2009/12/15 Noel O'Boyle <[email protected]>: > 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.
Sorry - I see that the code is already in OpenBabel with the "C" option to the SMILES writer. >>> 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
