Hello, I have just installed psearch and all the env dependencies in conda. I downloaded the acetylcholinestarase (AChE) dataset to do a test and in the phase of preparing the dataset I came across the following error:
**Traceback (most recent call last):
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)Traceback (most recent call last):
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/prepare_dataset.py", line 61, in common
create_db.main_params(dbout_fname=filenames[4],
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/scripts/create_db.py", line 156, in main_params
for i, res in enumerate(p.imap_unordered(map_process_mol,
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 873, in next
raise value
OSError: File error: Invalid input file /home/juliana/Downloads/Ache/compounds/inactive_conf.sdf
Process Process-1:
Traceback (most recent call last):
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/prepare_dataset.py", line 61, in common
create_db.main_params(dbout_fname=filenames[4],
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/scripts/create_db.py", line 156, in main_params
for i, res in enumerate(p.imap_unordered(map_process_mol,
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 873, in next
raise value
OSError: File error: Invalid input file /home/juliana/Downloads/Ache/compounds/active_conf.sdf
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/prepare_dataset.py", line 61, in common
create_db.main_params(dbout_fname=filenames[4],
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/scripts/create_db.py", line 156, in main_params
for i, res in enumerate(p.imap_unordered(map_process_mol,
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 873, in next
raise value
OSError: File error: Invalid input file /home/juliana/Downloads/Ache/compounds/inactive_conf.sdf
Process Process-1:
Traceback (most recent call last):
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, self._kwargs)
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/prepare_dataset.py", line 61, in common
create_db.main_params(dbout_fname=filenames[4],
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/site-packages/psearch/scripts/create_db.py", line 156, in main_params
for i, res in enumerate(p.imap_unordered(map_process_mol,
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/juliana/anaconda3/envs/psearch/lib/python3.12/multiprocessing/pool.py", line 873, in next
raise value
OSError: File error: Invalid input file /home/juliana/Downloads/Ache/compounds/active_conf.sdf
No file in the "compounds" folder was generated... Any suggestions on how to move forward?
Thanks in advance...
Juliana
From which branch did you install psearch? You have to use gen_pharms branch, it is the most recent. Unfortunately we still did not fix all remaining bugs and merge it to the master.
Another aspect, I never used psearch with python 3.12, maximum it was 3.9. However, it should be a problem.
Running psearch on my current working dataset got my trainset list stuck... I tried some checking in select_training_set_rdkit.py to understand the problem, but to no avail...
>> psearch -p my_models_2/created_pharmacophores/ -i beta_2_short.smi -d dbs/beta.dat -c 4
Size of df before generating fingerprints: (101, 3)
Size of df after generating fingerprints: (101, 4)
Size of df_mols before concatenation: (101, 4)
Size of df_mols after concatenation: (101, 5)
100 molecules screened 00:00:01
external_statistics.txt: (0.009s)
Any light?
Does it return any pharmacophore model? If not, it may happen that it cannot create training sets. I got something similar in the past and it would be reasonable to implement another modeling mode, where all input ligands will be taken as a training set without selection like now. It may also be some bug. If you can share your data set, I may look on it when I'll have time, but I do not promise that will do this quickly.
Increasing the number of active compounds solved the problem...
meddwl
