Updates to molfile_to_params_polymer.py to better accomodate non-alpha residues. #419
+299
−109
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…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
approved these changes
Jun 19, 2025
There was a problem hiding this comment.
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.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.