Updates to molfile_to_params_polymer.py to better accomodate non-alpha residues.#419
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roccomoretti wants to merge 3 commits intoRosettaCommons:mainfrom
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Updates to molfile_to_params_polymer.py to better accomodate non-alpha residues.#419roccomoretti wants to merge 3 commits intoRosettaCommons:mainfrom
roccomoretti wants to merge 3 commits intoRosettaCommons:mainfrom
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…a residues. The current molfile_to_params_polymer.py is not suited to creating params file for non-alpha amino acids, but I was able to make some tweaks to generalize things. Critically, there's now a M POLY_BACKBONE setting which can take the place of the alpha-amino-acid specific designations. You just need the ROOT, POLY_UPPER, POLY_LOWER and POLY_BACKBONE for things to work. -- Well, assuming you now use mol2 input and the new --keep_names flags, to avoid the alpha-amino-acid specific renaming code.
woodsh17
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Jun 19, 2025
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My understanding is if you have a non-alpha amino acid, then you need to use mol2 input and set the --keep_names to true. Where should we document this? I saw David linked this in the previous PR: https://docs.rosettacommons.org/docs/latest/rosetta_basics/non_protein_residues/Noncanonical-Amino-Acids. Is there anywhere else?
Fix merge conflict with Eric's changes.
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This is PR RosettaCommons/main#6462 which was already approved by @nannemdp
The current molfile_to_params_polymer.py is not suited to creating params file for non-alpha amino acids, but I was able to make some tweaks to generalize things.
Critically, there's now a M POLY_BACKBONE setting which can take the place of the alpha-amino-acid specific designations. You just need the ROOT, POLY_UPPER, POLY_LOWER and POLY_BACKBONE for things to work. -- Well, assuming you now use mol2 input and the new --keep_names flags, to avoid the alpha-amino-acid specific renaming code.