great thanks for you help
however the next line of code got crushed and here it is

1 # Write docked ligands conformations to a file (including scores)
----> 2 pipeline.write('mol2', 'ampc_docked.mol2', overwrite=True, opt={'c':None})

D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\virtualscreening.py in write(self, fmt, filename, csv_filename, **kwargs)
403 filename,
404 overwrite=True,
--> 405 **kwargs)
406 if csv_filename:
407 f = open(csv_filename, 'w')

TypeError: type object got multiple values for keyword argument 'overwrite'

please help me out
thanks

from oddt.

Hi, sorry for the inconvenience but
One more issue
At the same line I get
D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\virtualscreening.py:345: UserWarning: The chunksize (100) seams to be to large.
% self.chunksize)

RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "D:\Anaconda3\envs\drugdesign\lib\multiprocessing\pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\utils.py", line 89, in compose_iter
iterable = func(iterable)
File "D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\utils.py", line 112, in method_caller
return getattr(obj, methodname)(*args, **kwargs)
File "D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\docking\AutodockVina.py", line 242, in dock
ligand_dir = mkdtemp(dir=self.tmp_dir, prefix='ligands_')
File "D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\docking\AutodockVina.py", line 137, in tmp_dir
self.tmp_dir = mkdtemp(dir=self.dir, prefix='autodock_vina')
File "D:\Anaconda3\envs\drugdesign\lib\tempfile.py", line 370, in mkdtemp
_os.mkdir(file, 0o700)
FileNotFoundError: [WinError 3] Le chemin d’accès spécifié est introuvable: '/tmp\autodock_vina_yfo3z7ya'
"""

The above exception was the direct cause of the following exception:

FileNotFoundError Traceback (most recent call last)
in
1 # Write docked ligands conformations to a file (including scores)
----> 2 pipeline.write('mol2', 'ampc_docked.mol2', opt={'c':None})

D:\Anaconda3\envs\drugdesign\lib\site-packages\oddt\virtualscreening.py in write(self, fmt, filename, csv_filename, **kwargs)
407 f = open(csv_filename, 'w')
408 csv_file = None
--> 409 for mol in self.fetch():
410 if csv_filename:
411 data = mol.data.to_dict()

D:\Anaconda3\envs\drugdesign\lib\multiprocessing\pool.py in next(self, timeout)
759 if success:
760 return value
--> 761 raise value
762
763 next = next # XXX

FileNotFoundError: [Errno 2] Le chemin d’accès spécifié est introuvable: '/tmp\autodock_vina_yfo3z7ya'

Very grateful and sorry one more time
I m just obsessed with your pecular job

from oddt.

Automated discovery of Vina binary is flawed on Windows, I will try to find a better way of doing it.

In the meantime you can use executable argument of of dock/autodock_vina to point it to a vina binary:

pipeline.dock('autodock_vina', 'ampc/receptor.pdbqt', 'ampc/crystal_ligand.mol2', executable='path/to/vina.exe')

PS.
Sorry that I missed #90

from oddt.

Just remove overwrite=True, it was removed and is a default now.

from oddt.

I will try to reproduce the error on my Windows machine, although it seam that you are still missing Autodock Vina. How did you installed ODDT and other dependencies?

from oddt.

hi,
for the installation, I flowed through on the steps of the readme file and all seemed to be ok (i presume so!)
for the autodock vina ; i pointed to the executable path just as you have already suggested and i run the command without any warnings thank you for helping out, i really need your package for my paper.
thanks

from oddt.

I managed to reproduce that error, and some of the variables have default values that do not work smooth on Windows - this needs to be fixed. In the meantime you have to submit a temporary path for vina files with prefix_dir argument (default is /tmp which obviously is not there on windows).

I run the notebook by changinfg the dock line to:

# Dock entire library to receptor, autocenter docking box on  ligand
pipeline.dock('autodock_vina', 'ampc/receptor.pdbqt', 'ampc/crystal_ligand.mol2', 
              executable='C:\Users\maciek\Miniconda3\envs\py27\\bin\Windows-vina.exe', prefix_dir='.')

The . means that the temp files are going to be placed next to the notebook itself.

from oddt.

hi, trying to run the code, very slow and get stuck with this message

":\Anaconda3\envs\drugdesign\lib\site-packages\oddt\virtualscreening.py:345: UserWarning: The chunksize (100) seams to be to large.
% self.chunksize)"

even if i downsized the chunksize=30,
the only result i got until now is the creation of 'autodock_vina_d04d1aal' file (empty) in the notebook directory what to do, keep it running or shut it down?
regards

from oddt.

Two additional things:

• training NNscore takes ~1h, so you might want to disable (hash) nnscore rescoring;
• I have noticed an OpenBabel bug that surfaces in Windows, I'm preparing a fix for that issue.

from oddt.

i m still at the previous step

Write docked ligands conformations to a file (including scores)

pipeline.write('mol2', 'ampc_docked.mol2', opt={'c':None})

and the code is blocked ???
how did you manage to pass over to the next line of code ?

from oddt.

If it is blocked it probably is docking. Check your task manager. Invoking vs.write(...) actually triggers the computations. Until then they are lazy and are queued until write or fetch is called.

from oddt.

yes your right there is an issue with openbabel

*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot initialize database 'types.txt' which may cause further errors.
[I 10:01:25.458 NotebookApp] Saving file at /Snippet_1.ipynb
[I 10:03:24.927 NotebookApp] Saving file at /Snippet_1.ipynb

from oddt.

actually, openbabel is complicated to set up on google collab which humper seriously the possibility to run ODDT on the cloud,???!!!
i will very grateful if you could screw this away
1000 thanks

from oddt.

I need to retest it on Windows, but #93 should take care of those you had. I plan to add Appveyor Windows testing to CI for the future.

from oddt.

hi,
still getting the same error even after the amendments (93)
*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot initialize database 'types.txt' which may cause further errors.
hope the windows appveyr is coming soon

from oddt.

I managed to identify the problem - the logp was failing, and all molecules were filtered out. You have to hash the logp filter in the pipeline and the docking will be done.

# pipeline.apply_filter('0 < mol.logp < 5')

from oddt.

I will try it out and get back to you,
I need your mail I m holding a data science event a need to discuss it with you
Thanks

from oddt.

hi
the same issue with open babel even with hashing the logp filter

*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot initialize database 'types.txt' which may cause further errors.

do i need to reset the #93 amendments

from oddt.

hi any news

from oddt.

@aminemosbah Have you tried the latest OpenBabel from conda-forge?

from oddt.