ur-whitelab/exmol

The module 'exmol' has no attribute 'lime_explain'

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andresilvapimentel commented

In the notebook RF-lime.ipynb, the command

exmol.lime_explain(space, descriptor_type=descriptor_type)

gives a error module 'exmol' has no attribute 'lime_explain'

Please, let me know how to fix this error. Thanks.

whitead commented

lime_explain is available in the pre-release version. Use this command to install/upgrade it: pip install --pre --upgrade exmol

andresilvapimentel commented

It worked. Thanks.
Another question.... How can I plot the image ECFP.svg using the notebook RF-lime.ipynb?

I used descriptor_type = "ECFP" but the image is different from the image used in the https://github.com/ur-whitelab/exmol main page.
It shows up with no substructures and no structure in the right. The y-axis in the figure shows up many numbers only (no substructures) .

whitead commented

@hgandhi2411 may answer better here, but I believe to display SVGs you need to use the command skunk.display(svg) by importing the skunk package import skunk. Also, the README page results are from the other notebook (RNN) I believe so you may not get the same results. I put the code from the other notebook below on how to plot the explanations:

svg = exmol.plot_descriptors(samples, descriptor_type='ECFP')
skunk.display(svg)
hgandhi2411 commented

@andresilvapimentel use exmol.plot_descriptors() function as shown by @whitead to get descriptor plots. RF-lime.ipynb was used to create figure 3 in the paper and contains code only for that.

andresilvapimentel commented

It works, but I used:
svg = exmol.plot_descriptors(space, descriptor_type='ECFP')
skunk.display(svg)

Thanks!!! Nice work you did!!! I am working with something similar using LIME. Thanks!!!
I may have more questions later when I will try more.
Thanks anyway!!!

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