receptors directory missing from repo?

[dotsdl]

When I execute 02-generate-poses.py on branch sprint-5 under sprint-5-retrospective, I get:

sprint-5 [sprint-5-retrospective] ! python 02-generate-poses.py 
Warning: Unable to open "../../receptors/monomer/Mpro-x11498_0A_bound-receptor.oeb.gz" for reading molecules.
Warning: Unable to open receptor file ../../receptors/monomer/Mpro-x11498_0A_bound-receptor.oeb.gz for reading
Warning: Unable to open "../../receptors/monomer/Mpro-x11498_0A_bound-ligand.mol2" for reading molecules.
Traceback (most recent call last):
  File "02-generate-poses.py", line 702, in <module>
    refmol = load_fragment(fragment, title=fragments[fragment])
  File "02-generate-poses.py", line 577, in load_fragment
    raise Exception(f'Could not read {refmol_filename}')
Exception: Could not read ../../receptors/monomer/Mpro-x11498_0A_bound-ligand.mol2

The directory does not appear to exist in the repository; is it local to your workspace @jchodera?

[jchodera]

@dotsdl : Shoot, I realize I never responded to this!

The covid-moonshot/receptors/ path is generated by the covid-moonshot/scripts/00-prep-all-receptors.py script, and it's possible the paths have changed since sprint-5.

We also need to update the infrastructure to use the new fah_prep tool for preparing the receptors/ structures from @RobertArbon. This tool can correctly handle both the x (monomer in asymmetric unit) and P (dimer in asymmetric unit) crystal forms.