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@paobtorres paobtorres commented Nov 12, 2024

Added

  • Unit tests for pmb.create_protein, pmb.enable_motion_of_rigid_object, pmb.protein_sequence_parser, pmb.define_protein, pmb.read_protein_vtf_in_df

Fixed

  • Wrong parsing in pmb.protein_sequence_parser of input sequences provided as a list of aminoacids using the three letter code.
  • Wrong setup of the rigid object in pmb.enable_motion_of_rigid_object, leading to crashes in samples/globular_protein.py when enabling the protein motion.
  • The argparse argument --move_protein of samples/globular_protein.py is now a boolean flag instead of taking arbitrary float values.

@paobtorres paobtorres requested a review from pm-blanco November 12, 2024 21:49
@pm-blanco pm-blanco assigned pm-blanco and paobtorres and unassigned pm-blanco Nov 12, 2024
@pm-blanco pm-blanco added bug Something isn't working ci-improvement labels Nov 12, 2024
@pm-blanco pm-blanco added this to the pyMBE 1.0.0 milestone Nov 12, 2024
@pm-blanco pm-blanco changed the title Unit tests protein functions Add unit tests for features for globular proteins Nov 13, 2024
…erge tests, add switch for ideal tests in sample script for globular proteins
pm-blanco
pm-blanco previously approved these changes Nov 13, 2024
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@paobtorres I have reviewed the code and overall it looks good to me. I had to do a few changes because some parts were not fully covered:

  • In the functional test for the feature to have a moving protein, small ions were also created. Therefore, the test would always pass even if the protein would not move because the small ions motion would cause the trajectory to be different. I fixed that by setting up an ideal system with no small ions for this test.
  • The unit tests for globular proteins, I changed the test globular protein to 1f6s because in this way it also covers the case in which a metal ion is present in the PDB.
  • Some corner cases were still missing in protein_sequence_parser
  • I merged all unit tests for globular proteins in a single file globular_protein_unit_tests
    Take a look to my changes and if you are OK then I think we are now ready to merge this PR

I also tested that all unit and functional test ran properly.

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pm-blanco commented Nov 13, 2024

@Zitzeronion here we have fixed the issue you raised in #98

@jngrad once we merge this PR, we finally have a robust testing of the features of globular proteins so you can move forward with #13 when you have the time. The core features of pyMBE are now covered, although we still need to keep working on improving the coverage until we cover all the corners of the code.

@pm-blanco pm-blanco changed the title Add unit tests for features for globular proteins Add unit tests for globular proteins features Nov 13, 2024
@pm-blanco pm-blanco merged commit f73b582 into pyMBE-dev:main Nov 13, 2024
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