Performing a reaction

A program that uses a SMIRKS to perform reactions on single molecules. The OpenEye OEUniMolecularRxn class is designed to react every instance of the reactant pattern in the input molecules and so is useful for normalization reactions.

Example

prompt> unimolrxn.py '[NH2:1]>>[Nh3+:1]' dbase.oeb.gz output.oeb.gz

Code

Download code

unimolrxn.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").
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# 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.

#############################################################################
# Perform reactions on the given compounds
#############################################################################
import sys
from openeye import oechem


def UniMolRxn(ifs, ofs, umr):
    for mol in ifs.GetOEGraphMols():
        if umr(mol):
            oechem.OEWriteMolecule(ofs, mol)


def main(argv=[__name__]):
    if not (3 <= len(argv) <= 4):
        oechem.OEThrow.Usage("%s SMIRKS <infile> [<outfile>]" % argv[0])

    qmol = oechem.OEQMol()
    if not oechem.OEParseSmirks(qmol, argv[1]):
        oechem.OEThrow.Fatal("Unable to parse SMIRKS: %s" % argv[1])

    umr = oechem.OEUniMolecularRxn()
    if not umr.Init(qmol):
        oechem.OEThrow.Fatal("Failed to initialize reaction with %s SMIRKS" % argv[1])
    umr.SetClearCoordinates(True)

    ifs = oechem.oemolistream()
    if not ifs.open(argv[2]):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[2])

    ofs = oechem.oemolostream(".ism")
    if len(argv) == 4:
        if not ofs.open(argv[3]):
            oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[3])

    UniMolRxn(ifs, ofs, umr)


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