core::pack::rotamers Namespace Reference

Classes
class	SingleBasicRotamerLibrary
	A simple Rotamer library, which serves as a default for ResidueTypes which don't have some other more specific rotamer library. More...
class	SingleBasicRotamerLibraryCreator
class	SingleLigandRotamerLibrary
	A fixed library of conformations for some residue type (doesn't have to be a ligand). More...
class	SingleLigandRotamerLibraryCreator
class	SingleNCAARotamerLibraryCreator
class	SingleResidueRotamerLibrary
	SingleResidueRotamerLibrary pure virtual base class. More...
class	SingleResidueRotamerLibraryCreator
class	SingleResidueRotamerLibraryFactory
class	SingleResidueRotamerLibraryRegistrator
	This templated class will register an instance of an SingleResidueRotamerLibraryCreator (class T) with the SingleResidueRotamerLibraryFactory. It will ensure that no SingleResidueRotamerLibrary creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	StoredRotamerLibraryCreator

Typedefs
typedef utility::pointer::shared_ptr < SingleBasicRotamerLibrary >	SingleBasicRotamerLibraryOP
typedef utility::pointer::shared_ptr < SingleBasicRotamerLibrary const >	SingleBasicRotamerLibraryCOP
typedef utility::pointer::shared_ptr < SingleBasicRotamerLibraryCreator >	SingleBasicRotamerLibraryCreatorOP
typedef utility::pointer::shared_ptr < SingleBasicRotamerLibraryCreator const >	SingleBasicRotamerLibraryCreatorCOP
typedef utility::pointer::shared_ptr < SingleLigandRotamerLibrary >	SingleLigandRotamerLibraryOP
typedef utility::pointer::shared_ptr < SingleLigandRotamerLibrary const >	SingleLigandRotamerLibraryCOP
typedef utility::pointer::weak_ptr < SingleLigandRotamerLibrary >	SingleLigandRotamerLibraryAP
typedef utility::pointer::weak_ptr < SingleLigandRotamerLibrary const >	SingleLigandRotamerLibraryCAP
typedef std::map< std::string, core::Vector >	NamePosMap
typedef utility::pointer::shared_ptr < SingleLigandRotamerLibraryCreator >	SingleLigandRotamerLibraryCreatorOP
typedef utility::pointer::shared_ptr < SingleLigandRotamerLibraryCreator const >	SingleLigandRotamerLibraryCreatorCOP
typedef utility::pointer::shared_ptr < SingleNCAARotamerLibraryCreator >	SingleNCAARotamerLibraryCreatorOP
typedef utility::pointer::shared_ptr < SingleNCAARotamerLibraryCreator const >	SingleNCAARotamerLibraryCreatorCOP
typedef utility::pointer::shared_ptr < SingleResidueRotamerLibrary >	SingleResidueRotamerLibraryOP
typedef utility::pointer::shared_ptr < SingleResidueRotamerLibrary const >	SingleResidueRotamerLibraryCOP
typedef utility::pointer::weak_ptr < SingleResidueRotamerLibrary >	SingleResidueRotamerLibraryAP
typedef utility::pointer::weak_ptr < SingleResidueRotamerLibrary const >	SingleResidueRotamerLibraryCAP
typedef utility::vector1 < conformation::ResidueOP >	RotamerVector
typedef utility::pointer::shared_ptr < SingleResidueRotamerLibraryCreator >	SingleResidueRotamerLibraryCreatorOP
typedef utility::pointer::shared_ptr < SingleResidueRotamerLibraryCreator const >	SingleResidueRotamerLibraryCreatorCOP

Functions
static basic::Tracer	TR ("core.pack.rotamers.SingleBasicRotamerLibrary")
static basic::Tracer	TR ("core.pack.rotamers.SingleLigandRotamerLibrary")
void	dump_library (std::string filename, RotamerVector const &rotamers)
conformation::ResidueOP	dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
	Helper function for superposition. More...
void	rotamer_information_from_PDB_stream (std::istream &conformers_stream, chemical::ResidueType const &restype, utility::vector1< NamePosMap > &atom_positions, core::Real &e_ref)
	read a PDB-formatted string of conformers into the data types held by SingleLigandRotamerLibrary atom_positions and e_ref are return values More...
static basic::Tracer	TR ("core.pack.rotamers.SingleLigandRotamerLibraryCreator")
static basic::Tracer	TR ("core.pack.rotamers.SingleNCAARotamerLibraryCreator")
static basic::Tracer	TR ("core.pack.rotamers.SingleResidueRotamerLibrary")
static basic::Tracer	TR ("core.pack.rotamers.SingleResidueRotamerLibraryFactory")
static basic::Tracer	TR ("core.pack.rotamers.StoredRotamerLibraryCreator")

Typedef Documentation

typedef std::map< std::string, core::Vector > core::pack::rotamers::NamePosMap

typedef utility::vector1< conformation::ResidueOP > core::pack::rotamers::RotamerVector

typedef utility::pointer::shared_ptr< SingleBasicRotamerLibrary const > core::pack::rotamers::SingleBasicRotamerLibraryCOP

typedef utility::pointer::shared_ptr< SingleBasicRotamerLibraryCreator const > core::pack::rotamers::SingleBasicRotamerLibraryCreatorCOP

typedef utility::pointer::shared_ptr< SingleBasicRotamerLibraryCreator > core::pack::rotamers::SingleBasicRotamerLibraryCreatorOP

typedef utility::pointer::shared_ptr< SingleBasicRotamerLibrary > core::pack::rotamers::SingleBasicRotamerLibraryOP

typedef utility::pointer::weak_ptr< SingleLigandRotamerLibrary > core::pack::rotamers::SingleLigandRotamerLibraryAP

typedef utility::pointer::weak_ptr< SingleLigandRotamerLibrary const > core::pack::rotamers::SingleLigandRotamerLibraryCAP

typedef utility::pointer::shared_ptr< SingleLigandRotamerLibrary const > core::pack::rotamers::SingleLigandRotamerLibraryCOP

typedef utility::pointer::shared_ptr< SingleLigandRotamerLibraryCreator const > core::pack::rotamers::SingleLigandRotamerLibraryCreatorCOP

typedef utility::pointer::shared_ptr< SingleLigandRotamerLibraryCreator > core::pack::rotamers::SingleLigandRotamerLibraryCreatorOP

typedef utility::pointer::shared_ptr< SingleLigandRotamerLibrary > core::pack::rotamers::SingleLigandRotamerLibraryOP

typedef utility::pointer::shared_ptr< SingleNCAARotamerLibraryCreator const > core::pack::rotamers::SingleNCAARotamerLibraryCreatorCOP

typedef utility::pointer::shared_ptr< SingleNCAARotamerLibraryCreator > core::pack::rotamers::SingleNCAARotamerLibraryCreatorOP

typedef utility::pointer::weak_ptr< SingleResidueRotamerLibrary > core::pack::rotamers::SingleResidueRotamerLibraryAP

typedef utility::pointer::weak_ptr< SingleResidueRotamerLibrary const > core::pack::rotamers::SingleResidueRotamerLibraryCAP

typedef utility::pointer::shared_ptr< SingleResidueRotamerLibrary const > core::pack::rotamers::SingleResidueRotamerLibraryCOP

typedef utility::pointer::shared_ptr< SingleResidueRotamerLibraryCreator const > core::pack::rotamers::SingleResidueRotamerLibraryCreatorCOP

typedef utility::pointer::shared_ptr< SingleResidueRotamerLibraryCreator > core::pack::rotamers::SingleResidueRotamerLibraryCreatorOP

typedef utility::pointer::shared_ptr< SingleResidueRotamerLibrary > core::pack::rotamers::SingleResidueRotamerLibraryOP

Function Documentation

void core::pack::rotamers::dump_library	(	std::string	filename,
		RotamerVector const &	rotamers
	)

References core::io::pdb::dump_pdb_residue(), and core::conformation::membrane::out.

conformation::ResidueOP core::pack::rotamers::dup_residue	(	conformation::Residue const &	existing,
		conformation::Residue const &	conformer
	)

Helper function for superposition.

Helper function, combines existing's metadata with conformer's conformation.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), and core::conformation::Residue::seqpos().

Referenced by core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector().

void core::pack::rotamers::rotamer_information_from_PDB_stream	(	std::istream &	conformers_stream,
		chemical::ResidueType const &	restype,
		utility::vector1< NamePosMap > &	atom_positions,
		core::Real &	e_ref
	)

read a PDB-formatted string of conformers into the data types held by SingleLigandRotamerLibrary atom_positions and e_ref are return values

read an istream containing conformers (formatted as concatenated PDBs) into the data types held by SingleLigandRotamerLibrary atom_positions and e_ref are return values

This function was refactored out of init_from_file of this class its purpose is to allow PDB-formatted conformers to come from stream objects rather than necessarily files it is a separate utility function instead of a member function so that the data can be held in a StoredRotamerLibrarySpecification until needed

Author

refactored by Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

References core::chemical::ResidueTypeBase::name(), and TR().

Referenced by core::pack::rotamers::SingleLigandRotamerLibrary::init_from_file().

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.StoredRotamerLibraryCreator"  )

static

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleLigandRotamerLibraryCreator"  )

static

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleResidueRotamerLibraryFactory"  )

static

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleResidueRotamerLibrary"  )

static

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleBasicRotamerLibrary"  )

static

Referenced by core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(), core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_missing_atoms(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleLigandRotamerLibrary::init_from_file(), core::pack::rotamers::SingleResidueRotamerLibrary::operator==(), rotamer_information_from_PDB_stream(), and core::pack::rotamers::SingleResidueRotamerLibraryFactory::type_for_residuetype().

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleNCAARotamerLibraryCreator"  )

static

static basic::Tracer core::pack::rotamers::TR ( "core.pack.rotamers.SingleLigandRotamerLibrary"  )

static