8. OEChem Classes and Member Functions

Subsections

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 $\vert\vert$
- 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