[PardhavMaradani]

Changes made in this Pull Request:

• Added Vibrational Density of States (VDoS) widget
  • Uses HeydenLabASU-collab/trvdos as a reference

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

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• Tests?
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• CHANGELOG updated?
• Issue raised/referenced?
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---

cc: @HeydenLabASU , @amruthesht

Given mdadash now has weights support for ACF (as part of PR #112), I added support for showing VDoS calculated from the mass weighted VACF. I used HeydenLabASU-collab/trvdos as a reference for this implementation.

The values are a match to the ones from trvdos. Here are more details about the comparisons:

• I used the data from this comment
  • topol.tpr and traj.trr - 1001 frames
• For trvdos data, I used the devtools/examples/example.ipynb notebook with the above input files
  • mdadash is run with the same topology and trajectory files
• Lag time of 100 frames
• mdadash shows normalized values for both VACF and VDoS

First, here are the VACF comparisons for different selections:

selection	trvdos	mdadash
protein
resid 1
resid 100:115

Here are the VDoS comparisons for the above selecitons:

selection	trvdos	mdadash
protein
resid 1
resid 100:115

A few notes about the data above:

• trvdos starts calculating VACF after the window is full (if(tStep>=nCorr-1) {), where as mdadash accounts for the lags from the very first frame - there could be very minor differences due to this
• mdadash uses normalized (to 1) values for VDoS and the normalization for VACF is configurable in the widget (enabled for plots above)
• mass weights were used in the mdadash VACF widget to be comparable to trvdos, the new VDoS widget implicitly uses mass weighting for the VACF
• trvdos has an issue with arbitrary selections - see Arbitrary selections do not work and lead to memory corruption HeydenLabASU-collab/trvdos#11
  • Only selections that return all residue atoms in the ag were used above due to this (mdadash allows arbitrary selections)

@HeydenLabASU , @amruthesht, I'd be happy to update this if you think any other changes are needed here. Thanks

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (c1c25ad) to head (1ff8c32).

Additional details and impacted files

Components	Coverage Δ
frontend	100.00% <ø> (ø)
backend	100.00% <100.00%> (ø)

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Documentation build overview

📚 mdadash | 🛠️ Build #35697253 | 📁 Comparing 1ff8c32 against latest (c1c25ad)

  🔍 Preview build  

11 files changed · + 4 added · ± 7 modified

+ Added

• autosummary/mdadash.backend.analyses.common.html
• autosummary/mdadash.backend.analyses.vdos.html
• _modules/mdadash/backend/analyses/common.html
• _modules/mdadash/backend/analyses/vdos.html

± Modified

• built_in_widgets.html
• genindex.html
• py-modindex.html
• _modules/index.html
• autosummary/mdadash.backend.analyses.acf.html
• autosummary/mdadash.backend.analyses.html
• _modules/mdadash/backend/analyses/acf.html