Re: [Cdk-user] PubChem database with search

[Rajarshi G. <raj...@gm...>]

On Mon, Nov 14, 2011 at 7:31 AM, Jochen Schreiber <jo...@go...> wrote:

> The databases that i could download from the pubchem ftp for the substances
> havnt any 3D informations.

Pubchem has a 3D version, though they only store a 1 or 10 conformers.
See ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound_3D

> So the following code (which i test for iterating
> through all informations) will fail:

Note that if you want to read through an SD file that contains
multiple conformers (numbered contiguously) then you should be using
the IteratingMDLCoformerReader and ConformerContainer classes

> 1. Converting structure files into sdf (with babel)

Do you mean generate 3D structures?

> 2. CDK for creating the query.xml for CDKPSearch

You could also construct the query by hand (probably easier)

> 3. CDKPSearch for searching structures in the database (pubchem)
> 4. CDK for analyse the results (output the results etc.)
> Is this the right way?

This is certainly one way, though you might want to consider whether
10 conformers per structure is appropriate for a pharmacophore search

-- 
Rajarshi Guha
NIH Chemical Genomics Center