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Explain residue-level evidence in the shared inspector - #30

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CedricHermansBIT merged 6 commits into
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feature/residue-evidence-inspector
Oct 7, 2026
Merged

CedricHermansBIT merged 6 commits into
mainfrom
feature/residue-evidence-inspector

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Adds an evidence explanation panel for the currently selected residue without introducing a composite quality score.

The inspector can explain, when present:

  • Rama8000 Allowed/Outlier status;
  • native RamplotR Not allowed or near-contour positions;
  • low/very-low pLDDT;
  • very-high pLDDT combined with a Rama8000 outlier;
  • cis/twisted peptide geometry;
  • official wwPDB Ramachandran/rotamer outliers;
  • official local clashes and covalent-geometry outliers.

Each signal keeps its source and explanation. Quiet residues explicitly report that no unusual signal is present in the currently available evidence. Unit tests cover warning composition and the browser workflow verifies that every selected residue exposes the explanation panel.

@CedricHermansBIT
CedricHermansBIT marked this pull request as ready for review October 7, 2026 07:52
Copilot AI balanced review requested due to automatic review settings October 7, 2026 07:52
@CedricHermansBIT
CedricHermansBIT merged commit 9669fd0 into main Oct 7, 2026
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Copilot review overview

🟡 Changes recommended

The source labels do not meet minimum contrast requirements for normal text.

Review effort: Balanced
Findings: 1 Medium severity

Open (1)
What changed in this PR

Adds residue-level evidence explanations to the shared inspector without creating a composite quality score.

Changes:

  • Adds evidence composition and severity ordering.
  • Renders and documents the expandable evidence panel.
  • Adds unit and browser coverage.
File Description
shinyRam/​R/​inspection.R Builds residue evidence signals.
shinyRam/​app.R Renders evidence in the inspector.
shinyRam/​www/​styles.css Styles evidence cards and severity levels.
docs/​inspection-user-guide.md Documents evidence interpretation.
tests/​inspection.R Tests evidence composition.
tests/​ui-browser.cjs Verifies panel availability.

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Comment thread shinyRam/www/styles.css
}
.ram-evidence-item-head strong { color:#294f55; font-size:10px; }
.ram-evidence-item-head span {
color:#75898d; font-size:8px; text-transform:uppercase; letter-spacing:.04em;
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2 participants