Enumerating Tautomers

This following example shows a fast informatics technique using tautomer enumeration which is capped at 200 states per molecule. Formal charge of each input molecule is removed first, and then tautomers are enumerated. The tautomers are saved to the output file after setting a favorable ionization state at neutral pH.

Command Line Interface

A description of the command line interface is shown as follows:

prompt> python getreasonabletautomers.py <mol-infile> <mol-outfile>

Code

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getreasonabletautomers.py

#!/usr/bin/env python
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import sys
from openeye import oechem
from openeye import oequacpac


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

    tautomerOptions = oequacpac.OETautomerOptions()
    pKaNorm = True

    for mol in ifs.GetOEGraphMols():
        for tautomer in oequacpac.OEGetReasonableTautomers(mol, tautomerOptions, pKaNorm):
            oechem.OEWriteMolecule(ofs, tautomer)

    return 0


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