OESpicoli Toolkit: Generation, Manipulation, and Comparison of Surfaces

Previous: Front Matter Up: OESpicoli Toolkit: Generation, Manipulation, Next: List of Figures

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Contents

• List of Figures
• 1. Introduction
  • 1.1 How to Read this Manual
  • 1.2 What You Should Already Know
  • 1.3 History
• 2. Theory
  • 2.1 Surfaces
    • 2.1.1 Vertices
    • 2.1.2 Triangles
    • 2.1.3 Normal Vectors
    • 2.1.4 Specific Data
    • 2.1.5 Associative Data
  • 2.2 Generation of Surfaces
    • 2.2.1 Accessible vs Molecular
    • 2.2.2 Grids
    • 2.2.3 Subsets
  • 2.3 Manipulation
    • 2.3.1 Cliques
    • 2.3.2 Grids
  • 2.4 Storage
    • 2.4.1 Formats
    • 2.4.2 Attached to Molecules
• 3. Examples
  • 3.1 Molecular Volume Overlap
  • 3.2 Polar Surface Area
  • 3.3 Largest Hydrophobic Patch
• 4. OESpicoli Classes
  • 4.1 OESurface
    • 4.1.1 Constructors
    • 4.1.2 operator bool
    • 4.1.3 operator+=
    • 4.1.4 operator=
    • 4.1.5 Clear
    • 4.1.6 ClearVertexClique
    • 4.1.7 CreateCopy
    • 4.1.8 GetAtoms
    • 4.1.9 GetAtomsElement
    • 4.1.10 GetColor
    • 4.1.11 GetColorElement
    • 4.1.12 GetCurvature
    • 4.1.13 GetCurvatureElement
    • 4.1.14 GetDataType
    • 4.1.15 GetDistance
    • 4.1.16 GetDistanceElement
    • 4.1.17 GetFaceNormals
    • 4.1.18 GetFaceNormalsElement
    • 4.1.19 GetNormals
    • 4.1.20 GetNormalsElement
    • 4.1.21 GetNumTriangles
    • 4.1.22 GetNumVertices
    • 4.1.23 GetPotential
    • 4.1.24 GetPotentialElement
    • 4.1.25 GetPotentialName
    • 4.1.26 GetResolution
    • 4.1.27 GetTitle
    • 4.1.28 GetTriangles
    • 4.1.29 GetTrianglesElement
    • 4.1.30 GetVertexClique
    • 4.1.31 GetVertexCliqueElement
    • 4.1.32 GetVertices
    • 4.1.33 GetVerticesElement
    • 4.1.34 IsAtomsSet
    • 4.1.35 IsColorSet
    • 4.1.36 IsCurvatureSet
    • 4.1.37 IsDataType
    • 4.1.38 IsDistanceSet
    • 4.1.39 IsFaceNormalsSet
    • 4.1.40 IsNormalsSet
    • 4.1.41 IsPotentialSet
    • 4.1.42 IsVertexCliqueSet
    • 4.1.43 SetAtoms
    • 4.1.44 SetAtomsElement
    • 4.1.45 SetColor
    • 4.1.46 SetColorElement
    • 4.1.47 SetCurvature
    • 4.1.48 SetCurvatureElement
    • 4.1.49 SetDistance
    • 4.1.50 SetDistanceElement
    • 4.1.51 SetFaceNormals
    • 4.1.52 SetFaceNormalsElement
    • 4.1.53 SetNormals
    • 4.1.54 SetNormalsElement
    • 4.1.55 SetNumTriangles
    • 4.1.56 SetNumVertices
    • 4.1.57 SetPotential
    • 4.1.58 SetPotentialElement
    • 4.1.59 SetPotentialName
    • 4.1.60 SetTitle
    • 4.1.61 SetTriangles
    • 4.1.62 SetTrianglesElement
    • 4.1.63 SetVertexClique
    • 4.1.64 SetVertexCliqueElement
    • 4.1.65 SetVertices
    • 4.1.66 SetVerticesElement
  • 4.2 Implementation Classes
• 5. OESpicoli Functions
  • 5.1 OEAddSurfaces
  • 5.2 OECalculateFaceNormals
  • 5.3 OECalculateNormals
  • 5.4 OECalculateSurfaceCurvature
  • 5.5 OECalculateTriangleAreas
  • 5.6 OEGetCenterAndExtents
  • 5.7 OEGetSurfaceFileType
  • 5.8 OEGetSurfaceFormatExtension
  • 5.9 OEGetSurfaceFormatString
  • 5.10 OEInitSurfaceHandlers
  • 5.11 OEInvertSurface
  • 5.12 OEIsReadableSurface
  • 5.13 OEIsWriteableSurface
  • 5.14 OEMakeAccessibleSurface
  • 5.15 OEMakeBoxSurface
  • 5.16 OEMakeCavitySurfaces
  • 5.17 OEMakeCliqueSurface
  • 5.18 OEMakeComplexCavities
  • 5.19 OEMakeConnectedSurfaceCliques
  • 5.20 OEMakeEllipsoidSurface
  • 5.21 OEMakeGridFromSurface
  • 5.22 OEMakeMolecularSurface
  • 5.23 OEMakeSphericalSurface
  • 5.24 OEMakeSurfaceFromGrid
  • 5.25 OEMakeVoidVolume
  • 5.26 OEReadSurface
  • 5.27 OESetSurfaceColor
  • 5.28 OESetSurfacePotentials
  • 5.29 OESpicoliGetPlatform
  • 5.30 OESpicoliGetRelease
  • 5.31 OESpicoliGetVersion
  • 5.32 OESpicoliIsLicensed
  • 5.33 OESurfaceArea
  • 5.34 OESurfaceCliqueArea
  • 5.35 OESurfaceCliqueCentroid
  • 5.36 OESurfaceCliqueVolume
  • 5.37 OESurfaceCropToClique
  • 5.38 OESurfaceIsOpen
  • 5.39 OESurfaceToMoleculeDistance
  • 5.40 OESurfaceVolume
  • 5.41 OEWriteSurface
• 6. OESpicoli Namespaces
  • 6.1 OEVoxelizeMethod
  • 6.2 OESurfaceFileType
• 7. Release Notes
  • 7.1 OESpicoli 1.0.1
    • 7.1.1 Bug fixes
  • 7.2 OESpicoli 1.0
• Bibliography
• Index

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				OESpicoli Toolkit: Generation, Manipulation, and Comparison of Surfaces

Previous: Front Matter Up: OESpicoli Toolkit: Generation, Manipulation, Next: List of Figures

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Documentation released on June 4, 2008.