I accidentally sent the first part of this prematurely. Repeating:
--
Consider the following excerpt:
svg = drawer.GetDrawingText()
svg2 = svg.replace('svg:','')
svg3 = SVG(svg2)
print 'displaying svg:'
display(svg)
print 'displaying svg2:'
display(svg2)
print 'displaying svg3:'
display(svg3)
svg and svg2 display as xml text. svg3 displays as the image. All this is
in a Jupyter notebook in Chrome.
If I "print", rather than "display", svg and svg2 and copy the contents to
.svg files, then try to read the files into Chrome:
- Chrome thinks svg.svg is empty
- When I load svg2.svg, Chrome complains, "This XML file does not appear
to have any style information associated with it. The document tree is
shown below...."
svg3 cannot be printed; I'm just told that it's a <IPython.core.display.SVG
object>.
My first conclusion is that I don't know s**t about this stuff, but I
already knew that.... ;-)
My second conclusion (based on the .svg-file experiments) is that it's not
an iPython problem and, since you see the same thing on Firefox, it's
unlikely to be a Chrome problem.
-P.
-
On Mon, Oct 24, 2016 at 6:44 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> On 10/24/2016 04:39 PM, Peter S. Shenkin wrote:
>
> > Or is it
> > rather because chemists in your target audience will be thinking of the
> > first atom in, say, a structure from an sd file as atom #1?
>
> That
>
> > 2. Regarding the last line, most of the RDKit code I've seen in past
> > examples displays the molecule using code like the following. When is it
> > necessary/not necessary to remove the "svg" string from the results of
> > GetDrawingText()?
>
> Not sure: it's a namespace, I'm assuming ipython can't deal with xml
> namespaces. Properly written programs should show it either way,
> unfortunately my target viewer is firefox (it's a web application and
> the user's default browser is firefox) and firefox isn't one of them.
> Without svg:'s it'll show the file as xml text instead of the image.
>
> HTH
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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