I know :-) - personally though I look at it like this...
- If I want to handle PDB (protein) structures I would use BioJava - it as a
better object model for proteins. Docking is of course valid use case for
proteins but the protein structure and small molecule will usually be handled
separately.
- If I want to handle PDB small molecule structures I would use CDK - e.g. from
CCDC like data.
- Loading Diamond etc.. what can you do that is useful with that in the CDK?
SMILES? InChI? SMARTS query? Fingerprint? Ring Perception? Aromaticity? QSAR? I
would think are more appropriate 'physicsy' libraries might doing useful
things.
Cheers,
J
On 6 Oct 2013, at 22:08, Egon Willighagen <[email protected]> wrote:
> On Sun, Oct 6, 2013 at 11:01 PM, John May <[email protected]> wrote:
>> http://cdk.github.io/cdk/1.5/docs/api/index.html?org/openscience/cdk/Crystal.html
>>
>> "Class representing a molecular crystal. The crystal is described with
>> molecules in fractional coordinates and three cell axes: a,b and c."
>
> Ah, but that *is* about molecular crystals (e.g. the crystal structure
> of estrone). That's because I wrote that crappy text when I was biased
> to such crystals... I get your point, but it's not valid, but that is
> my fault :) But crystals can be much more... think diamond, think PDB
> structures.
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
>
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