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 make any progress. In case somebody has already faced the same
problem please let me know.
Best,
Markus
On 05/07/2013 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 the output using 'print' the notebook will always use
string rendering (AFAIK). Just try 'm' alone (instead of 'print m').
Alternatively, you can always force the notebook to do a HTML
rendering (useful for large dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
<markus.hartenfel...@molecularhealth.com> wrote:
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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