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 (both in tables and by just printing out a single molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB
...
a very long string with the base64 encoding of the image, but not the
image itself. Plotting from matplotlib works fine. Did I forget to
import 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 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 mining. Moreover, it integrates nicely with the ipython notebook
producing rendered HTML tables for the dataframes. The RDKit
integration allows to have molecule-type columns and functionality to
perform substructure-based row filtering directly on the pandas table.
Additionally, if a dataframe is exported as HTML or shown within an
ipython notebook, the molecules in the table are rendered as 2D
structures.
The new module is available in the current SF trunk and contains a
doctest header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug reports,
comments, ideas... are very much appreciated.
Best,
Nikolas
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