Thanks again for your reply. That's what I have tried:
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
df = PandasTools.LoadSDF('test.sdf', includeFingerprints=False)
display(HTML(df.to_html()))
So it is a dataframe and .to_html() works fine in general. I see all sdf
fields. It's just that the molecule column contains string value of this
kind:
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAASwAAAEsCAYAAAB ...
The notebook somehow does not realize that it is an html tag with an
image, but instead renders it as a normal string (just like before with
the single molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
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 ...
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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Molecular Health GmbH
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Fax: +49 6221 43851 100
Email: markus.hartenfel...@molecularhealth.com
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