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Add conformational change explorer - #22
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CedricHermansBIT
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October 6, 2026 17:58
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🟡 Changes recommended
The track omits valid aligned endpoints, rebuilds on every selection, has accessibility gaps, and its browser tests do not verify the claimed linked behavior.
Review effort: Balanced
Findings: 4
Open (6)
What changed in this PR
Adds a residue-level Conformational Change Explorer to linked structure comparisons.
Changes:
- Computes and classifies wrapped φ/ψ displacement.
- Adds an interactive residue track, ranking, filters, metrics, and linked selection.
- Extends unit, browser, and user documentation coverage.
| File | Description |
|---|---|
shinyRam/R/inspection.R |
Calculates displacement and display bands. |
shinyRam/app.R |
Integrates explorer UI and comparison behavior. |
shinyRam/www/custom.js |
Handles track selections. |
shinyRam/www/styles.css |
Styles the explorer. |
tests/inspection.R |
Tests calculations and thresholds. |
tests/ui-browser.cjs |
Adds browser checks for the explorer. |
README.md |
Advertises the new comparison workflow. |
docs/inspection-user-guide.md |
Documents usage and interpretation. |
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| finite <- which(is.finite(data$angular_displacement) & | ||
| data$alignment %in% c("Match","Substitution")) |
| finite <- which(is.finite(data$angular_displacement) & | ||
| data$alignment %in% c("Match","Substitution")) | ||
| if (!length(finite)) return(NULL) | ||
| selected <- selected_comparison() |
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| assert.ok(changeTrack.topLabels.length > 0 && changeTrack.topLabels.length <= 5, | ||
| "Explorer should expose the largest local shifts as navigation targets."); |
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| const stage = window.getNGLStage && window.getNGLStage("NGLCompare"); | ||
| return cell && stage && | ||
| stage.getRepresentationsByName("ram-compare-highlight-a").list.length === 1 && | ||
| stage.getRepresentationsByName("ram-compare-highlight-b").list.length === 1 && | ||
| document.querySelector(".ram-compare-selection-pair"); |
| band_class(data$shift_band[[i]]), | ||
| if (!is.null(selected) && identical(data$row_id[[i]],selected)) | ||
| "is-selected" else ""), | ||
| "data-row-id"=data$row_id[[i]], |
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| "aria-label"=sprintf( | ||
| "Inspect aligned residue pair with %.1f degree backbone shift",shift) |
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Adds the first residue-level Conformational Change Explorer to the pairwise Compare workflow.
What it does
sqrt(Δφ² + Δψ²)after wrapping each angular component across ±180°;Interpretation
The combined angular displacement is explicitly presented as a navigation/ranking measure, not a statistical significance score, RMSD, free-energy metric or proof of biological motion.
Coverage