OEChem Toolkit¶
OEChem Theory¶
Introduction to Molecules
Atoms and Bonds
- Atom and Bond Traversal
- Atom, Bond, and Conformer Indices
- Atom Properties
- Bond Properties
- Valence Models
Molecules
- Molecule Properties
- Ring Perception
- Aromaticity Perception
- Connectivity Perception
- Stereochemistry Perception
- Formal and Partial Charges
Molecule Algorithms
- Pattern Matching
- Substructure Search with MDL Queries
- Reactions
Advanced OEChem
Reference Appendices
OESystem Theory¶
OEBio Theory¶
Working With Macromolecules
OEGrid Theory¶
Examples¶
- OEChem Examples Summary
- Molecule processing
- Convert molecule files
- Concatenating molecules
- Splitting multicomponent molecules
- Extract molecules by title
- Write out unique molecules
- Randomize atoms of molecules
- Generate canonical smiles
- Filter molecules by weight or heavy atom count
- Strip salts
- Extract rings
- Extract molecule scaffolds
- Extract random molecule subset
- Reactions
- Molecule searching
- Molecule alignment
- SDF specific
- Molecule information
- Molecule processing
- OEChem Examples
- Convert molecule files
- Concatenating molecules
- Splitting multicomponent molecules
- Extract molecules by title
- Write out unique molecules
- Randomize atoms of molecules
- Generate canonical smiles
- Filter molecules by weight or heavy atom count
- Strip salts
- Extract rings
- Extract molecule scaffolds
- Extract random molecule subset
- Performing a reaction
- Library generation
- Perform substructure searches
- Align molecules by maximum common substructure
- Align molecules by clique match
- Align molecules by SMARTS
- Modifying SD tags
- Exporting SD data to a csv file
- Adding csv data as SD tags
- Renaming molecules by SD field
- Filter molecules by SD data
- Counting molecules
- Print OEChem and format information
- Get molecule titles
- Print dots
- Print simple molecule information
- Print rotor count distribution
- Find minimum path in a molecule
- Print molecule atom names
- OEBio Examples
API¶
- OEBio Classes
- OEBio Constants
- OEBio Functions
- OEBuildUnitCell
- OECopyCrystalSymmetry
- OEExpandCrystalSymmetry
- OEGetAlignment
- OEGetAlignmentMethodName
- OEGetChis
- OEGetCrystalSymmetry
- OEGetPhi
- OEGetProteinTorsionName
- OEGetPsi
- OEGetResidueAtoms
- OEGetRotamers
- OEGetSpaceGroup
- OEGetSpaceGroupNumber
- OEGetTorsion
- OEHasBondedResidues
- OEHasCrystalSymmetry
- OEIsStandardProteinResidue
- OEIsTypicalPrimaryLocationCode
- OERMSD
- OESetCrystalSymmetry
- OESetRotamer
- OESetTorsion
- OESwapAIEResidueAtoms
- OESymmetryCartesianToFractional
- OESymmetryFractionalToCartesian
- OEWriteAlignment
- OEChem Classes
- OEAbsCanonicalConfTest
- OEAbsoluteConfTest
- OEAtomBase
- OEAtomBondSet
- OEAtomIsInResidue
- OEAtomIsInRing
- OEBondBase
- OEBondIsInRing
- OECliqueSearch
- OEConfBaseT
- OEConfTestBase
- OECoordArray
- OEDefaultConfTest
- OEExprBase
- OEFuzzy
- OEGetNbrAtom
- OEGraphMol
- OEHasAtomName
- OEHasAtomStereoSpecified
- OEHasAtomicNum
- OEHasBondStereoSpecified
- OEHasChainID
- OEHasFragmentNumber
- OEHasIdx
- OEHasMapIdx
- OEHasOrder
- OEHasResidueNumber
- OEIdxSelected
- OEInSamePart
- OEIsAromaticAtom
- OEIsAromaticBond
- OEIsAtomHybridization
- OEIsCAlpha
- OEIsCarbon
- OEIsChiralAtom
- OEIsChiralBond
- OEIsHalide
- OEIsHalogen
- OEIsHeavy
- OEIsHydrogen
- OEIsMember
- OEIsMemberPtr
- OEIsNitrogen
- OEIsNonRingAtomDoubleBondedToRing
- OEIsOxygen
- OEIsPhosphorus
- OEIsPolar
- OEIsPolarHydrogen
- OEIsRGroup
- OEIsRotor
- OEIsSulfur
- OEIsomericConfTest
- OELibraryGen
- OELingoSim
- OEMCMolBaseT
- OEMCSFunc
- OEMCSMaxAtoms
- OEMCSMaxAtomsCompleteCycles
- OEMCSMaxBonds
- OEMCSMaxBondsCompleteCycles
- OEMCSSearch
- OEMatch
- OEMatchBase
- OEMatchFunc
- OEMatchPair
- OEMol
- OEMolBase
- OENbrs
- OENearestNbrs
- OENthAtom
- OEPartPredT
- OEQAtomBase
- OEQBase
- OEQBondBase
- OEQMol
- OEQMolBase
- OEQuaternion
- OEResidue
- OERotMatrix
- OESDDataPair
- OESubSearch
- OETrans
- OETransBase
- OETranslation
- OEUniMolecularRxn
- OEVectorBindings
- oemolistream
- oemolithread
- oemolostream
- oemolothread
- oemolstreambase
- oemolthreadbase
- OEChem Constants
- OEChem
- OEAtomStereo
- OEBondStereo
- OECIPAtomStereo
- OECIPBondStereo
- OEElemNo
- OEExprOpts
- OEFormat
- OEFuzzVal
- OEHybridization
- OEIFlavor
- OELingoType
- OEMCMolType
- OEMCSType
- OEMDLQueryOpts
- OEMModType
- OEMolBaseType
- OENearestNbrsMethod
- OEOFlavor
- OEPDBAtomName
- OEPerceived
- OEPreserveResInfo
- OEProperty
- OEQMolType
- OEResidueIndex
- OERxnRole
- OESLNFlag
- OESMILESFlag
- OESmartsParseOpts
- OETriposType
- OEWriteMolReturnCode
- OEChem Functions
- OE3DToAtomStereo
- OE3DToBondStereo
- OE3DToInternalStereo
- OEAcyclicPath
- OEAddExplicitHydrogens
- OEAddMols
- OEAddPDBData
- OEAddSDData
- OEAssignAromaticFlags
- OEAssignBondiVdWRadii
- OEAssignCovalentRadii
- OEAssignDelphiRadii
- OEAssignFormalCharges
- OEAssignHonigIonicCavityRadii
- OEAssignHybridization
- OEAssignImplicitHydrogens
- OEAssignMDLHydrogens
- OEAssignPaulingVdWRadii
- OEAssignResidueNumbers
- OEAssignSerialNumbers
- OEAssignZap9Radii
- OEAtomGetMDLParity
- OEAtomGetResidue
- OEAtomGetSmallestRingSize
- OEAtomIsInAromaticRingSize
- OEAtomIsInRingSize
- OEAtomSetMDLParity
- OEAtomSetResidue
- OEBAtomIntTypeOpts
- OEBDefaultOpts
- OEBGZipCompressOpts
- OEBRotCompressOpts
- OEBondGetSmallestRingSize
- OEBondIsInAromaticRingSize
- OEBondIsInRingSize
- OEBuildMDLQueryExpressions
- OECalcCartesianCoord
- OECalcInternalCoord
- OECalculateMolecularWeight
- OECanonicalOrderAtoms
- OECanonicalOrderBonds
- OECenter
- OEChemGetArch
- OEChemGetLicensee
- OEChemGetPlatform
- OEChemGetRelease
- OEChemGetSite
- OEChemGetVersion
- OEChemIsLicensed
- OEClearAromaticFlags
- OEClearPDBData
- OEClearPartialCharges
- OEClearResidue
- OEClearResidues
- OEClearRotorCompressData
- OEClearSDData
- OEComposeDMCSFromCliques
- OECopyPDBData
- OECopySDData
- OECorrectAcidProtonGeometry
- OECount
- OECreateAbsSmiString
- OECreateCanSmiString
- OECreateIsoSmiString
- OECreateSlnString
- OECreateSmiString
- OEDefaultImplicitHCount
- OEDefaultMDLHCount
- OEDeleteEverythingExceptTheFirstLargestComponent
- OEDeletePDBData
- OEDeleteSDData
- OEDetermineAromaticRingSystems
- OEDetermineComponents
- OEDetermineConnectivity
- OEDetermineReactants
- OEDetermineRingSystems
- OEDisassembleExpressions
- OEDoubleBondCount
- OEDoubleBondOCount
- OEElementHistogram
- OEEulerRotate
- OEExactGraphMatch
- OEExpandSuperAtoms
- OEFindRingAtomsAndBonds
- OEFormalPartialCharges
- OEGasteigerInitialCharges
- OEGasteigerPartialCharges
- OEGetAbsTorsion
- OEGetAminoAcidCode
- OEGetAngle
- OEGetAnisou
- OEGetAromatic
- OEGetAtomComment
- OEGetAtomicNum
- OEGetAtomicSymbol
- OEGetAutomorphs
- OEGetAverageWeight
- OEGetBondOrder
- OEGetBondiVdWRadius
- OEGetCenterAndExtents
- OEGetCenterOfMass
- OEGetComment
- OEGetCovalentRadius
- OEGetDefaultMass
- OEGetDelphiRadius
- OEGetDistance
- OEGetDistance2
- OEGetDoubleBondNeighbor
- OEGetFileExtension
- OEGetFileType
- OEGetFormalCharge
- OEGetFormatExtension
- OEGetFormatString
- OEGetHCount
- OEGetHonigIonicCavityRadius
- OEGetHybridization
- OEGetImplicitHCount
- OEGetIsotopicWeight
- OEGetNearestNbrs
- OEGetOtherNeighbor
- OEGetPDBAtomIndex
- OEGetPDBAtomName
- OEGetPDBBaseData
- OEGetPDBData
- OEGetPDBDataPairs
- OEGetPackedCoords
- OEGetPathLength
- OEGetPaulingVdWRadius
- OEGetResidueIndex
- OEGetResidueName
- OEGetSDBaseData
- OEGetSDData
- OEGetSDDataPairs
- OEGetSingleBondNeighbor
- OEGetSmallestSubtree
- OEGetSoleBond
- OEGetSoleDoubleBond
- OEGetSoleNeighbor
- OEGetSoleSingleBond
- OEGetSoleTripleBond
- OEGetStereo
- OEGetSubtree
- OEGetTokenizer
- OEGetTorsion
- OEGetTorsions
- OEGetTripleBondNeighbor
- OEGetUniMolecularRxnIter
- OEHasAtomStereoHydrogens
- OEHasBondStereoHydrogens
- OEHasDoubleBond
- OEHasDoubleBondO
- OEHasExplicitHydrogens
- OEHasImplicitHydrogens
- OEHasMultipleBond
- OEHasPDBData
- OEHasPartialCharges
- OEHasResidue
- OEHasResidues
- OEHasSDData
- OEHasSingleBond
- OEHasStereoHydrogens
- OEHasTokenizer
- OEHasTripleBond
- OEHistogramFormula
- OEInitDefaultHandler
- OEInitHandler
- OEInvertCenter
- OEIs3DFormat
- OEIsBinary
- OEIsCommonIsotope
- OEIsExtension
- OEIsGZip
- OEIsReadable
- OEIsSingleOrAromatic
- OEIsTerminalOxygen
- OEIsTerminalSulfur
- OEIsWriteable
- OEKekulize
- OEMDLClearParity
- OEMDLCorrectBondStereo
- OEMDLHasIncorrectBondStereo
- OEMDLHasParity
- OEMDLParityTag
- OEMDLPerceiveBondStereo
- OEMDLPerceiveParity
- OEMDLStereoFromBondStereo
- OEMDLStereoFromParity
- OEMMFF94InitialCharges
- OEMMFF94PartialCharges
- OEMMFFAtomType
- OEMMFFAtomTypeNames
- OEMMFFAtomTypes
- OEMMFFClearRemappedElements
- OEMMFFRemapElement
- OEMMFFTypeIndex
- OEMMFFTypeName
- OEMMFFTypeNames
- OEMacroModelAtomTypeNames
- OEMacroModelAtomTypes
- OEMacroModelTypeElement
- OEMacroModelTypeName
- OEMacroModelTypeNames
- OEMolecularFormula
- OEMultipleBondCount
- OENetCharge
- OENewMCMolBase
- OENewMolBase
- OENewQMolBase
- OENormalize
- OEPDBOrderAtoms
- OEParseSmarts
- OEParseSmiles
- OEParseSmirks
- OEPerceiveBondOrders
- OEPerceiveChiral
- OEPerceiveCIPStereo
- OEPerceiveResidues
- OEPerceiveSymmetry
- OERMSD
- OERandomizeTorsions
- OEReadCDXFile
- OEReadFASTAFile
- OEReadMDLFile
- OEReadMDLQueryFile
- OEReadMDLReactionQueryFile
- OEReadMacroModelFile
- OEReadMol2File
- OEReadMolecule
- OEReadOldBinary
- OEReadPDBFile
- OEReadRxnFile
- OEReadSketchFile
- OEReadXYZFile
- OEResidueHydrogens
- OERotate
- OESameChain
- OESameResidue
- OEScrambleMolecule
- OESet3DHydrogenGeom
- OESetAngle
- OESetAnisou
- OESetAtomComment
- OESetCIPStereo
- OESetComment
- OESetDefaultFlavors
- OESetDefaultIFlavors
- OESetDefaultOFlavors
- OESetDimensionFromCoords
- OESetDistance
- OESetPDBData
- OESetPackedCoords
- OESetSDData
- OESetTorsion
- OEShortestPath
- OESingleBondCount
- OESmilesAtomCount
- OEString2OEAtomExpr
- OEString2OEBondExpr
- OESubsetMol
- OESuppressHydrogens
- OESymmetryNumber
- OETerminalOCount
- OETerminalSCount
- OETheFunctionFormerlyKnownAsStripSalts
- OETranslate
- OETripleBondCount
- OETriposAtomNames
- OETriposAtomType
- OETriposAtomTypeNames
- OETriposAtomTypes
- OETriposBondTypeNames
- OETriposOrderAtoms
- OETriposResonantTypeNames
- OETriposTypeElement
- OETriposTypeIndex
- OETriposTypeName
- OETriposTypeNames
- OEWriteCDXFile
- OEWriteConstMolecule
- OEWriteFASTAFile
- OEWriteMDLFile
- OEWriteMOPACInputFile
- OEWriteMol2File
- OEWriteMolecule
- OEWritePDBFile
- OEWriteXYZFile
- SmartsLexReplace
- OEMath Constants
- OEMath Functions
- OEGeom2DAdd
- OEGeom2DAngle
- OEGeom2DCopy
- OEGeom2DDistance
- OEGeom2DDistance2
- OEGeom2DDotProd
- OEGeom2DNormalize
- OEGeom2DRotate
- OEGeom2DScale
- OEGeom2DSetLength
- OEGeom2DSubtract
- OEGeom2DTranslate
- OEGeom3DAbsTorsion
- OEGeom3DAdd
- OEGeom3DAngle
- OEGeom3DAngleCoord
- OEGeom3DCopy
- OEGeom3DCrossProd
- OEGeom3DDistance
- OEGeom3DDistance2
- OEGeom3DDotProd
- OEGeom3DEulerRotate
- OEGeom3DEulerToQuaternion
- OEGeom3DEulerToRotMatrix
- OEGeom3DGetCenterAndExtents
- OEGeom3DGetCenterOfMass
- OEGeom3DMagnitude
- OEGeom3DMakeQuaternion
- OEGeom3DMatrixIdentity
- OEGeom3DMatrixInvert
- OEGeom3DMatrixMultiply
- OEGeom3DNormalize
- OEGeom3DPlanarCoord
- OEGeom3DQuaternionInvert
- OEGeom3DQuaternionRotate
- OEGeom3DQuaternionToRotMatrix
- OEGeom3DRotVectorToTransform
- OEGeom3DRotate
- OEGeom3DScale
- OEGeom3DSetLength
- OEGeom3DSubtract
- OEGeom3DTetraCoord
- OEGeom3DTorsion
- OEGeom3DTranslate
- OEGeom3DUnitQuaternionRotate
- OEGeom3DVolume
- OEGeomDotProd
- OEGeomNormalizeQuaternion
- OEGeomQuaternionMultiply
- OEPlatform Classes
- OEPlatform Constants
- OEPlatform Functions
- OEAddLicenseKey
- OEBigEndian
- OECallOnce
- OECloseIStream
- OECloseOStream
- OECompress
- OECompressionAvailable
- OECreateDirectory
- OECurrentTime
- OECycleTime
- OEDeletePtr
- OEFileCorrectSeparators
- OEFileCreate
- OEFileDelete
- OEFileDetermineName
- OEFileDeterminePath
- OEFileDeterminePathAndName
- OEFileExists
- OEFileIsDirectory
- OEFileIsFile
- OEFileIsLink
- OEFileIsReadable
- OEFileIsWritable
- OEFileRandomName
- OEFileSize
- OEFileTempPath
- OEGetCurrentWorkingDirectory
- OEGetDomainName
- OEGetHostIdent
- OEGetHostName
- OEGetIPAddress
- OEGetMachineName
- OEGetPlatformInfo
- OEGetProcessMemUsage
- OEGetProcessorInfo
- OEGetTimeOfDay
- OEGetUserAppDataDir
- OEGetUserDocumentsDir
- OEGetUserHomeDir
- OEGetUserName
- OEIsNaN
- OEIsNormalNum
- OEMarkMalloca
- OEOpenIStream
- OEOpenOStream
- OEProcessFileName
- OEProcessSystemCommand
- OERegisterIStream
- OERegisterOStream
- OERenameFile
- OESetLicenseFile
- OESleep
- OEUncompress
- OEUnlink
- OEUnlinkDirectory
- oeendl
- oeends
- oeflush
- OESystem Classes
- OEAnd
- OEBase
- OEBaseData
- OEBaseDataT
- OEBaseDataTPtr
- OEBinaryAnd
- OEBinaryFalse
- OEBinaryFunction
- OEBinaryNot
- OEBinaryOr
- OEBinaryPredicate
- OEBitVector
- OEBoundedBuffer
- OEColor
- OEColorStop
- OEDots
- OEErrorHandler
- OEErrorHandlerImplBase
- OEFixedGrid
- OEFixedMultiGrid
- OEGaussian
- OEGaussianBase
- OEGaussianContainer
- OEGaussianContainerBase
- OEGrid
- OEGridAbstractBase
- OEGridBase
- OEInterface
- OEIter
- OEIterBase
- OELinearColorGradient
- OEMultiGrid
- OENot
- OEOr
- OEParameter
- OEProtectedBuffer
- OERandom
- OEScalarGrid
- OESkewGrid
- OEStopwatch
- OETypedParameter
- OEUnaryFalse
- OEUnaryFunction
- OEUnaryPredicate
- OEWallTimer
- OESystem Constants
- OESystem Functions
- OEAddContour
- OEAddGrid
- OEAnnotateArrow
- OEAnnotateBox
- OEAnnotateCylinder
- OEAnnotateEllipsoid
- OEAnnotateLine
- OEAnnotateSphere
- OEAnnotateSpline
- OEAnnotateSplineSurface
- OEAnnotateSymbol
- OEAnnotateText
- OEAnnotateTorus
- OEAttachData
- OEBDataLengthBytes
- OEBFloatEndian
- OEBIntEndian
- OEBPeekTag
- OEBReadData
- OEBReadDataLength
- OEBReadOEBase
- OEBReadPOD
- OEBReadTag
- OEBShortEndian
- OEBWriteDataLength
- OEBWriteOEBase
- OEBWritePOD
- OEBWriteTag
- OEBinaryRead
- OEBinaryWrite
- OEBitVectorAnd
- OEBitVectorEqual
- OEBitVectorNot
- OEBitVectorNumBytes
- OEBitVectorNumWords
- OEBitVectorOr
- OEBitVectorSub
- OEBitVectorXor
- OECastData
- OECheckHelp
- OEClearGridBoundary
- OEColorCreate
- OEColorGet
- OEColorPacked
- OEColorSet
- OEConfigure
- OECopyArray
- OECopyBaseData
- OECopyBits
- OEDivideGrid
- OEFileExtension
- OEFileExtensions
- OEGetBitCounts
- OEGetCenterAndExtents
- OEGetContourColor
- OEGetContourLevel
- OEGetDataType
- OEGetGridFileType
- OEGetGridFormatExtension
- OEGetGridFormatString
- OEGetKappa
- OEGetMemPoolMode
- OEGetOEBReturnString
- OEGetPrefactor
- OEGetRadius
- OEGetTag
- OEGetThreadSafe
- OEGetWidth
- OEGridAvgVal
- OEGridCopyContents
- OEGridCopyGeometry
- OEGridGetArch
- OEGridGetLicensee
- OEGridGetPlatform
- OEGridGetRelease
- OEGridGetSite
- OEGridGetVersion
- OEGridHasNonZeroValue
- OEGridIsLicensed
- OEGridMaxVal
- OEGridMinVal
- OEGridSameGeometry
- OEGridSetAllElements
- OEHasTag
- OEInitAnnotationHandlers
- OEInitGridHandlers
- OEInitializeHandler
- OEInterpolateBetweenGrids
- OEIsGrid
- OEIsReadableGrid
- OEIsSameTypeTester
- OEIsWriteableGrid
- OELinearInterpolate
- OEMakeGaussians
- OEMakeGridFromCenterAndExtents
- OEMakeHex
- OEMakeMolecularGaussianGrid
- OEMakeRegularGrid
- OEMakeRegularSubGrid
- OEMaskGrid
- OEMaskGridByCoordsAndRadii
- OEMaskGridByMolecule
- OEMaskGridValues
- OEMoveArray
- OEMultiplyGrid
- OENumContours
- OENumberToString
- OEPRIMITIVE_ITER
- OEParseCommandLine
- OEParseCommandLineLW
- OEParseParameterFile
- OEReadGrid
- OEReadOldStyleGrid
- OERegisterMolParameters
- OERegisterOEBInitializer
- OERotate
- OESetMemPoolMode
- OESetThreadSafe
- OESetupGrid
- OESigmaNormalizeGrid
- OEStaticGetTag
- OEStringJoin
- OEStringLower
- OEStringMatch
- OEStringSimplifyWhiteSpace
- OEStringStripWhiteSpace
- OEStringToNumber
- OEStringTokenize
- OEStringTokenizeQuoted
- OEStringTranslate
- OEStringUpper
- OESubtractGrid
- OETanimoto
- OETranslate
- OEUnknownOEBDataTagName
- OEWriteGrid
- OEWriteHtml
- OEWriteInterfaceConfigurationFile
- OEWriteOldStyleGrid
- OEWriteSettings
- PopBaseDataT
- PopBaseDataTPtr
- PushBaseDataT
- PushBaseDataTPtr
- RegisterMolParameters
- __typehash__
- hanoisort
- OEBitVector Operators
Glossary and Bibliography¶
Release Notes¶
- OEChem 1.7.7
- OEBio 1.7.7
- OESystem 1.7.7
- OEPlatform 1.7.7
- OESystem 1.7.6
- OEBio 1.7.6
- OEChem 1.7.5
- OEBio 1.7.5
- OEGrid 1.3.5
- OESystem 1.7.5
- OEPlatform 1.7.5
- OEChem 1.7.4
- OESystem 1.7.4
- OEPlatform 1.7.4
- OEBio 1.7.4
- OEGrid 1.3.4
- OEChem 1.7.3
- OEChem 1.7.2
- OESystem 1.7.2
- OEPlatform 1.7.2
- OEBio 1.7.2
- OEGrid 1.3.3
- OEChem 1.7.1
- OEChem 1.7.0
- OEGrid 1.3.2
- OESystem 1.7.0
- OEPlatform 1.7.0
- OEChem 1.6.1
- OESystem 1.6.1
- OEPlatform 1.6.1
- OEChem 1.6.0
- OESystem 1.6.0
- OEPlatform 1.6.0
- OEChem 1.5.1
- OEChem 1.5.0
- OEChem 1.4.2
- OEBio 1.4.2
- OESystem 1.4.2
- OEPlatform 1.4.2
- OEChem 1.4.1
- OEChem 1.4.0
- OEBio 1.4.0
- OESystem 1.4.0
- OEPlatform 1.4.0
- OEChem 1.3.4
- OEChem 1.3.3
- OESystem 1.3.3
- OEPlatform 1.3.3
- OEChem 1.3.2
- OESystem 1.3.2
- OEPlatform 1.3.2
- OEChem 1.3.1
- OESystem 1.3.1
- OEChem 1.3.0
- OESystem 1.3.0
- OEPlatform 1.3.0
