Python2 script in Rosetta3.13

[Anonymous]

Good morning,



I am trying to use Rosetta (v3.13) for  drug screening analysis and I

found a specific script in the Rosetta3.13 package (also in other

versions) which has some python2 code that hampers its use in the

current python3.



The script is:

rosetta_bin_linux_2021.16.61629_bundle/main/source/scripts/python/public/batch_molfile_to_params.py



Python2 code:



1) Lines 110, 114, 117: print without brackets



2) Lines 40, 116: "is not" instead of "!="



3) Line 103: ".next()" method on itertools.product (should iterate over

the itertools.product instead)





Also, in line 89 the function "get_disallowed_ligands" iterates over the

folders in "main/database/chemical/residue_type_sets" and works with the

files in them. However, in this "residue_type_sets" folder there is also

a file "how_to_add_new_residue_types.txt" which yields an error, as the

"get_disallowed_ligands" function tries to use it as a folder. Moving

the "how_to" file to a previous folder solves the problem.





Thank you for your attention, I hope this helps.



Best regards,



Dani

[Anonymous]

This does not answer your question… but I had similar strong issues with `molfile_to_params.py` being Python2. I updated it to Python3, but it was in violation of Rosetta licence, so I took it down and rewrote my own and tailored for my use, i.e. as Python3 module called within a script or notebook: https://github.com/matteoferla/rdkit_to_params (`pip install rdkit-to-params`). It optionally (but majorly) relies on RDKit, the most used Python package for CompChemistry (`pip install rdkit-pypi`).

[Author]

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