Saving the fp object

[ale94mleon]

Hello, excelent work!
I am trying to save the fingerprint (becasue the calculation is expensive). I tried with:

import pickle
with open('fp.pkl', 'wb') as file:
    pickle.dump(fp, file)

However, I got the error:

PicklingError: Can't pickle <function _Distance.detect at 0x7f77fa3725e0>: it's not the same object as prolif.interactions._Distance.detect

Any idea why this? Or even better, how to save the fp for future works?

[cbouy]

Hi @ale94mleon and thanks!

I'll have a look into exporting the fingerprint object as a pickle in the future.

In the meantime, you can convert the fingerprint to a dataframe, and then export the dataframe to a pickle object :

df = fp.to_dataframe()
df.to_pickle("dataframe.pkl")

Upon converting the fingerprint to a dataframe, you have several options available to include or exclude some info (namely drop_empty and return_atoms). Type help(fp.to_dataframe) to get more details on that.

So to be safe I would suggest saving both fp.to_dataframe() and fp.to_dataframe(return_atoms=True) just in case you need them later.
Both of these dataframes should contain everything you need for subsequent analysis!

Hope that helps,

Cédric

[ale94mleon]

Thanks for the advice! That is a good idea.