split molecule file to separate components and save to multiple files.

split_ligand.py

### split molecule file to separate components and save to multiple files.

import pybel
from openbabel import *

mol = pybel.readfile('mol2', 'ligand.mol2').next()
separated = mol.OBMol.Separate()

def writeOut( theConformer, outputPath ):
  myConversion = OBConversion()
  outputFormat = myConversion.FormatFromExt( outputPath )
  myConversion.SetOutFormat( outputFormat )
  myConversion.WriteFile( theConformer, outputPath )

i = 0
for singlemol in separated:
  i+=1
  print "Writing part %i" % (i)
  writeOut(singlemol, "output-%i.mol2" %(i) )