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> 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 > > On Thu, Aug 18, 2016 at 5:13 AM, Peter Murray-Rust <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 >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> Blueobelisk-discuss mailing list >> Blueobelisk-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > >
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