OK, my turn: that went out too soon.
It seems to me that jypiter, ipython, or whatever, has no idea how
render MIME type image/svg+xml. It can display an "SVG" object, but the
bit that turned image/svg+xml into "SVG" does not understand XML
namespaces (that's been around since at least 2009).
Hi,
Dima wrote:
>
> Try saving the text (svg/svg2) to a file and opening it in chrome (if you
> can actually open a file in chrome) or some other application.
I actually did that, and in a second email I reported:
>
>- Chrome thinks svg.svg is empty
>
>
>- When I load svg2.svg, Chrome
On 2016-10-24 19:04, Peter S. Shenkin wrote:
> 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.
Well, what I got it from (Greg's I think) tutorial that if you
Stuart,
The PAINS file is available in the RDKIT Github repository. If that's
too complicated deal with at this early stage, try some of the workflows
on myexperiment.org:
http://www.myexperiment.org/workflows/1841.html (embedded file)
or
http://www.myexperiment.org/workflows/4748.html (just
Hello everyone,
I am a new user of RDkit and I was looking in the documentation for an easy
way to load multiple conformers from a structure file like .sdf. The code
must 1) distinguish between different protonation states of the same
molecule, 2) create a new Mol() object for each protonation
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, in a
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
Hi, Dimitri,
I have two questions about your code.
1. Why are you incrementing the atom index by 1? Are there functions in
RDKit, for example, that use atom indices using index-origin 1? Or is it
rather because chemists in your target audience will be thinking of the
first atom in, say, a
Since you already got your answer I'll just post this for posterity:
import sys
import rdkit
import rdkit.Chem
import rdkit.Chem.AllChem
import rdkit.Chem.Draw
import rdkit.Chem.Draw.rdMolDraw2D
mol=rdkit.Chem.SupplierFromFilename(sys.argv[1],removeHs=False).next()
Hello All,
I have been trying to get the 09901004_Filtering A Hitlist workflow from KNIME
working but cannot set the location of the sieve files containing the pains
data. When I try and configure the node, an error is thrown stating this data
is missing. Since this workflow was downloaded
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