Extracting Biounits from PDB header remarks

Biounit (BU) extraction is one of the more basic functionalities offered through the Spruce TK. This example shows how to extract BUs using the PDB header remarks.

Command Line Interface

This example takes in a PDB file, and optionally the maximum number of atoms to be considered a BU as well as a boolean flag to instruct the code to prefer author or software generated headers (see OEExtractBioUnits for details on the API).

prompt> extract_biounits_remarks <extract protein PDB> [max atoms] [prefer author]

Code

Download code

extract_biounits_remarks.py and 4re6.pdb (the extraction PDB file)

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
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# subject to these terms. Cadence claims no rights to Customer's
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# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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# or its use.

#############################################################################
# Simple superimposition of a fit protein on to a reference protein
#############################################################################
import sys
import os
from openeye import oechem
from openeye import oespruce
import tempfile


def ReadProteinMol(pdb_file, mol):
    ifs = oechem.oemolistream()
    ifs.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_SpruceDefault)
    ifs.SetFlavor(oechem.OEFormat_MMCIF, oechem.OEIFlavor_MMCIF_SpruceDefault)

    if not ifs.open(pdb_file):
        oechem.OEThrow.Fatal("Unable to open %s for reading." % pdb_file)

    temp_mol = oechem.OEGraphMol()
    if not oechem.OEReadMolecule(ifs, temp_mol):
        oechem.OEThrow.Fatal("Unable to read molecule from %s." % pdb_file)
    ifs.close()

    fact = oechem.OEAltLocationFactory(temp_mol)
    mol.Clear()
    fact.MakePrimaryAltMol(mol)
    return (mol)


def main(argv=[__name__]):
    if len(argv) not in [2, 4, 5]:
        oechem.OEThrow.Usage("%s <extract protein PDB> [max atoms] [prefer author] [nowrite]" % argv[0])  # noqa

    do_write = True
    if len(argv) == 5:
        if argv[4] != "nowrite":
            oechem.OEThrow.Warning("%s is not a valid option.\n" % argv[4])
            sys.exit(1)
        else:
            do_write = False

    opts = oespruce.OEBioUnitExtractionOptions()
    if len(argv) >= 4:
        opts.SetMaxAtoms(int(argv[2]))
        opts.SetPreferAuthorRecord(bool(argv[3]))

    extract_prot_file = argv[1]
    extract_prot = oechem.OEGraphMol()
    extract_success = ReadProteinMol(extract_prot_file, extract_prot)
    if not extract_success:
        oechem.OEThrow.Fatal("Unable to read protein(s) from PDB file.")

    # @ <SNIPPET-OEExtractBioUnits-REMARKS>
    biounits = oespruce.OEExtractBioUnits(extract_prot, opts)
    # @ </SNIPPET-OEExtractBioUnits-REMARKS>

    if do_write:
        pdb_ext = ".pdb"
        str_pos = extract_prot_file.find(pdb_ext)
        base_name = extract_prot_file[0:str_pos]
        temp_dir = tempfile.mkdtemp()

        for i, biounit in enumerate(biounits):
            output_biounit_file = os.path.join(temp_dir, base_name + "_BU_{}.oeb.gz".format(i))  # noqa
            print("Writing biounit {} to {}".format(i, output_biounit_file))
            ofs = oechem.oemolostream(output_biounit_file)
            oechem.OEWriteMolecule(ofs, biounit)


if __name__ == "__main__":
    sys.exit(main(sys.argv))

Example

prompt> extract_biounits_remarks.py 4re6.pdb

will generate the following output:

Writing biounit 0 to 4re6_BU_0.oeb.gz
Writing biounit 1 to 4re6_BU_1.oeb.gz