core::scoring::disulfides Namespace Reference

Classes
class	CaCbCb_Angle_Func
class	CaCbCbCa_Dihedral_Func
class	CB_Angle_Func
class	Cb_Distance_Func
	Score based on the distance between Cb. More...
class	CBSG_Dihedral_Func
class	Cen_Distance_Func
class	CentroidDisulfideEnergyComponents
	Storage for Disulfide Energy Terms. More...
class	CentroidDisulfideEnergyContainer
class	CentroidDisulfideNeighborConstIterator
	Just a const version of CentroidDisulfideNeighborIterator. More...
class	CentroidDisulfideNeighborIterator
	An iterator over the disulfide bonds a residue forms. More...
class	CentroidDisulfidePotential
class	DisulfideAtomIndices
	This class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that's known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow. More...
class	DisulfideMatchingDatabase
class	DisulfideMatchingEnergyComponents
	Storage for Disulfide Energy Terms. More...
class	DisulfideMatchingEnergyContainer
class	DisulfideMatchingNeighborConstIterator
	Just a const version of DisulfideMatchingNeighborIterator. More...
class	DisulfideMatchingNeighborIterator
	An iterator over the disulfide bonds a residue forms. More...
class	DisulfideMatchingPotential
class	DisulfResNeighbConstIterator
class	DisulfResNeighbIterator
class	FullatomDisulfideEnergyComponents
class	FullatomDisulfideEnergyContainer
struct	FullatomDisulfideParams13
class	FullatomDisulfidePotential
class	NCaCaC_Dihedral_Func
class	RT_helper
class	SG_Dist_Func
class	SGSG_Dihedral_Func

Typedefs
typedef utility::pointer::shared_ptr < CentroidDisulfideEnergyContainer >	CentroidDisulfideEnergyContainerOP
typedef utility::pointer::shared_ptr < CentroidDisulfideEnergyContainer const >	CentroidDisulfideEnergyContainerCOP
typedef utility::pointer::weak_ptr < CentroidDisulfideEnergyContainer >	CentroidDisulfideEnergyContainerAP
typedef utility::pointer::weak_ptr < CentroidDisulfideEnergyContainer const >	CentroidDisulfideEnergyContainerCAP
typedef utility::pointer::shared_ptr < CentroidDisulfidePotential >	CentroidDisulfidePotentialOP
typedef utility::pointer::shared_ptr < CentroidDisulfidePotential const >	CentroidDisulfidePotentialCOP
typedef utility::pointer::weak_ptr < CentroidDisulfidePotential >	CentroidDisulfidePotentialAP
typedef utility::pointer::weak_ptr < CentroidDisulfidePotential const >	CentroidDisulfidePotentialCAP
typedef utility::pointer::shared_ptr < Cb_Distance_Func >	Cb_Distance_FuncOP
typedef utility::pointer::shared_ptr < Cen_Distance_Func >	Cen_Distance_FuncOP
typedef utility::pointer::shared_ptr < CaCbCb_Angle_Func >	CaCbCb_Angle_FuncOP
typedef utility::pointer::shared_ptr < NCaCaC_Dihedral_Func >	NCaCaC_Dihedral_FuncOP
typedef utility::pointer::shared_ptr < CaCbCbCa_Dihedral_Func >	CaCbCbCa_Dihedral_FuncOP
typedef utility::pointer::shared_ptr < Cb_Distance_Func const >	Cb_Distance_FuncCOP
typedef utility::pointer::shared_ptr < Cen_Distance_Func const >	Cen_Distance_FuncCOP
typedef utility::pointer::shared_ptr < CaCbCb_Angle_Func const >	CaCbCb_Angle_FuncCOP
typedef utility::pointer::shared_ptr < NCaCaC_Dihedral_Func const >	NCaCaC_Dihedral_FuncCOP
typedef utility::pointer::shared_ptr < CaCbCbCa_Dihedral_Func const >	CaCbCbCa_Dihedral_FuncCOP
typedef utility::pointer::weak_ptr < Cb_Distance_Func >	Cb_Distance_FuncAP
typedef utility::pointer::weak_ptr < Cen_Distance_Func >	Cen_Distance_FuncAP
typedef utility::pointer::weak_ptr < CaCbCb_Angle_Func >	CaCbCb_Angle_FuncAP
typedef utility::pointer::weak_ptr < NCaCaC_Dihedral_Func >	NCaCaC_Dihedral_FuncAP
typedef utility::pointer::weak_ptr < CaCbCbCa_Dihedral_Func >	CaCbCbCa_Dihedral_FuncAP
typedef utility::pointer::weak_ptr < Cb_Distance_Func const >	Cb_Distance_FuncCAP
typedef utility::pointer::weak_ptr < Cen_Distance_Func const >	Cen_Distance_FuncCAP
typedef utility::pointer::weak_ptr < CaCbCb_Angle_Func const >	CaCbCb_Angle_FuncCAP
typedef utility::pointer::weak_ptr < NCaCaC_Dihedral_Func const >	NCaCaC_Dihedral_FuncCAP
typedef utility::pointer::weak_ptr < CaCbCbCa_Dihedral_Func const >	CaCbCbCa_Dihedral_FuncCAP
typedef utility::pointer::shared_ptr < DisulfideMatchingEnergyContainer >	DisulfideMatchingEnergyContainerOP
typedef utility::pointer::shared_ptr < DisulfideMatchingEnergyContainer const >	DisulfideMatchingEnergyContainerCOP
typedef utility::pointer::weak_ptr < DisulfideMatchingEnergyContainer >	DisulfideMatchingEnergyContainerAP
typedef utility::pointer::weak_ptr < DisulfideMatchingEnergyContainer const >	DisulfideMatchingEnergyContainerCAP
typedef utility::pointer::shared_ptr < DisulfideMatchingPotential >	DisulfideMatchingPotentialOP
typedef utility::pointer::shared_ptr < DisulfideMatchingPotential const >	DisulfideMatchingPotentialCOP
typedef utility::pointer::weak_ptr < DisulfideMatchingPotential >	DisulfideMatchingPotentialAP
typedef utility::pointer::weak_ptr < DisulfideMatchingPotential const >	DisulfideMatchingPotentialCAP
typedef utility::pointer::shared_ptr < FullatomDisulfideEnergyContainer >	FullatomDisulfideEnergyContainerOP
typedef utility::pointer::shared_ptr < FullatomDisulfideEnergyContainer const >	FullatomDisulfideEnergyContainerCOP
typedef utility::pointer::weak_ptr < FullatomDisulfideEnergyContainer >	FullatomDisulfideEnergyContainerAP
typedef utility::pointer::weak_ptr < FullatomDisulfideEnergyContainer const >	FullatomDisulfideEnergyContainerCAP
typedef utility::pointer::shared_ptr < FullatomDisulfidePotential >	FullatomDisulfidePotentialOP
typedef utility::pointer::shared_ptr < FullatomDisulfidePotential const >	FullatomDisulfidePotentialCOP
typedef utility::pointer::weak_ptr < FullatomDisulfidePotential >	FullatomDisulfidePotentialAP
typedef utility::pointer::weak_ptr < FullatomDisulfidePotential const >	FullatomDisulfidePotentialCAP
typedef utility::pointer::shared_ptr < CBSG_Dihedral_Func >	CBSG_Dihedral_FuncOP
typedef utility::pointer::shared_ptr < SGSG_Dihedral_Func >	SGSG_Dihedral_FuncOP
typedef utility::pointer::shared_ptr < CB_Angle_Func >	CB_Angle_FuncOP
typedef utility::pointer::shared_ptr < SG_Dist_Func >	SG_Dist_FuncOP

Enumerations
enum	DisulfideDerivativeAtom {   NO_DERIVATIVES_FOR_ATOM = 0, CYS_C_ALPHA, CYS_C_BETA, CYS_S_GAMMA,   CYS_CEN }

Functions
static basic::Tracer	TR ("core.scoring.disulfides.CentroidDisulfideEnergyContainer")
static HistogramCOP< Real, Real >::Type	histogram_from_db (string file)
	Helper function for initializing Histograms from the database. More...
static basic::Tracer	TR ("core.scoring.disulfides.DisulfideAtomIndices")
static basic::Tracer	TR ("core.scoring.disulfides.DisulfideMatchingEnergyContainer")

Typedef Documentation

typedef utility::pointer::weak_ptr< CaCbCb_Angle_Func > core::scoring::disulfides::CaCbCb_Angle_FuncAP

typedef utility::pointer::weak_ptr< CaCbCb_Angle_Func const > core::scoring::disulfides::CaCbCb_Angle_FuncCAP

typedef utility::pointer::shared_ptr< CaCbCb_Angle_Func const > core::scoring::disulfides::CaCbCb_Angle_FuncCOP

typedef utility::pointer::shared_ptr< CaCbCb_Angle_Func > core::scoring::disulfides::CaCbCb_Angle_FuncOP

typedef utility::pointer::weak_ptr< CaCbCbCa_Dihedral_Func > core::scoring::disulfides::CaCbCbCa_Dihedral_FuncAP

typedef utility::pointer::weak_ptr< CaCbCbCa_Dihedral_Func const > core::scoring::disulfides::CaCbCbCa_Dihedral_FuncCAP

typedef utility::pointer::shared_ptr< CaCbCbCa_Dihedral_Func const > core::scoring::disulfides::CaCbCbCa_Dihedral_FuncCOP

typedef utility::pointer::shared_ptr< CaCbCbCa_Dihedral_Func > core::scoring::disulfides::CaCbCbCa_Dihedral_FuncOP

typedef utility::pointer::shared_ptr< CB_Angle_Func > core::scoring::disulfides::CB_Angle_FuncOP

typedef utility::pointer::weak_ptr< Cb_Distance_Func > core::scoring::disulfides::Cb_Distance_FuncAP

typedef utility::pointer::weak_ptr< Cb_Distance_Func const > core::scoring::disulfides::Cb_Distance_FuncCAP

typedef utility::pointer::shared_ptr< Cb_Distance_Func const > core::scoring::disulfides::Cb_Distance_FuncCOP

typedef utility::pointer::shared_ptr< Cb_Distance_Func > core::scoring::disulfides::Cb_Distance_FuncOP

typedef utility::pointer::shared_ptr< CBSG_Dihedral_Func > core::scoring::disulfides::CBSG_Dihedral_FuncOP

typedef utility::pointer::weak_ptr< Cen_Distance_Func > core::scoring::disulfides::Cen_Distance_FuncAP

typedef utility::pointer::weak_ptr< Cen_Distance_Func const > core::scoring::disulfides::Cen_Distance_FuncCAP

typedef utility::pointer::shared_ptr< Cen_Distance_Func const > core::scoring::disulfides::Cen_Distance_FuncCOP

typedef utility::pointer::shared_ptr< Cen_Distance_Func > core::scoring::disulfides::Cen_Distance_FuncOP

typedef utility::pointer::weak_ptr< CentroidDisulfideEnergyContainer > core::scoring::disulfides::CentroidDisulfideEnergyContainerAP

typedef utility::pointer::weak_ptr< CentroidDisulfideEnergyContainer const > core::scoring::disulfides::CentroidDisulfideEnergyContainerCAP

typedef utility::pointer::shared_ptr< CentroidDisulfideEnergyContainer const > core::scoring::disulfides::CentroidDisulfideEnergyContainerCOP

typedef utility::pointer::shared_ptr< CentroidDisulfideEnergyContainer > core::scoring::disulfides::CentroidDisulfideEnergyContainerOP

typedef utility::pointer::weak_ptr< CentroidDisulfidePotential > core::scoring::disulfides::CentroidDisulfidePotentialAP

typedef utility::pointer::weak_ptr< CentroidDisulfidePotential const > core::scoring::disulfides::CentroidDisulfidePotentialCAP

typedef utility::pointer::shared_ptr< CentroidDisulfidePotential const > core::scoring::disulfides::CentroidDisulfidePotentialCOP

typedef utility::pointer::shared_ptr< CentroidDisulfidePotential > core::scoring::disulfides::CentroidDisulfidePotentialOP

typedef utility::pointer::weak_ptr< DisulfideMatchingEnergyContainer > core::scoring::disulfides::DisulfideMatchingEnergyContainerAP

typedef utility::pointer::weak_ptr< DisulfideMatchingEnergyContainer const > core::scoring::disulfides::DisulfideMatchingEnergyContainerCAP

typedef utility::pointer::shared_ptr< DisulfideMatchingEnergyContainer const > core::scoring::disulfides::DisulfideMatchingEnergyContainerCOP

typedef utility::pointer::shared_ptr< DisulfideMatchingEnergyContainer > core::scoring::disulfides::DisulfideMatchingEnergyContainerOP

typedef utility::pointer::weak_ptr< DisulfideMatchingPotential > core::scoring::disulfides::DisulfideMatchingPotentialAP

typedef utility::pointer::weak_ptr< DisulfideMatchingPotential const > core::scoring::disulfides::DisulfideMatchingPotentialCAP

typedef utility::pointer::shared_ptr< DisulfideMatchingPotential const > core::scoring::disulfides::DisulfideMatchingPotentialCOP

typedef utility::pointer::shared_ptr< DisulfideMatchingPotential > core::scoring::disulfides::DisulfideMatchingPotentialOP

typedef utility::pointer::weak_ptr< FullatomDisulfideEnergyContainer > core::scoring::disulfides::FullatomDisulfideEnergyContainerAP

typedef utility::pointer::weak_ptr< FullatomDisulfideEnergyContainer const > core::scoring::disulfides::FullatomDisulfideEnergyContainerCAP

typedef utility::pointer::shared_ptr< FullatomDisulfideEnergyContainer const > core::scoring::disulfides::FullatomDisulfideEnergyContainerCOP

typedef utility::pointer::shared_ptr< FullatomDisulfideEnergyContainer > core::scoring::disulfides::FullatomDisulfideEnergyContainerOP

typedef utility::pointer::weak_ptr< FullatomDisulfidePotential > core::scoring::disulfides::FullatomDisulfidePotentialAP

typedef utility::pointer::weak_ptr< FullatomDisulfidePotential const > core::scoring::disulfides::FullatomDisulfidePotentialCAP

typedef utility::pointer::shared_ptr< FullatomDisulfidePotential const > core::scoring::disulfides::FullatomDisulfidePotentialCOP

typedef utility::pointer::shared_ptr< FullatomDisulfidePotential > core::scoring::disulfides::FullatomDisulfidePotentialOP

typedef utility::pointer::weak_ptr< NCaCaC_Dihedral_Func > core::scoring::disulfides::NCaCaC_Dihedral_FuncAP

typedef utility::pointer::weak_ptr< NCaCaC_Dihedral_Func const > core::scoring::disulfides::NCaCaC_Dihedral_FuncCAP

typedef utility::pointer::shared_ptr< NCaCaC_Dihedral_Func const > core::scoring::disulfides::NCaCaC_Dihedral_FuncCOP

typedef utility::pointer::shared_ptr< NCaCaC_Dihedral_Func > core::scoring::disulfides::NCaCaC_Dihedral_FuncOP

typedef utility::pointer::shared_ptr< SG_Dist_Func > core::scoring::disulfides::SG_Dist_FuncOP

typedef utility::pointer::shared_ptr< SGSG_Dihedral_Func > core::scoring::disulfides::SGSG_Dihedral_FuncOP

Enumeration Type Documentation

enum core::scoring::disulfides::DisulfideDerivativeAtom

Enumerator
NO_DERIVATIVES_FOR_ATOM
CYS_C_ALPHA
CYS_C_BETA
CYS_S_GAMMA
CYS_CEN

Function Documentation

static HistogramCOP<Real,Real>::Type core::scoring::disulfides::histogram_from_db ( string  file )

static

Helper function for initializing Histograms from the database.

Note

The static functions in FullatomDisulfidePotential are a more elegant way to initialize the Histograms

Referenced by core::scoring::disulfides::Cen_Distance_Func::func(), core::scoring::disulfides::CaCbCb_Angle_Func::func(), core::scoring::disulfides::NCaCaC_Dihedral_Func::func(), and core::scoring::disulfides::CaCbCbCa_Dihedral_Func::func().

static basic::Tracer core::scoring::disulfides::TR ( "core.scoring.disulfides.DisulfideAtomIndices"  )

static

static basic::Tracer core::scoring::disulfides::TR ( "core.scoring.disulfides.DisulfideMatchingEnergyContainer"  )

static

static basic::Tracer core::scoring::disulfides::TR ( "core.scoring.disulfides.CentroidDisulfideEnergyContainer"  )

static

Referenced by core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), and core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides().