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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>

Inheritance diagram for core::chemical::ChemicalManager:
Inheritance graph
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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, MMAtomTypeSetOP > core::chemical::ChemicalManager::MMAtomTypeSets
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)
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().

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_.

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_.

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_.

Friends And Related Function Documentation

friend class utility::SingletonBase< ChemicalManager >
friend

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().

GlobalResidueTypeSets core::chemical::ChemicalManager::residue_type_sets_
private

lookup map for querying residue_type_set by name tag

Referenced by has_residue_type_set(), and residue_type_set().


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