First I'd like to welcome these discussions as it shows that the Blue
Obelisk community continues to attract new ideas and collaborators. You are
all very welcome. Open Data, Open Standards, Open Source and Open
Discussion.
On Tue, Aug 4, 2009 at 6:14 AM, <[email protected]> wrote:
> >If it were a line drawing. But there are cylinders and spheres
> >representing bonds and atoms. And then there is the question of sorting
>
>
> Can your program export those structures in some chemical format, like
> V2000 molfile? Then it might be easier to use e.g. the CDK to generate
> real 2D stuctures from that...
>
> I'd strongly suggest using CML as the export format. It interoperates with
SVG and is widely supported in the BO. There are also many structures for
wich MOL files are not suitable (e.g. crystal structures). The value of XML
languages are that you can add annotations and additional information to
elements. For example you might wish to annotate some spheres/circle as
being atoms and others have a different purpose. It's perfectly ok to write:
<svg:circle cx="1.0" cy="2.0" r="3.0" style="fill:green">
<cml:atom id="a1" elementType="Cl" x3="4.0" y3="5.0" z3="6.0"/>
</svg:circle>
This is then able to carry two coordinate systems into the next part of the
processing - indeed we can probably ensure that the graphics information
survives through the chemical processing and vice versa.
I use SVG+CML a lot and they work very well together. With simple XML tools
you ensure syntactic validation of the XML (e.g. the writer() will
automatically escape & and <). Modern web tools will be able to process it
in other valuable ways we haven't thought of (e.g. Google's wave is based on
XML, rather than legacy formats).
--
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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