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

• OEOmegaOptions class

• OEOmega class

• OESimpleAppOptions class

Listing 1: Generating Conformers

#!/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.

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))

Download code

simple_omega.py

Generating a Single Conformer

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

See also

• OEConformerBuilder class

Listing 2: Generating a Single Conformer

#!/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.

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))

Download code

single_conformer.py

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

• OEOmegaOptions class

• OEOmega class

• OEOmegaSampling namespace

• OESimpleAppOptions class

Listing 3: Generating Densely Sampled Conformers

#!/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.

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))

Download code

dense_omega.py

Flipper 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

• OEOmegaOptions class

• OEOmega class

• OEFlipper function

• OESimpleAppOptions class

Listing 4: Generating Stereoisomers

#!/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.

import sys
from openeye import oechem
from openeye import oeomega


def main(argv=[__name__]):
    flipperOpts = oeomega.OEFlipperOptions()
    
    opts = oechem.OESimpleAppOptions(flipperOpts, "stereo_and_torsion", oechem.OEFileStringType_Mol, oechem.OEFileStringType_Mol)
    if oechem.OEConfigureOpts(opts, argv, False) == oechem.OEOptsConfigureStatus_Help:
        return 0

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

    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())

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

    return 0


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

Download code

stereo_and_torsion.py

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

• OETorDriveOptions class

• OETorDriver class

• OESimpleAppOptions class

Listing 5: Torsion Driving to Generating Conformer Ensemble

#!/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.

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))

Download code

torsion_drive.py

Fragment Library generation Examples

Making Fragment Library

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

See also

• OEFragBuilderOptions class

• OEMakeFragLib class

• OESimpleAppOptions class

Listing 6: Making Fragment Library

#!/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.

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))

Download code

make_fraglib.py

Macrocycle Examples

Generating Macrocycle Conformers

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

See also

• OEMacrocycleOmegaOptions class

• OEMacrocycleOmega class

• OESimpleAppOptions class

Listing 7: Generating Macrocycle Conformers

#!/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.

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))

Download code

macrocycle.py

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.

See also

• OEMacrocycleBuilderOptions class

• OEMacrocycleBuilder class

• OESimpleAppOptions class

Listing 8: Generating a Single Macrocycle Conformer

#!/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.

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))

Download code

single_conf_macrocycle.py