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core::scoring::disulfides Namespace Reference

Classes

class  CentroidDisulfideNeighborIterator
 An iterator over the disulfide bonds a residue forms. More...
 
class  CentroidDisulfideNeighborConstIterator
 Just a const version of CentroidDisulfideNeighborIterator. More...
 
class  CentroidDisulfideEnergyComponents
 Storage for Disulfide Energy Terms. More...
 
class  CentroidDisulfideEnergyContainer
 
class  CentroidDisulfidePotential
 
class  Cb_Distance_Func
 Score based on the distance between Cb. More...
 
class  Cen_Distance_Func
 
class  CaCbCb_Angle_Func
 
class  NCaCaC_Dihedral_Func
 
class  CaCbCbCa_Dihedral_Func
 
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  DisulfideMatchingNeighborIterator
 An iterator over the disulfide bonds a residue forms. More...
 
class  DisulfideMatchingNeighborConstIterator
 Just a const version of DisulfideMatchingNeighborIterator. More...
 
class  DisulfideMatchingEnergyComponents
 Storage for Disulfide Energy Terms. More...
 
class  DisulfideMatchingEnergyContainer
 
class  DisulfideMatchingPotential
 
class  RT_helper
 
class  DisulfResNeighbIterator
 
class  DisulfResNeighbConstIterator
 
class  FullatomDisulfideEnergyComponents
 
class  FullatomDisulfideEnergyContainer
 
struct  FullatomDisulfideParams13
 
class  FullatomDisulfidePotential
 
class  CBSG_Dihedral_Func
 
class  SGSG_Dihedral_Func
 
class  CB_Angle_Func
 
class  SG_Dist_Func
 

Typedefs

typedef utility::pointer::shared_ptr< CentroidDisulfideEnergyContainerCentroidDisulfideEnergyContainerOP
 
typedef utility::pointer::shared_ptr< CentroidDisulfideEnergyContainer const > CentroidDisulfideEnergyContainerCOP
 
typedef utility::pointer::weak_ptr< CentroidDisulfideEnergyContainerCentroidDisulfideEnergyContainerAP
 
typedef utility::pointer::weak_ptr< CentroidDisulfideEnergyContainer const > CentroidDisulfideEnergyContainerCAP
 
typedef utility::pointer::shared_ptr< CentroidDisulfidePotentialCentroidDisulfidePotentialOP
 
typedef utility::pointer::shared_ptr< CentroidDisulfidePotential const > CentroidDisulfidePotentialCOP
 
typedef utility::pointer::weak_ptr< CentroidDisulfidePotentialCentroidDisulfidePotentialAP
 
typedef utility::pointer::weak_ptr< CentroidDisulfidePotential const > CentroidDisulfidePotentialCAP
 
typedef utility::pointer::shared_ptr< Cb_Distance_FuncCb_Distance_FuncOP
 
typedef utility::pointer::shared_ptr< Cen_Distance_FuncCen_Distance_FuncOP
 
typedef utility::pointer::shared_ptr< CaCbCb_Angle_FuncCaCbCb_Angle_FuncOP
 
typedef utility::pointer::shared_ptr< NCaCaC_Dihedral_FuncNCaCaC_Dihedral_FuncOP
 
typedef utility::pointer::shared_ptr< CaCbCbCa_Dihedral_FuncCaCbCbCa_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_FuncCb_Distance_FuncAP
 
typedef utility::pointer::weak_ptr< Cen_Distance_FuncCen_Distance_FuncAP
 
typedef utility::pointer::weak_ptr< CaCbCb_Angle_FuncCaCbCb_Angle_FuncAP
 
typedef utility::pointer::weak_ptr< NCaCaC_Dihedral_FuncNCaCaC_Dihedral_FuncAP
 
typedef utility::pointer::weak_ptr< CaCbCbCa_Dihedral_FuncCaCbCbCa_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< DisulfideMatchingEnergyContainerDisulfideMatchingEnergyContainerOP
 
typedef utility::pointer::shared_ptr< DisulfideMatchingEnergyContainer const > DisulfideMatchingEnergyContainerCOP
 
typedef utility::pointer::weak_ptr< DisulfideMatchingEnergyContainerDisulfideMatchingEnergyContainerAP
 
typedef utility::pointer::weak_ptr< DisulfideMatchingEnergyContainer const > DisulfideMatchingEnergyContainerCAP
 
typedef utility::pointer::shared_ptr< DisulfideMatchingPotentialDisulfideMatchingPotentialOP
 
typedef utility::pointer::shared_ptr< DisulfideMatchingPotential const > DisulfideMatchingPotentialCOP
 
typedef utility::pointer::weak_ptr< DisulfideMatchingPotentialDisulfideMatchingPotentialAP
 
typedef utility::pointer::weak_ptr< DisulfideMatchingPotential const > DisulfideMatchingPotentialCAP
 
typedef utility::pointer::shared_ptr< FullatomDisulfideEnergyContainerFullatomDisulfideEnergyContainerOP
 
typedef utility::pointer::shared_ptr< FullatomDisulfideEnergyContainer const > FullatomDisulfideEnergyContainerCOP
 
typedef utility::pointer::weak_ptr< FullatomDisulfideEnergyContainerFullatomDisulfideEnergyContainerAP
 
typedef utility::pointer::weak_ptr< FullatomDisulfideEnergyContainer const > FullatomDisulfideEnergyContainerCAP
 
typedef utility::pointer::shared_ptr< FullatomDisulfidePotentialFullatomDisulfidePotentialOP
 
typedef utility::pointer::shared_ptr< FullatomDisulfidePotential const > FullatomDisulfidePotentialCOP
 
typedef utility::pointer::weak_ptr< FullatomDisulfidePotentialFullatomDisulfidePotentialAP
 
typedef utility::pointer::weak_ptr< FullatomDisulfidePotential const > FullatomDisulfidePotentialCAP
 
typedef utility::pointer::shared_ptr< CBSG_Dihedral_FuncCBSG_Dihedral_FuncOP
 
typedef utility::pointer::shared_ptr< SGSG_Dihedral_FuncSGSG_Dihedral_FuncOP
 
typedef utility::pointer::shared_ptr< CB_Angle_FuncCB_Angle_FuncOP
 
typedef utility::pointer::shared_ptr< SG_Dist_FuncSG_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")
 
static basic::Tracer TR ("core.scoring.disulfides.FullatomDisulfidePotential")
 

Typedef Documentation

◆ CaCbCb_Angle_FuncAP

◆ CaCbCb_Angle_FuncCAP

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

◆ CaCbCb_Angle_FuncCOP

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

◆ CaCbCb_Angle_FuncOP

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

◆ CaCbCbCa_Dihedral_FuncAP

◆ CaCbCbCa_Dihedral_FuncCAP

◆ CaCbCbCa_Dihedral_FuncCOP

◆ CaCbCbCa_Dihedral_FuncOP

◆ CB_Angle_FuncOP

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

◆ Cb_Distance_FuncAP

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

◆ Cb_Distance_FuncCAP

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

◆ Cb_Distance_FuncCOP

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

◆ Cb_Distance_FuncOP

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

◆ CBSG_Dihedral_FuncOP

◆ Cen_Distance_FuncAP

◆ Cen_Distance_FuncCAP

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

◆ Cen_Distance_FuncCOP

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

◆ Cen_Distance_FuncOP

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

◆ CentroidDisulfideEnergyContainerAP

◆ CentroidDisulfideEnergyContainerCAP

◆ CentroidDisulfideEnergyContainerCOP

◆ CentroidDisulfideEnergyContainerOP

◆ CentroidDisulfidePotentialAP

◆ CentroidDisulfidePotentialCAP

◆ CentroidDisulfidePotentialCOP

◆ CentroidDisulfidePotentialOP

◆ DisulfideMatchingEnergyContainerAP

◆ DisulfideMatchingEnergyContainerCAP

◆ DisulfideMatchingEnergyContainerCOP

◆ DisulfideMatchingEnergyContainerOP

◆ DisulfideMatchingPotentialAP

◆ DisulfideMatchingPotentialCAP

◆ DisulfideMatchingPotentialCOP

◆ DisulfideMatchingPotentialOP

◆ FullatomDisulfideEnergyContainerAP

◆ FullatomDisulfideEnergyContainerCAP

◆ FullatomDisulfideEnergyContainerCOP

◆ FullatomDisulfideEnergyContainerOP

◆ FullatomDisulfidePotentialAP

◆ FullatomDisulfidePotentialCAP

◆ FullatomDisulfidePotentialCOP

◆ FullatomDisulfidePotentialOP

◆ NCaCaC_Dihedral_FuncAP

◆ NCaCaC_Dihedral_FuncCAP

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

◆ NCaCaC_Dihedral_FuncCOP

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

◆ NCaCaC_Dihedral_FuncOP

◆ SG_Dist_FuncOP

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

◆ SGSG_Dihedral_FuncOP

Enumeration Type Documentation

◆ DisulfideDerivativeAtom

Enumerator
NO_DERIVATIVES_FOR_ATOM 
CYS_C_ALPHA 
CYS_C_BETA 
CYS_S_GAMMA 
CYS_CEN 

Function Documentation

◆ histogram_from_db()

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().

◆ TR() [1/4]

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

◆ TR() [2/4]

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

◆ TR() [3/4]

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

◆ TR() [4/4]

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