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coleygroup / pyscreener

pythonic interface to virtual screening software
MIT License
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Question about running error #8

Closed rebirthjin closed 3 years ago

rebirthjin commented 3 years ago

Dear Authors,

I installed pyscreener in conda env.

When I run the command "python run.py --config test_configs/test_vina.ini", I got the error message like:

ERROR: failed to convert "testing_inputs/5WIU.pdb" Traceback (most recent call last): File "", line 1, in File "/home/njgoo/Data1/program/pyscreener/pyscreener/docking/init.py", line 8, in screener return Vina(software=software, **kwargs) File "/home/njgoo/Data1/program/pyscreener/pyscreener/docking/vina.py", line 102, in init super().init(receptors=receptors, pdbids=pdbids, File "/home/njgoo/Data1/program/pyscreener/pyscreener/docking/base.py", line 102, in init self.receptors = receptors File "/home/njgoo/Data1/program/pyscreener/pyscreener/docking/base.py", line 203, in receptors raise RuntimeError('Preparation failed for all receptors!') RuntimeError: Preparation failed for all receptors!

Could you provide information for solving the error? I also added external software path to PATH in bach_profile.

Thank you!

davidegraff commented 3 years ago

can you provide more information on what the contents of the file were and what your $PATH configuration is?

rebirthjin commented 3 years ago

The test_vina.ini file was distributed in github. The contents like this:

**name = test_vina

mode = docking software = vina receptors = [testing_inputs/5WIU.pdb] ligands = [testing_inputs/test_ligands.csv]

center = [-18, 13.5, -17] size = [14, 12, 15]**

I only changed qvina into vina for docking software.

Also, External software added in ~/.bah_profile.

export PATH=$PATH:/ADFRsuite-1.0/bin export PATH=$PATH:/autodock_vina_1_1_2_linux_x86/bin

Thank you for response!

davidegraff commented 3 years ago

Sorry that we never followed up on this question. if you haven't figured it out by now, could you try re-running this example after porting your code to the new pyscreener version that currently resides in the refactor branch. let me know!

-david

davidegraff commented 3 years ago

we've just released a huge refactor of pyscrener on the main branch. If this issue still persists with the new pyscreener version (which may now be installed via pip install pyscreener!), I can reopen this issue