prepare_dataset issue

[julianaamorim]

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

[DrrDom]

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.

[julianaamorim]

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?

[DrrDom]

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.

[julianaamorim]

Increasing the number of active compounds solved the problem...