problem with smart_open ?

[slchan3]

I tried generating conformers by
python $E3FP/conformer/generate.py -s temp.smi -o ~/outdir -n 3
where temp.smi is simply
Brc4cccc(Nc2ncnc3cc1ccccc1cc23)c4 CHEMBL63786

I encountered the following error.

2020-10-22 21:19:30,180|INFO|Input type: Detected SMILES file(s)
2020-10-22 21:19:30,180|INFO|Input file number: 1
2020-10-22 21:19:30,180|INFO|Parallel Type: processes
2020-10-22 21:19:30,180|INFO|Out Directory: ......outdir
2020-10-22 21:19:30,180|INFO|Overwrite Existing Files: False
2020-10-22 21:19:30,180|INFO|Target Conformer Number: 3
2020-10-22 21:19:30,181|INFO|First Conformers Number: all
2020-10-22 21:19:30,181|INFO|Pool Multiplier: 1
2020-10-22 21:19:30,181|INFO|RMSD Cutoff: 0.5
2020-10-22 21:19:30,181|INFO|Maximum Energy Difference: None
2020-10-22 21:19:30,181|INFO|Forcefield: UFF
2020-10-22 21:19:30,181|INFO|Starting.
Traceback (most recent call last):
File "generate.py", line 413, in
run(**kwargs)
File "generate.py", line 338, in run
for result, data in results_iterator:
File "....../envs/e3fp_env/lib/python3.6/site-packages/sdaxen_python_utilities-0.1.4-py3.6.egg/python_utilities/parallel.py", line 304, in
File "....../envs/e3fp_env/lib/python3.6/site-packages/sdaxen_python_utilities-0.1.4-py3.6.egg/python_utilities/parallel.py", line 353, in concurrent_run
File "generate.py", line 279, in
data_iterator = make_data_iterator((x for x in mol_iter
File "generate.py", line 265, in
mol_iter = (mol_from_smiles(_smiles, _name,
File "....../envs/e3fp_env/lib/python3.6/site-packages/e3fp/conformer/util.py", line 165, in smiles_generator
values = line.rstrip('\r\n').split()
TypeError: a bytes-like object is required, not 'str'

I think it is a problem with smart_open because this part worked when I changed smart_open to a simple open. (Then there comes a problem of a similar nature when it tried to output.)

[sethaxen]

Thanks for the issue, and I apologize for the delayed reply. This looks like it might be due to a change in rdkit.Chem.SDWriter. I'll look into a workaround.

[slchan3]

Please don't worry, Seth. I don't need this fix as of now. Thank you. Ling

…

On Thu, Jan 14, 2021 at 12:38 AM Seth Axen ***@***.***> wrote: Thanks for the issue, and I apologize for the delayed reply. This looks like it might be due to a change in rdkit.Chem.SDWriter. I'll look into a workaround. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARHCUCAMTJIRED4QCLDQRILSZ2UR3ANCNFSM4S4BWFRQ> .