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provides a running blackbox for Rosetta #222

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Merged
merged 49 commits into from
Nov 7, 2024
Merged

provides a running blackbox for Rosetta #222

merged 49 commits into from
Nov 7, 2024

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SimonBartels
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@miguelgondu
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miguelgondu commented Jul 31, 2024 •
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Some tutorials on pyrosetta:

https://rosettacommons.github.io/PyRosetta.notebooks/

https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb

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@RMichae1 @SimonBartels I feel we should revive this PR before the end of my tenure at MLLS.

@RMichae1 RMichae1 self-assigned this Sep 25, 2024
Simon Bartels and others added 24 commits September 25, 2024 16:31
provides a running blackbox
5ee292c
@miguelgondu
Starts playing around with PyRosetta
c915c13
add opt in wrapping for PyRosetta licensing
0133838
add get_inner_function
c3199dd
provides a running blackbox
4a6524a
@miguelgondu
Starts playing around with PyRosetta
e61c060
add opt in wrapping for PyRosetta licensing
fe36658
update environment, poli, numpy, biopython required
f1d7354
add isolated function with pack/relax algo, ddG prediction, score fxns
8b74b0e
update info
26d0cc7
fig score computation, by applying mutants to deepcopy of reference pose
3c9aa8f
add register on main
d8b190b
implement register
d0fbaea
add tests
af9c9a0
Merge remote-tracking branch 'origin/feature-blackbox-rosetta' into f…
813fc44 
…eature-blackbox-rosetta
add black-box and factory
7bde9dd
fix import error on init
7788a6a
wrap inner function with opt in
15431d4
correct zero DDG test, PDB file, REU equal
d1c5de2
fix import and pdb variable ref
2bc770f
specify pytest markers
623c165
add to tox
075c6f5
correct numerical stability values
07f03f1
correct test, set isolated seed
20f85eb
@RMichae1 RMichae1 marked this pull request as ready for review October 22, 2024 08:06
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@miguelgondu

  • added the discussed opt-in.
  • corrected the fast-protocol use, via Rosetta pose mutations instead of reading from sequences, which yielded erroneous values.
  • added a pack&relax protocol (standard Rosetta use)
  • added different relevant output units: REU (raw), delta-REU, and ddGs (default)
  • added multiple standard Rosetta protocols
  • added cartesian treatment if required
  • added user-manual seeding

I've added the tests analogue to the Rasp testing, which includes a opt-in session fixture.

@RMichae1 RMichae1 requested a review from miguelgondu October 22, 2024 08:32
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Let me know if you can check-out, setup the env, and run the tests.

miguelgondu
miguelgondu requested changes Oct 22, 2024
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Hi Richard!

Amazing work! Thanks for all the effort you've put into this.

Here are some minor comments related to some changes we did on poli recently.

I'll pull and test at some point after the camera-ready deadline.

miguelgondu
miguelgondu approved these changes Nov 7, 2024
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LGTM.

src/poli/objective_repository/rosetta_energy/register.py
constraint_weight=self.constraint_weight,
n_threads=self.n_threads,
)
self.inner_function = opt_in_wrapper(inner_function)
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how fancy!

@miguelgondu miguelgondu merged commit 1fd2c0b into dev Nov 7, 2024
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@miguelgondu miguelgondu deleted the feature-blackbox-rosetta branch November 7, 2024 15:40
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@SimonBartels @miguelgondu @RMichae1