On Mon, Dec 12, 2011 at 2:13 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > > It took me a while to understand what you wrote. I'm so SMARTS oriented that > I was thinking that if the user draws a carbon (yielding the SMILES of "C") > then it would not match against a "c" in the target. > > Your point, I believe, is that a sketched carbon should match aliphatic or > aromatic, while a sketched aromatic carbon should only match an aromatic > carbon. >
Well, a sketched aromatic carbon is normally a SMARTS, but that's a different story. :-S With queries it is essential to distinguish between SMILES and SMARTS. In the tests that I have been doing, I treat both the pool and query molecules as SMILES. > Are the semantics of a SMILES-based Molecule to SMILES-based Molecule > described somewhere? Sure, in the code. ;-) A non-query atom (like what you get from parsing SMILES) matches another non-query atom with the same atomic number; nothing else matches and isotopic information is ignored (this probably should be changed). Dummies (atoms with atomic number zero) are handled somewhat differently (and will be handled differently still as soon as I check in a change that I've been meaning to migrate to the open-source side for a while now). > For that matter, I looked but couldn't find a detailed description of what > "sanitize" does. I know we've talked about it, and I know some of what it > does, but written information would be better. > There's some information here (collected for another purpose): http://code.google.com/p/rdkit/wiki/MoleculeConstructionOptimization but there should be something in the "RDKit book" describing the process as well. -greg ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss