Hi Niko,
I tried this piece of code adapted from the doctest and got the same
result (table is fine, but no rendering of molecules):
from rdkit.Chem import PandasTools
import pandas as pd
import os
from rdkit import RDConfig
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
antibiotics = pd.DataFrame(columns=['Name','Smiles'])
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C','Name':'Penicilline
G'}, ignore_index=True)#Penicilline G
antibiotics =
antibiotics.append({'Smiles':'CC1(C2CC3C(C(=O)C(=C(C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O','Name':'Tetracycline'},
ignore_index=True)#Tetracycline
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)C(C3=CC=CC=C3)N)C(=O)O)C','Name':'Ampicilline'},
ignore_index=True)#Ampicilline
PandasTools.AddMoleculeColumnToFrame(antibiotics,'Smiles','Molecule',includeFingerprints=True)
display(HTML(antibiotics.to_html()))
The img tag and the png encoding themselves are fine. If I paste one in
a simple html page and open it with the same browser the molecule is
rendered.
Best,
Markus
On 05/08/2013 09:03 AM, Fechner, Nikolas wrote:
Hi Markus,
Could you try the examples that are included as doctests in the
PandasTools.py module? These should definitely work and show rendered
molecules in the tables.
Best,
Niko
From: Markus Hartenfeller <markus.hartenfel...@molecularhealth.com
<mailto:markus.hartenfel...@molecularhealth.com>>
Date: Tuesday, May 7, 2013 1:40 PM
To: "rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>"
<rdkit-discuss@lists.sourceforge.net
<mailto:rdkit-discuss@lists.sourceforge.net>>
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want to paste the whole beast. The fields contain
the full strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had problems with *very*
long png strings, because the pandas maximal column width applies to
the string, which is what is stored in the dataframe, before the
image rendering. As an effect the truncated png string was shown in
the table (exactly the "...' ending shown in your example).
You could try manually setting the maximal width very high (e.g.
pandas.set_option("display.max_colwidth",100000)). This should be
done automatically by the PandasTools, which sets it the len(PNG)+100
for the longest string found during rendering, but because this
rarely had an impact I could very well have overseen some problems
with this strategy.
Best,
Niko
On May 7, 2013 at 1:13 PM Markus Hartenfeller
<markus.hartenfel...@molecularhealth.com> wrote:
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>
<mailto: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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