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

#include <ChemicalManager.hh>

Inheritance diagram for core::chemical::ChemicalManager:

Public Member Functions
AtomTypeSetCOP	atom_type_set (TypeSetMode type_set_type)
	query atom_type_set by mode More...

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

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

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

MMAtomTypeSetCOP	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::OrbitalTypeSetCOP	orbital_type_set (std::string const &tag)
	query orbital_type_set by a name tag More...

ResidueTypeSetCOP	residue_type_set (TypeSetMode type_set_type)
	query residue_type_set by a type More...

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

bool	has_residue_type_set (std::string const &tag)
	Check if residue_type_set is instantiated... 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, GlobalResidueTypeSetOP >	GlobalResidueTypeSets

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...

GlobalResidueTypeSetOP	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...

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...

GlobalResidueTypeSets	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...

Friends
class	utility::SingletonBase< ChemicalManager >

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, GlobalResidueTypeSetOP > core::chemical::ChemicalManager::GlobalResidueTypeSets

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

Constructor & Destructor Documentation

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

privatedefault

private constructor

private constructor to guarantee the singleton

Member Function Documentation

AtomTypeSetCOP core::chemical::ChemicalManager::atom_type_set ( TypeSetMode type_set_type )

query atom_type_set by mode

query residue_type_set by a type

References core::chemical::string_from_type_set_mode().

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::rdkit::RDMolToRestype::generate_restype(), and core::chemical::IdealBondLengthSet::get_bond_length().

AtomTypeSetCOP 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().

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(), core::chemical::add_atom_types_from_command_line(), 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 protocols::abinitio::filename().

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 protocols::abinitio::filename().

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 core::chemical::add_mm_atom_type_set_parameters_from_command_line(), and protocols::abinitio::filename().

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.

Referenced by orbital_type_set().

GlobalResidueTypeSetOP 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 core::chemical::CENTROID, core::chemical::FA_STANDARD, and core::chemical::TR().

Referenced by residue_type_set().

ElementSetCOP 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 gasteiger_atom_type_set(), and core::chemical::rdkit::RDMolToRestype::generate_restype().

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(), protocols::abinitio::filename(), and gasteiger_atom_type_sets_.

bool core::chemical::ChemicalManager::has_residue_type_set ( std::string const & tag )

Check if residue_type_set is instantiated...

References residue_type_sets_.

IdealBondLengthSetCOP 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().

MMAtomTypeSetCOP 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::rdkit::RDMolToRestype::generate_restype().

orbitals::OrbitalTypeSetCOP 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 core::chemical::rdkit::RDMolToRestype::generate_restype().

ResidueTypeSetCOP core::chemical::ChemicalManager::residue_type_set ( TypeSetMode type_set_type )

query residue_type_set by a type

Note: If you have access to a Pose/Conformation, you probably don't want to use this function. The Conformation can have custom ResidueTypeSets which add additional ResidueTypes to the ResidueTypeSet. Instead, use the residue_type_set_for_*() function on the pose. Those will fall back to this function if there isn't a custom ResidueTypeSet.

References core::chemical::string_from_type_set_mode().

Referenced by protocols::ligand_docking::generate_unique_name(), protocols::ligand_docking::LigandDesign::set_fragments(), and protocols::ligand_docking::GrowLigand::set_fragments().

ResidueTypeSetCOP core::chemical::ChemicalManager::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.

References create_residue_type_set(), and residue_type_sets_.