On Mon, Apr 2, 2012 at 12:00 PM, Ola Spjuth <ola.spj...@farmbio.uu.se>wrote:
> 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.
>
>
Yes it would be great and you would be an author. The emphasis is on the
CML and any downstream functionality that uses or otherwise relies on CML.
And I am keen that we have a checklist (approximate) of the elements and
other relavent aspects of CML
> 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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>
--
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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