[JOSS review] Criptic error running example

[rvhonorato]

When running the provided example:

# example/benzene_5wiu.py
import pyscreener as ps
import ray
ray.init()

metadata = ps.build_metadata("vina")
virtual_screen = ps.virtual_screen("vina", ["integration-tests/inputs/5WIU.pdb"], (-18.2, 14.4, -16.1), (15.4, 13.9, 14.5), metadata, ncpu=8)

scores = virtual_screen("c1ccccc1")
scores

$ python example/benzene_5wiu.py 
2022-01-12 14:20:06,884 INFO services.py:1338 -- View the Ray dashboard at http://127.0.0.1:8265
Traceback (most recent call last):
  File "example/benzene_5wiu.py", line 9, in <module>
    scores = virtual_screen("c1ccccc1")
  File "/Users/rodrigo/repos/pyscreener/pyscreener/docking/screen.py", line 169, in __call__
    planned_simulationsss = self.plan(sources, smiles)
  File "/Users/rodrigo/repos/pyscreener/pyscreener/docking/screen.py", line 243, in plan
    planned_simulationsss = [
  File "/Users/rodrigo/repos/pyscreener/pyscreener/docking/screen.py", line 244, in <listcomp>
    [
  File "/Users/rodrigo/repos/pyscreener/pyscreener/docking/screen.py", line 245, in <listcomp>
    [
  File "/Users/rodrigo/repos/pyscreener/pyscreener/docking/screen.py", line 246, in <listcomp>
    replace(
  File "/Users/rodrigo/software/anaconda3/envs/pyscreener_env/lib/python3.8/dataclasses.py", line 1264, in replace
    raise TypeError("replace() should be called on dataclass instances")
TypeError: replace() should be called on dataclass instances
(prepare_receptors pid=47498) Traceback (most recent call last):
(prepare_receptors pid=47498)   File "/Users/rodrigo/ADFRsuite-1.0/CCSBpckgs/AutoDockTools/Utilities24/prepare_receptor4.py", line 9, in <module>
(prepare_receptors pid=47498)     from MolKit import Read
(prepare_receptors pid=47498) ImportError: No module named MolKit
(prepare_receptors pid=47498) 
(prepare_receptors pid=47498) ERROR: failed to convert "integration-tests/inputs/5WIU.pdb"

[rvhonorato]

Actually just as I posted this I realized it is because there was something wrong with my ADFRsuite-1.0 suite. Also it seems that pyscreener depends on this prepare_receptor, which is still python2, very unfortunate...

I see that ADFR is also available as a conda package: https://anaconda.org/hcc/adfr-suite, is this a viable substitute?

[davidegraff]

It is unfortunate that prepare_receptor is still in python2. Even more unfortunate is that openbabel functions to prepare receptor result in different files than prepare_receptor, so it doesn't seem like there's a python3 method by which to do this. Though I guess, there's no native python3 support for any of these docking programs, which is the whole thing we're trying to address here (basically hiding all the ugly parts of integrating docking into your own python workflow)

[davidegraff]

re: conda ADFR- I haven't tried with that package. The only requirement for it to work is that prepare_receptor is accessible on your path and produces the same results as the prepare_receptor when installing from source. Though I suspect that latter point is not much concern here...