Date: Tuesday, May 7, 2013 1:40 PM
To: rdkit-discuss@lists.sourceforge.net
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rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I
-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
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Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want
...@molecularhealth.com
Date: Tuesday, May 7, 2013 1:40 PM
To: rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS
integration
Sorry
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think this
is going to be useful for many rdkit users. I'm looking forward to using
it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython
notebook though
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 the
output using 'print' the notebook will always use string
Thanks for your help, Niko. Importing the iPythonConsole from rdkit +
removing the 'print' command did the trick for a single molecule :)
Unfortunately, molecules in data frames are still shown as strings, even
when forcing html rendering. I will try to get this working and report
here if I
Just for clarification, are you trying to render a dataframe or a series/single
column? The pandas series object has no to_html() method and is therefore
rendered as string only. Moreover, if you select a single column, e.g. 'ROMol'
from a dataframe by df['ROMol'] you will get a series object that
When developing the module I occasionally had problems with *very* long png
strings, because the pandas maximal column width applies to the string, which is
what is stored in the dataframe, before the image rendering. As an effect the
truncated png string was shown in the table (exactly the ...'
Sorry for the confusion, I truncated the string myself in the mail
because I did not want 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
I just started playing around with the Pandas module, this is very cool
stuff. Thanks so much Nikolas for the contribution. I definitely owe you
a beer at the UGM. It might be worth noting that the you need to install
PIL in order to use the Pandas module. Everything will install without a
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 Takayuki,
On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote:
I'm interested in this work
I want to use PandasTools.
But I got error message, ImportError: cannot import name pyAvalonTools.
I just checked in a modified version that will work when the avalon
tools are not
Dear Greg.
Thank you your quick reply !
The modified version was worked without AvalonTools .
That's nice tool .
I appreciate your kindness.
Takayuki
2013/4/22 Greg Landrum greg.land...@gmail.com
Dear Takayuki,
On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote:
I'm
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
I think Nikolas is being a bit modest... the Pandas integration is
pretty cool. :-)
Here's an example of using it from the IPython prompt (it's better in
the notebook, but that doesn't paste so nicely into email)
Loading an SD file:
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import
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