On Mon, Feb 6, 2012 at 11:37 AM, Peter Murray-Rust <pm...@cam.ac.uk> wrote:
> As a follow-up to the workshop we ran on Semantic Physical Science (see
> http://blogs.ch.cam.ac.uk/pmr/2012/01/15/semantic-physical-science/ and
> later blog posts ) we are publishing a thematic issue in J. Cheminform.
> (cf. last years http://www.jcheminf.com/series/semantic_mol_future )..
> The emphasis is on implementing semantic systems particularly in the area
> of chemistry and materials science. I will publish the proposed papers in
> the next day or so.
>
> One of the papers is:
> "Building a CML code library"
> In this we formulate the essential and optional components of a software
> library to support CML. The scope is ingest, building, modification,
> serialization, and validation. There may also be scope for code-specific
> dictionaries.
>
> This is being copied to the Blue Obelisk to gather current practice in CML
> libraries. This is not limited to Open Source implementations. These
> implementations need not be "complete" - in fact the theme of the paper is
> to show that subsets can be addressed robustly. The implementations should
> be at least show a willingness to address problems of conformance ("Open
> Standards" in the BO ODOSOS).
>
> At present I am aware of roughly
>
> JUMBO (PMR-group, Java)
> Cameron Neylon, Python
> FoX (Andrew Walker et al, FORTRAN90)
> CDK Java
> cclib ??
> Open Babel C++ (Avogadro)
> Chem4Word (C#)
> InChi-interface (C++), PMR group
>
> I believe that some other implementations exist, not sure of whether there
> is an identifiable library/API and conformance
> Chemdraw
> ACDLabs
> Chemaxon
>
The Cactvs toolkit has a pretty good implementation, including I/O of
reactions and NMR spectra.
>
> I believe there are others - I just haven't come across them recently
>
> I'd like to make a reasonably comprehensive list and add objective
> comments if possible.
>
>
> --
> 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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