mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-27 05:37:38 -05:00
Eisuke Kawashima
6b57788a05
- `from __future__ import print_function` - replace deprecated `unittest.TestCase.assertEquals` with `assertEqual`, `assertTrue`, or `assertFalse` - use `obj is None` instead of `obj == None` - remove modules and functions that are imported but not used
57 lines
1.6 KiB
Python
57 lines
1.6 KiB
Python
######################################################################
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#
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# wgtRotorSrch.py: weighted rotor search (conformer search)
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#
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######################################################################
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from __future__ import print_function
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import openbabel
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import sys
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# Make sure we have a filename
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try:
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filename = sys.argv[1]
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except:
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print("Usage: python energy.py filename")
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sys.exit(1)
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# Read the file.
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mol = openbabel.OBMol()
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conv = openbabel.OBConversion()
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format = conv.FormatFromExt(filename)
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conv.SetInAndOutFormats(format, format)
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conv.ReadFile(mol, filename)
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# Find the MMFF94 force field.
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ff = openbabel.OBForceField.FindForceField("MMFF94")
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if ff == 0:
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print("Could not find forcefield")
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# Set the log level to low since we only want to print out the conformer search
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# steps and not all individual interactions for each call to Energy()
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ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
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# python specific, python doesn't have std::ostream so the SetLogFile()
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# function is replaced by SetLogToStdOut and SetLogToStdErr in the SWIG
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# interface file
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ff.SetLogToStdErr()
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# Setup the molecule. This assigns atoms types, charges and parameters
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if ff.Setup(mol) == 0:
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print("Could not setup forcefield")
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# Weighted rotor search: generate 25 conformers, optimize each conformer for
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# 500 steps.
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ff.WeightedRotorSearch(25, 500)
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# Get all the coordinates back from the force field. The best conformer is also
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# set in mol
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ff.GetConformers(mol)
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# Write the best conformer back to the file
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conv.WriteFile(mol, filename)
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# Other conformers can also be written by calling:
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# mol.SetConformer(0)
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# conv.Write(mol)
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# mol.SetConformer(1)
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# conv.Write(mol)
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# ...
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