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Please help me checking my script to predict on my ./coreset:
import os
import pandas as pd
import csv
import oddt
from oddt.scoring.functions import RFScore
oddt.toolkit = oddt.toolkits.rdk
# create RFScore model from trained model
# rf = RFScore.load('/path/to/your/model.pkl')
rf = RFScore.rfscore(version=1, n_jobs=-1)
with open('result_csv.csv', 'w', newline='') as csvfile:
fieldnames = ['pdb_id', 'rf_score_v1']
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
for root, dirs, _ in os.walk('./coreset'):
for dir in dirs:
pdb_id = dir
ligands_file = os.path.join(root, dir, f'{pdb_id}_ligand.sdf')
proteins_file = os.path.join(root, dir, f'{pdb_id}_pocket.pdb')
lig_mol = next(oddt.toolkit.readfile('sdf', ligands_file))
prot_mol = next(oddt.toolkit.readfile('pdb', proteins_file))
score = rf.predict(lig_mol, prot_mol)
print(f'{pdb_id}_ligand.sdf', score)
Traceback (most recent call last):
File "oddt_rfscore_Coreset.py", line 25, in
score = rf.predict(lig_mol, prot_mol)
File "/data2/rjli/mambaforge/envs/oddt/lib/python3.8/site-packages/oddt/scoring/init.py", line 260, in predict
descs = self.descriptor_generator.build(ligands)
File "/data2/rjli/mambaforge/envs/oddt/lib/python3.8/site-packages/oddt/scoring/descriptors/init.py", line 167, in build
for mol in ligands:
TypeError: 'NoneType' object is not iterable
The text was updated successfully, but these errors were encountered:
Please help me checking my script to predict on my ./coreset:
Traceback (most recent call last):
File "oddt_rfscore_Coreset.py", line 25, in
score = rf.predict(lig_mol, prot_mol)
File "/data2/rjli/mambaforge/envs/oddt/lib/python3.8/site-packages/oddt/scoring/init.py", line 260, in predict
descs = self.descriptor_generator.build(ligands)
File "/data2/rjli/mambaforge/envs/oddt/lib/python3.8/site-packages/oddt/scoring/descriptors/init.py", line 167, in build
for mol in ligands:
TypeError: 'NoneType' object is not iterable
The text was updated successfully, but these errors were encountered: