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
> <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/ <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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