Missing dependencies and package names

[sellersb]

Hi all.

Thanks for open sourcing the rf_interactions and line of sight code.

I have been unsuccessful in getting rf_interaction evaluations (e.g. running rf_values_from_pdb_and_sdf.py) to work.

I think there are some leftover naming and organization from internal Roche repo which makes this challenging.

• ccdc_roche package is referenced everywhere but is not a package.

  • recommend creating a new package "rfinteractions" under root dir, adding init.py and moving python and atom_types subfolders under the new "rfinteractions" folder. Then search replace all ccdc_roche package names with rfinteractions.

• lookup_files is referenced but is not available

  • See python/rf_structure_analysis.py
  • ImportError: cannot import name 'lookup_files' from 'ccdc_roche' (note this is not just a ccdc_roche naming issue. I can't find "lookup_files")

• global_ligand_xxxx files seem to be missing too.

Recommended changes

• Having gold docking required for parsing gold docking files make it required to have even more CCDC licenses (expensive). We just want rf_interactions for pdb and sdf files for the time being.

[jasonccole]

Hi,

Thanks for this. If I get some time in the next few weeks I will tkae a look. The roche package is a historical thing and I'm sure it could be factored out.

[sellersb]

Thanks for listening and your feedback.

On Tue, May 9, 2023 at 2:46 AM Jason Christopher Cole < @.***> wrote:

Hi,

Thanks for this. If I get some time in the next few weeks I will tkae a look. The roche package is a historical thing and I'm sure it could be factored out.

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