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core::chemical::ChemicalManager Class Reference

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

#include <ChemicalManager.hh>

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

Static Public Member Functions

static ChemicalManagerget_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 ChemicalManagerinstance_
 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.

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, MMAtomTypeSetOP > core::chemical::ChemicalManager::MMAtomTypeSets
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 get_instance().

Member Function Documentation

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

References ChemicalManager(), and instance_.

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), protocols::hybridization::HybridizeProtocol::add_template(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::domain_assembly::CombineChainsMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::match::MatcherMover::apply(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), protocols::features::AtomAtomPairFeatures::AtomAtomPairFeatures(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::MakeRotLib::calc_std_dev(), core::import_pose::centroid_pose_from_pdb(), protocols::jd2::JD2ResourceManagerJobInputter::cleanup_after_job_completion(), protocols::swa::StepWiseClusterer::cluster(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::chemical::IdealBondLengthSet::contains_bond_length(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), protocols::loophash::LoopHashLibrary::create_db(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), 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::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::sic_dock::dump_loophash_linkers(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::scoring::ScoringManager::etable(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), 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::ligand_docking::generate_unique_name(), core::chemical::sdf::SDFParser::GenerateResidues(), protocols::swa::rna::get_binary_rna_silent_struct_safe(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::enzdes::AddOrRemoveMatchCsts::get_EnzConstraintIO_for_cstfile(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_instance(), core::scoring::ScoringManager::get_MMBondAngleLibrary(), core::scoring::ScoringManager::get_MMBondLengthLibrary(), core::scoring::ScoringManager::get_MMLJLibrary(), core::scoring::ScoringManager::get_MMTorsionLibrary(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), protocols::inputter::FastaInputter::get_nth_pose(), protocols::inputter::PDBInputter::get_nth_pose(), protocols::inputter::SilentFileInputter::get_nth_pose(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::swa::rna::import_pose_from_silent_file(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::qsar::scoring_grid::SolvationMetaGrid::initialize(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line(), protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose(), 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::features::PoseConformationFeatures::load_sequence(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::rna::make_coarse_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::rna::make_extended_coarse_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::make_pose_from_sequence(), core::scoring::ScoringManager::memb_etable(), protocols::MakeRotLib::min_rotamers(), protocols::motifs::Motif::Motif(), protocols::jobdist::not_universal_main(), core::conformation::orient_residue_for_ideal_bond(), protocols::fldsgn::BluePrintBDR::parse_my_tag(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdb_stream(), core::import_pose::pose_from_pdbstring(), core::io::pdb::pose_from_pose(), core::import_pose::poseOPs_from_pdbs(), core::import_pose::poses_from_pdbs(), protocols::rna::RNA_ChunkLibrary::process_input_file(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), core::io::serialization::read_binary(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::jumping::ResiduePairJumpSetup::read_file(), protocols::wum::SilentStructStore::read_from_cmd_line(), protocols::ddG::ddGData::read_mut_data(), protocols::protein_interface_design::PatchdockReader::read_poses(), core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::MetalloClaimer::read_tag(), 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::ResidueTypeSet::ResidueTypeSet(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), core::chemical::rsd_set_from_cmd_line(), protocols::abinitio::run_boinc_debug(), protocols::frag_picker::scores::RDCScore::score(), core::pack::task::operation::util::select_coord_for_residue(), core::chemical::sdf::ctabV2000Parser::set_atom_type(), core::chemical::sdf::CtabBase::set_atom_type(), protocols::forge::constraints::InvrotTreeRCG::set_cstfile(), 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(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), protocols::motifs::single_residue_from_stream(), core::util::switch_to_residue_type_set(), protocols::jobdist::universal_main(), protocols::rna::RNA_HelixAssembler::use_phenix_geo(), and protocols::frag_picker::VallProvider::vallChunksFromLibrary().

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 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.

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)
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.

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.

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

Referenced by atom_type_set().

ElementSets core::chemical::ChemicalManager::element_sets_
private

lookup map for querying element_type_set by name tag

Referenced by element_set().

IdealBondLengthSets core::chemical::ChemicalManager::ideal_bond_length_sets_
private

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

Referenced by get_instance().

MMAtomTypeSets core::chemical::ChemicalManager::mm_atom_type_sets_
private

lookup map for querying mm_atom_type_set by name tag

Referenced by mm_atom_type_set().

OrbitalTypeSets core::chemical::ChemicalManager::orbital_type_sets_
private

lookup map for querying orbital_type_set by name tag.

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

Referenced by nonconst_residue_type_set(), and residue_type_set().


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