Enumerate ionization states at neutral pH using OEMultistatepKaModel and OEMultistatepKaModelOptions

The following code example shows how to use OEMultistatepKaModel and OEMultistatepKaModelOptions classes to enumerate ionization states at neutral pH. The program reads an input molecules file, create an instance of OEMultistatepKaModelOptions class. Use it in OEMultistatepKaModel class object and writes generated ionization states at neutral pH to specified output file.

Command Line Interface

A description of the command line interface is as following.

prompt> python enumerateionizationstatesatneutralph.py [<oedu infile>] [<oedu outfile>]

Code

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enumerateionizationstatesatneutralph.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])

    logfs = oechem.oeofstream("enumerateionizationstatesatneutralph.log")
    # oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Verbose)
    # oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Info)
    oechem.OEThrow.SetLevel(oechem.OEErrorLevel_Warning)
    oechem.OEThrow.SetOutputStream(logfs)

    mol = oechem.OEGraphMol()
    while oechem.OEReadMolecule(ifs, mol):
        title = mol.GetTitle()
        opts = oequacpac.OEMultistatepKaModelOptions()
        # opts.SetMaxNumMicrostates(128)

        multistatepka = oequacpac.OEMultistatepKaModel(mol, opts)

        if (multistatepka.GenerateMicrostates()):
            for a in multistatepka.GetMicrostates():
                a.SetTitle(title)
                oechem.OEWriteMolecule(ofs, a)
                ofs.flush()

        else:
            msg = ("No microstates are generated for molecule: %s"
                   % title)
            oechem.OEThrow.Warning(msg)
            oechem.OEWriteMolecule(ofs, mol)
            ofs.flush()

    return 0


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