ZAP
Electrostatics at OpenEye
Java Programming Manual
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Front Matter
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ZAP Electrostatics at OpenEye
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1 Theory Manual
Contents
1 Theory Manual
1. The What of ZAP
2. The Why of ZAP
3. The Way of ZAP
3.1 Partial Charges and Atomic Radii
3.2 Get a Grid
3.3 Atom Potentials
3.4 Solvation Energies: PBSA
3.5 Binding Energies
3.6 Focussing
3.7 Gradients/Forces
3.8 Electrostatic Similarity
2 API
4. OEZap Classes
4.1 OEArea
4.1.1 Constructors
4.1.2 operator=
4.1.3 GetArea
4.1.4 GetMethod
4.1.5 GetUseHydrogens
4.1.6 SetMethod
4.1.7 SetUseHydrogens
4.2 OEBind
4.2.1 Constructors
4.2.2 operator=
4.2.3 Bind
4.2.4 GetZap
4.2.5 SetProtein
4.2.6 SetZap
4.2.7 SimpleBind
4.3 OEBindResults
4.3.1 Constructors
4.3.2 operator=
4.3.3 GetAnalyticCoulombicBindingEnergy
4.3.4 GetBoundLigandCoulombEnergy
4.3.5 GetBoundProteinCoulombEnergy
4.3.6 GetComplexCoulombEnergy
4.3.7 GetCoulombEnergy
4.3.8 GetDesolvationEnergy
4.3.9 GetLigandDesolvationEnergy
4.3.10 GetProteinDesolvationEnergy
4.3.11 GetUnboundLigandCoulombEnergy
4.3.12 GetUnboundProteinCoulombEnergy
4.3.13 Print
4.4 OEET
4.4.1 Constructors
4.4.2 operator=
4.4.3 GetDielectric
4.4.4 GetGridBuffer
4.4.5 GetGridSpacing
4.4.6 GetInnerMask
4.4.7 GetJoin
4.4.8 GetOuterMask
4.4.9 GetSaltConcentration
4.4.10 SetDielectric
4.4.11 SetGridBuffer
4.4.12 SetGridSpacing
4.4.13 SetInnerMask
4.4.14 SetJoin
4.4.15 SetOuterMask
4.4.16 SetRefMol
4.4.17 SetSaltConcentration
4.4.18 Tanimoto
4.5 OESimpleBindResults
4.5.1 Constructors
4.5.2 operator=
4.5.3 GetBindingEnergy
4.5.4 GetBoundLigandArea
4.5.5 GetBoundLigandAreaEnergy
4.5.6 GetBoundLigandZapEnergy
4.5.7 GetBoundProteinArea
4.5.8 GetBoundProteinAreaEnergy
4.5.9 GetBoundProteinZapEnergy
4.5.10 GetBuriedArea
4.5.11 GetBuriedAreaEnergy
4.5.12 GetComplexArea
4.5.13 GetComplexAreaEnergy
4.5.14 GetComplexZapEnergy
4.5.15 GetConf
4.5.16 GetUnboundLigandArea
4.5.17 GetUnboundLigandAreaEnergy
4.5.18 GetUnboundLigandZapEnergy
4.5.19 GetUnboundProteinArea
4.5.20 GetUnboundProteinAreaEnergy
4.5.21 GetUnboundProteinZapEnergy
4.5.22 GetZapEnergy
4.5.23 Print
4.6 OEZap
4.6.1 Constructors
4.6.2 operator=
4.6.3 CalcAtomPotentials
4.6.4 CalcForces
4.6.5 CalcPotentialGrid
4.6.6 CalcSolvationEnergy
4.6.7 ClearFocusTarget
4.6.8 GetBoundarySpacing
4.6.9 GetDielectricModel
4.6.10 GetFocusTarget
4.6.11 GetGridSpacing
4.6.12 GetInnerDielectric
4.6.13 GetIterations
4.6.14 GetMolecule
4.6.15 GetOuterDielectric
4.6.16 GetProbeRadius
4.6.17 GetSaltConcentration
4.6.18 IsFocusTargetSet
4.6.19 SetBoundarySpacing
4.6.20 SetDielectricModel
4.6.21 SetFocusTarget
4.6.22 SetGridSpacing
4.6.23 SetInnerDielectric
4.6.24 SetIterations
4.6.25 SetMolecule
4.6.26 SetOuterDielectric
4.6.27 SetProbeRadius
4.6.28 SetSaltConcentration
5. OEZap Functions
5.1 OECalculateCoulombicBinding
5.2 OECoulombicAtomPotentials
5.3 OECoulombicSelfEnergy
5.4 OEMakeETGrid
5.5 OEZapBind
5.6 OEZapGetRelease
5.7 OEZapGetVersion
5.8 OEZapIsLicensed
6. Release Notes
6.1 Zap 2.1.0
6.1.1 Bug fixes
6.1.2 New features
6.2 Zap 2.0.0
Index
ZAP
Electrostatics at OpenEye
Java Programming Manual
Previous:
Front Matter
Up:
ZAP Electrostatics at OpenEye
Next:
1 Theory Manual
Documentation released on June 4, 2008.
