Re: [Rdkit-discuss] New module for RDKit - PANDAS integration

[Markus H. <mar...@mo...>]

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 
> <mar...@mo...> 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 
>>> <mar...@mo...> 
>>> <mailto:mar...@mo...> 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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-- 
*Markus Hartenfeller*
Chemoinformatics Specialist
Molecular Health GmbH
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Email: mar...@mo...
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