Indeed, when the file under discussion most recently named "svg2.html" is
modified so that "xmlns:svg=" is replaced with "xmlns=", and the file is
renamed "svg2.svg", double-clicking it opens it and correctly correctly
displays the image in the browser.
But trying this in the Jupyter notebook fails. the original code had the
lines:
svg = drawer.GetDrawingText().replace('svg:','')
display(SVG(svg))
This succeeded. If i add Dimitri's latest sugesstion:
svg =
drawer.GetDrawingText().replace('svg:','').replace('xmlns:svg=','xmlns=')
display(SVG(svg))
this also succeeds. If I only carry out the second replacement, this fails
with an error several levels down.
So apparently, SVG() can create an svg object out of the contents of a
correctly formed svg file, but is insensitive to some constructs that make
the such a file invalid for direct use in a browser.
I'm still not sure why GetDrawingText() doesn't return a properly formatted
svg string. Is there some use its output can be put to without these
.replacements?
-P
On Tue, Oct 25, 2016 at 1:35 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> On 10/25/2016 11:21 AM, Peter S. Shenkin wrote:
> > Hi, Hongbin,
> >
> > Thanks. Indeed. svg2.svg, when renamed to svg2.html, shows the correct
> > image in Chrome. svg.html shows garbage.
> >
> > Still, it would be good to be able to create a real .svg file from RDKit.
>
> OK, you made me look and I learned something today.
>
> Mozilla claims valid SVG must include the namespace declarations
> (https://developer.mozilla.org/en-US/docs/Web/SVG/FAQ) citing this
> document: https://jwatt.org/svg/authoring/#namespace-binding
>
> There it states
> """
> <svg xmlns="http://www.w3.org/2000/svg";
> ...
> Be careful not to type xmlns:svg instead of just xmlns when you bind the
> SVG namespace. This is an easy mistake to make, but one that can break
> everything. Instead of making SVG the default namespace, it binds it to
> the namespace prefix 'svg', and this is almost certainly not what you
> want to do in an SVG file. A standards compliant browser will then fail
> to recognise any tags and attributes that don't have an explicit
> namespace prefix (probably most if not all of them) and fail to render
> your document as SVG.
> """
>
> Sure enough, rdkit's files start with
> """
> <svg:svg version='1.1' baseProfile='full'
> xmlns:svg='http://www.w3.org/2000/svg'
> ...
> """
>
> With that declaration any standards-compliant viewer should only
> recognize tags with "svg:" prefix, and removing svg:'s results in a
> technically invalid file. Anything that displays it as an image is what
> we "it professionals" call b0rk3d.
>
> According to this, what RDKit writes out is wrong: you actually *want
> to* remove :svg from the root tag's "xmlns" attribute, then you *may*
> remove the svg: prefixes from all tags (including the root one).
>
> Of course, that was last edited in 2007, maybe something changed in the
> 10 years since.
>
> HTH,
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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