Add elbow-form layout for plot_tRNA_structure()#28
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Adds a `layout = c("cloverleaf", "elbow")` argument to
`plot_tRNA_structure()` and `structure_trnas()`. The elbow form stacks
the acceptor stem and T-arm coaxially at the top, with the D-arm
extending horizontally and the anticodon arm hanging vertically —
matching the L-shape depiction common in structural biology figures.
Geometry is derived from canonical Sprinzl labels via
`inst/extdata/sprinzl/ecoliK12_global_coords.tsv.gz`, so a single
coordinate table works across all standard tRNAs. The new generator
`data-raw/structures/generate_elbow.py` reads each cloverleaf JSON's
sequence, looks up Sprinzl labels, and writes elbow SVG + JSON in the
same schema as cloverleaf — overlay code (modifications, outlines,
linkages, position markers, end labels) works unchanged.
v1 ships 29 E. coli standard 3-arm tRNAs. Variable-arm tRNAs
(Leu, Ser, SeC, Tyr) are deferred to v2.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Initial elbow layout drew the D-arm horizontally with D-loop at the far left. The reference figure (Matsumoto 2026 JBC fig 2A) shows the L-shape with D-arm and AC-arm both VERTICAL — sitting side-by-side as parallel helices below the horizontal acceptor+T stack: * D-arm on the LEFT, 4 bp going DOWN, D-loop curling at bottom-left * AC-arm on the RIGHT, 5 bp going DOWN, AC-loop at the bottom * pos 26 hinge bridges D-arm top-right to AC-arm top-left * variable region curves from AC-arm top-right up to T-stem 5' Updates the geometry constants and the D-arm + D-loop placement code in generate_elbow.py and regenerates all 29 bundled E. coli elbow SVG/JSON pairs. Visual check on Phe, Asp, and Val now matches the reference. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The first elbow layout had loop residues only 4-5 SVG units apart and the variable region as tight as 2.5 units — too tight for the radius-4.3 modification circles and stroke outlines drawn by plot_tRNA_structure(). Fixes: * Loop radii now solved analytically so chord between adjacent residues equals the backbone spacing S: R = S / (2 sin(π/(2N))) for N residues on a 180° arc. Previous formula (N-1)*S/π underestimated R by ~17%. * Variable region (44..48) now sampled by ARC LENGTH along the bezier rather than by uniform t, so neighbors are evenly spaced instead of bunching at the apex. * Wider canvas (240×170 vs 215×132) and deeper D-arm/AC-arm (D_TOP_Y pushed down by 14 units) give the variable-region path enough room. * Acceptor stem widened (ACC_X1 220 vs 195) for more horizontal room. Result: minimum neighbor distance is now 7.55 (matching the cloverleaf median of 7.56), so modification circles fit without overlapping neighboring letters. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
layout = c("cloverleaf", "elbow")toplot_tRNA_structure()andstructure_trnas(). Default is"cloverleaf"— fully backwards compatible.inst/extdata/structures/Escherichia_coli/elbow/.data-raw/structures/generate_elbow.pyderives geometry from canonical Sprinzl labels (so a single coordinate table covers all standard tRNAs across organisms), reads each cloverleaf JSON's sequence, and writes elbow SVG + JSON in the same schema as cloverleaf — so all overlay machinery (modifications, outlines, linkages, position markers, end labels) works unchanged.The elbow form stacks the acceptor stem and T-arm coaxially at the top, with the D-arm extending horizontally and the anticodon arm hanging vertically — matching the L-shape depiction common in structural biology figures.
Variable-arm tRNAs (Leu, Ser, SeC, Tyr) are deferred to v2; the generator skips them with a clear log message and the R-side path errors cleanly when callers request elbow layout for an unbundled tRNA.
Test plan
devtools::test()— all 47 new + existing tests pass (8 pre-existing skips for rsvg/tidygraph/ggraph)pkgdown::check_pkgdown()clean<circle>annotations are placed correctlylayoutrenders identical cloverleaf output🤖 Generated with Claude Code