[Rdkit-discuss] problems with 'Ames mutagenicity dataset analysis using RDKit and PANDAS' tutorial

[Andrew D. <da...@da...>]

I'm trying out the "Ames mutagenicity dataset analysis using RDKit and PANDAS" notebook at

  http://nbviewer.ipython.org/1223fc7f1ec7ae4165c5

I have two problems. First, the data frame is supposed to show an inline image, but I get the actual text "<img src=..." with the data: url rather than the image. (See the first attached screen grab with the head(2) to see what I mean.)

Regular images do work. (See the second attached screen grab which shows the Molecule depiction.)

 
Second, the inline plots are severely truncated. (See the third attached screen grab, with In/Out[24].)

It appears to have something to do with the unstack(), since if I remove that transformation then I get something viewable. (See the 4th screen grab, with In/Out[33] and [35].) Though of course the plot isn't what it's supposed to be in the tutorial.

I don't know enough about pandas to figure this out myself.


I'm using the latest build of RDKit, built from version control.

>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2014.03.1pre'
>>> 

and I have PANDAS version  0.10.1.


BTW, the tutorial also needs an "import numpy" because In[14] has a '    res = numpy.zeros(len(fp),numpy.int32)' and numpy wasn't previously imported.


Cheers,


				Andrew
				da...@da...