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Python2 script in Rosetta3.13

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Python2 script in Rosetta3.13
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: 

    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,

Post Situation: 
Wed, 2021-09-15 04:05

This does not answer your question... but I had similar strong issues with `` 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: (`pip install rdkit-to-params`). It optionally (but majorly) relies on RDKit, the most used Python package for CompChemistry (`pip install rdkit-pypi`).

Wed, 2021-09-15 06:04