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

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