Shape Toolkit Java Programming Manual

Previous: Front Matter Up: Shape Toolkit Java Programming Next: 1 OEShape Programming Manual

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Contents

• 1 OEShape Programming Manual
  • 1. Introduction
    • 1.1 History
  • 2. Theory
    • 2.1 Molecular Shape
    • 2.2 Shape Characteristics and the Use of Gaussians
  • 3. Calculating simple overlap
    • 3.1 Overlap methods
    • 3.2 Radii approximations
    • 3.3 Using hydrogens
    • 3.4 Adding scores to molecules using SD data
  • 4. Color overlap
    • 4.1 Overlap of color atoms
    • 4.2 Using built-in color force fields
    • 4.3 OEColorForceField
      • 4.3.1 User-defined interactions
      • 4.3.2 Writing color force field files (CFF)
  • 5. Best Overlay
    • 5.1 Starting positions for optimization
    • 5.2 Ways to deal with OEBestOverlay results
    • 5.3 Saving aligned structures
    • 5.4 Using color along with shape
  • 6. Calculating shape characteristics
• 2 OEShape API
  • 7. Classes
    • 7.1 OEBestOverlay
      • 7.1.1 Constructors
      • 7.1.2 operator=
      • 7.1.3 ClearColorForceField
      • 7.1.4 GetAllColor
      • 7.1.5 GetCarbonRadius
      • 7.1.6 GetInertialAxialDivisions
      • 7.1.7 GetInitialOrientation
      • 7.1.8 GetMaxRandomTranslation
      • 7.1.9 GetMethod
      • 7.1.10 GetMinimizeType
      • 7.1.11 GetNumRandomStarts
      • 7.1.12 GetRadiiApproximation
      • 7.1.13 GetRandomSeed
      • 7.1.14 GetRefGrid
      • 7.1.15 GetRefMol
      • 7.1.16 GetRefSelfColor
      • 7.1.17 GetRefSymmetry
      • 7.1.18 GetRepresentationLevel
      • 7.1.19 GetSymmetryThreshold
      • 7.1.20 GetUseHydrogens
      • 7.1.21 Overlay
      • 7.1.22 SetAllColor
      • 7.1.23 SetCarbonRadius
      • 7.1.24 SetColorForceField
      • 7.1.25 SetColorOptimize
      • 7.1.26 SetInertialAxialDivisions
      • 7.1.27 SetInitialOrientation
      • 7.1.28 SetMaxRandomTranslation
      • 7.1.29 SetMethod
      • 7.1.30 SetMinimizeType
      • 7.1.31 SetNumRandomStarts
      • 7.1.32 SetRadiiApproximation
      • 7.1.33 SetRandomSeed
      • 7.1.34 SetRefGrid
      • 7.1.35 SetRefMol
      • 7.1.36 SetRepresentationLevel
      • 7.1.37 SetSymmetryThreshold
      • 7.1.38 SetUseHydrogens
    • 7.2 OEBestOverlayResults
      • 7.2.1 Constructors
      • 7.2.2 operator=
      • 7.2.3 AddScore
      • 7.2.4 Clear
      • 7.2.5 GetScores
    • 7.3 OEBestOverlayScore
      • 7.3.1 Constructors
      • 7.3.2 GetColorTanimoto
      • 7.3.3 GetColorTversky
      • 7.3.4 GetComboScore
      • 7.3.5 GetTanimotoCombo
      • 7.3.6 GetFitColorTversky
      • 7.3.7 GetFitTversky
      • 7.3.8 GetFitTverskyCombo
      • 7.3.9 GetRefColorTversky
      • 7.3.10 GetRefTversky
      • 7.3.11 GetRefTverskyCombo
      • 7.3.12 GetTversky
      • 7.3.13 Transform
    • 7.4 OEColorForceField
      • 7.4.1 Constructors
      • 7.4.2 operator=
      • 7.4.3 AddColorer
      • 7.4.4 AddInteraction
      • 7.4.5 AddType
      • 7.4.6 Clear
      • 7.4.7 ClearInteractions
      • 7.4.8 GetTitle
      • 7.4.9 GetType
      • 7.4.10 GetTypeName
      • 7.4.11 Init
      • 7.4.12 Ready
      • 7.4.13 SetTitle
      • 7.4.14 Write
    • 7.5 OEColorOverlap
      • 7.5.1 Constructors
      • 7.5.2 operator=
      • 7.5.3 ColorScore
      • 7.5.4 GetAllColor
      • 7.5.5 GetSelfColor
      • 7.5.6 SetAllColor
      • 7.5.7 SetColorForceField
      • 7.5.8 SetFitMol
      • 7.5.9 SetRefMol
    • 7.6 OEColorResults
      • 7.6.1 Constructors
      • 7.6.2 GetFitTversky
      • 7.6.3 GetRefTversky
      • 7.6.4 GetTanimoto
      • 7.6.5 GetTversky
    • 7.7 OEHighestColorTanimoto
    • 7.8 OEHighestComboScore
    • 7.9 OEHighestFitColorTversky
    • 7.10 OEHighestFitTversky
    • 7.11 OEHighestFitTverskyCombo
    • 7.12 OEHighestOverlap
    • 7.13 OEHighestRefColorTversky
    • 7.14 OEHighestRefTversky
    • 7.15 OEHighestRefTverskyCombo
    • 7.16 OEHighestScaledColor
    • 7.17 OEHighestTanimoto
    • 7.18 OEHighestTanimotoCombo
    • 7.19 OEOverlap
      • 7.19.1 Constructors
      • 7.19.2 operator=
      • 7.19.3 GetCarbonRadius
      • 7.19.4 GetHandle
      • 7.19.5 GetMethod
      • 7.19.6 GetRadiiApproximation
      • 7.19.7 GetRepresentationLevel
      • 7.19.8 GetUseHydrogens
      • 7.19.9 Overlap
      • 7.19.10 SetCarbonRadius
      • 7.19.11 SetFitGrid
      • 7.19.12 SetFitMol
      • 7.19.13 SetMethod
      • 7.19.14 SetRadiiApproximation
      • 7.19.15 SetRefGrid
      • 7.19.16 SetRefMol
      • 7.19.17 SetRepresentationLevel
      • 7.19.18 SetUseHydrogens
    • 7.20 OEOverlapResults
      • 7.20.1 Constructors
      • 7.20.2 GetFitTversky
      • 7.20.3 GetRefTversky
      • 7.20.4 GetTversky
  • 8. OEShape Functions
    • 8.1 OEAddColorAtoms
    • 8.2 OECalcShapeMultipoles
    • 8.3 OECalcVolume
    • 8.4 OECountColorAtoms
    • 8.5 OEHasColorAtoms
    • 8.6 OERemoveColorAtoms
    • 8.7 OESelfColor
    • 8.8 OEShapeGetRelease
    • 8.9 OEShapeGetPlatform
    • 8.10 OEShapeGetVersion
    • 8.11 OEShapeIsLicensed
    • 8.12 OESortOverlayScores
  • 9. OEShape Namespaces
    • 9.1 OEBOMinType
    • 9.2 OEBOOrientation
    • 9.3 OEColorFFType
    • 9.4 OEOverlapMethod
    • 9.5 OEOverlapRadii
    • 9.6 OEOverlapRepresentation
  • A. Bibliography
• Index

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				Shape Toolkit Java Programming Manual

Previous: Front Matter Up: Shape Toolkit Java Programming Next: 1 OEShape Programming Manual

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Documentation released on June 4, 2008.