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LinaDongXMU / XLPFE

XLPFE: a Simple and Effective Machine Learning Scoring Function for Protein-ligand Scoring and Ranking
https://pubs.acs.org/doi/10.1021/acsomega.2c01723
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XLPFE running errors #4

Closed mglgc closed 3 months ago

mglgc commented 3 months ago

Hi, After a successful conda env XLPFE installation, the XLPFE.sh main script ends up with errors messages coming from the python scripts as I'm copying below. Please, could you give me some clues to fix it? Thank you very much in advance for your reply.

Traceback (most recent call last): File "/user/XLPFE-main/application/for_feature/pocket.py", line 17, in if a[5].isalnum()==True: IndexError: list index out of range Traceback (most recent call last): File "/user/XLPFE-main/application/for_feature/fullprotein.py", line 17, in if a[5].isalnum()==True: IndexError: list index out of range Traceback (most recent call last): File "/user/XLPFE-main/application/for_model/XLPFE.py", line 14, in x_tests=transfer.fit_transform(x_test) File "/user/miniconda3/lib/python3.9/site-packages/sklearn/base.py", line 852, in fit_transform return self.fit(X, fit_params).transform(X) File "/user/miniconda3/lib/python3.9/site-packages/sklearn/preprocessing/_data.py", line 806, in fit return self.partial_fit(X, y, sample_weight) File "/user/miniconda3/lib/python3.9/site-packages/sklearn/preprocessing/_data.py", line 841, in partial_fit X = self._validate_data( File "/user/miniconda3/lib/python3.9/site-packages/sklearn/base.py", line 566, in _validate_data X = check_array(X, check_params) File "/user/miniconda3/lib/python3.9/site-packages/sklearn/utils/validation.py", line 805, in check_array raise ValueError( ValueError: Found array with 0 sample(s) (shape=(0, 63)) while a minimum of 1 is required by StandardScaler. cp: cannot stat 'results.csv': No such file or directory

mglgc commented 3 months ago

Further clarifying, the issue comes from the pocket.py script:

Traceback (most recent call last): File "/user/XLPFE-main/application/for_feature/pocket.py", line 17, in if a[5].isalnum()==True: IndexError: list index out of range

mglgc commented 3 months ago

Digging into the code I realized if the pocket pdb files contain chain identifiers (PDB column #22) the pocket.py script will reproduce such issue. Fixed by leaving blank that PDB column.

Further clarifying, the issue comes from the pocket.py script:

Traceback (most recent call last): File "/user/XLPFE-main/application/for_feature/pocket.py", line 17, in if a[5].isalnum()==True: IndexError: list index out of range

LinaDongXMU commented 3 months ago

examples have pocket.pdb and protein.pdb to be referred. Congratulations on being able to debug on yourself.

mglgc commented 3 months ago

Anyway, thanks for your reply.

examples have pocket.pdb and protein.pdb to be referred. Congratulations on being able to debug on yourself.