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Classes | Typedefs | Functions
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
 
struct  TorsionEnergy
 
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< SingleBasicRotamerLibrarySingleBasicRotamerLibraryOP
 
typedef utility::pointer::shared_ptr< SingleBasicRotamerLibrary const > SingleBasicRotamerLibraryCOP
 
typedef utility::pointer::shared_ptr< SingleBasicRotamerLibraryCreatorSingleBasicRotamerLibraryCreatorOP
 
typedef utility::pointer::shared_ptr< SingleBasicRotamerLibraryCreator const > SingleBasicRotamerLibraryCreatorCOP
 
typedef utility::pointer::shared_ptr< SingleLigandRotamerLibrarySingleLigandRotamerLibraryOP
 
typedef utility::pointer::shared_ptr< SingleLigandRotamerLibrary const > SingleLigandRotamerLibraryCOP
 
typedef utility::pointer::weak_ptr< SingleLigandRotamerLibrarySingleLigandRotamerLibraryAP
 
typedef utility::pointer::weak_ptr< SingleLigandRotamerLibrary const > SingleLigandRotamerLibraryCAP
 
typedef std::map< std::string, core::VectorNamePosMap
 
typedef utility::pointer::shared_ptr< SingleLigandRotamerLibraryCreatorSingleLigandRotamerLibraryCreatorOP
 
typedef utility::pointer::shared_ptr< SingleLigandRotamerLibraryCreator const > SingleLigandRotamerLibraryCreatorCOP
 
typedef utility::pointer::shared_ptr< SingleNCAARotamerLibraryCreatorSingleNCAARotamerLibraryCreatorOP
 
typedef utility::pointer::shared_ptr< SingleNCAARotamerLibraryCreator const > SingleNCAARotamerLibraryCreatorCOP
 
typedef utility::pointer::shared_ptr< SingleResidueRotamerLibrarySingleResidueRotamerLibraryOP
 
typedef utility::pointer::shared_ptr< SingleResidueRotamerLibrary const > SingleResidueRotamerLibraryCOP
 
typedef utility::pointer::weak_ptr< SingleResidueRotamerLibrarySingleResidueRotamerLibraryAP
 
typedef utility::pointer::weak_ptr< SingleResidueRotamerLibrary const > SingleResidueRotamerLibraryCAP
 
typedef utility::vector1< conformation::ResidueOPRotamerVector
 
typedef utility::pointer::shared_ptr< SingleResidueRotamerLibraryCreatorSingleResidueRotamerLibraryCreatorOP
 
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

◆ NamePosMap

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

◆ RotamerVector

◆ SingleBasicRotamerLibraryCOP

◆ SingleBasicRotamerLibraryCreatorCOP

◆ SingleBasicRotamerLibraryCreatorOP

◆ SingleBasicRotamerLibraryOP

◆ SingleLigandRotamerLibraryAP

◆ SingleLigandRotamerLibraryCAP

◆ SingleLigandRotamerLibraryCOP

◆ SingleLigandRotamerLibraryCreatorCOP

◆ SingleLigandRotamerLibraryCreatorOP

◆ SingleLigandRotamerLibraryOP

◆ SingleNCAARotamerLibraryCreatorCOP

◆ SingleNCAARotamerLibraryCreatorOP

◆ SingleResidueRotamerLibraryAP

◆ SingleResidueRotamerLibraryCAP

◆ SingleResidueRotamerLibraryCOP

◆ SingleResidueRotamerLibraryCreatorCOP

◆ SingleResidueRotamerLibraryCreatorOP

◆ SingleResidueRotamerLibraryOP

Function Documentation

◆ dump_library()

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

◆ dup_residue()

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().

◆ rotamer_information_from_PDB_stream()

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().

◆ TR() [1/7]

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

◆ TR() [2/7]

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

◆ TR() [3/7]

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

◆ TR() [4/7]

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

◆ TR() [5/7]

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

◆ TR() [6/7]

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

◆ TR() [7/7]

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