Constraint optimization in Python with Open Babel

This post is just a quick post to show, how you can optimize molecules with harmonic constraints in Python with Open Babel. This requires Open Babel to be compiled with Python SWIG-bindings.

There are three types of constraints, distances, angles and torsions. Here is a gist that might help get you started.

	import openbabel as ob
	# Standard openbabel molecule load
	conv = ob.OBConversion()
	conv.SetInAndOutFormats('xyz','xyz')
	mol = obOBMol()
	conv.ReadFile(mol,'my_mol.xyz')
	# Define constraints
	constraints = ob.OBFFConstraints()
	constraints.AddDistanceConstraint(1, 10, 3.4) # Angstroms
	constraints.AddAngleConstraint(1, 2, 3, 120.0) # Degrees
	constraints.AddTorsionConstraint(1, 2, 3, 4, 180.0) # Degrees
	# Setup the force field with the constraints
	forcefield = ob.OBForceField.FindForceField("MMFF94")
	forcefield.Setup(mol, constraints)
	forcefield.SetConstraints(constraints)
	# Do a 500 steps conjugate gradient minimiazation
	# and save the coordinates to mol.
	forcefield.ConjugateGradients(500)
	forcefield.GetCoordinates(mol)
	# Write the mol to a file
	conv.WriteFile(mol,'my_mol.xyz')

view raw pbconstraint.py hosted with ❤ by GitHub

Acknowledgements: Kasper Thofte pretty much wrote the above gist back in the days.