Hi Horacio,
you might want to have a look at KNIME:
http://www.knime.org/
Certain functions from CDK (and other Chemistry Toolkits) can be used
within Knime.
With Knime you can:
read from database -> comvert data to Molecule objects -> do stuff
-> export or report result
Best Regards,
Joos
Am 23.03.2012 10:51, schrieb Egon Willighagen:
> Dear Horacio,
>
> ---------- Forwarded message ----------
> From: Horacio Pérez-Sánchez
> Date: 2012/3/23
> Subject: Molecular flexibility analysis
>
>> I wonder whether Chemistry Development kit tools can be used for, given a
>> database with thousands of ligands, analyzing each ligand and reporting
>> which fragments are rigid and which parts or connetors can be modelled as
>> flexible.
> Yes, the CDK can do that. Just as an example, there is a Rotatable
> Bond Count descriptor implemented.
>
> There are various approaches you can take, and it depends a bit on
> what you qualify something as a rigid bond. We have functionality to
>
> - identify ring bonds (SpanningTree class)
> - detect double/triple bonds (simple iteration over all bonds)
> - detect ring systems (we have at least three algorithms to find ring systems)
> - classes to do fragmentation, such as the Murcko approach
>
> With kind regards,
>
> Egon
>
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