[Cdk-devel] Re: [Jchempaint-devel] SVG output for molecules

[Peter Murray-R. <pm...@ca...>]

At 11:05 07/06/2004 +0200, E.L. Willighagen wrote:
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Thanks Egon,

>On Monday 07 June 2004 10:45, Peter Murray-Rust wrote:
> > [This might also be relevant to CDK]
> >
> > Currently if we want re-usable SVG output for molecules we use our own XSLT
> > stylesheets. These are becoming increasingly clunky and we'd like to have
> > Java routines instead. What are the current options? I'd suggest
> >
> > - write it in native SVG output
>
>A few options here I think:
>
>1. a true CDK class 2 SVG convertor (and use the Batik SVG viewer for display)
>2. keep using the XSLT stylesheets and do CDK 2 CML 2 SVG
>
> > - write it in Java2D and use their facilities for rescaling, etc
>
>Peter, IIRC you told be that Java2D was a bit buggy... it potentially would
>improve the 2D rendering considerably... but only if the implementation of
>Java2D among platforms is reasonably stable...

Miguel affirmed that JCP was using Java2D anyway. My experience was ca 2 
years ago when I found it didn't do affine transformations. This could be 
anything from my incompetence to buggy Java. I would expect that if others 
had another go it might disappear.

> > - write to a JCP panel and convert.
> >
> > Presumably 3 requires SVGGEN (and maybe 2)
>
>That's the Batik route... I have not had very good results though... The
>exported SVG does not generally work, which seems to be caused by the
>stroke="none" in theSVG output...

Again - is this recent or might Batik have mended it?

> > I couldn't find huge amounts in CDK and JCP but I didn't look very hard
>
>The code is in CDK:
>
>org.openscience.cdk.io.CDKWriter
>
>and uses Batik for the actual conversion...
>
> > One of the attractions of SVG over current JCP is that it looks nicer
> > (antialiasing, etc.)
>
>Agreed.
>
> > Does JCP support antialiasing or if not does it plan
> > to? For printed output (e.g. converted by FOP) it's fairly important
>
>I'll ask Miguel what he needed to do to get anti-aliasing in Jmol...

Thanks.

There are several reasons but an obvious one is using JCP as a toolkit for 
rendering molecules and reactions. The user might specify the dimensions, 
fonts, etc to be used and the toolkit return an SVG file. This might 
include multiple pictures per page or alternatively FOP might be used for that.

P.


>Egon
>
>- --
>eg...@sc...
>PhD on Molecular Representation in Chemometrics
>Nijmegen University
>http://www.cac.sci.kun.nl/people/egonw/
>GPG: 1024D/D6336BA6
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Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069