Re: [Cdk-devel] Extended fingerprinter question

[Andrew D. <da...@da...>]

On Feb 20, 2009, at 10:57 AM, ma...@eb... wrote:
> Thanks Andrew and Chris. I'm still a bit puzzled - first of all I  
> think
> the rings in 35623 are aromatic (I just checked the rings' bond
> aromaticity flags using that Java program I attached before).

They could be. I only checked the SD file and I'm not so experienced
with SD files as I am with SMILES. But the query structure was
definitely not aromatic.

> Secondly Chris, if you draw that query in Pubchem for substructure  
> query
> searching, you get 1625 hits of which mant look to me suspiciously  
> like
> 35623..

That's a different question. Now you're asking "why is the CDK  
definition of substructure different than the PubChem definition?"

Here's your query as a SMILES, generated via PubChem's sketcher.

C1C2C(CCC1)CC4C3C2CCCC3CCN4

Here's an example matched target, CID 2215
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2215&loc=ec_rcs
It has the SMILES

CN1CCC2=CC=CC3=C2C1CC4=C3C(=C(C=C4)O)O

Clearly the latter contains many double bonds while the former only  
contains single bonds.

This is a guess: PubChem might treat single, double, and aromatic
bonds as the same if they are between carbons in a ring.

For example, I did a search for this
   C1=CC=C=C=CC1
which is a 7-member ring containing 3 double-bonds in a row (C=C=C=C).

One of the PubChem matches was
   http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi? 
cid=10330236&loc=ec_rcs
SMILES C1C=CC=CC2=C1C3=CC=CC=CC3=N2

Looking at the structure, there's no place with 3 connected double  
bonds. Or even two for that matter.

I suspect this is a PubChem tweak because aromaticity is an ambiguous  
definition and people sketching the structure might not be as  
sensitive to the problems that can arise.


				Andrew
				da...@da...