can not use from_pkl function

[Lili-Cao]

Hi,

I was trying to use the from_pkl function to get the interaction fps saved as a pkl file. But I encountered an error.
Below shows how I generate the ifp, save the file and read the file

Could you please tell me what is the problem? Thank you!

fp = plf.Fingerprint()
ifp = plf.Fingerprint(fp.interactions)
ifp.run_from_iterable([ref_mol], protein_mol)
ifp.to_pickle(path=Path(ligdir)/"ifps"/(Path(name).with_suffix(".pkl"))

however, I cannot use
plf.Fingerprint.from_pkl('path_to_pkl.pkl')
to get the fps,
The error message I get was from
/dill/_dill.py:
obj = StockUnpickler.load(self)
UnpicklingError: state is not a dictionary

[cbouy]

I'll need a bit more info: which version and platform are you using, are you defining custom interactions? Also are you running this from a plain python script or from a jupyter/colab notebook?

[Lili-Cao]

Hi,

I am using version '2.0.3', running it in a jupyternote book in vscode.
I didn't define a custom interaction, just used the default ones.
Here are the related codes in my case

for index, name in enumerate(sys):
print (name)
records[index]=name
reflig_file = Path(ligdir)/Path(name).with_suffix(".pdb")
protein_file = Path(prodir)/Path(name).with_suffix(".pdb")
print ("reflig_file", reflig_file)
print ("protein_file", protein_file)
u1 = mda.Universe(reflig_file.as_posix(), guess_bonds=True)
ref_mol = plf.Molecule.from_mda(u1)
u2 = mda.Universe(protein_file.as_posix(), guess_bonds=True)
protein_mol = plf.Molecule.from_mda(u2)

fp = plf.Fingerprint()
ifp = plf.Fingerprint(fp.interactions)
ifp.run_from_iterable([ref_mol], protein_mol)
ifp.to_pickle(path=Path(ligdir)/"ifps"/(Path(name).with_suffix(".pkl")))

[cbouy]

I can't reproduce your issue, could you try to run your script with the tutorial files?
You should only need to switch these:

reflig_file = plf.datafiles.datapath / "vina" / "lig.pdb"
protein_file = plf.datafiles.datapath / "vina" / "rec.pdb"

Also which OS are you using?

And as a side-note, this line ifp = plf.Fingerprint(fp.interactions) is not necessary, you can directly use the fp object instead of ifp