Strip salts

A program that removes all but the largest molecule from molecules that contain more than one part. If the molecule contains two or more parts that are equal in size it keeps the larger.

Example

prompt> stripsalts.py dbase.oeb.gz output.oeb.gz

Code

Download code

stripsalts.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.

#############################################################################
# Remove salts and/or remove all but the largest molecule
#############################################################################
import sys
from openeye import oechem


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

    ifs = oechem.oemolistream()
    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])

    for mol in ifs.GetOEMols():
        oechem.OEDeleteEverythingExceptTheFirstLargestComponent(mol)
        oechem.OEWriteMolecule(ofs, mol)


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