uffminimize.py

#!/usr/bin/python

import sys,string
from rdkit.Chem import AllChem as Chem
from optparse import OptionParser

#minimize sdf structures with the UFF forcefiled and rdkit

parser = OptionParser(usage="Usage: %prog [options] <input>.sdf <output>.sdf")
parser.add_option("-v","--verbose", dest="verbose",action="store_true",default=False,
                  help="verbose output")
parser.add_option("-a","--add_hydrogens", dest="addh",action="store_true",default=False,
                  help="add hydrogens")

    
(options, args) = parser.parse_args()
input = args[0]
output = args[1]

inmols = Chem.SDMolSupplier(input)
if inmols is None:
    print("Could not open ".input)
    sys.exit(-1)
    
sdwriter = Chem.SDWriter(output)
if sdwriter is None:
    print("Could not open ".output)
    sys.exit(-1)
        
for mol in inmols:
    if mol is not None:
        try:
            if options.addh:
                mol = Chem.AddHs(mol,addCoords=True)
            orig = Chem.UFFGetMoleculeForceField(mol).CalcEnergy()
            a=Chem.UFFOptimizeMolecule(mol)
            
            #sometimes the UFF Optimization does not converge (returns a 1 instead of 0)
            if a==1:
              a=Chem.UFFOptimizeMolecule(mol, maxIters=1000)
            
            if options.verbose:
                e = Chem.UFFGetMoleculeForceField(mol).CalcEnergy()
                print(mol.GetProp('_Name'),orig,"->",e)
            sdwriter.write(mol)
        except (KeyboardInterrupt, SystemExit):
            raise            
        except:            
            print("Exception occurred",mol.GetProp('_Name'))
    else:
        print("ERROR")