OEChem - API Manual
Previous:
Front Matter
Up:
OEChem - API Manual
Next:
1 Introduction
Contents
1 Introduction
1. Overview
2. C++ Compilers and Platforms
2.1 Native Compilers
2.2 GNU C/C++ Compilers
2 OEBio Library
3. OEBIO
4. OEBio Classes and Member Functions
4.1 OEHierChain
4.1.1 Constructors
4.1.2 operator =
4.1.3 Destructor
4.1.4 GetChainID
4.1.5 GetOEResidue
4.1.6 GetFragments
4.1.7 GetResidue
4.1.8 GetAtom
4.2 OEHierFragment
4.2.1 Constructors
4.2.2 operator =
4.2.3 Destructor
4.2.4 GetFragmentNumber
4.2.5 GetOEResidue
4.2.6 GetResidues
4.2.7 GetAtom
4.2.8 GetResidue
4.3 OEHierResidue
4.3.1 Constructors
4.3.2 operator =
4.3.3 Destructor
4.3.4 GetResidueNumber
4.3.5 GetOEResidue
4.3.6 GetAtom
4.3.7 GetAtoms
4.4 OEHierView
4.4.1 Constructors
4.4.2 Assignment Operators
4.4.3 Destructors
4.4.4 GetChains
4.4.5 GetFragments
4.4.6 GetResidues
4.4.7 GetAtom
4.4.8 GetAtoms
4.4.9 GetResidue
4.5 OESequenceAlignment
4.5.1 Constructors
4.5.2 operator =
4.5.3 Destructor
4.5.4 Clear
4.5.5 GetMethod
4.5.6 GetGap
4.5.7 GetExtend
4.5.8 GetScore
4.5.9 GetMaxSeqIdx
4.5.10 GetBackboneMatch
4.5.11 GetCAlphaMatch
5. OEBio Functions
5.1 OECopyCrystalSymmetry
5.2 OEExpandCrystalSymmetry
5.3 OEGetAlignmentMethodName
5.4 OEGetChis
5.5 OEGetCrystalSymmetry
5.6 OEGetSpaceGroup
5.7 OEGetSpaceGroupNumber
5.8 OEGetPhi
5.9 OEGetPsi
5.10 OEGetProteinTorsionName
5.11 OEGetResidueAtoms
5.12 OEGetSequenceAlignment
5.13 OEGetTorsion
5.14 OEHasBondedResidues
5.15 OEHasCrystalSymmetry
5.16 OEIsStandardProteinResidue
5.17 OERMSD
5.18 OESetCrystalSymmetry
5.19 OESetTorsion
5.20 OESwapAIEResidueAtoms
5.21 OEWriteAlignment
6. OEBio Functors
6.1 OEHasPDBAtomIndex
6.2 OEIsAlphaCarbon
6.3 OEIsBackboneAtom
7. OEBio Namespaces
7.1 OEAssumption
7.2 OEProtTorType
7.3 OESeqAlignmentMethod
3 OEChem Library
8. OEChem Classes and Member Functions
8.1 OEAbsCanonicalConfTest
8.2 OEAbsoluteConfTest
8.3 OEAtomBase
8.3.1 GetAtomicNum
8.3.2 GetAtoms
8.3.3 GetBond
8.3.4 GetBonds
8.3.5 GetDegree
8.3.6 GetExplicitDegree
8.3.7 GetExplicitHCount
8.3.8 GetExplicitValence
8.3.9 GetFormalCharge
8.3.10 GetHvyDegree
8.3.11 GetHvyValence
8.3.12 GetHyb
8.3.13 GetIdx
8.3.14 GetImplicitHCount
8.3.15 GetIntType
8.3.16 GetIsotope
8.3.17 GetMapIdx
8.3.18 GetName
8.3.19 GetParent
8.3.20 GetPartialCharge
8.3.21 GetRadius
8.3.22 GetRxnRole
8.3.23 GetStereo
8.3.24 GetSymmetryClass
8.3.25 GetTotalHCount
8.3.26 GetType
8.3.27 GetValence
8.3.28 HasStereoSpecified
8.3.29 IsAromatic
8.3.30 IsCarbon
8.3.31 IsChiral
8.3.32 IsConnected
8.3.33 IsHalogen
8.3.34 IsHydrogen
8.3.35 IsInRing
8.3.36 IsMetal
8.3.37 IsNitrogen
8.3.38 IsOxygen
8.3.39 IsPhosphorus
8.3.40 IsPolar
8.3.41 IsPolarHydrogen
8.3.42 IsSulfur
8.3.43 SetAromatic
8.3.44 SetAtomicNum
8.3.45 SetFormalCharge
8.3.46 SetHyb
8.3.47 SetImplicitHCount
8.3.48 SetIntType
8.3.49 SetInRing
8.3.50 SetIsotope
8.3.51 SetMapIdx
8.3.52 SetName
8.3.53 SetPartialCharge
8.3.54 SetRadius
8.3.55 SetRxnRole
8.3.56 SetStereo
8.3.57 SetSymmetryClass
8.3.58 SetType
8.4 OEBondBase
8.4.1 GetBgn
8.4.2 GetBgnIdx
8.4.3 GetEnd
8.4.4 GetEndIdx
8.4.5 GetIdx
8.4.6 GetIntType
8.4.7 GetNbr
8.4.8 GetOrder
8.4.9 GetParent
8.4.10 GetStereo
8.4.11 GetType
8.4.12 HasStereoSpecified
8.4.13 IsAromatic
8.4.14 IsChiral
8.4.15 IsInRing
8.4.16 IsRotor
8.4.17 SetAromatic
8.4.18 SetBgn
8.4.19 SetEnd
8.4.20 SetIntType
8.4.21 SetInRing
8.4.22 SetOrder
8.4.23 SetStereo
8.4.24 SetType
8.4.25 SwapEnds
8.5 OECartesianToInternal
8.5.1 reset
8.5.2 update
8.6 OECliqueSearch
8.6.1 Constructors
8.6.2 AddConstraint
8.6.3 ClearConstraints
8.6.4 GetMaxMatches
8.6.5 GetMinAtoms
8.6.6 GetPattern
8.6.7 GetSaveRange
8.6.8 Init
8.6.9 Match
8.6.10 SingleMatch
8.7 OEConfBase
8.8 OEConfBaseT
8.8.1 coord type
8.8.2 Copy
8.8.3 Constructors
8.8.4 operator=
8.8.5 AddAtom
8.8.6 AddBond
8.8.7 RemoveAtom
8.8.8 RemoveBond
8.8.9 MCMol
8.8.10 Conformer Indices
8.8.11 SetCoords
8.8.12 GetCoords
8.8.13 Deletion
8.8.14 Torsions
8.8.15 Transformations
8.8.16 Title
8.8.17 OEMolBase
8.8.18 OEBase
8.9 OEConfTest
8.9.1 CompareMols
8.9.2 CreateCopy
8.10 OEDefaultConfTest
8.11 OEEuler
8.12 OEExprBase
8.12.1 IsEquivalent
8.12.2 CreateCopy
8.12.3 GetType
8.13 OEFuzzy
8.13.1 Constructor
8.13.2 operator bool
8.13.3 operator !
8.13.4 operator &&
8.13.5 operator
8.13.6 operator ==
8.13.7 operator !=
8.14 OEInternalToCartesian
8.14.1 reset
8.14.2 update
8.15 OEIsomericConfTest
8.16 OELibaryGen
8.16.1 Constructors
8.16.2 AddStartingMaterial
8.16.3 operator()
8.16.4 operator bool
8.16.5 ClearStartingMaterial
8.16.6 GetExplicitHydrogens
8.16.7 GetProducts
8.16.8 GetReactants
8.16.9 GetTitleSeparator
8.16.10 GetValenceCorrection
8.16.11 Init
8.16.12 NumReactants
8.16.13 SetExplicitHydrogens
8.16.14 SetStartingMaterial
8.16.15 SetTitleSeparator
8.16.16 SetValenceCorrection
8.17 OELingoSim
8.17.1 Constructors
8.17.2 OELingoType
8.17.3 operator =
8.17.4 IsValid
8.17.5 Init
8.17.6 Similarity
8.17.7 Implementation
8.18 OEMatch
8.18.1 OEMatch Constructors
8.18.2 operator =
8.18.3 AddPair
8.18.4 CreateCopy
8.18.5 GetAtoms
8.18.6 GetBonds
8.18.7 GetPatternAtoms
8.18.8 GetPatternBonds
8.18.9 GetTargetAtoms
8.18.10 GetTargetBonds
8.18.11 NumAtoms
8.18.12 NumBonds
8.19 OEMatchBase
8.19.1 CreateCopy
8.19.2 GetAtoms
8.19.3 GetBonds
8.19.4 GetPatternAtoms
8.19.5 GetPatternBonds
8.19.6 GetTargetAtoms
8.19.7 GetTargetBonds
8.19.8 NumAtoms
8.19.9 NumBonds
8.20 OEMatchPair
8.20.1 Constructors
8.20.2 operator =
8.21 OEMCMolBase
8.22 OEMCMolBaseT
8.22.1 ConfType
8.22.2 Copy
8.22.3 Constructors
8.22.4 operator=
8.22.5 Active Conformer
8.22.6 GetMaxConfIdx
8.22.7 NewConf
8.22.8 NumConfs
8.22.9 GetConf
8.22.10 Delete Conformers
8.22.11 SweepConfs
8.22.12 OrderConfs
8.22.13 GetConfs
8.22.14 OEMolBase
8.22.15 OEBase
8.23 OEMCSFunc
8.23.1 operator()
8.23.2 CreateCopy
8.24 OEMCSMaxAtoms
8.25 OEMCSMaxBonds
8.26 OEMCSMaxAtomsCompleteCycles
8.26.1 Constructor
8.27 OEMCSMaxBondsCompleteCycles
8.27.1 Constructor
8.28 OEMCSSearch
8.28.1 Constructor
8.28.2 operator=
8.28.3 operator bool
8.28.4 AddConstraint
8.28.5 ClearConstraints
8.28.6 GetMaxMatches
8.28.7 GetMinAtoms
8.28.8 GetPattern
8.28.9 GetSaveRange
8.28.10 Init
8.28.11 Match
8.28.12 SetMCSFunc
8.28.13 SetMaxMatches
8.28.14 SetMinAtoms
8.28.15 SetSaveRange
8.28.16 SingleMatch
8.29 OEMol
8.29.1 Constructors
8.29.2 operator =
8.29.3 operator bool
8.29.4 ConfIdxArraySize
8.29.5 DeleteConfs
8.29.6 DeleteConf
8.29.7 GetActive
8.29.8 GetConf
8.29.9 GetConfs
8.29.10 IsDeleted
8.29.11 NewConf
8.29.12 NumConfs
8.29.13 OrderConfs
8.29.14 PopActive
8.29.15 PushActive
8.29.16 ResetConf
8.29.17 SetActive
8.29.18 SweepConfs
8.30 OEMolBase
8.30.1 operator =
8.30.2 operator +=
8.30.3 operator bool
8.30.4 Clear
8.30.5 Compress
8.30.6 DeleteAtom
8.30.7 DeleteBond
8.30.8 GetAtom
8.30.9 GetAtoms
8.30.10 GetBond
8.30.11 GetBonds
8.30.12 GetCoords
8.30.13 GetDimension
8.30.14 GetEnergy
8.30.15 GetMaxAtomIdx
8.30.16 GetMaxBondIdx
8.30.17 GetTitle
8.30.18 IsRxn
8.30.19 NewAtom
8.30.20 NewBond
8.30.21 NumAtoms
8.30.22 NumBonds
8.30.23 OrderAtoms
8.30.24 OrderBonds
8.30.25 SetCoords
8.30.26 SetDimension
8.30.27 SetEnergy
8.30.28 SetRxn
8.30.29 SetTitle
8.30.30 Sweep
8.30.31 UnCompress
8.31 oemolistream
8.31.1 Constructors
8.31.2 operator
8.31.3 close
8.31.4 GetFlavor
8.31.5 GetFormat
8.31.6 Getgz
8.31.7 open
8.31.8 openstring
8.31.9 SetConfTest
8.31.10 SetFlavor
8.31.11 SetFormat
8.31.12 Setgz
8.31.13 seek
8.31.14 size
8.31.15 tell
8.32 oemolostream
8.32.1 Constructors
8.32.2 operator
8.32.3 close
8.32.4 GetFlavor
8.32.5 GetFormat
8.32.6 Getgz
8.32.7 GetString
8.32.8 Getgz
8.32.9 open
8.32.10 openstring
8.32.11 SetFlavor
8.32.12 SetFormat
8.32.13 Setgz
8.32.14 SetString
8.33 oemolstreambase
8.34 OEQAtomBase
8.34.1 GetQAtoms
8.34.2 GetQBonds
8.35 OEQBase
8.35.1 SetExpr
8.35.2 GetExpr
8.36 OEQBondBase
8.37 OEQMol
8.37.1 Constructors
8.37.2 operator +=
8.37.3 operator OEMolBase
8.37.4 operator OEQMolBase
8.37.5 SCMol
8.37.6 QMol
8.38 OEQMolBase
8.38.1 operator=
8.38.2 operator +=
8.38.3 BuildExpressions
8.38.4 GetQAtoms
8.38.5 GetQBonds
8.39 OEQuaternion
8.40 OERotMatrix
8.41 OEResidue
8.41.1 operator =
8.41.2 operator bool
8.41.3 GetAlternateLocation
8.41.4 GetBFactor
8.41.5 GetChainID
8.41.6 GetFragmentNumber
8.41.7 GetInsertCode
8.41.8 GetModelNumber
8.41.9 GetName
8.41.10 GetOccupancy
8.41.11 GetResidueNumber
8.41.12 GetSecondaryStructure
8.41.13 GetSerialNumber
8.41.14 IsHetAtom
8.41.15 SetAlternateLocation
8.41.16 SetBFactor
8.41.17 SetChainID
8.41.18 SetFragmentNumber
8.41.19 SetHetAtom
8.41.20 SetInsertCode
8.41.21 SetModelNumber
8.41.22 SetName
8.41.23 SetOccupancy
8.41.24 SetResidueNumber
8.41.25 SetSecondaryStructure
8.41.26 SetSerialNumber
8.42 OESubSearch
8.42.1 Constructors
8.42.2 operator =
8.42.3 operator bool
8.42.4 AddConstraint
8.42.5 AtomMatch
8.42.6 ClearConstraints
8.42.7 GetMaxMatches
8.42.8 GetPattern
8.42.9 Init
8.42.10 Match
8.42.11 SingleMatch
8.42.12 SetMaxMatches
8.43 OETrans
8.43.1 Construction and Initialization
8.43.2 Adding Transformations
8.43.3 OETransBase Access
8.43.4 Transform
8.44 OETransBase
8.44.1 CreateCopy
8.44.2 Transform
8.44.3 Protected Transformations
8.45 OETranslation
8.46 OEUniMolecularRxn
8.46.1 Constructors
8.46.2 Init
8.46.3 operator()
8.46.4 operator bool
8.47 OEVectorBindings
8.47.1 Constructors
8.47.2 operator=
8.47.3 Add
8.47.4 Get
9. OEChem Functions
9.1 OE3DToAtomStereo
9.2 OE3DToBondStereo
9.3 OE3DToInternalStereo
9.4 OEAddExplicitHydrogens
9.5 OEAddMols
9.6 OEAssignAromaticFlags
9.7 OEAssignBondiVdWRadii
9.8 OEAssignCovalentRadii
9.9 OEAssignDelphiRadii
9.10 OEAssignFormalCharges
9.11 OEAssignHybridization
9.12 OEAssignImplicitHydrogens
9.13 OEAssignMDLHydrogens
9.14 OEAssignPaulingVdWRadii
9.15 OEAssignResidueNumbers
9.16 OEAssignSerialNumbers
9.17 OEAtomGetMDLParity
9.18 OEAtomGetResidue
9.19 OEAtomGetSmallestRingSize
9.20 OEAtomIsInAromaticRingSize
9.21 OEAtomIsInRingSize
9.22 OEAtomSetMDLParity
9.23 OEAtomSetResidue
9.24 OEBondGetSmallestRingSize
9.25 OEBondIsInAromaticRingSize
9.26 OEBondIsInRingSize
9.27 OECalcCartesianCoord
9.28 OECalcInternalCoord
9.29 OECalculateMolecularWeight
9.30 OECanonicalOrderAtoms
9.31 OECanonicalOrderBonds
9.32 OEChemGetPlatform
9.33 OEChemGetRelease
9.34 OEChemGetVersion
9.35 OEChemIsLicensed
9.36 OECenter
9.37 OEClearAromaticFlags
9.38 OEClearPartialCharges
9.39 OECreateAbsSmiString
9.40 OECreateCanSmiString
9.41 OECreateIsoSmiString
9.42 OECreateSlnString
9.43 OECreateSmiString
9.44 OEDefaultImplicitHCount
9.45 OEDefaultMDLHCount
9.46 OEDeleteEverythingExceptTheFirstLargestComponent
9.47 OEDetermineComponents
9.48 OEDetermineConnectivity
9.49 OEDetermineRingSystems
9.50 OEDoubleBondCount
9.51 OEEulerRotate
9.52 OEExactGraphMatch
9.53 OEExpandSuperAtoms
9.54 OEFindRingAtomsAndBonds
9.55 OEFormalPartialCharges
9.56 OEGasteigerInitialCharges
9.57 OEGasteigerPartialCharges
9.58 OEGetAbsTorsion
9.59 OEGetAminoAcidCode
9.60 OEGetAngle
9.61 OEGetAtomComment
9.62 OEGetAtomicNum
9.63 OEGetAtomicSymbol
9.64 OEGetAutomorphs
9.65 OEGetAverageWeight
9.66 OEGetBondiVdWRadius
9.67 OEGetComment
9.68 OEGetCovalentRadius
9.69 OEGetDefaultMass
9.70 OEGetDelphiRadius
9.71 OEGetDistance
9.72 OEGetDistance2
9.73 OEGetFileExtension
9.74 OEGetFileType
9.75 OEGetFormatExtension
9.76 OEGetFormatString
9.77 OEGetHybridization
9.78 OEGetIsotopicWeight
9.79 OEGetPackedCoords
9.80 OEGetPaulingVdWRadius
9.81 OEGetPDBAtomIndex
9.82 OEGetPDBAtomName
9.83 OEGetPathLength
9.84 OEGetResidueIndex
9.85 OEGetResidueName
9.86 OEGetSmallestSubtree
9.87 OEGetSubtree
9.88 OEGetTorsion
9.89 OEHasDoubleBond
9.90 OEHasExplicitHydrogens
9.91 OEHasImplicitHydrogens
9.92 OEHasMultipleBond
9.93 OEHasPartialCharges
9.94 OEHasStereoHydrogens
9.95 OEHasResidue
9.96 OEHasResidues
9.97 OEHasSingleBond
9.98 OEHasTripleBond
9.99 OEInvertCenter
9.100 OEIsBinary
9.101 OEIsCommonIsotope
9.102 OEIsReadable
9.103 OEIsWriteable
9.104 OEKekulize
9.105 OEMacroModelAtomTypes
9.106 OEMacroModelAtomTypeNames
9.107 OEMacroModelTypeElement
9.108 OEMacroModelTypeName
9.109 OEMacroModelTypeNames
9.110 OEMDLClearParity
9.111 OEMDLCorrectBondStereo
9.112 OEMDLHasIncorrectBondStereo
9.113 OEMDLHasParity
9.114 OEMDLPerceiveBondStereo
9.115 OEMDLPerceiveParity
9.116 OEMDLStereoFromBondStereo
9.117 OEMDLStereoFromParity
9.118 OEMolecularFormula
9.119 OEMultipleBondCount
9.120 OENetCharge
9.121 OENewMCMolBase
9.122 OENewMolBase
9.123 OENewQMolBase
9.124 OEParseSmarts
9.125 OEParseSmiles
9.126 OEParseSmirks
9.127 OEPDBOrderAtoms
9.128 OEPerceiveBondOrders
9.129 OEPerceiveChiral
9.130 OEPerceiveResidues
9.131 OEPerceiveSymmetry
9.132 OERandomizeTorsions
9.133 OEReadCDXFile
9.134 OEReadFASTAFile
9.135 OEReadMacroModelFile
9.136 OEReadMDLFile
9.137 OEReadMol2File
9.138 OEReadMolecule
9.139 OEReadMOPACFile
9.140 OEReadOldBinary
9.141 OEReadPDBFile
9.142 OEReadSketchFile
9.143 OEReadXYZFile
9.144 OEResidueHydrogens
9.145 OERMSD
9.145.1 Array-Based OERMSD
9.145.2 Full Molecule-Based OERMSD
9.145.3 Partial Molecule-Based OERMSD
9.146 OERotate
9.147 OESameChain
9.148 OESameResidue
9.149 OEScrambleMolecule
9.150 OESet3DHydrogenGeom
9.151 OESetAtomComment
9.152 OESetComment
9.153 OESetDimensionFromCoords
9.154 OESetPackedCoords
9.155 OESetTorsion
9.156 OESingleBondCount
9.157 OESmilesAtomCount
9.158 OESubsetMol
9.159 OESuppressHydrogens
9.160 OETheFunctionFormerlyKnownAsStripSalts
9.161 OETranslate
9.162 OETripleBondCount
9.163 OETriposAtomNames
9.164 OETriposAtomType
9.165 OETriposAtomTypes
9.166 OETriposAtomTypeNames
9.167 OETriposBondTypeNames
9.168 OETriposTypeElement
9.169 OETriposTypeIndex
9.170 OETriposTypeName
9.171 OETriposTypeNames
9.172 OEWriteCDXFile
9.173 OEWriteFASTAFile
9.174 OEWriteMacroModelFile
9.175 OEWriteMDLFile
9.176 OEWriteMOPACInputFile
9.177 OEWriteMol2File
9.178 OEWritePDBFile
9.179 OEWriteMolecule
9.180 OEWriteXYZFile
10. OEChem Functors
10.1 OEAtomIsInResidue
10.1.1 Constructor
10.1.2 operator()
10.2 OEAtomIsInRing
10.2.1 Constructor
10.2.2 operator()
10.3 OEBondIsInRing
10.3.1 Constructor
10.3.2 operator()
10.4 OEGetNbrAtom
10.4.1 Constructor
10.4.2 operator()
10.5 OEHasAlphaBetaUnsat
10.5.1 Constructor
10.5.2 operator()
10.6 OEHasAtomicNum
10.6.1 Constructor
10.6.2 operator()
10.7 OEHasAtomIdx
10.7.1 Constructor
10.7.2 operator()
10.8 OEHasAtomName
10.8.1 Constructor
10.8.2 operator()
10.9 OEHasAtomStereoSpecified
10.9.1 Constructor
10.9.2 operator()
10.10 OEHasBondIdx
10.10.1 Constructor
10.10.2 operator()
10.11 OEHasBondStereoSpecified
10.11.1 Constructor
10.11.2 operator()
10.12 OEHasChainID
10.12.1 Constructor
10.12.2 operator()
10.13 OEHasConfIdx
10.13.1 Constructor
10.13.2 operator()
10.14 OEHasFragmentNumber
10.14.1 Constructor
10.14.2 operator()
10.15 OEHasIdx
10.15.1 Constructor
10.15.2 operator()
10.16 OEHasMapIdx
10.16.1 Constructor
10.16.2 operator()
10.17 OEHasOrder
10.17.1 Constructor
10.17.2 operator()
10.18 OEHasResidueNumber
10.18.1 Constructor
10.18.2 operator()
10.19 OEIsAromaticAtom
10.19.1 Constructor
10.19.2 operator()
10.20 OEIsAromaticBond
10.20.1 Constructor
10.20.2 operator()
10.21 OEIsCAlpha
10.21.1 Constructor
10.21.2 operator()
10.22 OEIsCarbon
10.22.1 Constructor
10.22.2 operator()
10.23 OEIsChiralAtom
10.23.1 Constructor
10.23.2 operator()
10.24 OEIsChiralBond
10.24.1 Constructor
10.24.2 operator()
10.25 OEIsHalogen
10.25.1 Constructor
10.25.2 operator()
10.26 OEIsHeavy
10.26.1 Constructor
10.26.2 operator()
10.27 OEIsHydrogen
10.27.1 Constructor
10.27.2 operator()
10.28 OEIsMember
10.28.1 Constructors
10.28.2 operator()
10.29 OEIsMemberPtr
10.29.1 Constructors
10.29.2 operator()
10.29.3 CreateCopy()
10.30 OEIsNitrogen
10.30.1 Constructor
10.30.2 operator()
10.31 OEIsOxygen
10.31.1 Constructor
10.31.2 operator()
10.32 OEIsPhosphorus
10.32.1 Constructor
10.32.2 operator()
10.33 OEIsPolar
10.33.1 Constructor
10.33.2 operator()
10.34 OEIsPolarHydrogen
10.34.1 Constructor
10.34.2 operator()
10.35 OEIsRGroup
10.35.1 Constructor
10.35.2 operator()
10.36 OEIsRotor
10.36.1 Constructor
10.36.2 operator()
10.37 OEIsSulfur
10.37.1 Constructor
10.37.2 operator()
10.38 OEMatchFunc
10.38.1 Constructor
10.38.2 operator()
10.38.3 typedefs
10.39 OENthAtom
10.39.1 Constructor
10.39.2 operator()
10.40 OEPartPred
10.40.1 Constructor
10.40.2 SelectPart
10.40.3 operator()
11. OEChem Constants
11.1 OEAroModel Constants
12. OEChem Template Functions
12.1 OECalcInertialTensor
12.2 OESetCoordsToInertialFrame
13. OEChem Namespaces
13.1 OEAroType
13.2 OECounts
13.3 OEElemNo
13.4 OEExprOpts
13.4.1 Mass
13.4.2 HCount
13.4.3 ImplicitHCount
13.4.4 FormalCharge
13.4.5 StrictFormalCharge
13.4.6 Degree
13.4.7 ExplicitDegree
13.4.8 Valence
13.4.9 Hybridization
13.4.10 AtomicNumber
13.4.11 EqMetal
13.4.12 EqHalogen
13.4.13 EqON
13.4.14 EqONS
13.4.15 EqPS
13.4.16 EqAromatic
13.4.17 EqCHalogen
13.4.18 EqCAliphaticONS
13.4.19 EqCPSAcidRoot
13.4.20 EqKetoneSulfoneRoot
13.4.21 BondOrder
13.4.22 EqSingleDouble
13.4.23 EqDoubleTriple
13.4.24 EqNotAromatic
13.4.25 Aromaticity
13.4.26 RingMember
13.4.27 Chiral/Stereo
13.4.28 IntType
13.4.29 StringType
13.4.30 DefaultAtoms
13.4.31 DefaultBonds
13.4.32 ExactAtoms
13.4.33 ExactBonds
13.4.34 AutomorphAtoms
13.4.35 AutomorphBonds
13.5 OEExprType
13.6 OEFormat
13.7 OEFuzzVal
13.8 OEIFlavor
13.8.1 OEIFlavor::Generic
13.8.2 OEIFlavor::MMOD
13.8.3 OEIFlavor::MOL2
13.8.4 OEIFlavor::PDB
13.8.5 OEIFlavor::SMI
13.8.6 OEIFlavor::XYZ
13.9 OEOFlavor
13.9.1 OEOFlavor::CAN
13.9.2 OEOFlavor::Generic
13.9.3 OEOFlavor::ISM
13.9.4 OEOFlavor::MDL
13.9.5 OEOFlavor::MF
13.9.6 OEOFlavor::MMOD
13.9.7 OEOFlavor::MOL2
13.9.8 OEOFlavor::MOL2H
13.9.9 OEOFlavor::MOPAC
13.9.10 OEOFlavor::PDB
13.9.11 OEOFlavor::RDF
13.9.12 OEOFlavor::SDF
13.9.13 OEOFlavor::SMI
13.10 OEHybridization
13.11 OEHydrogenMode
13.12 OEMCMolType
13.13 OEMDLOFlag
13.14 OEMModTypes
13.15 OEMolBaseType
13.16 OEMOPACOFlag
13.17 OEPDBAtomName
13.18 OEPDBIFlag
13.19 OEPDBOFlag
13.20 OEPreserveResInfo
13.21 OEProperty
13.22 OEQMolType
13.23 OEResidueIndex
13.24 OERxnRole
13.25 OESmiFlag
13.26 OETriposType
13.27 OEWriteMolReturnCode
4 OESystem Library
14. OESystem Classes and Member Functions
14.1 OEBase
14.1.1 Constructors
14.1.2 AddData
14.1.3 Clear
14.1.4 CreateCopy
14.1.5 DeleteData
14.1.6 GetBoolData
14.1.7 GetData
14.1.8 GetDataIter
14.1.9 GetDataType
14.1.10 GetDoubleData
14.1.11 GetFloatData
14.1.12 GetIntData
14.1.13 GetStringData
14.1.14 HasData
14.1.15 IsDataType
14.1.16 SetBoolData
14.1.17 SetData
14.1.18 SetDoubleData
14.1.19 SetFloatData
14.1.20 SetIntData
14.1.21 SetStringData
14.2 OEBaseData
14.2.1 Constructor
14.2.2 CreateCopy
14.2.3 GetDataType
14.2.4 GetSize
14.2.5 GetTag
14.3 OEBitVector
14.3.1 Constructors
14.3.2 ClearBits
14.3.3 CountBits
14.3.4 FirstBit
14.3.5 FromHexString
14.3.6 GetData
14.3.7 GetSize
14.3.8 IsBitOn
14.3.9 IsEmpty
14.3.10 LastBit
14.3.11 NegateBits
14.3.12 NextBit
14.3.13 PrevBit
14.3.14 SetBitOff
14.3.15 SetBitOn
14.3.16 SetSize
14.3.17 ToggleBit
14.3.18 ToHexString
14.4 OEContainer
14.4.1 Constructors
14.5 OEDots
14.5.1 Constructors
14.5.2 GetCounts
14.5.3 Total
14.5.4 Update
14.6 OEErrorHandler
14.6.1 Error
14.6.2 Fatal
14.6.3 GetStrict
14.6.4 Info
14.6.5 SetOutputStream
14.6.6 SetStrict
14.6.7 Usage
14.6.8 Warning
14.7 OEErrorHandlerImplBase
14.8 OEInterface
14.8.1 Factory
14.8.2 Has
14.8.3 Get
14.8.4 SetOrderPriority
14.8.5 SetName
14.8.6 SetBrief
14.8.7 AddDetail
14.8.8 GetOrderPriority
14.8.9 GetName
14.8.10 GetBrief
14.8.11 GetDetail
14.8.12 AddParameter
14.8.13 DeleteParameter
14.8.14 GetParameter
14.8.15 GetTypedParameter
14.8.16 GetParameters
14.8.17 AddInterface
14.8.18 DeleteInterface
14.8.19 GetInterface
14.8.20 GetInterfaces
14.8.21 Parent
14.8.22 Clear
14.8.23 Constructor
14.8.24 Destructor
14.8.25 Copy Constructor
14.8.26 Assignment operator
14.9 OEParameter
14.9.1 IsSet
14.9.2 SetName
14.9.3 SetBrief
14.9.4 SetStringValue
14.9.5 SetStringDefault
14.9.6 SetHasValue
14.9.7 SetHasDefault
14.9.8 SetRequired
14.9.9 SetKeyless
14.9.10 SetVisibility
14.9.11 SetOrderPriority
14.9.12 AddDetail
14.9.13 AddAlias
14.9.14 AddLegalValue
14.9.15 AddIllegaValue
14.9.16 AddLegalRange
14.9.17 AddIllegalRange
14.9.18 GetName
14.9.19 GetBrief
14.9.20 GetStringValue
14.9.21 GetStringDefault
14.9.22 GetHasValue
14.9.23 GetHasDefault
14.9.24 GetRequired
14.9.25 GetKeyless
14.9.26 GetVisibility
14.9.27 GetOrderPriority
14.9.28 GetDetail
14.9.29 GetAlaises
14.9.30 GetLegalValues
14.9.31 GetIllegalValues
14.9.32 GetLegalRanges
14.9.33 GetIllegalRanges
14.9.34 Load
14.9.35 LoadValue
14.9.36 LoadDefault
14.9.37 IsLegalString
14.9.38 IsSetToString
14.9.39 TypeParameterTypeID
14.9.40 ClassID
14.9.41 WriteValueAndDefaultBinary
14.9.42 ReadValueAndDefaultBinary
14.9.43 ValueAndDefaultBinarySize
14.9.44 CreateCopy
14.9.45 Destructor
14.10 OERandom
14.10.1 Constructor
14.10.2 NextFloat
14.10.3 Seed
14.10.4 TimeSeed
14.11 OEStopwatch
14.11.1 Elapsed
14.11.2 Lap
14.11.3 Start
15. OESystem Functions
15.1 OEBitVectorAnd
15.2 OEBitVectorEqual
15.3 OEBitVectorNot
15.4 OEBitVectorOr
15.5 OEBitVectorSub
15.6 OEBitVectorXor
15.7 OEGetTag
15.8 OEGetThreadSafe
15.9 OEHasTag
15.10 OENumberToString
15.11 OESetThreadSafe
15.12 OEStringJoin
15.13 OEStringLower
15.14 OEStringMatch
15.15 OEStringSimplifyWhiteSpace
15.16 OEStringStripWhiteSpace
15.17 OEStringTokenize
15.18 OEStringTokenizeQuoted
15.19 OEStringToNumber
15.20 OEStringTranslate
15.21 OEStringUpper
15.22 OETanimoto
15.23 OEConfigure
15.23.1 Parameter record format
15.23.2 Category record format
15.24 OECheckHelp
15.25 OEParseCommandLine
15.26 OEParseCommandLineLW
15.27 OEWriteSettings
16. OESystem Templates
16.1 OEAnd
16.1.1 Constructor
16.2 OEFactory
16.2.1 Construct
16.2.2 Register
16.3 OEGetDataType
16.4 OEIter
16.4.1 Constructors
16.4.2 operator =
16.4.3 operator ==
16.4.4 operator !=
16.4.5 operator bool
16.4.6 operator
16.4.7 operator *
16.4.8 operator ++
16.4.9 operator -
16.4.10 operator +=
16.4.11 operator -=
16.4.12 Copy
16.4.13 ToFirst
16.4.14 ToLast
16.4.15 Sort
16.5 OEIterBase
16.6 OENot
16.6.1 Constructor
16.7 OEOr
16.7.1 Constructor
16.8 OETypedParameter
16.8.1 GetDefault
16.8.2 GetSetting
16.8.3 GetValue
16.8.4 SetDefault
16.8.5 SetValue
16.8.6 TypedParameterTypedID
16.9 OETypeId
16.10 OEUnaryFunction
16.10.1 Specializations
16.11 OEUnaryPredicate
17. OESystem Globals
17.1 OEThrow
5 OEMath Library
18. OEMath Constants
18.1 Deg2Rad
18.2 Pi
18.3 Pi2
18.4 Rad2Deg
19. OEMath Template Functions
19.1 OEGeom2DAdd
19.2 OEGeom2DAngle
19.3 OEGeom2DCopy
19.4 OEGeom2DDistance
19.5 OEGeom2DDistance2
19.6 OEGeom2DDotProd
19.7 OEGeom2DMidpoint
19.8 OEGeom2DNormalize
19.9 OEGeom2DSubtract
19.10 OEGeom2DScale
19.11 OEGeom3DAbsTorsion
19.12 OEGeom3DAdd
19.13 OEGeom3DAngle
19.14 OEGeom3DAngleCoord
19.15 OEGeom3DCopy
19.16 OEGeom3DCrossProd
19.17 OEGeom3DDistance
19.18 OEGeom3DDistance2
19.19 OEGeom3DDotProd
19.20 OEGeom3DEulerRotate
19.21 OEGeom3DMidpoint
19.22 OEGeom3DNormalize
19.23 OEGeom3DRotate
19.24 OEGeom3DRotVectorToTransform
19.25 OEGeom3DSubtract
19.26 OEGeom3DScale
19.27 OEGeom3DTorsion
19.28 OEGeom3DTranslate
19.29 OEGeom3DVolume
19.30 OEGeom3DPlanarCoord
19.31 OEGeom3DTetraCoord
19.32 OEGeom3DEulerToRotMatrix
19.33 OEGeomQuaternionMultiply
19.34 OEGeomNormalizeQuaternion
19.35 OEGeom3DQuaternionToRotMatrix
19.36 OEGeom3DMatrixMultiply
19.37 OEGeom3DQuaternionRotate
19.38 OEGeom3DUnitQuaternionRotate
6 OEPlatform Library
20. OEPlatform Classes and Member Functions
20.1 OEDirectoryScan
20.1.1 Constructors
20.1.2 operator bool
20.1.3 Close
20.1.4 Next
20.2 oeifstream
20.2.1 Constructors
20.2.2 fd
20.2.3 openfd
20.3 oeigzstream
20.3.1 Constructors
20.4 oeipstream
20.4.1 Constructors
20.5 oeisstream
20.5.1 Constructors
20.5.2 Operators
20.5.3 clear
20.5.4 getbuffer
20.5.5 reset
20.5.6 set
20.6 oeistdstream
20.6.1 Constructors
20.6.2 clear
20.6.3 set
20.6.4 stream
20.7 oeistream
20.7.1 Constructors
20.7.2 operator
20.7.3 close
20.7.4 get
20.7.5 getbyte
20.7.6 getline
20.7.7 gettoken
20.7.8 open
20.7.9 peekbyte
20.7.10 read
20.7.11 skip
20.7.12 skipbyte
20.7.13 skipline
20.8 oeiwrapperstream
20.8.1 Constructors
20.8.2 clear
20.8.3 set
20.8.4 stream
20.9 OEMutex
20.9.1 Acquire
20.9.2 Release
20.10 oeofstream
20.10.1 Constructors
20.10.2 append
20.10.3 fd
20.10.4 openfd
20.11 oeogzstream
20.11.1 Constructors
20.12 oeopstream
20.12.1 Constructors
20.13 oeosstream
20.13.1 Constructors
20.13.2 Operators
20.13.3 clear
20.13.4 set
20.13.5 str
20.14 oeostdstream
20.14.1 Constructors
20.14.2 clear
20.14.3 set
20.14.4 stream
20.15 oeostream
20.15.1 Constructors
20.15.2 operator
20.15.3 close
20.15.4 flush
20.15.5 open
20.15.6 putbyte
20.15.7 write
20.16 oeowrapperstream
20.16.1 Constructors
20.16.2 clear
20.16.3 set
20.16.4 stream
20.17 oestream
20.17.1 Constructors
20.17.2 operator bool
20.17.3 eof
20.17.4 length
20.17.5 rewind
20.17.6 seek
20.17.7 size
20.17.8 tell
20.18 OETryMutex
20.18.1 Acquire
20.18.2 Release
20.18.3 Try
21. OEPlatform Functions
21.1 OECloseIStream
21.2 OECloseOStream
21.3 OECompressionAvailable
21.4 OECompress
21.5 OECreateDirectory
21.6 oeendl
21.7 oeends
21.8 oeflush
21.9 OEGetUserName
21.10 OEOpenIStream
21.11 OEOpenOStream
21.12 OERegisterIStream
21.13 OERegisterOStream
21.14 OERenameFile
21.15 OESleep
21.16 OEUncompress
21.17 OEUnlink
21.18 OEUnlinkDirectory
21.19 operator
22. OEPlatform Globals
22.1 oeerr
22.2 oein
22.3 oenul
22.4 oeout
OEChem - API Manual
Previous:
Front Matter
Up:
OEChem - API Manual
Next:
1 Introduction
Documentation released on June 4, 2008.
