2009/12/15 Noel O'Boyle <[email protected]>: > 2009/12/14 Geoffrey Hutchison <[email protected]>: >>> So I thought about changing the fragment to be composed of C atoms and >>> using that to derive the canonical representation. >> >> The problem is that if you change the fragment to C atoms, you have lots of >> un-filled valence. Consider, changing the "N" in pyrrole (or S in thiophene) >> to carbon. It's no longer aromatic. So with that approach (making fragments, >> changing atoms to carbon, writing output), the resulting SMARTS patterns >> weren't > > Got you. > >> I see your point. Perhaps the "best" solution is to look for similar SMARTS >> in the post-processing step and merge them? > > Aha, finally a use for canonical SMARTS strings! Which I'm afraid we > don't have. But I might be able to identify at least the simpler > duplicates.
Actually just thought of a way to create canonical SMARTS string. Craig, do you have code for generating all possible SMILES strings for a particular molecule? If so, then I could do this for each fragment, do string replacement to create the corresponding SMARTS, and pick the 'canonical SMARTS' with the lowest alphabetical order. >> Craig, do you have another solution? Is there a wild-card or dummy atom for >> the canonical SMILES? >> >> -Geoff > ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
