Spruce TK Examples

The following table lists the currently available Spruce TK examples:

Program	Description
make_design_units	Constructing design units from a PDB (due to loop modeling, this example takes ~10 min)
make_apo_design_units	Constructing apo design units from a PDB using a site residue input (due to loop modeling, this example takes ~10 min)
superposition	Superposition of two proteins
extract_biounits_remarks	Extract biounits from PDB header remarks
extract_biounits_ref	Extract biounits from a sequence alignment to a reference protein
findpockets	Find pockets and some of their properties from a protein or uesign unit
convert_du_to_mmcif	Writing DU to MMCIF file
write_metadata_json_file	Writing a metadata JSON file from a FASTA file

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