Extracting Protein Backbone

A program that extracts the backbone from a protein. An example command would be:

prompt> python backbone.py input.pdb output.pdb

Code

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backbone.py

#!/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
# provided to current licensees or subscribers of Cadence products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

#############################################################################
# This program demonstrates how to extract the backbone of a protein.
#############################################################################
import sys
from openeye import oechem


def BackBone(ifs, ofs):
    adjustHCount = True
    mol = oechem.OEGraphMol()
    backboneMol = oechem.OEGraphMol()

    while oechem.OEReadMolecule(ifs, mol):
        if not oechem.OEHasResidues(mol):
            oechem.OEPerceiveResidues(mol, oechem.OEPreserveResInfo_All)
        aiter = mol.GetAtoms(oechem.OEIsBackboneAtom())
        member = oechem.OEIsAtomMember(aiter)

        oechem.OESubsetMol(backboneMol, mol, member, adjustHCount)
        oechem.OEWriteMolecule(ofs, backboneMol)


def main(argv=[__name__]):
    if len(sys.argv) != 3:
        oechem.OEThrow.Usage("%s <infile> <outfile>" % argv[0])

    ifs = oechem.oemolistream()
    ifs.SetFlavor(oechem.OEFormat_PDB, oechem.OEIFlavor_PDB_Default ^ oechem.OEIFlavor_PDB_DATA)
    if not ifs.open(argv[1]):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])

    ofs = oechem.oemolostream()
    if not ofs.open(argv[2]):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])

    BackBone(ifs, ofs)


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