OMEGA Examples

The following table lists the currently available Omega TK examples:

Program

Description

simple_omega.py

generating conformers

single_conformer.py

generating a single conformer

dens_omega.py

generating densely sampled conformers

stereo_and_torsion.py

generating stereoisomers

torsion_drive.py

torsion driving to generating conformer ensemble

make_fraglib.py

making fragment library

macrocycle.py

generating macrocycle conformers

single_conf_macrocycle.py

generating single macrocycle conformer

Note

If the input molecule has SD tag data, the data will be copied to every conformer in the results molecule.

Classic OEOmega Examples

Generating Conformers

The following code example is a simple example of how to generate conformers using the OEOmega object.

See also

Listing 1: Generating Conformers

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    omegaOpts = oeomega.OEOmegaOptions()
    omegaOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    omegaOpts.SetParameterVisibility("-rms", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-ewindow", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-maxconfs", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-useGPU", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(omegaOpts, "Omega", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    omegaOpts.UpdateValues(opts)
    omega = oeomega.OEOmega(omegaOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        ret_code = omega.Build(mol)
        if ret_code == oeomega.OEOmegaReturnCode_Success:
            oechem.OEWriteMolecule(ofs, mol)
        else:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

Generating a Single Conformer

The following code example is a simple example of how to generate a single conformer.

See also

Listing 2: Generating a Single Conformer

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


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])

    if not oechem.OEIs3DFormat(ofs.GetFormat()):
        oechem.OEThrow.Fatal("Invalid output file format for 3D coordinates!")

    builder = oeomega.OEConformerBuilder()

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        ret_code = builder.Build(mol)
        if ret_code == oeomega.OEOmegaReturnCode_Success:
            oechem.OEWriteMolecule(ofs, mol)
        else:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

Generating Densely Sampled Conformers

The following code example is a simple example of how to generate densely sampled conformers, as used in OEFreeFormConf calculations, using the OEOmega object.

See also

Listing 3: Generating Densely Sampled Conformers

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
    omegaOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    omegaOpts.SetParameterVisibility("-rms", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-ewindow", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-maxconfs", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-useGPU", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-searchFF", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(omegaOpts, "Omega", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    omegaOpts.UpdateValues(opts)
    omega = oeomega.OEOmega(omegaOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        ret_code = omega.Build(mol)
        if ret_code == oeomega.OEOmegaReturnCode_Success:
            oechem.OEWriteMolecule(ofs, mol)
        else:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

StereoAndTorsion Examples

Generating Stereoisomers

The following code example is a simple example of how to use the OEFlipper function to generate stereoisomers. The code example also demonstrates that stereoisomers should be generated before generating conformers.

See also

Listing 4: Generating Stereoisomers

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    omegaOpts = oeomega.OEOmegaOptions()
    omegaOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    omegaOpts.SetParameterVisibility("-rms", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-ewindow", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-maxconfs", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(omegaOpts, "Omega", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    omegaOpts.UpdateValues(opts)
    omega = oeomega.OEOmega(omegaOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    flipperOpts = oeomega.OEFlipperOptions()
    flipperOpts.SetEnumSpecifiedStereo(True)
    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())

        for enantiomer in oeomega.OEFlipper(mol.GetActive(), flipperOpts):
            enantiomer = oechem.OEMol(enantiomer)
            ret_code = omega.Build(enantiomer)
            if ret_code == oeomega.OEOmegaReturnCode_Success:
                oechem.OEWriteMolecule(ofs, enantiomer)
            else:
                oechem.OEThrow.Warning("%s: %s" %
                                       (enantiomer.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

Generating Torsion Driven Conformation Examples

Torsion Driving to Generating Conformer Ensemble

The following code example is a simple example of how to torsion drive from given 3D structure, to generate a conformer ensemble.

See also

Listing 5: Torsion Driving to Generating Conformer Ensemble

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    torOpts = oeomega.OETorDriveOptions()
    torOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    torOpts.SetParameterVisibility("-rms", oechem.OEParamVisibility_Simple)
    torOpts.SetParameterVisibility("-ewindow", oechem.OEParamVisibility_Simple)
    torOpts.SetParameterVisibility("-maxconfs", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(torOpts, "Omega", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    torOpts.UpdateValues(opts)
    tordriver = oeomega.OETorDriver(torOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        ret_code = tordriver.GenerateConfs(mol)
        if ret_code == oeomega.OEOmegaReturnCode_Success:
            oechem.OEWriteMolecule(ofs, mol)
        else:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

Fragment Library generation Examples

Making Fragment Library

The following code example is a simple example of how to generate a fragment library.

Listing 6: Making Fragment Library

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    libOpts = oeomega.OEFragBuilderOptions()
    libOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    libOpts.SetParameterVisibility("-buildFF", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(libOpts, "Makefraglib", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    libOpts.UpdateValues(opts)
    makefraglib = oeomega.OEMakeFragLib(libOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    if ofs.GetFormat() != oechem.OEFormat_OEB:
        oechem.OEThrow.Fatal("Output file has to have OEB format!")

    makefraglib.ClearFragLibs()
    makefraglib.GenerateMissingFrags(ifs, ofs)
    return 0


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

Macrocycle Examples

Generating Macrocycle Conformers

The following code example is a simple example of how to generate conformers using the OEMacrocycleOmega object.

Listing 7: Generating Macrocycle Conformers

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    omegaOpts = oeomega.OEMacrocycleOmegaOptions()
    omegaOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    omegaOpts.SetParameterVisibility("-rms", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-ewindow", oechem.OEParamVisibility_Simple)
    omegaOpts.SetParameterVisibility("-maxconfs", oechem.OEParamVisibility_Simple)

    opts = oechem.OESimpleAppOptions(omegaOpts, "Omega", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol3D)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    omegaOpts.UpdateValues(opts)
    mcomega = oeomega.OEMacrocycleOmega(omegaOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        ret_code = mcomega.Build(mol)
        if ret_code == oeomega.OEOmegaReturnCode_Success:
            oechem.OEWriteMolecule(ofs, mol)
        else:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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

Generating a Single Macrocycle Conformer

The following code example is a simple example of how to generate a single macrocycle conformer using the OEMacrocycleBuilder object.

Listing 8: Generating a Single Macrocycle Conformer

#!/usr/bin/env python
# (C) 2017 OpenEye Scientific Software Inc. All rights reserved.
#
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
# provided to current licensees or subscribers of OpenEye products or
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# subject to these terms. OpenEye 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 OpenEye 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 OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    buildOpts = oeomega.OEMacrocycleBuilderOptions()
    buildOpts.SetParameterVisibility(oechem.OEParamVisibility_Hidden)
    buildOpts.SetParameterVisibility("-seed", oechem.OEParamVisibility_Simple)
    buildOpts.SetParameterVisibility("-dielectric_constant", oechem.OEParamVisibility_Simple)

    inType = oechem.OEFileStringType_Mol
    outType = oechem.OEFileStringType_Mol3D
    opts = oechem.OESimpleAppOptions(buildOpts, "macrocycle_builder", inType, outType)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

    buildOpts.UpdateValues(opts)
    #builder = oeomega.OEMacrocycleBuilder(buildOpts)

    ifs = oechem.oemolistream()
    if not ifs.open(opts.GetInFile()):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % opts.GetInFile())

    ofs = oechem.oemolostream()
    if not ofs.open(opts.GetOutFile()):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % opts.GetOutFile())

    for mol in ifs.GetOEMols():
        oechem.OEThrow.Info("Title: %s" % mol.GetTitle())
        itlimit = 1000
        itnum = 0
        ret_code = oeomega.OEOmegaReturnCode_Failed
        while itnum <= itlimit:
            builder = oeomega.OEMacrocycleBuilder(buildOpts)
            ret_code = builder.Build(mol)
            if ret_code == oeomega.OEOmegaReturnCode_Success:
                oechem.OEWriteMolecule(ofs, mol)
                break
            else:
                buildOpts.SetRandomSeed(buildOpts.GetRandomSeed()+1)
            ++itnum
        if ret_code != oeomega.OEOmegaReturnCode_Success:
            oechem.OEThrow.Warning("%s: %s" % (mol.GetTitle(), oeomega.OEGetOmegaError(ret_code)))

    return 0


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