Transforming molecules into...well...other molecules

It's fairly straightforward to filter structures by SMARTS patterns using Open Babel, but how about if you want to transform all occurences of a particular substructure into something else? This may be useful for structure cleanup, tautomer normalisation, or even to carry out a reaction in silico.

Anyhoo, that's enough background. Let's suppose we want to hydrogenate all instances of C=C and C=O. Just copy and paste the following into the end of plugindefines.txt:

OpTransform
hydrogenate      # ID used for commandline option
*                # Asterisk means "no datafile specified"
Hydrogenate C=C and C=O double bonds
TRANSFORM [C:1]=[C:2] >> [C:1][C:2]
TRANSFORM [C:1]=[O:2] >> [C:1][O:2]

This gives a new obabel option, --hydrogenate, that will do the job:

C:\Tools\tmp>obabel -L ops
...
hydrogenate    Hydrogenate C=C and C=O double bonds
...
C:\Tools\tmp>obabel -:C=C -osmi --hydrogenate
CC
C:\Tools\tmp>obabel -:O=CSC=CC=S -osmi --hydrogenate
OCSCCC=S

Notes:
(1) This works best in the latest SVN as Chris sorted out some longstanding bugs.
(2) I've just enabled this in Python where it works as follows:

import pybel
transform = pybel.ob.OBChemTsfm()
success = transform.Init("[C:1]=[C:2]", "[C:1][C:2]")
assert success
mol = pybel.readstring("smi", "C=C")
transform.Apply(mol.OBMol)
assert mol.write("smi").rstrip() == "CC"