Hi Peter, Rajarshi and Wibe,
Thanks for your input.
There doesn't seem to be an obvious candidate for the 2D editor. We will
explore what's available.
Paul (and Garib).
On 18/08/16 17:18, Garib Murshudov wrote:
Begin forwarded message:
*From: *Wibe de Jong <wadej...@lbl.gov <mailto:wadej...@lbl.gov>>
*Subject: **Re: [BlueObelisk-discuss] Software for ligands*
*Date: *18 August 2016 17:16:03 BST
*To: *rajarshi.g...@gmail.com <mailto:rajarshi.g...@gmail.com>
*Cc: *Peter Murray-Rust <pm...@cam.ac.uk <mailto:pm...@cam.ac.uk>>,
BlueObelisk-Discuss <blueobelisk-discuss@lists.sourceforge.net
<mailto:blueobelisk-discuss@lists.sourceforge.net>>,
ga...@mrc-lmb.cam.ac.uk <mailto:ga...@mrc-lmb.cam.ac.uk>
That's a nice overview paper. Started to look more into descriptors,
so happy to see the listing of tools one can start from.
Some of the web components have been integrated into MongoChem
(https://openchemistry.kitware.com/). Here we use a greatly extended
version of Marcus' Chemical Json (reusing some of the CML naming
conventions) to generate data and populate a MongoDB. The
computational chemistry app used here is NWChem, for which we now
have a CJson writer directly in the code (using an open source son
fortran writer) and an extensive Python script (which I need to
integrate into cclib at some point in the near future).
Bert
On Thu, Aug 18, 2016 at 5:06 AM, Rajarshi Guha
<rajarshi.g...@gmail.com <mailto:rajarshi.g...@gmail.com>> wrote:
There is a nice listing of open tools by Pirhadi et al and covers
the spectrum from cheminformatics to computational chemistry
http://www.sciencedirect.com/science/article/pii/S1093326316301188
<http://www.sciencedirect.com/science/article/pii/S1093326316301188>
On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust
<pm...@cam.ac.uk <mailto:pm...@cam.ac.uk>> wrote:
I have been talking with the Computational Crystallography
group in Cambridge/LMB who develop ligand dictionaries for
protein crystallography and are building their system with
Open software (and Open data from Crystallography Open Database).
I have suggested that there are Open tools that they may not
yet have discovered. They have needs for (at least):
* 2-D chemical editor and display
* 3-D editor
* atom typing
* computational chemistry (e.g. DFT)
* chemical database software
They have filled some of this themselves, and use RDKIT, but
would benefit from other components. I pointed them at
JChempaint - which has matured a lot since I last used it. I
have also suggested NWChem.
I am not up-to-date with all the Open software. Do we have a
list of tools in this area? If not, perhaps people can
respond to the list? It would be a useful update.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069 <tel:%2B44-1223-763069>
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Rajarshi Guha | http://blog.rguha.net <http://blog.rguha.net/>
NIH Center for Advancing Translational Science
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Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk,
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