Appendix: Additional Examples in Python

These are full listings of programming examples that are excerpted or offered for download, elsewhere in this chapter.

For an overall guide to programming examples, see the earlier material in the Omega chapter.

Listing 1: Example of adding a new torsion rule.

#!/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

if len(sys.argv) != 2:
    oechem.OEThrow.Usage("%s <outfile>" % sys.argv[0])

mol = oechem.OEMol()
oechem.OESmilesToMol(mol, "O=COC")

ofs = oechem.oemolostream()
if not ofs.open(sys.argv[1]):
    oechem.OEThrow.Fatal("Unable to open %s for writing" % sys.argv[1])

omegaOpts = oeomega.OEOmegaOptions()
omega = oeomega.OEOmega(omegaOpts)
torlib = oeomega.OETorLib()

# Adding the torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 90" as a string
# This takes precedent over previous rule
rule = "[O:1]=[C:2]-[O:3][CH3:4] 90"
if not torlib.AddTorsionRule(rule):
    oechem.OEThrow.Fatal("Failed to add torsion rule: %s" % rule)

omegaOpts.SetTorLib(torlib)
omega.SetOptions(omegaOpts)
if omega(mol):
    oechem.OEWriteMolecule(ofs, mol)

# Adding torsion rule "[O:1]=[C:2]-[O:3][CH3:4] 45" as a query
# molecule. This takes precedent over default rule
qmol = oechem.OEQMol()
oechem.OEParseSmarts(qmol, "[O:1]=[C:2]-[O:3][CH3:4]")
degrees = oechem.OEIntVector([45])

if not torlib.AddTorsionRule(qmol, degrees):
    oechem.OEThrow.Fatal("Failed to add torsion rule")

omegaOpts.SetTorLib(torlib)
omega.SetOptions(omegaOpts)
if omega(mol):
    oechem.OEWriteMolecule(ofs, mol)

Listing 2: Example of turning off GPU-Omega and changing parameters.

#!/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.

from openeye import oechem
from openeye import oeff
from openeye import oeomega

mol = oechem.OEMol()
oechem.OESmilesToMol(mol, "C1CCCCC1N(=O)CCS")

omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.GetTorDriveOptions().SetUseGPU(False)
omega = oeomega.OEOmega(omegaOpts)
omega(mol)

omegaOpts = oeomega.OEOmegaOptions(oeomega.OEOmegaSampling_Dense)
if oeomega.OEOmegaIsGPUReady():
    omegaOpts.GetTorDriveOptions().SetForceField(oeff.OEMMFFSheffieldFFType_MMFF94Smod_NOESTAT)
    omegaOpts.GetMolBuilderOptions().SetSampleHydrogens(False)
omega = oeomega.OEOmega(omegaOpts)
omega(mol)