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 is rendered as
string. If you select a set of columns you get a dataframe, for which the HTML
rendering should work. The latter also works for a single column if you enclose
in double brackets df[ ['ROMol' ]], which will give a single-column dataframe.
This took me some time to figure out and the silent conversion that sometimes
occurs can be quite confusing.
Best,
Niko
On May 7, 2013 at 11:33 AM Markus Hartenfeller
<markus.hartenfel...@molecularhealth.com> wrote:
> 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>
> > <mailto: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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