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Szybki TK -- C\#, v1.7.0
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Szybki Toolkit
ΒΆ
Front Matter
SZYBKI Theory
Force Field
Bond stretching
Angle bending
Stretch-bend interaction
Out-of-plane bending
Torsion interactions
Van der Waals interactions
Electrostatic interactions
Entropy evaluation
Configurational entropy
Solvation entropy
Protein-bound ligand entropy
OEConstr Classes
OEHarmonicPotential
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetPred
Get_dc
Get_kc
NumVar
Set
Set_dc
Set_kc
Setup
SetupConf
OEMolMMFF Classes
OEMMFF
Constructors
OEMMFF94sParams
CreateCopy
GetOutOfPlaneParams
GetTorsionParams
OEMMFFBend
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMMFFCoulomb
Constructors
operator=
operator()
ClearPredicates
GetDielectric
GetExponent
GetFComponents
GetInteractions
NumVar
Set
SetDielectric
SetExponent
Setup
OEMMFFInterCoulomb
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetGrid
NumVar
Set
Setup
OEMMFFInterVdw
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetMolecule
NumVar
Set
Setup
OEMMFFInterVdwNN
Constructors
operator=
operator()
ClearPredicates
GetFComponents
NumVar
Set
Setup
OEMMFFOutOfPlane
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMMFFParams
CreateCopy
GetAtomTypeIndex
GetAtomTypeName
GetBendParams
GetContactDistance
GetCoulombParams
GetEquilibriumAngle
GetEquilibriumBondLength
GetOutOfPlaneParams
GetStretchBendParams
GetStretchParams
GetTorsionParams
GetVdwParams
GetVdwRadius
PrepMol
OEMMFFStretch
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMMFFStretchBend
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMMFFSubsetVdw
Constructors
operator=
operator()
Set
SetCutoff
Setup
OEMMFFTorsion
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMMFFVdw
Constructors
operator=
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
OEMolMMFF Functions
OEMMFFCalcVdw
OEMolPotential Classes
OEFFParams
CreateCopy
GetAtomTypeIndex
GetAtomTypeName
GetBendParams
GetContactDistance
GetCoulombParams
GetEquilibriumAngle
GetEquilibriumBondLength
GetOutOfPlaneParams
GetStretchBendParams
GetStretchParams
GetTorsionParams
GetVdwParams
GetVdwRadius
PrepMol
OEForceField
operator()
Add
ClearPredicates
GetFComponents
NumVar
PrepMol
Remove
Set
Setup
OEGenericFF
Constructors
operator()
Add
ClearPredicates
GetFComponents
GetInteractions
NumVar
PrepMol
Remove
Set
Setup
SetupConf
OEInterAdaptor
Constructors
operator()
AdaptGrad
AdaptVar
ClearPredicates
GetFComponents
GetInteractions
GetMolFunc
GetVar
NumVar
Set
SetMolFunc
SetVerbose
Setup
OEInteractParams
operator[]
Clear
OEInteraction
Constructors
operator=
GetAtoms
GetName
GetValues
NumAtoms
NumValues
OEMolAdaptor
operator()
AdaptVar
GetFComponents
GetMolFunc
GetVar
NumVar
SetMolFunc
Setup
OEMolFunc
ClearPredicates
GetInteractions
Set
OEMolFunc0
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
SetupConf
OEMolFunc1
operator()
ClearPredicates
GetFComponents
GetInteractions
NumVar
Set
Setup
SetupConf
OEMolSetup
Setup
OEQuatAdaptor
Constructors
operator()
AdaptGrad
AdaptVar
ClearPredicates
GetFComponents
GetInteractions
GetMolFunc
GetRefCoord
GetVar
NumVar
Set
SetMolFunc
Setup
OESubsetAdaptor
Constructors
operator()
AdaptGrad
AdaptVar
ClearPredicates
GetFComponents
GetInteractions
GetMolFunc
GetVar
NumVar
Set
SetMolFunc
Setup
OETorAdaptor
Constructors
operator()
AdaptGrad
AdaptVar
ClearPredicates
GetFComponents
GetInteractions
GetMolFunc
GetVar
NumVar
Set
SetMolFunc
Setup
SetupConf
OETorQuatAdaptor
Constructors
operator()
AdaptGrad
AdaptVar
ClearPredicates
GetFComponents
GetInteractions
GetMolFunc
GetVar
NumVar
Set
SetMolFunc
Setup
OEMolPotential Constants
OEFFParam
OEVarType
OEOpt Classes
OEAdaptor
AdaptVar
GetVar
OEBFGSOpt
Constructors
operator=
operator()
GetHessianDimension
GetInverseHessian
GetKeepHessian
SetIterLimit
SetKeepHessian
SetLineMinimize
SetTolerance
UseSavedHessian
OECGLineMinimize
operator()
CreateCopy
OECheckpoint0
operator()
OECheckpoint1
operator()
OEConjGradOpt
Constructors
operator=
operator()
SetIterLimit
SetLineMinimize
SetTolerance
OEDFPOpt
Constructors
operator=
operator()
SetIterLimit
SetLineMinimize
SetTolerance
OEFComponent
Constructors
OEFletcherReevesOpt
Constructors
operator=
operator()
SetIterLimit
SetLineMinimize
SetTolerance
OEFunc0
Constructors
operator()
GetFComponents
NumVar
OEFunc1
operator()
GetFComponents
NumVar
OEFunc2
operator()
OEHestenesStiefelOpt
Constructors
operator=
operator()
SetIterLimit
SetLineMinimize
SetTolerance
OELineMinimize
operator()
SetMaxStep
CreateCopy
OEMaxStepLineMinimize
Constructors
operator=
operator()
CreateCopy
SetMaxStep
OENRLineSearch
SetMaxStep
operator()
CreateCopy
OEOptimizer0
operator()
SetIterLimit
OEOptimizer1
operator()
SetIterLimit
SetTolerance
OEQNLineMinimize
operator()
CreateCopy
OERibierePolakOpt
Constructors
operator=
operator()
SetIterLimit
SetLineMinimize
SetTolerance
OESteepestDescentOpt
Constructors
operator()
SetInitialStep
SetIterLimit
SetTolerance
OEOpt Functions
OEGetStateName
OESheff Classes
OESheffield
Constructors
operator=
operator()
ClearPredicates
GetDielectricDerivative
GetFComponents
GetParameters
NumVar
Set
SetCharges
SetRadii
SetSoluteDielectricConstant
SetSolventDielectricConstant
Set_A
Set_B
Setup
OESz Classes
OESzybki
Constructors
operator()
GetAtomicRadiiType
GetCalculateGradients
GetEntropy
GetEveryConfAM1BCCCharges
GetSolutionEntropy
GetProteinBoundLigandEntropy
GetSaltConcentration
GetProteinDielectric()
ClearFixAtoms
ClearHarmonicConstraints
FixAtoms
GetCalculateFrozenTerms
GetCavitySolventParameter
GetExactVdWProteinLigand
GetFixPattern
GetFixPredicate
GetForceFieldType
GetHarmonicConstraints
GetLigandRMSHeavy
GetOptimizerType
GetPolarHFlexibility
GetProtein
GetProteinDielectric
GetProteinElectrostaticModel
GetProteinVdWCutoff
GetRemoveAttractiveVdWForces
GetRemoveCoulombTerms
GetResidueFlexibility
GetRunType
GetSheffieldParameters
GetSideChainsFlexibility
GetSolventModel
GetUseCurrentCharges
GetVerbose
LoadPotentialGrid
SavePotentialGrid
SetAtomicRadii
SetCavitySolventParameter
SetCalculateFrozenTerms
SetCalculateGradients
SetEveryConfAM1BCCCharges
SetExactVdWProteinLigand
SetForceFieldType
SetHarmonicConstraints
SetLigandRMSDHeavy
SetOptCriteria
SetOptimizerType
SetPolarHFlexibility
SetProtein
SetProteinDielectric
SetSaltConcentration
SetSolventDielectric
SetProteinElectrostaticModel
SetProteinVdWCutoff
SetRemoveAttractiveVdWForces
SetRemoveCoulombTerms
SetResidueFlexibility
SetRunType
SetSheffieldParameters
SetSideChainsFlexibility
SetSolventModel
SetUseCurrentCharges
SetVerbose
UnsetProtein
OESzybkiResults
Constructors
operator=
GetCPUTime
GetConfIdx
GetEnergyTerm
GetFinalRMSGradient
GetGradients
GetFinalTotalPotential
GetIntramolecularLigandEnergy
GetInitialRMSGradient
GetInitialTotalPotential
GetInterEnergy
GetMaxDisplacement
GetNumCycles
GetNumFixAtoms
GetNumRotors
GetProteinRMSD
GetRMSD
GetTotalEnergy
IsActiveTerm
Print
OESz Constants
OEEntropyMethod
OEEnvType
OEForceFieldType
OEOptType
OEPotentialTerms
OEProteinElectrostatics
OERunType
OESolventModel
OEAtomicRadii
OESz Functions
OEGetEnergyTermName
OESzybkiGetArch
OESzybkiGetLicensee
OESzybkiGetPlatform
OESzybkiGetRelease
OESzybkiGetSite
OESzybkiGetVersion
OESzybkiIsLicensed
Release Notes
SzybkiTK 1.7.0
New features
Bug fixes
SzybkiTK 1.6.0
New features
Bug fixes
SzybkiTK 1.5.0
New features
Bug fixes
SzybkiTK 1.4.0
New features
Bug fixes
SzybkiTK 1.3.4
New features
Bug fixes
Bibliography
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Szybki TK -- C\#, v1.7.0
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