[Cdk-user] Re: [Cdk-devel] CDK basics questions

[E.L. W. <eg...@sc...>]

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=46irst a minor remark: this question should have gone to the=20
cdk...@li... mailing list.=20

On Wednesday 12 May 2004 11:33, Ola Spjuth wrote:
> My group is investigating the possible use of CDK as framework/basis for
> constructing an integrated bio/chemoinformatics enterprise application.
> I have installed the CDK library and have a few newbie-questions that I
> hope someone might answer. We have also been looking at the commercial
> application Jchem (because of the good database support, descriptor
> analysis and 2D-visualization) but would of course prefer CDK!
>
> 1) We would like to read SMILES and convert to 2D-structure. What are
> the options after using the SmilesParser? Which algorithms should I use?

The SmilesParser creates a connectivity table.
The StructureDiagramGenerator will create 2D coordinates.

In between these steps can be done:
The HydrogenAdder can replace implicit hydrogens, eg. as in the CC smiles,
into explicit hydrogens, e.g. as in [H]C([H])=3DC([H])[H]
The ValencyChecker.saturate() can adjust bond orders to match common=20
situations

> StructureDiagramGenerator gives me something to visualize in Jmol but
> the bonds are incorrect.

The SMILES parser should interpret bond orders... Can you give an example?=
=20
Maybe you found a bug...

> 2) Can CDK output images (GIF/PNG etc) of 2D-structure of a molecule? If
> not, how do people address this matter with external programs (like
> JchemPaint)? We would like to put the 2D structures on the web, not in a
> java-panel.

Very good. I once made a sevlet system which did this... it had 2D structur=
es=20
in a database and made GIF on the fly... (See Chemistry & Internet=20
conference, 2000, Washington, USA). I used code similar to that in=20
JChemPaint. (Fairly easy to set up such a system...)

> 3) Are there any algorithms for converting 1D/2D structures to putative
> 3D (or just 3D)?=20

No, not in CDK at this moment...

> Any energy minimizing modules?

There are people working on force fields, and it is fairly easy to link Jav=
a=20
to Ghemical which can do structure optimization.

> 4) How extensive is the database support? Can CDK only store/retrieve
> molecules from a database?=20

That's what is in CDK right now...

> It would be nice with for example Hibernate support...

What's Hibernate?

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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