Spruce Toolkit 1.9.0.0
Attention
Spruce TK is currently only available in C++ and Python.
- Introduction
- Theory
- Iridium
- Advanced Macromolecular Preparation Workflow
- Inputs
- Filtering and Standardization
- Generating the Biological Unit
- Generating Packing Residues
- Enumerating Alternate Locations
- Componentizing the System
- Building Missing Pieces
- Optimizing the Hydrogen Bond Network
- Assignment on Radii and Partial Charges
- Prepared Biological Units (BioDUs)
- Enumerating Sites / Pockets
- Assigning an Iridium Category
- Generating a Docking Receptor
- Superposition to a Common Frame of Reference
- Design Unit Validation
- Examples
- Spruce TK Examples
- Creating OEDesignUnits from a PDB file
- Creating apo OEDesignUnits from a PDB file
- Creating mmcif file from an input DU
- Calculating superposition
- Extracting Biounits from PDB header remarks
- Extracting Biounits by aligning to a reference protein
- Finding pockets and their properties (like, Surface Area) from a PDB file
- Write a metadata JSON file from a FASTA file
- Validate Structure of the Design Unit
- Add Receptor Grid to Design Unit
- Creating OEDesignUnits Using Provided Metadata
- Spruce TK Examples
- Appendix: Additional Examples in Python
- OESpruce API
- OESpruce Classes
- OEBioUnitExtractionOptions
- OECapBuilderOptions
- OEDesignUnitBuildOptions
- OEDesignUnitEnumerateSitesOptions
- OEDesignUnitMutationOptions
- OEDesignUnitPrepOptions
- OEDesignUnitSplitOptions
- OEHeterogenMetadata
- OEIsModeledAtom
- OELoopBuilderOptions
- OEMakeDesignUnitOptions
- OEPocket
- OEPocketOptions
- OEProtonateDesignUnitOptions
- OESidechainBuilderOptions
- OESequenceMetadata
- OEStructureMetadata
- OESecondaryStructureSuperposition
- OESpruceFilter
- OESpruceFilterOptions
- OEStructuralSuperposition
- OESuperpositionOptions
- OESuperpose
- OESuperposeOptions
- OESuperposeResults
- OEValidateDesignUnit
- OESpruce Constants
- OESpruce Functions
- OEBuildLoops
- OEBuildSidechains
- OEBuildSingleLoop
- OECapCTermini
- OECapNTermini
- OECapTermini
- OEEnumerateSites
- OEExtractBioUnits
- OEFindPockets
- OEFixBackbone
- OEGetAlternateLocationOptionID
- OEGetAlternateLocationOptionName
- OEGetExperimentTypeID
- OEGetExperimentTypeName
- OEGetHeterogenTypeID
- OEGetHeterogenTypeName
- OEGetPartialResidues
- OEHeterogenMetadataFromJson
- OEHeterogenMetadataToJson
- OEIsRedundantDesignUnit
- OEMakeBioDesignUnits
- OEMakeDesignUnit
- OEMakeDesignUnits
- OEMakeDesignUnitFromPocket
- OEMutateResidue
- OEMutateResidues
- OEProtonateDesignUnit
- OESplitBioUnitToComponents
- OESpruceGetArch
- OESpruceGetLicensee
- OESpruceGetPlatform
- OESpruceGetRelease
- OESpruceGetSite
- OESpruceGetVersion
- OESpruceIsLicensed
- OESequenceMetadataFromJson
- OESequenceMetadataToJson
- OEStructureMetadataFromJson
- OEStructureMetadataToJson
- OEGetSuperposeMethodFromName
- OEGetSuperposeMethodName
- OESpruce Classes
- Release History