OESpruce Classes¶

OEBioUnitExtractionOptions
- Constructors
- operator=
- GetMaxAtoms
- GetMaxParts
- GetMinScore
- GetPreferAuthorRecord
- GetSuperpose
- SetMaxAtoms
- SetMaxParts
- SetMinScore
- SetPreferAuthorRecord
- SetSuperpose
OECapBuilderOptions
- Constructors
- operator=
- GetDeleteClashingSolvent
- GetAllowTruncate
- GetForceCapping
- SetDeleteClashingSolvent
- SetAllowTruncate
- SetForceCapping
OEDesignUnitBuildOptions
- Constructors
- operator=
- GetBuildLoops
- GetBuildSidechains
- GetCapCTermini
- GetCapNTermini
- GetSidechainBuilderOptions
- GetLoopBuilderOptions
- GetCapBuilderOptions
- SetBuildLoops
- SetBuildSidechains
- SetCapCTermini
- SetCapNTermini
- SetSidechainBuilderOptions
- SetCapBuilderOptions
- SetLoopBuilderOptions
OEDesignUnitEnumerateSitesOptions
- Constructors
- operator=
- GetAddInteractionHints
- GetAddStyle
- GetCollapseNonSiteAlts
- GetDuplicateRemoval
- GetEnumerateCofactorSites
- GetRestrictToRefSite
- GetSiteSize
- SetAddInteractionHints
- SetAddStyle
- SetCollapseNonSiteAlts
- SetDuplicateRemoval
- SetEnumerateCofactorSites
- SetRestrictToRefSite
- SetSiteSize
OEDesignUnitMutationOptions
- Constructors
- operator=
- AddMutation
- ClearMutations
- GetMutations
- SetMutations
OEDesignUnitPrepOptions
- Constructors
- operator=
- GetAssignPartialChargesAndRadii
- GetBuildOptions
- GetChargeEngine
- GetEnumerateSitesOptions
- GetProtonate
- GetStrictProtonationMode
- GetProtonateOptions
- SetAssignPartialChargesAndRadii
- SetBuildOptions
- SetChargeEngine
- SetEnumerateSitesOptions
- SetProtonate
- SetStrictProtonationMode
- SetProtonateOptions
OEDesignUnitSplitOptions
- Constructors
- operator=
- AddCofactorCode
- AddExcipientCode
- AddLipidCode
- ClearCofactorCodes
- ClearExcipientCodes
- ClearLipidCodes
- GetAlternateLocationHandling
- GetCofactorCodes
- GetExcipientCodes
- GetLipidCodes
- GetMakePackingResidues
- GetMaxLigAtoms
- GetMaxLigResidues
- GetMaxSystemAtoms
- GetMinLigAtoms
- GetTargetComponentID
- SetAlternateLocationHandling
- SetCofactorCodes
- SetExcipientCodes
- SetLipidCodes
- SetMakePackingResidues
- SetMaxLigAtoms
- SetMaxLigResidues
- SetMaxSystemAtoms
- SetMinLigAtoms
- SetTargetComponentID
OEHeterogenMetadata
- Constructors
- operator=
- AddTautomer
- AddTautomers
- ClearTautomers
- GetID
- GetSmiles
- GetTautomers
- GetTitle
- GetType
- SetID
- SetSmiles
- SetTitle
- SetType
OEIsModeledAtom
- Constructors
- operator()
- CreateCopy
OELoopBuilderOptions
- GetOptimizationStage2IterMultiplier
- GetOptimizationUseSolventModel
- GetOptimizationInclSurfaceAreaTerm
- GetOptimizationMaxLoops
- GetAllowBuildDisulfideBridges
- GetSeqAlignMethod
- GetSeqAlignGapPenalty
- GetSeqAlignExtendPenalty
- GetBuildTails
- SetLoopDBFilename
- SetUsePackingResidues
- SetCropLength
- SetTransformThreshold
- SetStrictProlineMatch
- SetConnectBufferDistance
- SetBackboneClashRejectThreshold
- SetLoopClashRejectThreshold
- SetOptimizationShell
- SetOptimizationTolerance
- SetOptimizationStage1IterMultiplier
- SetOptimizationStage2IterMultiplier
- SetOptimizationUseSolventModel
- SetOptimizationInclSurfaceAreaTerm
- SetOptimizationMaxLoops
- SetAllowBuildDisulfideBridges
- SetSeqAlignMethod
- SetSeqAlignGapPenalty
- SetSeqAlignExtendPenalty
- SetBuildTails
OEMakeDesignUnitOptions
- Constructors
- operator=
- GetBioUnitExtractionOptions
- GetPrepOptions
- GetSplitOptions
- GetSuperpose
- GetSuperpositionMethod
- SetBioUnitExtractionOptions
- SetPrepOptions
- SetSplitOptions
- SetSuperpose
- SetSuperpositionMethod
OEPocket
- Constructors
- operator=
- GetSurfaceArea
- GetLocalDensity
- GetPocketPredicate
- GetPocketSurface
- GetAtoms
- GetResidues
OEPocketOptions
- Constructors
- operator=
- GetMinSurfaceArea
- GetMaxSurfaceArea
- GetBurialFactor
- SetMinSurfaceArea
- SetMaxSurfaceArea
- SetBurialFactor
OEProtonateDesignUnitOptions
- Constructors
- operator=
- GetGenerateTautomers
- GetHetGroupNbrDist
- GetOptimizeExpProtons
- GetPlaceHydrogensOptions
- SetGenerateTautomers
- SetHetGroupNbrDist
- SetOptimizeExpProtons
- SetPlaceHydrogensOptions
OESidechainBuilderOptions
- Constructors
- operator=
- GetDeleteClashingSolvent
- GetRotamerLibrary
- GetStrictMode
- SetRotamerCoverage
- SetRotamerLibrary
- SetDeleteClashingSolvent
- SetStrictMode
OESequenceMetadata
- Constructors
- operator=
- GetChainID
- GetEndResidueInsertCode
- GetEndResidueNumber
- GetSequence
- GetStartResidueInsertCode
- GetStartResidueNumber
- SetChainID
- SetEndResidueInsertCode
- SetEndResidueNumber
- SetSequence
- SetStartResidueInsertCode
- SetStartResidueNumber
OEStructureMetadata
- Constructors
- operator=
- AddHeterogenMetadata
- AddKeyword
- AddKeywords
- AddSequenceMetadata
- ClearHeterogenMetadata
- ClearKeywords
- ClearSequenceMetadata
- GetAuthor
- GetExperimentDate
- GetExperimentType
- GetHeterogenMetadata
- GetIridiumData
- GetKeywords
- GetRevision
- GetRevisionDate
- GetSequenceMetadata
- GetStructureID
- SetAuthor
- SetExperimentDate
- SetExperimentType
- SetIridiumData
- SetRevision
- SetRevisionDate
- SetStructureID
OESecondaryStructureSuperposition
- Constructors
- operator=
- operator bool
- GetFitChains
- GetRefChains
- GetRotMatrix
- GetTanimoto
- GetTranslation
- Transform
OESpruceFilter
- Constructors
- operator=
- StandardizeAndFilter
- GetMessages
- GetAtoms
OESpruceFilterOptions
- Constructors
- operator=
- GetFixBondOrder
- SetFixBondOrder
- GetFixNames
- SetFixNames
- GetFixBondsToMetals
- SetFixBondsToMetals
- GetFixBackboneAtoms
- SetFixBackboneAtoms
- GetDeleteFloatingRes
- SetDeleteFloatingRes
- GetFixLigandState
- SetFixLigandState
OEStructuralSuperposition
- Constructors
- operator=
- operator bool
- ConstraintsMet
- GetFitChains
- GetRMSD
- GetRefChains
- GetRegion
- GetRotMatrix
- GetScore
- GetTranslation
- Transform
OESuperpositionOptions
- Constructors
- operator=
- AddSiteResidue
- ClearLigandConstraints
- ClearSiteResidues
- GetDist
- GetLigandConstraints
- GetSiteResidues
- GetSuperpositionType
- HasLigandConstraints
- SetDist
- SetLigandConstraints
- SetSiteResidues
- SetSuperpositionType
OESuperpose
- SetMethod
  - Superpose
OESuperposeOptions
- Constructors
- operator=
OESuperposeResults
- Constructors
- operator=
- operator bool
- IsValid
- Transform
- GetTransform
- GetRotMatrix
- GetTranslation
- HasRMSD
- HasTanimoto
- HasSeqScore
- GetRMSD
- GetTanimoto
- GetSeqScore
- GetRefChains
- GetFitChains
OEValidateDesignUnit
- Constructors
- operator=
- Validate
- GetMessages
- GetAtoms