Getting Started
Front Matter
Introduction
Prerequisites
Licensing
Download the OpenEye Java distribution
Installation
Using Apache Maven with OpenEye
Using Eclipse
Creating an Example on the command line
Creating a custom oejava jar file
How to import the toolkits
Release Notes
Release Highlights 2018.Oct
Detailed Release Notes
Previous Release Highlights
Toolkit API
Release Cycle
OEChem Toolkit
Introduction
OEChem Theory
OESystem Theory
OEBio Theory
OEGrid Theory
Examples
OEChem API
OESystem API
OEPlatform API
OEMath API
OEBio API
Release Notes
Glossary and Bibliography
Indices and tables
OEDepict Toolkit
Introduction
Theory
Examples
Appendices
API
Release Notes
Glossary and Bibliography
Indices and Tables
Grapheme Toolkit
Introduction
Theory
Examples
API
Preliminary API
Release Notes
Indices and Tables
GraphSim Toolkit
Introduction
Theory
Examples
API
Release Notes
Glossary and Bibliography
Indices and Tables
Lexichem Toolkit
Theory
Examples
API
Release Notes
Bibliography
Indices and Tables
OEMedChem Toolkit
Introduction
Theory
Examples
API
Release Notes
Bibliography
Indices and Tables
MolProp Tookit
Theory
Examples
API
Release Notes
Bibliography
Indices and Tables
Quacpac Toolkit
Theory
Examples
API
Release Notes
Bibliography
Indices and Tables
FastROCS Toolkit
Introduction
Theory
Examples
Tutorials
API
Release Notes
Bibliography
Indices and Tables
OEDocking Toolkit
Introduction
Theory
API
Release Notes
Bibliography
Indices and Tables
Omega Toolkit
Theory
Examples
API
Preliminary API
Release Notes
Bibliography
Indices and Tables
Shape Toolkit
Theory
Examples
API
Deprecated API
Release Notes
Bibliography
Indices and Tables
Spicoli Toolkit
Theory
API
Release Notes
Glossary and Bibliography
Indices and Tables
Szmap Toolkit
Introduction
Theory and Examples
API
Release Notes
Bibliography
Indices and Tables
Szybki Toolkit
Theory
API
Examples
Release Notes
Bibliography
Indices and Tables
Zap Toolkit
Theory and Examples
API
Release Notes
Reference
Toolkits-2018.Oct.1-java
Docs
»
OEDepict Toolkit 2.4.1
OEDepict Toolkit 2.4.1
¶
Introduction
Theory
¶
Basic Drawing Primitives
Coordinate System
Basic Shapes
Image File Formats
Molecule Depiction
Customizing Molecule Depiction
Controlling the Size of Depicted Molecules
Molecule Depiction with Transparent Background
Displaying Atom Properties
Displaying Bond Properties
Hiding Atoms and Bonds
Configuring Molecule Display
Highlighting
Using Highlighting Styles
Using Highlighting Classes
Highlighting Overlapped Patterns
Molecule Layouts
Depicting Molecules in an Arbitrary Position
Depicting Molecules in a Grid
Depicting Molecules in a Table
Multi Page Images
Multi Page Reports
MDL Query Depiction
Atom Query Features
Bond Query Features
R-group Depiction
MDL Reaction Depiction
Molecule Alignment
Molecule Alignment Based on MCS
Molecule Alignment Based on Substructure Search
Molecule Alignment Based on Molecular Similarity
Generating Interactive SVG Images
SVG group
SVG class
Examples of Generating Interactive SVG Images
Inserting SVG Images into HTML
How to Catch SVG Events
Examples
¶
OEDepict Examples
Generating 2D coordinates
Depicting Substructure Search Match
Aligning Molecule Based on MCS
Depicting MDL Query
Depicting MDL Reaction
Depicting a Single Molecule
Depicting Molecules In a Grid
Depicting Molecules in Multi-Page
Generating 2D Ring Dictionary Report
Aligning Molecules Based on Substructure Search
Depicting MDL Query Substructure Search Hits
Python Cookbook Examples
Appendices
¶
Element coloring (CPK)
API
¶
OEDepict Classes
OE2DAtomDisplay
OE2DBondDisplay
OE2DMolDisplay
OE2DMolDisplayOptions
OE2DPath
OE2DPathPoint
OE2DPoint
OEAlignmentOptions
OEAlignmentResult
OEAtomDisplayBase
OEAtomSVGAtomIdxMarkup
OEAtomSVGMarkupBase
OEAtomSVGNoMarkup
OEAtomSVGResidueMarkup
OEBondDisplayBase
OEBondSVGBondIdxMarkup
OEBondSVGMarkupBase
OEBondSVGNoMarkup
OEDisplayAtomIdx
OEDisplayAtomMapIdx
OEDisplayAtomPropBase
OEDisplayBondIdx
OEDisplayBondPropBase
OEDisplayNoAtomProp
OEDisplayNoBondProp
OEFont
OEHighlightBase
OEHighlightByBallAndStick
OEHighlightByCogwheel
OEHighlightByColor
OEHighlightByLasso
OEHighlightByStick
OEHighlightLabel
OEHighlightOverlayBase
OEHighlightOverlayByBallAndStick
OEImage
OEImageBase
OEImageFileBase
OEImageFileCreatorBase
OEImageFrame
OEImageGrid
OEImageTable
OEImageTableOptions
OEJavaImageBase
OELegendLayout
OELegendLayoutOptions
OEMolDisplayBase
OEMultiPageImageFile
OENearestAtom
OENearestBond
OEPen
OEPrepareDepictionOptions
OEReport
OEReportOptions
OESVGClass
OESVGGroup
OEDepict Constants
OE2DMolDisplaySetup
OE2DPathPointType
OEAlignment
OEAromaticStyle
OEAtomColorStyle
OEAtomStereoStyle
OEBondColorStyle
OEBondDisplayPosition
OEBondDisplayType
OEBondStereoStyle
OEDepict
OEDepictOrientation
OEFill
OEFontFamily
OEFontStyle
OEHighlightOverlayStyle
OEHighlightParamName
OEHighlightSetup
OEHighlightStyle
OEHydrogenPos
OEHydrogenStyle
OEIconLocation
OEImageGridParamName
OEImageGridSetup
OEImageParamName
OEImageSetup
OEImageTableStyle
OELayerPosition
OELegendColorStyle
OELegendInteractiveStyle
OELegendLayoutStyle
OELineCap
OELineJoin
OEMargin
OEMultiPageParamName
OEMultiPageSetup
OEPageOrientation
OEPageSize
OEPrepareDepictionSetup
OEProtectiveGroupStyle
OERadicalDisplayType
OEReportSetup
OEScale
OEStipple
OESuperAtomStyle
OETitleLocation
OEDepict Functions
OEAddBuiltInHiddenSVGClass
OEAddBuiltInVisibleSVGClass
OEAddDepictionHydrogens
OEAddHighlighting
OEAddHighlightOverlay
OEAddInteractiveIcon
OEAddLabel
OEAddOpenEyeIcon
OEAddSVGClickEvent
OEAddSVGHover
OEAddSVGToggle
OEAddWatermark
OEAnnotateDepictionProblems
OEAnnotateValenceProblems
OEConfigure2DMolDisplayOptions
OEConfigureColor
OEConfigureHighlightColor
OEConfigureHighlightParams
OEConfigureHighlightStyle
OEConfigureImageGridNumColumns
OEConfigureImageGridNumRows
OEConfigureImageGridParams
OEConfigureImageHeight
OEConfigureImageOptions
OEConfigureImageWidth
OEConfigureMultiPageOrientation
OEConfigureMultiPageParams
OEConfigureMultiPageSize
OEConfigurePrepareDepictionOptions
OEConfigureReportOptions
OECreateWin32GraphicsImage
OEDepictCoordinates
OEDepictGetArch
OEDepictGetLicensee
OEDepictGetPlatform
OEDepictGetRelease
OEDepictGetSite
OEDepictGetVersion
OEDepictIsLicensed
OEDrawBorder
OEDrawChevronArrow
OEDrawCurvedArrow
OEDrawCurvedBorder
OEDrawCurvedRectangle
OEDrawEquilibriumArrow
OEDrawHighlighting
OEDrawLegendLayout
OEDrawReactionArrow
OEDrawResonanceArrow
OEDrawSVGHoverText
OEDrawSVGToggleText
OEDrawText
OEDrawTextToCenter
OEEstimateTextWidth
OEGetAverageBondLengthInDispCoords
OEGetBuiltInHiddenSVGClass
OEGetBuiltInVisibleSVGClass
OEGetCenter
OEGetColor
OEGetDefaultAtomColor
OEGetDisplayCoords
OEGetHighlightColor
OEGetHighlightStyle
OEGetImageGridNumColumns
OEGetImageGridNumRows
OEGetImageHeight
OEGetImageWidth
OEGetMoleculeCoords
OEGetMoleculeScale
OEGetMultiPageOrientation
OEGetMultiPageSize
OEGetNearbyAtom
OEGetNearbyBond
OEGetNearestAtom
OEGetNearestBond
OEGetPageHeight
OEGetPageWidth
OEGetSupportedImageFileExtensions
OEGetSupportedMultiPageImageFileExtensions
OEHasDepictionHydrogens
OEIsRegisteredImageFile
OEIsRegisteredMultiPageImageFile
OEIsValidSVGClassName
OEIsValidSVGGroupId
OELengthenVector
OEOffsetMolDisplay
OEPrepareAlignedDepiction
OEPrepareDepiction
OEPrepareMultiAlignedDepiction
OEReduceFontSizeToFit
OERegisterImageFile
OERenderMolecule
OERenderMoleculeToString
OERotateVector
OESetup2DMolDisplayOptions
OESetupPrepareDepictionOptions
OESetupReportOptions
OESuppressNonDepictionHydrogens
OEWrite2DRingDictionaryReport
OEWriteImage
OEWriteImageToString
OEWriteMultiPageImage
OEWriteReport
OEWriteReportPageByPage
OEWriteReportToString
Release Notes
¶
Release Notes
Glossary and Bibliography
¶
Glossary
Bibliography
Indices and Tables
¶
Index