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

#include <ChemicalManager.hh>

Collaboration diagram for core::chemical::ChemicalManager:

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...

orbitals::OrbitalTypeSetCAP	orbital_type_set (std::string const &tag)
	query csd_atom_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, ResidueTypeSetOP >	ResidueTypeSets

Private Member Functions
	ChemicalManager ()
	private constructor 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...

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

IdealBondLengthSets	ideal_bond_length_sets_

Static Private Attributes
static ChemicalManager *	instance_
	static data member holding pointer to the singleton class itself 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.

Definition at line 66 of file ChemicalManager.hh.

Member Typedef Documentation

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

private

Definition at line 108 of file ChemicalManager.hh.

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

private

Definition at line 109 of file ChemicalManager.hh.

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

private

Definition at line 110 of file ChemicalManager.hh.

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

private

Definition at line 112 of file ChemicalManager.hh.

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

private

Definition at line 111 of file ChemicalManager.hh.

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

private

Definition at line 114 of file ChemicalManager.hh.

Constructor & Destructor Documentation

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

private

private constructor

private constructor to guarantee the singleton

Definition at line 92 of file ChemicalManager.cc.

Referenced by get_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.

Definition at line 97 of file ChemicalManager.cc.

References core::chemical::add_atom_type_set_parameters_from_command_line(), atom_type_sets_, and core::chemical::modify_atom_properties_from_command_line().

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::ResidueLoader::create_resource(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::chemical::sdf::SDFParser::GenerateResidues(), core::chemical::IdealBondLengthSet::get_bond_length(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::motifs::Motif::Motif(), core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential(), residue_type_set(), core::chemical::ResidueTypeSet::ResidueTypeSet(), core::chemical::sdf::ctabV2000Parser::set_atom_type(), and core::chemical::sdf::CtabBase::set_atom_type().

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.

Definition at line 117 of file ChemicalManager.cc.

References element_sets_, and protocols::abinitio::filename().

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

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

static

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

Definition at line 82 of file ChemicalManager.cc.

References ChemicalManager(), and instance_.

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.

Definition at line 402 of file ChemicalManager.cc.

References protocols::abinitio::filename(), 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.

Definition at line 148 of file ChemicalManager.cc.

References protocols::abinitio::filename(), and mm_atom_type_sets_.

Referenced by core::chemical::ResidueLoader::create_resource(), core::chemical::sdf::SDFParser::GenerateResidues(), residue_type_set(), 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.

Definition at line 391 of file ChemicalManager.cc.

References residue_type_set(), and residue_type_sets_.

Referenced by protocols::ligand_docking::AddHydrogen::apply(), protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion(), protocols::ligand_docking::generate_unique_name(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), and protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job().

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

query csd_atom_type_set by a name 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.

Definition at line 133 of file ChemicalManager.cc.

References orbital_type_sets_.

Referenced by core::chemical::ResidueLoader::create_resource(), residue_type_set(), 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.

Definition at line 184 of file ChemicalManager.cc.

References atom_type_set(), core::chemical::CENTROID, element_set(), core::chemical::FA_STANDARD, protocols::abinitio::filename(), core::chemical::ResidueDatabaseIO::get_all_residues_in_database(), mm_atom_type_set(), orbital_type_set(), core::chemical::sdf::MolFileParser::parse_mol_file(), core::chemical::ResidueDatabaseIO::read_residuetype_from_database(), residue_type_sets_, and core::chemical::tr().

Referenced by protocols::hybridization::HybridizeProtocol::add_template(), protocols::domain_assembly::CombineChainsMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::swa::StepWiseClusterer::cluster(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::loophash::LoopHashLibrary::create_db(), protocols::simple_moves::ConstrainToIdealMover::create_pose_reference(), protocols::simple_moves::HelicalPeptideLengthMover::create_residue_from_resname_(), core::chemical::ResidueLoader::create_resource(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::sic_dock::dump_loophash_linkers(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::wum::MPI_Relax::fill_outbound_queue(), core::io::silent::SilentStruct::fill_pose(), core::import_pose::PDBSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), core::conformation::form_disulfide(), protocols::kinmatch::FunGroupTK::FunGroupTK(), protocols::swa::protein::generate_beta_database_test(), protocols::inputter::FastaInputter::get_nth_pose(), protocols::inputter::PDBInputter::get_nth_pose(), protocols::inputter::SilentFileInputter::get_nth_pose(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), protocols::swa::StepWiseScreener::initialize_ghost_pose(), protocols::swa::protein::StepWiseProteinScreener::initialize_ghost_pose(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::rna::make_coarse_pose(), protocols::rna::make_extended_coarse_pose(), nonconst_residue_type_set(), protocols::jobdist::not_universal_main(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), core::import_pose::pose_from_pdb(), core::import_pose::poseOPs_from_pdbs(), protocols::rna::RNA_ChunkLibrary::process_input_file(), protocols::wum::SilentStructStore::read_from_cmd_line(), protocols::ddG::ddGData::read_mut_data(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::hybridization::HybridizeProtocol::read_template_structures(), protocols::ddG::ddGData::read_wt_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::chemical::rsd_set_from_cmd_line(), protocols::frag_picker::scores::RDCScore::score(), core::pack::task::operation::util::select_coord_for_residue(), protocols::ligand_docking::LigandDesign::set_fragments(), protocols::ligand_docking::GrowLigand::set_fragments(), protocols::jd2::set_native_in_mover(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::set_pair_and_func_map(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), protocols::jobdist::universal_main(), and protocols::rna::RNA_HelixAssembler::use_phenix_geo().

Member Data Documentation

AtomTypeSets core::chemical::ChemicalManager::atom_type_sets_

private

lookup map for querying atom_type_set by name tag

Definition at line 123 of file ChemicalManager.hh.

Referenced by atom_type_set().

ElementSets core::chemical::ChemicalManager::element_sets_

private

lookup map for querying element_type_set by name tag

Definition at line 125 of file ChemicalManager.hh.

Referenced by element_set().

IdealBondLengthSets core::chemical::ChemicalManager::ideal_bond_length_sets_

private

Definition at line 135 of file ChemicalManager.hh.

Referenced by ideal_bond_length_set().

ChemicalManager * core::chemical::ChemicalManager::instance_

staticprivate

static data member holding pointer to the singleton class itself

set initial value as no instance

Definition at line 120 of file ChemicalManager.hh.

Referenced by get_instance().

MMAtomTypeSets core::chemical::ChemicalManager::mm_atom_type_sets_

private

lookup map for querying mm_atom_type_set by name tag

Definition at line 129 of file ChemicalManager.hh.

Referenced by mm_atom_type_set().

OrbitalTypeSets core::chemical::ChemicalManager::orbital_type_sets_

private

lookup map for querying orbital_type_set by name tag.

Definition at line 127 of file ChemicalManager.hh.

Referenced by orbital_type_set().

ResidueTypeSets core::chemical::ChemicalManager::residue_type_sets_

private

lookup map for querying csd_atom_type_set by name tag

lookup map for querying residue_type_set by name tag

Definition at line 133 of file ChemicalManager.hh.

Referenced by nonconst_residue_type_set(), and residue_type_set().

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

src/core/chemical/ChemicalManager.hh
src/core/chemical/ChemicalManager.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation