Changelog
All notable changes to IgFold2D are documented here.
[0.2.0] — Interaction overlays
Added
- Interaction feature layer. Every residue cell now carries a vector of
interactions computed from the 3D structure: H‑bonds (with donor/acceptor
direction and bb/bs/ss subtype), salt bridges, π‑stacking, cation‑π, and the
disulfide bond. See
docs/interactions.md.
- iCn3D‑matched colors: green H‑bond, cyan salt/ionic, blue π‑stacking,
red cation‑π, yellow disulfide, magenta halogen (reserved), grey contacts.
- Hover tooltip lists a residue’s interaction partners; click shows the
full vector in the side panel with distances and lets you navigate the graph.
- Whole‑network “Show all” toggles (H‑bonds / salt / cation‑π / π–π / S‑S),
cumulative, drawn as faded dotted lines.
- Multi‑selection with Cmd‑click (macOS) / Ctrl‑click (Windows/Linux) to
combine several residues’ or strands’ subnetworks into one view.
- Click‑to‑select groups: clicking a strand label selects that whole strand;
clicking a SHEET A / SHEET B header selects the whole sheet.
- Fluorescent cell highlighting of a selection and its partners, colored by
interaction type; selected residues draw solid contact lines vs the dotted
whole‑network overview.
- “IgStrand colors” toggle to neutralize strand fills for interaction focus.
assignments/CD8a-P01732.interactions.json — interaction vectors (keyed by
IgStrand number).tools/compute_interactions.py — reproducible interaction computation from a
PDB with explicit hydrogens.
Fixed
- Restored 7 missing loop residues in the CD8α assignment (now 114/114,
previously 107). These were dropped because the hand‑curated template’s
IgStrand numbering diverged by ±1 from the iCn3D
refnum output in the
C′/loop regions. Restored residues (UniProt / PDB): 49/28 (N), 50/29 (P),
64/43 (A), 65/44 (A), 84/63 (L), 87/66 (Q), 107/86 (R). The two CDR1 residues
(UniProt 49, 50) were the originally reported gap.
- Header cleanup: removed the redundant numeric rows below the strand labels;
strand labels now sit directly under the (colored) SHEET A / SHEET B headers
and are colored by the canonical IgStrand palette.
Notes
- The interaction overlay currently lives in the standalone demo
(
examples/browser-widget/index.html). Factoring it into the core library
(src/igfold2d.js) is planned for a follow‑up.
[0.1.0] — Initial release
- Hand‑curated CD8α IgV template, folded‑lace 2D renderer, multi‑addressable
cells (Excel / row,col / IgStrand / UniProt / PDB), chain trace with direction,
browser widget, sequence ↔ map sync.