OEChem - API Manual
Version 1.3.1
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OEChem - API Manual
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3. OEChem Classes and
1 OEChem Library
Subsections
3. OEChem Classes and Member Functions
3.1 OEAtomBase
3.1.1 GetAtomicNum
3.1.2 GetAtoms
3.1.3 GetBond
3.1.4 GetBonds
3.1.5 GetDegree
3.1.6 GetExplicitDegree
3.1.7 GetExplicitHCount
3.1.8 GetExplicitValence
3.1.9 GetFormalCharge
3.1.10 GetHvyDegree
3.1.11 GetHvyValence
3.1.12 GetHyb
3.1.13 GetIdx
3.1.14 GetImplicitHCount
3.1.15 GetIntType
3.1.16 GetIsotope
3.1.17 GetMapIdx
3.1.18 GetName
3.1.19 GetParent
3.1.20 GetPartialCharge
3.1.21 GetRadius
3.1.22 GetRxnRole
3.1.23 GetSymmetryClass
3.1.24 GetTotalHCount
3.1.25 GetType
3.1.26 GetValence
3.1.27 IsAromatic
3.1.28 IsCarbon
3.1.29 IsConnected
3.1.30 IsHalogen
3.1.31 IsHydrogen
3.1.32 IsInRing
3.1.33 IsMetal
3.1.34 IsNitrogen
3.1.35 IsOxygen
3.1.36 IsPhosphorus
3.1.37 IsPolar
3.1.38 IsPolarHydrogen
3.1.39 IsSulfur
3.1.40 SetAromatic
3.1.41 SetAtomicNum
3.1.42 SetFormalCharge
3.1.43 SetHyb
3.1.44 SetImplicitHCount
3.1.45 SetIntType
3.1.46 SetInRing
3.1.47 SetIsotope
3.1.48 SetMapIdx
3.1.49 SetName
3.1.50 SetPartialCharge
3.1.51 SetRadius
3.1.52 SetRxnRole
3.1.53 SetStereo
3.1.54 SetSymmetryClass
3.1.55 SetType
3.2 OEBondBase
3.2.1 GetBgn
3.2.2 GetBgnIdx
3.2.3 GetEnd
3.2.4 GetEndIdx
3.2.5 GetIdx
3.2.6 GetIntType
3.2.7 GetNbr
3.2.8 GetOrder
3.2.9 GetParent
3.2.10 GetType
3.2.11 IsAromatic
3.2.12 IsInRing
3.2.13 IsRotor
3.2.14 SetAromatic
3.2.15 SetBgn
3.2.16 SetEnd
3.2.17 SetIntType
3.2.18 SetInRing
3.2.19 SetOrder
3.2.20 SetStereo
3.2.21 SetType
3.2.22 SwapEnds
3.3 OECartesianToInternal
3.3.1 reset
3.3.2 update
3.4 OECliqueSearch
3.4.1 Constructors
3.4.2 AddConstraint
3.4.3 ClearConstraints
3.4.4 GetMaxMatches
3.4.5 GetMinAtoms
3.4.6 GetPattern
3.4.7 GetSaveRange
3.4.8 Init
3.4.9 Match
3.4.10 SingleMatch
3.5 OEConfBase
3.6 OEConfBaseT
3.6.1 coord_type
3.6.2 Copy
3.6.3 Constructors
3.6.4 operator=
3.6.5 AddAtom
3.6.6 AddBond
3.6.7 RemoveAtom
3.6.8 RemoveBond
3.6.9 MCMol
3.6.10 Conformer Indices
3.6.11 SetCoords
3.6.12 GetCoords
3.6.13 Deletion
3.6.14
Torsions
3.6.15 Transformations
3.6.16 Title
3.6.17 OEMolBase
3.6.18 OEBase
3.7 OEConfTest
3.7.1 CompareMols
3.7.2 CreateCopy
3.7.3 OEDefaultConfTest
3.7.4 OEIsomericConfTest
3.7.5 OEAbsoluteConfTest
3.7.6 OEAbsCanonicalConfTest
3.8 OEEuler
3.9 OEExprBase
3.9.1 IsEquivalent
3.9.2 CreateCopy
3.9.3 GetType
3.10 OEFuzzy
3.10.1 Constructor
3.10.2 operator bool
3.10.3 operator !
3.10.4 operator &&
3.10.5 operator
3.10.6 operator ==
3.10.7 operator !=
3.11 OEInternalToCartesian
3.11.1 reset
3.11.2 update
3.12 OELibaryGen
3.12.1 Constructors
3.12.2 AddStartingMaterial
3.12.3 operator()
3.12.4 operator bool
3.12.5 ClearStartingMaterial
3.12.6 GetExplicitHydrogens
3.12.7 GetProducts
3.12.8 GetReactants
3.12.9 GetValenceCorrection
3.12.10 Init
3.12.11 NumReactants
3.12.12 SetExplicitHydrogens
3.12.13 SetStartingMaterial
3.12.14 SetValenceCorrection
3.13 OEMatch
3.13.1 OEMatch Constructors
3.13.2 operator =
3.13.3 AddPair
3.13.4 CreateCopy
3.13.5 GetAtoms
3.13.6 GetBonds
3.13.7 GetPatternAtoms
3.13.8 GetPatternBonds
3.13.9 GetTargetAtoms
3.13.10 GetTargetBonds
3.13.11 NumAtoms
3.13.12 NumBonds
3.14 OEMatchBase
3.14.1 CreateCopy
3.14.2 GetAtoms
3.14.3 GetBonds
3.14.4 GetPatternAtoms
3.14.5 GetPatternBonds
3.14.6 GetTargetAtoms
3.14.7 GetTargetBonds
3.14.8 NumAtoms
3.14.9 NumBonds
3.15 OEMatchPair
3.15.1 Constructors
3.15.2 operator =
3.16 OEMCMolBase
3.17 OEMCMolBaseT
3.17.1 ConfType
3.17.2 Copy
3.17.3 Constructors
3.17.4 operator=
3.17.5 Active Conformer
3.17.6 GetMaxConfIdx
3.17.7 NewConf
3.17.8 NumConfs
3.17.9 GetConf
3.17.10 Delete Conformers
3.17.11 SweepConfs
3.17.12 OrderConfs
3.17.13 GetConfs
3.17.14 OEMolBase
3.17.15 OEBase
3.18 OEMCSFunc
3.18.1 operator()
3.18.2 CreateCopy
3.19 OEMCSMaxAtoms
3.20 OEMCSMaxBonds
3.21 OEMCSMaxAtomsCompleteCycles
3.21.1 Constructor
3.22 OEMCSSearch
3.22.1 Constructor
3.22.2 operator=
3.22.3 operator bool
3.22.4 AddConstraint
3.22.5 ClearConstraints
3.22.6 GetMaxMatches
3.22.7 GetMinAtoms
3.22.8 GetPattern
3.22.9 GetSaveRange
3.22.10 Init
3.22.11 Match
3.22.12 SetMCSFunc
3.22.13 SetMaxMatches
3.22.14 SetMinAtoms
3.22.15 SetSaveRange
3.22.16 SingleMatch
3.23 OEMol
3.23.1 Constructors
3.23.2 operator =
3.23.3 operator bool
3.23.4 ConfIdxArraySize
3.23.5 DeleteConfs
3.23.6 DeleteConf
3.23.7 GetActive
3.23.8 GetConf
3.23.9 GetConfs
3.23.10 IsDeleted
3.23.11 NewConf
3.23.12 NumConfs
3.23.13 OrderConfs
3.23.14 PopActive
3.23.15 PushActive
3.23.16 ResetConf
3.23.17 SetActive
3.23.18 SweepConfs
3.24 OEMolBase
3.24.1 operator =
3.24.2 operator +=
3.24.3 operator bool
3.24.4 Clear
3.24.5 Compress
3.24.6 DeleteAtom
3.24.7 DeleteBond
3.24.8 GetAtom
3.24.9 GetAtoms
3.24.10 GetBond
3.24.11 GetBonds
3.24.12 GetCoords
3.24.13 GetDimension
3.24.14 GetEnergy
3.24.15 GetMaxAtomIdx
3.24.16 GetMaxBondIdx
3.24.17 GetTitle
3.24.18 IsRxn
3.24.19 NewAtom
3.24.20 NewBond
3.24.21 NumAtoms
3.24.22 NumBonds
3.24.23 OrderAtoms
3.24.24 OrderBonds
3.24.25 SetCoords
3.24.26 SetDimension
3.24.27 SetEnergy
3.24.28 SetRxn
3.24.29 SetTitle
3.24.30 Sweep
3.24.31 UnCompress
3.25 oemolistream
3.25.1 operator
3.25.2 close
3.25.3 GetFlavor
3.25.4 GetFormat
3.25.5 Getgz
3.25.6 open
3.25.7 SetConfTest
3.25.8 SetFormat
3.25.9 SetFlavor
3.26 oemolostream
3.26.1 operator
3.26.2 close
3.26.3 GetFormat
3.26.4 open
3.26.5 SetFormat
3.27 OEQAtomBase
3.27.1 GetQAtoms
3.27.2 GetQBonds
3.28 OEQBase
3.28.1 SetExpr
3.28.2 GetExpr
3.29 OEQBondBase
3.30 OEQMol
3.30.1 Constructors
3.30.2 operator +=
3.30.3 operator OEMolBase
3.30.4 operator OEQMolBase
3.30.5 SCMol
3.30.6 QMol
3.31 OEQMolBase
3.31.1 operator=
3.31.2 operator +=
3.31.3 BuildExpressions
3.31.4 GetQAtoms
3.31.5 GetQBonds
3.32 OEQuaternion
3.33 OERotMatrix
3.34 OEResidue
3.34.1 operator =
3.34.2 operator bool
3.34.3 GetAlternateLocation
3.34.4 GetBFactor
3.34.5 GetChainID
3.34.6 GetFragmentNumber
3.34.7 GetInsertCode
3.34.8 GetModelNumber
3.34.9 GetName
3.34.10 GetOccupancy
3.34.11 GetResidueNumber
3.34.12 GetSecondaryStructure
3.34.13 GetSerialNumber
3.34.14 IsHetAtom
3.34.15 SetAlternateLocation
3.34.16 SetBFactor
3.34.17 SetChainID
3.34.18 SetFragmentNumber
3.34.19 SetHetAtom
3.34.20 SetInsertCode
3.34.21 SetModelNumber
3.34.22 SetName
3.34.23 SetOccupancy
3.34.24 SetResidueNumber
3.34.25 SetSecondaryStructure
3.34.26 SetSerialNumber
3.35 OESubSearch
3.35.1 Constructors
3.35.2 operator =
3.35.3 operator bool
3.35.4 AddConstraint
3.35.5 AtomMatch
3.35.6 ClearConstraints
3.35.7 GetMaxMatches
3.35.8 GetPattern
3.35.9 Init
3.35.10 Match
3.35.11 SingleMatch
3.35.12 SetMaxMatches
3.36 OETrans
3.36.1 Construction and Initialization
3.36.2 Adding Transformations
3.36.3 OETransBase Access
3.36.4 Transform
3.37 OETransBase
3.37.1 CreateCopy
3.37.2 Transform
3.37.3 Protected Transformations
3.38 OETranslation
3.39 OEUniMolecularRxn
3.39.1 Constructors
3.39.2 Init
3.39.3 operator()
3.39.4 operator bool
3.40 OEVectorBindings
3.40.1 Constructors
3.40.2 operator=
3.40.3 Add
3.40.4 Get
4. OEChem Functions
4.1 OE3DToAtomStereo
4.2 OE3DToBondStereo
4.3 OE3DToInternalStereo
4.4 OEAddExplicitHydrogens
4.5 OEAddMols
4.6 OEAssignAromaticFlags
4.7 OEAssignFormalCharges
4.8 OEAssignHybridization
4.9 OEAssignImplicitHydrogens
4.10 OEAssignMDLHydrogens
4.11 OEAssignResidueNumbers
4.12 OEAssignSerialNumbers
4.13 OEAtomGetResidue
4.14 OEAtomGetSmallestRingSize
4.15 OEAtomIsInAromaticRingSize
4.16 OEAtomIsInRingSize
4.17 OEAtomSetResidue
4.18 OEBondGetSmallestRingSize
4.19 OEBondIsInAromaticRingSize
4.20 OEBondIsInRingSize
4.21 OECalcCartesianCoord
4.22 OECalcInternalCoord
4.23 OECalculateMolecularWeight
4.24 OECanonicalOrderAtoms
4.25 OECanonicalOrderBonds
4.26 OEChemGetRelease
4.27 OEChemGetVersion
4.28 OECenter
4.29 OEClearAromaticFlags
4.30 OEClearPartialCharges
4.31 OECreateAbsSmiString
4.32 OECreateCanSmiString
4.33 OECreateIsoSmiString
4.34 OECreateSlnString
4.35 OECreateSmiString
4.36 OEDefaultImplicitHCount
4.37 OEDefaultMDLHCount
4.38 OEDeleteEverythingExceptTheFirstLargestComponent
4.39 OEDetermineComponents
4.40 OEDetermineConnectivity
4.41 OEDetermineRingSystems
4.42 OEEulerRotate
4.43 OEExactGraphMatch
4.44 OEExpandSuperAtoms
4.45 OEFindRingAtomsAndBonds
4.46 OEFormalPartialCharges
4.47 OEGasteigerInitialCharges
4.48 OEGasteigerPartialCharges
4.49 OEGetAbsTorsion
4.50 OEGetAngle
4.51 OEGetAtomicNum
4.52 OEGetAtomicSymbol
4.53 OEGetAutomorphs
4.54 OEGetAverageWeight
4.55 OEGetBondiVdWRadius
4.56 OEGetCovalentRadius
4.57 OEGetDefaultMass
4.58 OEGetDistance
4.59 OEGetDistance2
4.60 OEGetFileExtension
4.61 OEGetFileType
4.62 OEGetFormatString
4.63 OEGetHybridization
4.64 OEGetIsotopicWeight
4.65 OEGetPackedCoords
4.66 OEGetPaulingVdWRadius
4.67 OEGetPDBAtomIndex
4.68 OEGetPDBAtomName
4.69 OEGetPathLength
4.70 OEGetResidueIndex
4.71 OEGetResidueName
4.72 OEGetSmallestSubtree
4.73 OEGetSubtree
4.74 OEGetSubtree
4.75 OEGetTorsion
4.76 OEHasDoubleBond
4.77 OEHasExplicitHydrogens
4.78 OEHasImplicitHydrogens
4.79 OEHasPartialCharges
4.80 OEHasResidue
4.81 OEHasResidues
4.82 OEHasSingleBond
4.83 OEHasTripleBond
4.84 OEIsCommonIsotope
4.85 OEIsReadable
4.86 OEIsWriteable
4.87 OEKekulize
4.88 OEMacroModelAtomTypes
4.89 OEMacroModelAtomTypeNames
4.90 OEMacroModelTypeElement
4.91 OEMacroModelTypeName
4.92 OEMacroModelTypeNames
4.93 OEMDLClearParity
4.94 OEMDLCorrectBondStereo
4.95 OEMDLHasIncorrectBondStereo
4.96 OEMDLHasParity
4.97 OEMDLPerceiveBondStereo
4.98 OEMDLPerceiveParity
4.99 OEMDLStereoFromBondStereo
4.100 OEMDLStereoFromParity
4.101 OEMolecularFormula
4.102 OENetCharge
4.103 OENewMCMolBase
4.104 OENewMolBase
4.105 OENewQMolBase
4.106 OEParseSmarts
4.107 OEParseSmiles
4.108 OEParseSmirks
4.109 OEPDBOrderAtoms
4.110 OEPerceiveBondOrders
4.111 OEPerceiveChiral
4.112 OEPerceiveResidues
4.113 OEPerceiveSymmetry
4.114 OERandomizeTorsions
4.115 OEReadCDXFile
4.116 OEReadFASTAFile
4.117 OEReadMacroModelFile
4.118 OEReadMDLFile
4.119 OEReadMol2File
4.120 OEReadMolecule
4.121 OEReadMOPACFile
4.122 OEReadOldBinary
4.123 OEReadPDBFile
4.124 OEReadXYZFile
4.125 OEResidueHydrogens
4.126 OERMSD
4.126.1 Array-Based OERMSD
4.126.2 Full Molecule-Based OERMSD
4.126.3 Partial Molecule-Based OERMSD
4.127 OERotate
4.128 OESameChain
4.129 OESameResidue
4.130 OEScrambleMolecule
4.131 OESet3DHydrogenGeom
4.132 OESetDimensionFromCoords
4.133 OESetPackedCoords
4.134 OESetTorsion
4.135 OESmilesAtomCount
4.136 OESubsetMol
4.137 OESuppressHydrogens
4.138 OETheFunctionFormerlyKnownAsStripSalts
4.139 OETranslate
4.140 OETriposAtomNames
4.141 OETriposAtomType
4.142 OETriposAtomTypes
4.143 OETriposAtomTypeNames
4.144 OETriposBondTypeNames
4.145 OETriposTypeElement
4.146 OETriposTypeIndex
4.147 OETriposTypeName
4.148 OETriposTypeNames
4.149 OEWriteCDXFile
4.150 OEWriteFASTAFile
4.151 OEWriteMacroModelFile
4.152 OEWriteMDLFile
4.153 OEWriteMOPACInputFile
4.154 OEWriteMol2File
4.155 OEWritePDBFile
4.156 OEWriteMolecule
4.157 OEWriteXYZFile
5. OEChem Functors
5.1 OEHasIdx
5.1.1 Constructor
5.1.2 operator()
5.1.3 Typedefs
5.2 OEHasAtomName
5.2.1 Constructor
5.2.2 operator()
5.3 OEHasChainID
5.3.1 Constructor
5.3.2 operator()
5.4 OEHasResidueNumber
5.4.1 Constructor
5.4.2 operator()
5.5 OEHasFragmentNumber
5.5.1 Constructor
5.5.2 operator()
5.6 OEHasMapIdx
5.6.1 Constructor
5.6.2 operator()
5.7 OEHasAtomicNum
5.7.1 Constructor
5.7.2 operator()
5.8 OEIsRGroup
5.8.1 Constructor
5.8.2 operator()
5.9 OENthAtom
5.9.1 Constructor
5.9.2 operator()
5.10 OEMatchFunc
5.10.1 Constructor
5.10.2 operator()
5.10.3 typedefs
5.11 OEIsHydrogen
5.11.1 Constructor
5.11.2 operator()
5.12 OEIsHeavy
5.12.1 Constructor
5.12.2 operator()
5.13 OEIsPolar
5.13.1 Constructor
5.13.2 operator()
5.14 OEIsPolarHydrogen
5.14.1 Constructor
5.14.2 operator()
5.15 OEIsCarbon
5.15.1 Constructor
5.15.2 operator()
5.16 OEIsCAlpha
5.16.1 Constructor
5.16.2 operator()
5.17 OEIsNitrogen
5.17.1 Constructor
5.17.2 operator()
5.18 OEIsOxygen
5.18.1 Constructor
5.18.2 operator()
5.19 OEIsHalogen
5.19.1 Constructor
5.19.2 operator()
5.20 OEIsSulfur
5.20.1 Constructor
5.20.2 operator()
5.21 OEIsPhosphorus
5.21.1 Constructor
5.21.2 operator()
5.22 OEIsAromaticAtom
5.22.1 Constructor
5.22.2 operator()
5.23 OEAtomIsInRing
5.23.1 Constructor
5.23.2 operator()
5.24 OEIsChiralAtom
5.24.1 Constructor
5.24.2 operator()
5.25 OEHasAtomStereoSpecified
5.25.1 Constructor
5.25.2 operator()
5.26 OEHasAlphaBetaUnsat
5.26.1 Constructor
5.26.2 operator()
5.27 OEAtomIsInResidue
5.27.1 Constructor
5.27.2 operator()
5.28 OEHasOrder
5.28.1 Constructor
5.28.2 operator()
5.29 OEBondIsInRing
5.29.1 Constructor
5.29.2 operator()
5.30 OEIsRotor
5.30.1 Constructor
5.30.2 operator()
5.31 OEIsChiralBond
5.31.1 Constructor
5.31.2 operator()
5.32 OEHasBondStereoSpecified
5.32.1 Constructor
5.32.2 operator()
5.33 OEIsAromaticBond
5.33.1 Constructor
5.33.2 operator()
5.34 OEGetNbrAtom
5.34.1 Constructor
5.34.2 operator()
5.35 OEPartPred
5.35.1 Constructor
5.35.2 SelectPart
5.35.3 operator()
5.36 OEIsMember
5.36.1 Constructors
5.36.2 operator()
5.37 OEIsMemberPtr
5.37.1 Constructors
5.37.2 operator()
5.37.3 CreateCopy()
6. OEChem Constants
6.1 OEAroModel Constants
7. OEChem Template Functions
7.1 OECalcInertialTensor
7.2 OESetCoordsToInertialFrame
8. OEChem Namespaces
8.1 OEAroType
8.2 OECounts
8.3 OEElemNo
8.4 OEExprOpts
8.4.1 Mass
8.4.2 HCount
8.4.3 ImplicitHCount
8.4.4 FormalCharge
8.4.5 StrictFormalCharge
8.4.6 Degree
8.4.7 ExplicitDegree
8.4.8 Valence
8.4.9 Hybridization
8.4.10 AtomicNumber
8.4.11 EqMetal
8.4.12 EqHalogen
8.4.13 EqON
8.4.14 EqONS
8.4.15 EqPS
8.4.16 EqAromatic
8.4.17 EqCHalogen
8.4.18 EqCAliphaticONS
8.4.19 EqCPSAcidRoot
8.4.20 EqKetoneSulfoneRoot
8.4.21 BondOrder
8.4.22 EqSingleDouble
8.4.23 EqDoubleTriple
8.4.24 EqNotAromatic
8.4.25 Aromaticity
8.4.26 RingMember
8.4.27 Chiral/Stereo
8.4.28 IntType
8.4.29 StringType
8.4.30 DefaultAtoms
8.4.31 DefaultBonds
8.4.32 ExactAtoms
8.4.33 ExactBonds
8.4.34 AutomorphAtoms
8.4.35 AutomorphBonds
8.5 OEExprType
8.6 OEFormat
8.7 OEFuzzVal
8.8 OEIFlavor
8.8.1 OEIFlavor::Generic
8.8.2 OEIFlavor::MMOD
8.8.3 OEIFlavor::MOL2
8.8.4 OEIFlavor::PDB
8.8.5 OEIFlavor::SMI
8.8.6 OEIFlavor::XYZ
8.9 OEOFlavor
8.9.1 OEOFlavor::CAN
8.9.2 OEOFlavor::Generic
8.9.3 OEOFlavor::ISM
8.9.4 OEOFlavor::MDL
8.9.5 OEOFlavor::MF
8.9.6 OEOFlavor::MMOD
8.9.7 OEOFlavor::MOL2
8.9.8 OEOFlavor::MOL2H
8.9.9 OEOFlavor::MOPAC
8.9.10 OEOFlavor::PDB
8.9.11 OEOFlavor::RDF
8.9.12 OEOFlavor::SDF
8.9.13 OEOFlavor::SMI
8.10 OEHybridization
8.11 OEHydrogenMode
8.12 OEMCMolType
8.13 OEMDLOFlag
8.14 OEMModTypes
8.15 OEMolBaseType
8.16 OEMOPACOFlag
8.17 OEPDBAtomName
8.18 OEPDBIFlag
8.19 OEPDBOFlag
8.20 OEProperty
8.21 OEQMolType
8.22 OEResidueIndex
8.23 OERxnRole
8.24 OESmiFlag
8.25 OETriposType
OEChem - API Manual
Version 1.3.1
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2.3 Third Party Compilers
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OEChem - API Manual
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3. OEChem Classes and
Documentation released on July 30, 2004.
