Apologies about the broken links - try now.
By the way, if you are interested in 2D layout code, you would be very
welcome to help us with ours...
- Noel
2010/1/28 Robert DeLisle <rkdeli...@gmail.com>:
> 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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