Hi Adrian, On Tue, Apr 8, 2008 at 5:06 PM, Adrian Schreyer <[email protected]> wrote: > I was wondering what would be the best way in RDKit to represent > molecules with a metal complex in SMILES, for instance heme. > Apparently different programs use different approaches, CACTVS uses a > non-standard notation > > CC1=C(CCC(O)=O)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(CCC(O)=O)c7C)C(=C(C=C)C6=Cc8n5c(C=C13)c(C=C)c8C)C, > some represent coordinate bonds as standard bonds and others use a > disconnected notation > > CC1=C(C2=CC3=NC(=CC4=C(C(=C([N-]4)C=C5C(=C(C(=N5)C=C1[N-]2)C=C)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C=C.[Fe+2].
I'm afraid I don't have a good answer for you. If you just want to be able to read the molecules in and do things like calculate MW, etc. then I'd probably go with the dot-disconnected form. Anything else just isn't going to work particularly well. > Will there be any openSMILES standard for this? There was a good proposal from Peter Ertl on the OpenSMILES mailing list for an extension to support organometallic bonding: http://sourceforge.net/mailarchive/forum.php?thread_name=5191c3b80710060104h8d16a03j66a3d2b4ee3f9585%40mail.gmail.com&forum_name=blueobelisk-smiles But it's an extension, so I guess that it will have to wait until after the OpenSMILES itself is finalized; and who knows when that will happen. If we can get a couple of people to agree on what should be done, I'd be happy to see an organometallic smiles extension added to the RDKit (probably as a separate parser that handles the extended smiles), but I'm unlikely to have the time to do it anytime soon. This is one of those wonderful opportunities for the open-source model to function and someone who needs this stuff and knows C++ to step forward and add it. It's not a particular easy addition (some core data structures may have to be modified), so I'm not holding my breath. :-) -greg
