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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::shared_ptr
< CentroidDisulfideEnergy
CentroidDisulfideEnergyOP
 
typedef
utility::pointer::shared_ptr
< CentroidDisulfideEnergy
const > 
CentroidDisulfideEnergyCOP
 
typedef
utility::pointer::shared_ptr
< DisulfideMatchingEnergy
DisulfideMatchingEnergyOP
 
typedef
utility::pointer::shared_ptr
< DisulfideMatchingEnergy
const > 
DisulfideMatchingEnergyCOP
 
using DisulfMinDataOP = utility::pointer::shared_ptr< DisulfMinData >
 
using DisulfMinDataCOP = utility::pointer::shared_ptr< const DisulfMinData >
 
typedef
utility::pointer::shared_ptr
< FullatomDisulfideEnergy
FullatomDisulfideEnergyOP
 
typedef
utility::pointer::shared_ptr
< FullatomDisulfideEnergy
const > 
FullatomDisulfideEnergyCOP
 
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.CentroidDisulfideEnergy")
 
static basic::Tracer TR ("core.scoring.disulfides.DisulfideMatchingEnergy")
 
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 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::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::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
using core::scoring::disulfides::DisulfMinDataCOP = typedef utility::pointer::shared_ptr<const DisulfMinData>
using core::scoring::disulfides::DisulfMinDataOP = typedef utility::pointer::shared_ptr<DisulfMinData>
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< SG_Dist_Func > core::scoring::disulfides::SG_Dist_FuncOP

Enumeration Type Documentation

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