I'm also very interested in the topic. More the CS theory behind it, so if
there are any specific references to the algorithms/math behind 2D structure
generation, I would appreciate to to know them.
Also, the links at Noel O'Blog (Cheminformatics toolkit face-off -
Depiction) seem to no longer exist. Have they moved?
-Kirk
On Wed, Jan 27, 2010 at 9:22 AM, Craig A. James <cja...@emolecules.com>wrote:
> Jean-Marc Nuzillard wrote:
> > I am interested in 2D structure diagram generation from atom
> connectivity,
> > as a part of LSD project (www.univ-reims.fr/LSD) for NMR-constrainted
> > structure generation
> > of small organic molecules.
> >
> > I have seen in previous posts to this mailing list that
> > pybel.readstring("smi", "CCO").draw() would do the job for ethanol.
> >
> > My questions are:
> > Which is the algorithms that works beyind the scenes? depict?
>
> The ab-initio 2D coordinates are generated by the MCDL algorithm by
> Trepalin and Gakh.
>
> > Which is the legal status of the algorithm?
> > I mean, is it free or is some kind of licence required?
>
> >From the OpenBabel file mcdlutil.c:
>
> Copyright (C) 2007,2008 by Sergei V. Trepalin
> sergey_trepa...@chemical-block.com
> Copyright (C) 2007,2008 by Andrei Gakh andrei.g...@nnsa.doe.gov
>
> This file is part of the Open Babel project.
> For more information, see <http://openbabel.sourceforge.net/>
>
> This program is free software; you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation version 2 of the License.
>
>
> > In which language is the algorithm written?
>
> C++, but I believe the original was written in Java, and is probably still
> available in that form.
>
> You might also find this instructive:
>
>
> http://baoilleach.blogspot.com/2008/05/cheminformatics-toolkit-face-off.html
>
> I don't know if Noel included a later arrival that received good reviews:
>
> http://opensource.scitouch.net/indigo/dingo
>
> Craig
>
>
>
>
>
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