Rosetta Core  2014.35
Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
core::chemical::ChemicalManager Class Reference

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...
 
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,
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 ChemicalManagercreate_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

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)
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.

References atom_type_set(), core::chemical::CENTROID, core::chemical::sdf::convert_to_ResidueType(), utility::sql_database::database_mode_from_name(), database_name, element_set(), basic::options::OptionKeys::in::file::extra_patch_cen, basic::options::OptionKeys::in::file::extra_patch_fa, basic::options::OptionKeys::in::file::extra_res, basic::options::OptionKeys::in::file::extra_res_batch_path, basic::options::OptionKeys::in::file::extra_res_cen, basic::options::OptionKeys::in::file::extra_res_database, basic::options::OptionKeys::in::file::extra_res_database_mode, basic::options::OptionKeys::in::file::extra_res_database_resname_list, basic::options::OptionKeys::in::file::extra_res_fa, basic::options::OptionKeys::in::file::extra_res_mol, basic::options::OptionKeys::in::file::extra_res_path, basic::options::OptionKeys::in::file::extra_res_pq_schema, core::chemical::FA_STANDARD, filename(), basic::database::full_name(), utility::pointer::owning_ptr< T >::get(), core::chemical::ResidueDatabaseIO::get_all_residues_in_database(), basic::database::get_db_session(), get_instance(), basic::options::OptionKeys::corrections::chemical::icoor_05_2009, utility::file::list_dir(), mm_atom_type_set(), utility::file::FileName::name(), utility::options::PathVectorOption::name(), basic::options::option, orbital_type_set(), core::chemical::sdf::MolFileIOReader::parse_file(), path, basic::options::OptionKeys::mistakes::chemical::pre_talaris2013_geometries, core::chemical::ResidueDatabaseIO::read_residuetype_from_database(), utility::options::FileVectorOption::size(), utility::options::PathVectorOption::size(), core::chemical::TR, and user.

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)

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().

GasteigerAtomTypeSets core::chemical::ChemicalManager::gasteiger_atom_type_sets_
private

lookup map for querying gasteiger_atom_type_set by name tag

Referenced by gasteiger_atom_type_set().

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

lookup map for the set of ideal bond lengths

Referenced by ideal_bond_length_set().

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 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: