe (and neccessary) to construct it.

References basic::database::full_name().

Referenced by orbital_type_set().

ResidueTypeSetOP core::chemical::ChemicalManager::create_residue_type_set ( std::string const & tag ) const

private

Go and create a residue type set. Should be called only after it's been determined safe (and neccessary) to construct it.

Referenced by residue_type_set().

ChemicalManager * core::chemical::ChemicalManager::create_singleton_instance ( )

staticprivate

private singleton creation function to be used with utility::thread::threadsafe_singleton

References ChemicalManager().

Referenced by get_instance().

ElementSetCAP core::chemical::ChemicalManager::element_set ( std::string const & tag )

query atom_type_set by a name tag

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References create_element_set(), and element_sets_.

Referenced by core::io::pdb::bonding_distance_threshold(), core::chemical::sdf::convert_to_ResidueType(), create_residue_type_set(), core::chemical::ResidueLoader::create_resource(), gasteiger_atom_type_set(), and core::chemical::ResidueTypeSet::ResidueTypeSet().

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ChemicalManager::gasteiger_atom_type_set ( std::string const & tag = "default" )

query gasteiger_atom_type_set by a name tag

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References element_set(), filename(), basic::database::full_name(), and gasteiger_atom_type_sets_.

Referenced by core::chemical::ResidueType::set_gasteiger_atom_type().

ChemicalManager * core::chemical::ChemicalManager::get_instance ( )

static

static function to get the instance of ( pointer to) this singleton class

References create_singleton_instance(), and utility::thread::safely_create_singleton().

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::util::add_covalent_linkage_helper(), core::pose::addVirtualResAsRoot(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::scoring::AtomVDW::AtomVDW(), core::io::pdb::bonding_distance_threshold(), core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff(), core::scoring::geometric_solvation::compute_exact_geosol(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::sdf::convert_to_ResidueType(), core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), core::pack::dunbrack::RotamerLibrary::create_centroid_rotamer_libraries_from_ASCII(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), create_residue_type_set(), core::chemical::ResidueLoader::create_resource(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::scoring::ScoringManager::etable(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::conformation::form_disulfide(), core::chemical::IdealBondLengthSet::get_bond_length(), core::scoring::ScoringManager::get_MMBondAngleLibrary(), core::scoring::ScoringManager::get_MMBondLengthLibrary(), core::scoring::ScoringManager::get_MMLJLibrary(), core::scoring::ScoringManager::get_MMTorsionLibrary(), core::pose::rna::RNA_IdealCoord::init(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::data::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), core::pose::make_pose_from_sequence(), core::scoring::ScoringManager::memb_etable(), core::conformation::orient_residue_for_ideal_bond(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdb_stream(), core::import_pose::pose_from_pdbstring(), core::scoring::methods::GoapEnergy::read_angle_definitions(), core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential(), core::scoring::constraints::BackboneStubLinearConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::chemical::ResidueTypeSet::ResidueTypeSet(), core::chemical::rsd_set_from_cmd_line(), core::pack::task::operation::util::select_coord_for_residue(), core::chemical::ResidueType::set_gasteiger_atom_type(), and core::util::switch_to_residue_type_set().

IdealBondLengthSetCAP core::chemical::ChemicalManager::ideal_bond_length_set ( std::string const & tag )

query ideal_bond_lengths

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References create_ideal_bond_length_set(), and ideal_bond_length_sets_.

Referenced by core::conformation::orient_residue_for_ideal_bond().

MMAtomTypeSetCAP core::chemical::ChemicalManager::mm_atom_type_set ( std::string const & tag )

query mm_atom_type_set by a name tag

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References create_mm_atom_type_set(), and mm_atom_type_sets_.

Referenced by core::chemical::sdf::convert_to_ResidueType(), create_residue_type_set(), core::chemical::ResidueLoader::create_resource(), and core::chemical::ResidueTypeSet::ResidueTypeSet().

ResidueTypeSet & core::chemical::ChemicalManager::nonconst_residue_type_set ( std::string const & tag )

query residue_type_set by a name tag

@ details if the tag is not in the map, input it from a database file and add it to the map for future look-up. THIS FUNCTION IS DECIDEDLY NOT THREADSAFE!

References residue_type_set(), and residue_type_sets_.

Referenced by core::util::add_covalent_linkage_helper().

orbitals::OrbitalTypeSetCAP core::chemical::ChemicalManager::orbital_type_set ( std::string const & tag )

query orbital_type_set by a name tag

if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References create_orbital_type_set(), and orbital_type_sets_.

Referenced by create_residue_type_set(), core::chemical::ResidueLoader::create_resource(), and core::chemical::ResidueTypeSet::ResidueTypeSet().

ResidueTypeSetCAP core::chemical::ChemicalManager::residue_type_set ( std::string tag )

query residue_type_set by a name tag

@ details if the tag is not in the map, input it from a database file and add it to the map for future look-up.

References basic::options::OptionKeys::rna::corrected_geo, corrected_geo, create_residue_type_set(), basic::options::option, residue_type_sets_, basic::options::OptionKeys::rna::rna_prot_erraser, rna_prot_erraser, and utility_exit_with_message.

Referenced by core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), core::pack::dunbrack::RotamerLibrary::create_centroid_rotamer_libraries_from_ASCII(), core::chemical::ResidueLoader::create_resource(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::conformation::form_disulfide(), core::pose::rna::RNA_IdealCoord::init(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::data::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), nonconst_residue_type_set(), core::import_pose::pose_from_pdb(), core::scoring::methods::GoapEnergy::read_angle_definitions(), core::scoring::constraints::BackboneStubLinearConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::chemical::rsd_set_from_cmd_line(), core::pack::task::operation::util::select_coord_for_residue(), and core::util::switch_to_residue_type_set().