Dear Peter,
CML is a central part of the Bioclipse API and toolset and ensures
interoperability between plugins locally in Bioclipse and over distributed web
services. While much relies on CDK for reading/writing, I can also contribute a
paragraph on CML extensions I implemented for a molecular dynamics project in
Bioclipse, as well as assist Egon with atom type info roundtripping. I would be
happy to contribute on these topics, please let me know if you think any of
this would be suitable additions to your paper.
Kind regards,
Ola
--
Ola Spjuth, PhD
Department of Pharmaceutical Biosciences
Box 541, Uppsala University
Sweden
Email: ola.spj...@farmbio.uu.se
Ph: +46 (0)70 425 06 28
Bioclipse: http://www.bioclipse.net
On 29 mar 2012, at 11.11, Peter Murray-Rust wrote:
> As a result of the "Semantic Physical Science" workshop earlier this year
> (http://www-pmr.ch.cam.ac.uk/wiki/Semantic_Physical_Science) we are writing a
> paper for J.Cheminformatics on "Building a code library for CML". We'd like
> information from anyone who has implemented a toolset to read and/or write
> CML. The paper will analyse some of these in depth and record others. The
> minimal amount of information is probably the coverage (through the usage of
> CML Elements) , the language and a few additional fields (this are mainly
> tickboxes). At present we are covering:
> Neylon/Python
> VTK
> Avogadro
> Chem4Word
> OpenBabel
> CDK/JChemPaint
> FoX
> Jmol
> JUMBO-system
> We'd very much like others to contribute - it can be closed source as well as
> Open, We are generally interested in systems that use Schema2.4 or Schema3.0
> as previous versions are deprecated. Note that Schema 2.4 has been used by
> the community for about 5 years with no emendations. Schema3 does not
> introduce new functionality but has a more modern approach using conventions
> rather than content-models.
>
> We are creating a spreadsheet and it may be simplest to share this in a
> dropbox.
>
> If you write a section on your code then this will generally mean that you
> are listed as an author. We only want descriptions of the CML
> interface/API/coverage - not the greater functionality of the program/library
> If you aren't on the list above, please mail either this list or me.
>
> Hoping for contributions
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
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