Problem using the last version of Prolif

[xavgit]

Hi, If I run the following using the last version of prolif:

fp = plf.Fingerprint() fp.run_from_iterable( docked_poses , receptor )

I receive the the error:

0%| | 0/5 [00:00<?, ?it/s] multiprocess.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/xxxx/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/parallel.py", line 233, in executor return cls.fp.generate(mol, cls.pmol, residues=cls.residues, metadata=True) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 371, in generate interactions = get_interactions(lres, pres) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 306, in metadata return { File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 309, in if (metadata := interaction(res1, res2, metadata=True)) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 54, in wrapped return next(interaction(args, **kwargs), None) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/interactions/base.py", line 48, in call for int_data in self.detect(lig_res, prot_res): File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/interactions/interactions.py", line 480, in detect yield self.metadata( File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/interactions/base.py", line 71, in metadata [get_mapindex(prot_res, index) for index in prot_indices] File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/interactions/base.py", line 71, in [get_mapindex(prot_res, index) for index in prot_indices] File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/interactions/utils.py", line 24, in get_mapindex return res.GetAtomWithIdx(index).GetUnsignedProp("mapindex") KeyError: 'mapindex' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "prolif_analysis.py", line 11, in fp.run_from_iterable( docked_poses , receptor ) File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 596, in run_from_iterable return self._run_iter_parallel( File "/home/xxxx/.local/lib/python3.8/site-packages/prolif/fingerprint.py", line 629, in _run_iter_parallel for i, ifp_data in enumerate(pool.process(lig_iterable)): File "/home/xxxx/.local/lib/python3.8/site-packages/tqdm/std.py", line 1180, in iter for obj in iterable: File "/home/xxxx/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 868, in next raise value KeyError: 'mapindex'

---

(program exited with code: 1) Press return to continue

If I downgrade to 1.1.0 version then it seems that all is fine obtaining:

100%|█████████████████████████████████████████████| 5/5 [00:00<00:00, 81.23it/s]

---

(program exited with code: 0) Press return to continue

Thanks. Saverio

PS: I have used the F5 key of Geany to run the code.

[cbouy]

How did you prepare docked_poses and receptor?

[xavgit]

Hi, thanks for the reply.

For the receptor I have used the following code; import pickle import prolif as plf import MDAnalysis as mda

u = mda.Universe( 'receptor_dock_prep.pdb' ) receptor = plf.Molecule.from_mda( u ) with open( 'receptor_dock_prep_mda.pkl' , 'wb' ) as outfile: pickle.dump( receptor , outfile )

Then from a file ZINCID_docked.sdf converted from the file ZINCID_docked.pdbqt ( obtained using vina with num_modes = 5 ) using mk_export.py the following code:

import pickle import prolif as plf

with open( 'receptor_dock_prep_mda.pkl' , 'rb' ) as infile: receptor = pickle.load( infile ) docked_poses = plf.sdf_supplier( 'ZINCID_docked.sdf' )

fp = plf.Fingerprint() fp.run_from_iterable( docked_poses , receptor ) df = fp.to_dataframe()

With prolif 1.1.0 it runs without errors.

Thanks.

Saverio ZINC000016999890_docked.pdbqt.txt ZINC000016999890_docked.sdf.txt

[cbouy]

Ah yes this might be because you're loading your receptor from a pickle file, by default RDKit does not transfer atomic properties when you do this. The previous version of ProLIF was applying a patch (on import) for this which wasn't very conservative, and the new version only applies the patch when necessary.

You can force-apply the patch by running this before pickling your receptor:

from prolif.pickling import PICKLE_HANDLER

PICKLE_HANDLER.set()

# pickle your receptor
...

or alternatively:

from rdkit import Chem

Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AtomProps ^ Chem.PropertyPickleOptions.MolProps)

which should do the same thing

[xavgit]

Hi, thanks for your help and the Prolif package. I will avoid to use pickle. The reason to use it is for save time and prepare the receptor from mda only one time for many different docked ligands.

Thanks. Saverio

[orgw]

Thank you!! this helped