Dear all,
This year’s RDKit UGM will offer for the first time the opportunity to present
posters. If you would like to bring a poster please send Sereina and me an
email. You do not have to provide a title right now, but as the available space
is limited, poster slots will be allocated on a
Dear Isidro,
I can’t test at the moment, but as I understand it so far I would guess the
reason for the behaviour is two-fold. First, the substructure search in the
pandas data frame just checks wether the substructure is present by calling the
HasSubstructMatch method from the molecule object.
Hi George,
Glad that Greg already helped you getting it working. Just to add some information: The methods RenderImagesInAllDataFrames and ChangeMoleculeRendering are related in their effects but doing slightly different things.
RenderImagesInAllDataFrames is patching
Hi Paul,
I'll answer directly below.
Dear Niko,
I was exactly looking for this functionality, great work!
A few follow-up questions:
* frame.set_index('_Name') did not work, but there is a name set in the SD
file.
The molecule name is contained in the column specified by the optional
Hi Paul,
I am not sure if it is easily doable to get the pandas read_table function to
handle sd-files. However, there is some basic functionality for this already
built-in in the PandasTools module. If you check the docktest header there is a
small example. Basically,
frame =
Dear all,
a tutorial ipython notebook for using the RDKit/Pandas integration is now
available on the wiki (http://code.google.com/p/rdkit/wiki/Tutorials - Using
Pandas in combination with RDKit).
There is also a new version of the PandasTools module in the rdkit trunk on
GitHub. This fixes the
to paste the whole beast. The fields contain the full
strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had
problems with *very* long png strings
something,
or could it be a browser issue? I am using centOS 6 and Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows for
using RDKit molecule
/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem, there are
two things: You have to import the RDKit IPythonConsole to enable the
molecule rendering (from rdkit.Chem.Draw import IPythonConsole) and if you
trigger
that it is an html tag with an image,
but instead renders it as a normal string (just like before with the single
molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
Just for clarification, are you trying to render a dataframe or
a series/single
Hi Pat,
I am glad you find it useful. Many thanks for pointing out the PIL dependency.
I had installed It already for different reasons and did not think about
mentioning it.
Best,
Niko
On 22 Apr 2013, at 17:52, Patrick Walters wpwalt...@gmail.com wrote:
I just started playing around with
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows for using
RDKit molecule objects directly in pandas dataframes. Pandas
(http://pandas.pydata.org/) is a python library that offers table-like
datacontainers, which are incredibly useful for anything related to data
, line 66, in
FormCorrelationMatrix
sumY = sum(y)
So, what version of RDKit are you using?
And if you don't care, could you show me some results ?
Thanks.
Takayuki
2013/1/18 Nikolas Fechner m...@fechner.cc
Hi Takayuki,
I was able to run your code snippet without any errors
Hi Takayuki,
I was able to run your code snippet without any errors (with different example
molecules of course). Could possible explain in more detail what is not working
for you? What version of RDKit are you using (from rdkit import rdBase;print
rdBase.rdkitVersion) ?
Niko
On Jan 17, 2013,
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