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	CentroidDisulfideEnergy
class	CentroidDisulfideEnergyComponents
	Storage for Disulfide Energy Terms. More...
class	CentroidDisulfideEnergyContainer
class	CentroidDisulfideEnergyCreator
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	DisulfideMatchingEnergy
class	DisulfideMatchingEnergyComponents
	Storage for Disulfide Energy Terms. More...
class	DisulfideMatchingEnergyContainer
class	DisulfideMatchingEnergyCreator
class	DisulfideMatchingNeighborConstIterator
	Just a const version of DisulfideMatchingNeighborIterator. More...
class	DisulfideMatchingNeighborIterator
	An iterator over the disulfide bonds a residue forms. More...
class	DisulfideMatchingPotential
class	DisulfMinData
class	DisulfResNeighbConstIterator
class	DisulfResNeighbIterator
class	FullatomDisulfideEnergy
class	FullatomDisulfideEnergyComponents
class	FullatomDisulfideEnergyContainer
class	FullatomDisulfideEnergyCreator
struct	FullatomDisulfideParams13
class	FullatomDisulfidePotential
class	NCaCaC_Dihedral_Func
class	RT_helper
class	SG_Dist_Func
class	SGSG_Dihedral_Func

Typedefs
typedef utility::pointer::owning_ptr < CentroidDisulfideEnergy >	CentroidDisulfideEnergyOP
typedef utility::pointer::owning_ptr < CentroidDisulfideEnergy const >	CentroidDisulfideEnergyCOP
typedef utility::pointer::owning_ptr < CentroidDisulfideEnergyContainer >	CentroidDisulfideEnergyContainerOP
typedef utility::pointer::owning_ptr < CentroidDisulfideEnergyContainer const >	CentroidDisulfideEnergyContainerCOP
typedef utility::pointer::access_ptr < CentroidDisulfideEnergyContainer >	CentroidDisulfideEnergyContainerAP
typedef utility::pointer::access_ptr < CentroidDisulfideEnergyContainer const >	CentroidDisulfideEnergyContainerCAP
typedef utility::pointer::owning_ptr < CentroidDisulfidePotential >	CentroidDisulfidePotentialOP
typedef utility::pointer::owning_ptr < CentroidDisulfidePotential const >	CentroidDisulfidePotentialCOP
typedef utility::pointer::access_ptr < CentroidDisulfidePotential >	CentroidDisulfidePotentialAP
typedef utility::pointer::access_ptr < CentroidDisulfidePotential const >	CentroidDisulfidePotentialCAP
typedef utility::pointer::owning_ptr < Cb_Distance_Func >	Cb_Distance_FuncOP
typedef utility::pointer::owning_ptr < Cen_Distance_Func >	Cen_Distance_FuncOP
typedef utility::pointer::owning_ptr < CaCbCb_Angle_Func >	CaCbCb_Angle_FuncOP
typedef utility::pointer::owning_ptr < NCaCaC_Dihedral_Func >	NCaCaC_Dihedral_FuncOP
typedef utility::pointer::owning_ptr < CaCbCbCa_Dihedral_Func >	CaCbCbCa_Dihedral_FuncOP
typedef utility::pointer::owning_ptr < Cb_Distance_Func const >	Cb_Distance_FuncCOP
typedef utility::pointer::owning_ptr < Cen_Distance_Func const >	Cen_Distance_FuncCOP
typedef utility::pointer::owning_ptr < CaCbCb_Angle_Func const >	CaCbCb_Angle_FuncCOP
typedef utility::pointer::owning_ptr < NCaCaC_Dihedral_Func const >	NCaCaC_Dihedral_FuncCOP
typedef utility::pointer::owning_ptr < CaCbCbCa_Dihedral_Func const >	CaCbCbCa_Dihedral_FuncCOP
typedef utility::pointer::access_ptr < Cb_Distance_Func >	Cb_Distance_FuncAP
typedef utility::pointer::access_ptr < Cen_Distance_Func >	Cen_Distance_FuncAP
typedef utility::pointer::access_ptr < CaCbCb_Angle_Func >	CaCbCb_Angle_FuncAP
typedef utility::pointer::access_ptr < NCaCaC_Dihedral_Func >	NCaCaC_Dihedral_FuncAP
typedef utility::pointer::access_ptr < CaCbCbCa_Dihedral_Func >	CaCbCbCa_Dihedral_FuncAP
typedef utility::pointer::access_ptr < Cb_Distance_Func const >	Cb_Distance_FuncCAP
typedef utility::pointer::access_ptr < Cen_Distance_Func const >	Cen_Distance_FuncCAP
typedef utility::pointer::access_ptr < CaCbCb_Angle_Func const >	CaCbCb_Angle_FuncCAP
typedef utility::pointer::access_ptr < NCaCaC_Dihedral_Func const >	NCaCaC_Dihedral_FuncCAP
typedef utility::pointer::access_ptr < CaCbCbCa_Dihedral_Func const >	CaCbCbCa_Dihedral_FuncCAP
typedef utility::pointer::owning_ptr < DisulfideMatchingEnergy >	DisulfideMatchingEnergyOP
typedef utility::pointer::owning_ptr < DisulfideMatchingEnergy const >	DisulfideMatchingEnergyCOP
typedef utility::pointer::owning_ptr < DisulfideMatchingEnergyContainer >	DisulfideMatchingEnergyContainerOP
typedef utility::pointer::owning_ptr < DisulfideMatchingEnergyContainer const >	DisulfideMatchingEnergyContainerCOP
typedef utility::pointer::access_ptr < DisulfideMatchingEnergyContainer >	DisulfideMatchingEnergyContainerAP
typedef utility::pointer::access_ptr < DisulfideMatchingEnergyContainer const >	DisulfideMatchingEnergyContainerCAP
typedef utility::pointer::owning_ptr < DisulfideMatchingPotential >	DisulfideMatchingPotentialOP
typedef utility::pointer::owning_ptr < DisulfideMatchingPotential const >	DisulfideMatchingPotentialCOP
typedef utility::pointer::access_ptr < DisulfideMatchingPotential >	DisulfideMatchingPotentialAP
typedef utility::pointer::access_ptr < DisulfideMatchingPotential const >	DisulfideMatchingPotentialCAP
typedef utility::pointer::owning_ptr < DisulfMinData >	DisulfMinDataOP
typedef utility::pointer::owning_ptr < DisulfMinData const >	DisulfMinDataCOP
typedef utility::pointer::owning_ptr < FullatomDisulfideEnergy >	FullatomDisulfideEnergyOP
typedef utility::pointer::owning_ptr < FullatomDisulfideEnergy const >	FullatomDisulfideEnergyCOP
typedef utility::pointer::owning_ptr < FullatomDisulfideEnergyContainer >	FullatomDisulfideEnergyContainerOP
typedef utility::pointer::owning_ptr < FullatomDisulfideEnergyContainer const >	FullatomDisulfideEnergyContainerCOP
typedef utility::pointer::access_ptr < FullatomDisulfideEnergyContainer >	FullatomDisulfideEnergyContainerAP
typedef utility::pointer::access_ptr < FullatomDisulfideEnergyContainer const >	FullatomDisulfideEnergyContainerCAP
typedef utility::pointer::owning_ptr < FullatomDisulfidePotential >	FullatomDisulfidePotentialOP
typedef utility::pointer::owning_ptr < FullatomDisulfidePotential const >	FullatomDisulfidePotentialCOP
typedef utility::pointer::access_ptr < FullatomDisulfidePotential >	FullatomDisulfidePotentialAP
typedef utility::pointer::access_ptr < FullatomDisulfidePotential const >	FullatomDisulfidePotentialCAP
typedef utility::pointer::owning_ptr < CBSG_Dihedral_Func >	CBSG_Dihedral_FuncOP
typedef utility::pointer::owning_ptr < SGSG_Dihedral_Func >	SGSG_Dihedral_FuncOP
typedef utility::pointer::owning_ptr < CB_Angle_Func >	CB_Angle_FuncOP
typedef utility::pointer::owning_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 HistogramCOP< Real, Real >::Type	histogram_from_db (string file)
	Helper function for initializing Histograms from the database. More...

Variables
static basic::Tracer	TR ("core.scoring.disulfides.CentroidDisulfideEnergy")
static basic::Tracer	TR ("core.scoring.disulfides.CentroidDisulfideEnergyContainer")
static basic::Tracer	TR ("core.scoring.disulfides.DisulfideMatchingEnergy")
static basic::Tracer	TR ("core.scoring.disulfides.DisulfideMatchingEnergyContainer")

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< CentroidDisulfideEnergy const > core::scoring::disulfides::CentroidDisulfideEnergyCOP

typedef utility::pointer::owning_ptr< CentroidDisulfideEnergy > core::scoring::disulfides::CentroidDisulfideEnergyOP

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< DisulfideMatchingEnergy const > core::scoring::disulfides::DisulfideMatchingEnergyCOP

typedef utility::pointer::owning_ptr< DisulfideMatchingEnergy > core::scoring::disulfides::DisulfideMatchingEnergyOP

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

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

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

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

typedef utility::pointer::owning_ptr< DisulfMinData const > core::scoring::disulfides::DisulfMinDataCOP

typedef utility::pointer::owning_ptr< DisulfMinData > core::scoring::disulfides::DisulfMinDataOP

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

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

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

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

typedef utility::pointer::owning_ptr< FullatomDisulfideEnergy const > core::scoring::disulfides::FullatomDisulfideEnergyCOP

typedef utility::pointer::owning_ptr< FullatomDisulfideEnergy > core::scoring::disulfides::FullatomDisulfideEnergyOP

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_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

References utility::io::izstream::close(), and basic::database::open().

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().

Variable Documentation

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

static

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

static

basic::Tracer core::scoring::disulfides::TR("core.scoring.disulfides.DisulfideMatchingEnergy")

static

basic::Tracer core::scoring::disulfides::TR("core.scoring.disulfides.CentroidDisulfideEnergy")

static

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