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49 lines
1.4 KiB
Python
49 lines
1.4 KiB
Python
######################################################################
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#
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# minSimple.py: minimize a molecule
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#
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######################################################################
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from __future__ import print_function
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from openbabel 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 minimization
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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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# Minimize using steepest descent for 2000 steps
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ff.SteepestDescent(2000)
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# Get the coordinates back from the force field.
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ff.GetCoordinates(mol)
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# Write the minimized molecule back to the file
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conv.WriteFile(mol, filename)
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