Refactor of universe creation and applying transformations by hannahbaumann · Pull Request #93 · OpenFreeEnergy/openfe_analysis

hannahbaumann · 2026-02-27T13:13:26Z

The make_Universe function did two things: Create a Universe for a state and then applying some transformations to it, hard coding selection strings for protein and ligand.
Here, I split off the creation of the universe and the applying of transformations into separate steps. This allows passing AtomGroups to the apply_transformations function. I thought that this might be useful for moving towards a more individual Protocol based analysis.

IAlibay

Mostly small things / nits, otherwise lgtm.

IAlibay · 2026-05-21T08:18:13Z

 from openfe_analysis.utils.multistate import _determine_position_indices


+def _create_universe_single_state(top, trj, state):


I think this should go into utils. The reader file should really concentrate on reader things rather than universe creation.

I moved it into it's own universe_utils.py file.

IAlibay · 2026-05-21T08:21:39Z

+    ligand: Optional[mda.AtomGroup] = None,
+):
+    """
+    Apply a collection of transformations to a Universe.


Since MDAnalysis transformations are meant to be quite flexible and additive, it might be good to be more descriptive about this sentence. Maybe be even just "collection of transformations usually required for X, Y, Z analyses" would be fine.

Added that they are typically used in RMSD analyses and other structural analyses.

IAlibay · 2026-05-21T08:22:44Z

+    u.trajectory.add_transformations(*transforms)
+
+
+def _apply_transformations_complex(protein, ligand=None):


Please do add type hints everywhere.

jthorton

Thanks @hannahbaumann looks great, nothing to add over @IAlibay so i'll approve early!

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

hannahbaumann · 2026-05-27T10:57:59Z

Tests are now in test_gather_rms_data.py and test_transformations.py

codecov · 2026-05-27T10:59:31Z

Codecov Report

❌ Patch coverage is 97.61905% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 97.63%. Comparing base (0911e9b) to head (03bb871).

Files with missing lines	Patch %	Lines
src/openfe_analysis/utils/apply_transformations.py	96.42%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #93      +/-   ##
==========================================
+ Coverage   96.93%   97.63%   +0.70%     
==========================================
  Files           6        8       +2     
  Lines         359      381      +22     
==========================================
+ Hits          348      372      +24     
+ Misses         11        9       -2

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IAlibay

Couple of small things that might be worth fixing, I'm going to eagerly approve.

IAlibay · 2026-05-27T11:36:51Z

+from ..reader import FEReader
+
+
+def create_universe_single_state(top: Path, trj: nc.Dataset, state: int) -> mda.Universe:


Suggested change

def create_universe_single_state(top: Path, trj: nc.Dataset, state: int) -> mda.Universe:

def create_universe_single_state(top: Path | mda.core.topology.Topology, trj: nc.Dataset, state: int) -> mda.Universe:

Or something like that - you can actually pass anything that Universe accepts for the topology argument. In practice we actually pass through a pre-existing Topology (see how it's called in gather_rms_data), so making it clear that it could at least be one of Path and Topology would be grand.

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

hannahbaumann · 2026-05-27T12:08:09Z

pre-commit.ci autofix

hannahbaumann and others added 6 commits February 20, 2026 11:08

Refactor RMSD analyses into MDAnalysis AnaysisBase classes

2977c01

Combine RMSD analyses

4a960a0

Merge branch 'main' into rmsd_refactor_analysisbase

afa829a

Refactor of universe creation and applying transformations

3e7f6d8

Add new file

5e65b34

more updates

8a8b20a

hannahbaumann requested a review from jthorton March 2, 2026 13:26

hannahbaumann commented Mar 2, 2026

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Comment thread src/openfe_analysis/utils/apply_transformations.py Outdated

hannahbaumann and others added 16 commits March 2, 2026 15:05

Add reference and superposition option

df017da

Apply suggestion from @hannahbaumann

d824ab6

Merge branch 'main' into rmsd_refactor_analysisbase

71a11d3

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

8c08fa6

Merge branch 'main' into rmsd_refactor_analysisbase

5cabcf4

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

b7ba29f

Some changes

e16b2e3

Fix mda 2D analysis example

616bf42

Add RMSD test using mda test data

90ed39e

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

113dc6d

Split complex and ligand only treatment into separate functions

a73f096

Fix docstring

2f7a441

Some fixes

7d6e49f

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

e4e778f

Some more updates

4bf598f

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

edca537

hannahbaumann requested a review from IAlibay May 21, 2026 11:32

IAlibay requested changes May 21, 2026

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jthorton reviewed May 21, 2026

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Comment thread src/openfe_analysis/utils/apply_transformations.py Outdated

jthorton approved these changes May 21, 2026

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hannahbaumann linked an issue May 21, 2026 that may be closed by this pull request

API work - RMSD #82

Closed

Update src/openfe_analysis/rmsd.py

80b984d

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

hannahbaumann commented May 26, 2026

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Comment thread environment.yml Outdated

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hannahbaumann commented May 26, 2026

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Comment thread pyproject.toml Outdated

hannahbaumann and others added 2 commits May 26, 2026 10:14

Apply suggestion from @hannahbaumann

cb242dd

Make universe creation function not private

8d0a811

hannahbaumann linked an issue May 26, 2026 that may be closed by this pull request

Expose the atom selection in the gather_rms_data function #103

Closed

hannahbaumann and others added 5 commits May 26, 2026 14:08

add more tests for classes

e4c5417

Update tests

984bcbb

Merge branch 'rmsd_refactor_analysisbase' into code_refactor

6237d11

move transformation test to test_transformations.py

0f4b380

Rename test file

93cc1ad

Base automatically changed from rmsd_refactor_analysisbase to main May 27, 2026 09:45

hannahbaumann closed this May 27, 2026

hannahbaumann reopened this May 27, 2026

hannahbaumann added 3 commits May 27, 2026 12:48

Merge conflicts

d840014

fix test

c35e222

remove test file since tests were put into two separate other files

ee66a92

hannahbaumann commented May 27, 2026

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hannahbaumann requested review from IAlibay and jthorton May 27, 2026 11:12

IAlibay approved these changes May 27, 2026

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hannahbaumann and others added 4 commits May 27, 2026 13:45

Update src/openfe_analysis/reader.py

9d1bfaf

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Update src/openfe_analysis/utils/universe_utils.py

e700a60

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

Apply review comments

9e58328

Merge branch 'main' into code_refactor

b483c66

small fix

03bb871

hannahbaumann merged commit e093451 into main May 27, 2026
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hannahbaumann deleted the code_refactor branch May 27, 2026 12:27

		from openfe_analysis.utils.multistate import _determine_position_indices


		def _create_universe_single_state(top, trj, state):

		u.trajectory.add_transformations(*transforms)


		def _apply_transformations_complex(protein, ligand=None):

		from ..reader import FEReader


		def create_universe_single_state(top: Path, trj: nc.Dataset, state: int) -> mda.Universe:

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