> I have a number of multimolecular complexes that I'm converting into > canonical SMILES. Some of these molecules are carbon monoxide, and I am > noticing that sometimes they are written as [C]=O, and sometimes as O=[C]. > > Is the expected behavior of canonical SMILES - or should it instead be > canonicalizing each molecule in the complex?
I'm not sure that there is specific code in place for multi molecular systems. What you describe (that each fragment have a canonical ordering) is a useful idea, since it makes it much easier to parse the string into canonical pieces. Could you file a bug to remind me to get through this before the next release? Basically, I'd just make sure that in a multi-fragment SMILES, each fragment is canonicallized separately and then the result is put into a canonical ordering of fragments. Thanks, -Geoff ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
