Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
core::scoring::disulfides Namespace Reference

Classes

class  CentroidDisulfideEnergy
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  CentroidDisulfideEnergyCreator
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  DisulfideMatchingEnergy
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  DisulfideMatchingEnergyCreator
class  DisulfideMatchingPotential
class  RT_helper
class  DisulfMinData
class  FullatomDisulfideEnergy
class  DisulfResNeighbIterator
class  DisulfResNeighbConstIterator
class  FullatomDisulfideEnergyComponents
class  FullatomDisulfideEnergyContainer
class  FullatomDisulfideEnergyCreator
class  FullatomDisulfidePotential
class  CBSG_Dihedral_Func
class  SGSG_Dihedral_Func
class  CB_Angle_Func
class  SG_Dist_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 basic::Tracer TR ("core.scoring.disulfides.CentroidDisulfideEnergy")
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.
static basic::Tracer TR ("core.scoring.disulfides.DisulfideMatchingEnergy")
static basic::Tracer TR ("core.scoring.disulfides.DisulfideMatchingEnergyContainer")

Typedef Documentation


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

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