@motionscript/molecule 0.0.0-stage → 0.1.0-alpha.0

package/dist/protein/ribbon.js

@@ -0,0 +1,468 @@
+/**
+ * The cartoon: a chain's backbone swept as a **ribbon** rather than as a tube.
+ *
+ * This is the one representation whose whole job is to be recognised. A figure
+ * in a paper draws a helix as a twisted band and a strand as a flat arrow, and
+ * has since Jane Richardson drew the first one by hand in 1980 — the convention
+ * is old enough that a reader decodes it without a legend, which is exactly why
+ * a picture that departs from it reads as *wrong* rather than as different.
+ *
+ * The node drew that with `Geo.tube` before this module existed, and the two
+ * things it could not express are the two the convention is made of:
+ *
+ * **A cross-section has a width and a thickness, not a radius.** A tube's is a
+ * circle, so a helix could only be told from a coil by being *fatter* — and a
+ * fat circle swept along the α-carbons of a helix is close to self-intersecting,
+ * because those carbons corkscrew about the helix axis at ~2.3 Å with a 5.4 Å
+ * pitch. What comes out is a lumpy sausage: the tube's own diameter is most of
+ * the coil's, so the spiral fills in and the shape stops being legible. Swept
+ * flat instead — ~2.2 Å across and ~0.5 Å thick — the same spiral reads as the
+ * band every textbook draws, because the eye is now reading the *face* turning
+ * rather than a diameter changing.
+ *
+ * **A band has a side, and a curve through α-carbons does not say which.** So
+ * the frame is built from the residue's own carbonyl (see
+ * {@link TracePoint.normal}), which is what turns with the fold. A ribbon swept
+ * on an arbitrary frame twists at random and looks like a misprint.
+ *
+ * Everything here is derived **per structure**, cached by the node against the
+ * inputs that produced it, and never rebuilt for a camera move — the same
+ * bargain the instance lists make in `shared.ts`.
+ */
+import { resolveColor3D } from "@motionscript/core/component";
+/**
+ * How wide and how thick each secondary structure's ribbon is, as multiples of
+ * the node's `ribbonRadius`.
+ *
+ * Stated as a ratio to one control rather than as six numbers in the inspector:
+ * "how heavy is the cartoon" is one question an author actually asks, and the
+ * *proportions* between a helix, a strand and a loop are the convention rather
+ * than a preference. The absolute values are the ones the established viewers
+ * settled on — a helix band about 2.2 Å across and half an Ångström thick, a
+ * strand slightly wider still, and a loop a thin round cord.
+ *
+ * A coil stays round (width equals thickness), which is the other half of the
+ * statement: a loop has no face to turn, so giving it one would claim a
+ * structure the file did not annotate.
+ */
+const SECTION = {
+    helix: { width: 2.4, thickness: 0.5 },
+    sheet: { width: 2.6, thickness: 0.45 },
+    coil: { width: 1, thickness: 1 },
+};
+/** How wide a strand's arrowhead is at its base, in the same multiples. */
+const ARROW_WIDTH = 4.4;
+/**
+ * How many residues at the C-terminal end of a strand the arrowhead occupies.
+ *
+ * Residues rather than a fraction of the span, because an arrowhead is a fixed
+ * *shape* — the same barb whether the strand is five residues or fifteen. A
+ * fraction would draw a stubby wedge on a short strand and a long spike on a
+ * β-hairpin's arm. Capped below at a third of the span so a three-residue
+ * strand is still a strand with a point on it rather than one long taper.
+ */
+const ARROW_RESIDUES = 2.4;
+/** What a strand's arrow narrows to at its tip, so the point is a point. */
+const ARROW_TIP = 0.08;
+/**
+ * How many samples each residue-to-residue step is drawn with.
+ *
+ * The curve is the picture here. Consecutive α-carbons are 3.8 Å apart and a
+ * helix turns fully in 3.6 of them, so a ribbon drawn straight between residues
+ * is a polygon with about five sides per turn — which is exactly the faceted,
+ * angular look that separates a rendering nobody trusts from one that reads as
+ * a molecule. Tied to the node's mesh detail so the same control that coarsens
+ * the spheres coarsens this.
+ */
+function subdivisionsFor(quality) {
+    return Math.min(10, Math.max(3, Math.round(quality / 2)));
+}
+/**
+ * Splits a chain's trace into the spans a cartoon is built from — one per
+ * unbroken stretch of the same secondary structure.
+ *
+ * Consecutive spans overlap by one point, for the reason `backboneRuns`'
+ * consecutive runs do: the shared residue is the last sample of one sweep and
+ * the first of the next, so the two meshes butt up rather than leaving a hole
+ * at every helix-to-loop transition.
+ */
+export function cartoonSpans(chain, colors) {
+    const spans = [];
+    chain.trace.forEach((point, index) => {
+        const color = colors[index] ?? colors[0] ?? "#ffffff";
+        let current = spans[spans.length - 1];
+        if (!current || current.secondary !== point.secondary) {
+            const previous = current;
+            current = { secondary: point.secondary, points: [], colors: [] };
+            // Carry the previous span's last residue in as this one's first.
+            if (previous) {
+                current.points.push(previous.points[previous.points.length - 1]);
+                current.colors.push(previous.colors[previous.colors.length - 1]);
+            }
+            spans.push(current);
+        }
+        current.points.push(point);
+        current.colors.push(color);
+    });
+    // A lone point is not a curve: there is no direction to sweep along and no
+    // tangent to build a frame from. Only ever the first span, since every later
+    // one is seeded with its predecessor's last point.
+    return spans.filter((span) => span.points.length > 1);
+}
+/**
+ * One span, as a mesh.
+ *
+ * `null` when there is nothing to sweep, so the caller can skip the op rather
+ * than hand the renderer an empty buffer.
+ *
+ * The arrays are freshly allocated and never mutated afterwards, which is what
+ * makes `staticData` honest: the renderer then compares them by identity and
+ * uploads each exactly once, where re-deriving them per frame would re-upload
+ * the whole fold sixty times a second to spin the camera.
+ */
+export function cartoonGeometry(span, options) {
+    const samples = sampleSpan(span, options);
+    if (samples.length < 2)
+        return null;
+    return sweep(samples, profileFor(span.secondary, options.quality));
+}
+/**
+ * The span, resampled onto a smooth curve with a frame and a size at every
+ * sample.
+ *
+ * Three things happen here that each fix something visible:
+ *
+ * **Catmull-Rom through the residues**, so the ribbon is a curve rather than a
+ * five-sided polygon per helical turn — see {@link subdivisionsFor}.
+ *
+ * **The frames are made continuous before anything is interpolated.** A
+ * β-strand's carbonyls point alternately to one side and the other, which is
+ * chemistry rather than noise: hydrogen bonds go to the neighbouring strand on
+ * both sides. Swept as given, the ribbon would flip 180° at every residue and
+ * come out as a chain of triangles. Flipping each frame to agree with its
+ * predecessor is what every viewer does and what makes a strand flat.
+ *
+ * **The arrow is measured in residues from the C-terminal end**, before
+ * subdivision, so it is the same barb on a long strand and a short one.
+ */
+function sampleSpan(span, options) {
+    const points = span.points;
+    const count = points.length;
+    const section = SECTION[span.secondary];
+    const radius = Math.max(0.01, options.radius);
+    const frames = continuousFrames(points);
+    const tints = span.colors.map((color) => linearRgb(color));
+    // Where the arrowhead starts, as a position along the span in *residues*.
+    // A strand shorter than the barb gives up a third of itself to it rather than
+    // becoming one long taper.
+    const arrow = span.secondary === "sheet"
+        ? Math.max(count - 1 - ARROW_RESIDUES, (count - 1) * (2 / 3))
+        : Infinity;
+    const steps = subdivisionsFor(options.quality);
+    const samples = [];
+    // Positions first, frames second: a tangent is a finite difference over the
+    // *sampled* curve, so every position has to exist before any of them can be
+    // taken. Doing it in one pass would take each tangent from the residues
+    // instead, which is the polyline this subdivision exists to get away from.
+    const curve = [];
+    const carried = [];
+    const colors = [];
+    const positions = [];
+    for (let i = 0; i < count - 1; i++) {
+        // The last segment emits its endpoint too, so the sweep reaches the final
+        // residue rather than stopping one sample short of it.
+        const last = i === count - 2;
+        for (let s = 0; s < steps + (last ? 1 : 0); s++) {
+            const t = s / steps;
+            curve.push(catmullRom(points[i - 1] ?? points[i], points[i], points[i + 1], points[i + 2] ?? points[i + 1], t));
+            carried.push(lerpVector(frames[i], frames[i + 1], t));
+            colors.push(lerpRgb(tints[i], tints[i + 1], t));
+            positions.push(i + t);
+        }
+    }
+    for (let i = 0; i < curve.length; i++) {
+        const position = curve[i];
+        const tangent = normalize(subtract(curve[Math.min(curve.length - 1, i + 1)], curve[Math.max(0, i - 1)]));
+        // Squared against the tangent, so the frame is orthonormal even though the
+        // carbonyl it came from is not perpendicular to the chain.
+        const normal = perpendicular(carried[i], tangent);
+        const binormal = normalize(cross(tangent, normal));
+        const along = positions[i];
+        const width = along <= arrow
+            ? section.width
+            : // Linear from the barb's base to its point. The base is *wider* than
+                // the strand, which is what makes an arrowhead read as one rather
+                // than as the strand simply stopping.
+                ARROW_WIDTH +
+                    (ARROW_TIP - ARROW_WIDTH) *
+                        clamp01((along - arrow) / Math.max(1e-6, count - 1 - arrow));
+        samples.push({
+            position,
+            tangent,
+            normal,
+            binormal,
+            halfWidth: radius * width,
+            halfThickness: radius * section.thickness,
+            color: colors[i],
+        });
+    }
+    return samples;
+}
+/**
+ * Each residue's ribbon direction, made to agree with its predecessor.
+ *
+ * Falls back to the curve's own binormal — the axis its turn is about — where
+ * the file gives no carbonyl. That is the right stand-in rather than an
+ * arbitrary perpendicular: in a helix the carbonyl points very nearly along the
+ * helix axis, and so does the binormal of the curve the α-carbons trace, so a
+ * Cα-only model comes out with its bands lying the same way a complete file's
+ * do.
+ */
+function continuousFrames(points) {
+    const frames = [];
+    for (let i = 0; i < points.length; i++) {
+        const point = points[i];
+        let direction = point.normal ?? binormalAt(points, i);
+        // Degenerate — three collinear residues with no carbonyl. Any perpendicular
+        // will do, and the frame is squared against the tangent anyway.
+        if (lengthOf(direction) < 1e-6)
+            direction = { x: 0, y: 0, z: 1 };
+        const previous = frames[i - 1];
+        // The 180° flip a β-strand's alternating carbonyls would otherwise put into
+        // the sweep. See {@link sampleSpan}.
+        if (previous && dot(previous, direction) < 0)
+            direction = negate(direction);
+        frames.push(normalize(direction));
+    }
+    return frames;
+}
+/** The curve's binormal at a residue — the axis its local turn is about. */
+function binormalAt(points, index) {
+    const before = points[Math.max(0, index - 1)];
+    const here = points[index];
+    const after = points[Math.min(points.length - 1, index + 1)];
+    return cross(subtract(here, before), subtract(after, here));
+}
+/**
+ * The cross-section a secondary structure is swept with.
+ *
+ * A loop is a round cord and a helix or a strand is a flat band — the whole
+ * distinction the convention rests on, and the one a radius could not express.
+ * The band is a rectangle rather than an ellipse because its *edge* is what the
+ * eye reads a twist by: an ellipse turning through 90° goes smoothly from wide
+ * to narrow and reads as a tube pinching, where a rectangle's corner catches the
+ * light and reads as a face turning over.
+ */
+function profileFor(secondary, quality) {
+    if (secondary === "coil") {
+        const sides = Math.min(16, Math.max(5, Math.round(quality / 2)));
+        const profile = [];
+        for (let i = 0; i < sides; i++) {
+            const angle = (i / sides) * Math.PI * 2;
+            const u = Math.cos(angle);
+            const v = Math.sin(angle);
+            // Smooth: one vertex per side, its normal radial, so a cord reads as
+            // round rather than as a faceted prism.
+            profile.push({ u, v, nu: u, nv: v });
+        }
+        return profile;
+    }
+    // Four faces, each with its own pair of corners, walked so consecutive
+    // entries are consecutive around the section.
+    return [
+        { u: 1, v: 1, nu: 0, nv: 1 },
+        { u: -1, v: 1, nu: 0, nv: 1 },
+        { u: -1, v: 1, nu: -1, nv: 0 },
+        { u: -1, v: -1, nu: -1, nv: 0 },
+        { u: -1, v: -1, nu: 0, nv: -1 },
+        { u: 1, v: -1, nu: 0, nv: -1 },
+        { u: 1, v: -1, nu: 1, nv: 0 },
+        { u: 1, v: 1, nu: 1, nv: 0 },
+    ];
+}
+/**
+ * The samples and the profile, as one indexed mesh.
+ *
+ * Ends are **capped**: a ribbon is a solid band and an open end shows the
+ * inside of the far face, which at a helix-to-loop transition would be a
+ * visible hole rather than a join. Cheap — one fan per end — and it is what
+ * lets a span be drawn as its own mesh at all.
+ */
+function sweep(samples, profile) {
+    const ring = profile.length;
+    const position = [];
+    const normal = [];
+    const color = [];
+    const index = [];
+    for (const sample of samples) {
+        for (const vertex of profile) {
+            const u = vertex.u * sample.halfWidth;
+            const v = vertex.v * sample.halfThickness;
+            position.push(sample.position.x + sample.normal.x * u + sample.binormal.x * v, sample.position.y + sample.normal.y * u + sample.binormal.y * v, sample.position.z + sample.normal.z * u + sample.binormal.z * v);
+            // A normal does not survive a non-uniform scale the way a position does:
+            // squashing a circle to a 5:1 ellipse tips every one of its normals
+            // toward the wide axis. Dividing by the half-extents is the inverse
+            // transpose of that scale, written out for two dimensions.
+            const n = normalize2(vertex.nu / sample.halfWidth, vertex.nv / sample.halfThickness);
+            normal.push(sample.normal.x * n[0] + sample.binormal.x * n[1], sample.normal.y * n[0] + sample.binormal.y * n[1], sample.normal.z * n[0] + sample.binormal.z * n[1]);
+            color.push(sample.color[0], sample.color[1], sample.color[2]);
+        }
+    }
+    for (let i = 0; i < samples.length - 1; i++) {
+        for (let j = 0; j < ring; j++) {
+            const next = (j + 1) % ring;
+            const a = profile[j];
+            const b = profile[next];
+            // The two halves of a hard corner sit in the same place, so the quad
+            // between them has no area. Skipping it keeps the index buffer honest
+            // rather than filling it with degenerate triangles.
+            if (a.u === b.u && a.v === b.v)
+                continue;
+            const i0 = i * ring + j;
+            const i1 = i * ring + next;
+            const i2 = (i + 1) * ring + next;
+            const i3 = (i + 1) * ring + j;
+            index.push(i0, i1, i2, i0, i2, i3);
+        }
+    }
+    capEnd(samples[0], profile, position, normal, color, index, false);
+    capEnd(samples[samples.length - 1], profile, position, normal, color, index, true);
+    return {
+        type: "buffer",
+        position: new Float32Array(position),
+        normal: new Float32Array(normal),
+        color: new Float32Array(color),
+        index: new Uint32Array(index),
+        // Built once per structure and cached by the node; nothing mutates these
+        // arrays afterwards, so the renderer may compare them by identity alone.
+        staticData: true,
+    };
+}
+/** A triangle fan closing one end of the sweep, facing along the tangent. */
+function capEnd(sample, profile, position, normal, color, index, forward) {
+    const sign = forward ? 1 : -1;
+    const nx = sample.tangent.x * sign;
+    const ny = sample.tangent.y * sign;
+    const nz = sample.tangent.z * sign;
+    const center = position.length / 3;
+    position.push(sample.position.x, sample.position.y, sample.position.z);
+    normal.push(nx, ny, nz);
+    color.push(sample.color[0], sample.color[1], sample.color[2]);
+    const first = position.length / 3;
+    for (const vertex of profile) {
+        const u = vertex.u * sample.halfWidth;
+        const v = vertex.v * sample.halfThickness;
+        position.push(sample.position.x + sample.normal.x * u + sample.binormal.x * v, sample.position.y + sample.normal.y * u + sample.binormal.y * v, sample.position.z + sample.normal.z * u + sample.binormal.z * v);
+        normal.push(nx, ny, nz);
+        color.push(sample.color[0], sample.color[1], sample.color[2]);
+    }
+    for (let j = 0; j < profile.length; j++) {
+        const next = (j + 1) % profile.length;
+        // Wound the opposite way at the two ends, so both caps face outward.
+        if (forward)
+            index.push(center, first + j, first + next);
+        else
+            index.push(center, first + next, first + j);
+    }
+}
+// --- Small vector maths ----------------------------------------------------
+//
+// Written out rather than reached for, on the same terms as `chemistry.ts`:
+// this package has to stay loadable in a bare Node process, and none of it is
+// more than a few lines.
+function catmullRom(p0, p1, p2, p3, t) {
+    const t2 = t * t;
+    const t3 = t2 * t;
+    const a = -0.5 * t3 + t2 - 0.5 * t;
+    const b = 1.5 * t3 - 2.5 * t2 + 1;
+    const c = -1.5 * t3 + 2 * t2 + 0.5 * t;
+    const d = 0.5 * t3 - 0.5 * t2;
+    return {
+        x: p0.x * a + p1.x * b + p2.x * c + p3.x * d,
+        y: p0.y * a + p1.y * b + p2.y * c + p3.y * d,
+        z: p0.z * a + p1.z * b + p2.z * c + p3.z * d,
+    };
+}
+function subtract(a, b) {
+    return { x: a.x - b.x, y: a.y - b.y, z: a.z - b.z };
+}
+function cross(a, b) {
+    return {
+        x: a.y * b.z - a.z * b.y,
+        y: a.z * b.x - a.x * b.z,
+        z: a.x * b.y - a.y * b.x,
+    };
+}
+function dot(a, b) {
+    return a.x * b.x + a.y * b.y + a.z * b.z;
+}
+function negate(v) {
+    return { x: -v.x, y: -v.y, z: -v.z };
+}
+function lengthOf(v) {
+    return Math.hypot(v.x, v.y, v.z);
+}
+function normalize(v) {
+    const length = lengthOf(v);
+    if (length < 1e-9)
+        return { x: 0, y: 0, z: 1 };
+    return { x: v.x / length, y: v.y / length, z: v.z / length };
+}
+function normalize2(u, v) {
+    const length = Math.hypot(u, v);
+    if (length < 1e-9)
+        return [1, 0];
+    return [u / length, v / length];
+}
+/** `v` with everything along `axis` taken out of it, normalized. */
+function perpendicular(v, axis) {
+    const along = dot(v, axis);
+    const out = {
+        x: v.x - axis.x * along,
+        y: v.y - axis.y * along,
+        z: v.z - axis.z * along,
+    };
+    // The carbonyl parallel to the chain — vanishingly rare, but it would leave
+    // no frame at all. Any perpendicular is correct; take one from the axis.
+    if (lengthOf(out) < 1e-6) {
+        const fallback = Math.abs(axis.x) < 0.9 ? { x: 1, y: 0, z: 0 } : { x: 0, y: 1, z: 0 };
+        return normalize(cross(axis, fallback));
+    }
+    return normalize(out);
+}
+function lerpVector(a, b, t) {
+    return {
+        x: a.x + (b.x - a.x) * t,
+        y: a.y + (b.y - a.y) * t,
+        z: a.z + (b.z - a.z) * t,
+    };
+}
+function lerpRgb(a, b, t) {
+    return [
+        a[0] + (b[0] - a[0]) * t,
+        a[1] + (b[1] - a[1]) * t,
+        a[2] + (b[2] - a[2]) * t,
+    ];
+}
+function clamp01(value) {
+    return Math.min(1, Math.max(0, value));
+}
+/**
+ * A colour as the **linear** RGB triple a vertex attribute holds.
+ *
+ * The same conversion `grid3d.ts` documents and for the same reason: three
+ * reads vertex colours as linear, so an sRGB channel uploaded raw paints far
+ * too bright. Skipping it here would wash every ribbon out against the atoms
+ * beside it, which take their colour through the material instead.
+ */
+function linearRgb(value) {
+    const [r, g, b] = resolveColor3D(value);
+    return [srgbToLinear(r), srgbToLinear(g), srgbToLinear(b)];
+}
+/** The sRGB transfer function, inverted. three's own `SRGBToLinear`. */
+function srgbToLinear(channel) {
+    return channel < 0.04045
+        ? channel * 0.0773993808
+        : Math.pow(channel * 0.9478672986 + 0.0521327014, 2.4);
+}
+//# sourceMappingURL=ribbon.js.map

package/dist/protein/ribbon.js.map

@@ -0,0 +1 @@
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* The cartoon: a chain's backbone swept as a **ribbon** rather than as a tube.\n *\n * This is the one representation whose whole job is to be recognised. A figure\n * in a paper draws a helix as a twisted band and a strand as a flat arrow, and\n * has since Jane Richardson drew the first one by hand in 1980 — the convention\n * is old enough that a reader decodes it without a legend, which is exactly why\n * a picture that departs from it reads as *wrong* rather than as different.\n *\n * The node drew that with `Geo.tube` before this module existed, and the two\n * things it could not express are the two the convention is made of:\n *\n * **A cross-section has a width and a thickness, not a radius.** A tube's is a\n * circle, so a helix could only be told from a coil by being *fatter* — and a\n * fat circle swept along the α-carbons of a helix is close to self-intersecting,\n * because those carbons corkscrew about the helix axis at ~2.3 Å with a 5.4 Å\n * pitch. What comes out is a lumpy sausage: the tube's own diameter is most of\n * the coil's, so the spiral fills in and the shape stops being legible. Swept\n * flat instead — ~2.2 Å across and ~0.5 Å thick — the same spiral reads as the\n * band every textbook draws, because the eye is now reading the *face* turning\n * rather than a diameter changing.\n *\n * **A band has a side, and a curve through α-carbons does not say which.** So\n * the frame is built from the residue's own carbonyl (see\n * {@link TracePoint.normal}), which is what turns with the fold. A ribbon swept\n * on an arbitrary frame twists at random and looks like a misprint.\n *\n * Everything here is derived **per structure**, cached by the node against the\n * inputs that produced it, and never rebuilt for a camera move — the same\n * bargain the instance lists make in `shared.ts`.\n */\n\nimport type { BufferGeometry3D, Color, Vector3 } from \"@motionscript/core\"\n\nimport { resolveColor3D } from \"@motionscript/core/component\"\nimport type { ProteinChain, SecondaryStructure, TracePoint } from \"./structure\"\n\n/**\n * A run of backbone drawn as one mesh: a whole stretch of one secondary\n * structure, with its per-residue colours carried as a vertex attribute.\n *\n * The unit is the **span**, not the run of constant colour that a tube is swept\n * as (see `backboneRuns`), and both halves of that matter. An arrowhead is a\n * statement about where a strand *ends*, so it can only be placed by something\n * that can see the whole strand — split the strand into four differently\n * coloured pieces first and each piece grows an arrow of its own. And a colour\n * that varies along the span is what a vertex attribute is for, which is also\n * what retires the faceted-polyline compromise the tube path has to make under\n * the residue spectrum.\n */\nexport interface CartoonSpan {\n  /** What this stretch is doing, which decides its cross-section. */\n  secondary: SecondaryStructure\n  /**\n   * The residues of the span, N→C, **overlapping its neighbours by one point**\n   * at each end so consecutive spans meet rather than leaving a gap.\n   */\n  points: TracePoint[]\n  /** One sRGB colour per entry of {@link points}. */\n  colors: string[]\n}\n\n/**\n * How wide and how thick each secondary structure's ribbon is, as multiples of\n * the node's `ribbonRadius`.\n *\n * Stated as a ratio to one control rather than as six numbers in the inspector:\n * \"how heavy is the cartoon\" is one question an author actually asks, and the\n * *proportions* between a helix, a strand and a loop are the convention rather\n * than a preference. The absolute values are the ones the established viewers\n * settled on — a helix band about 2.2 Å across and half an Ångström thick, a\n * strand slightly wider still, and a loop a thin round cord.\n *\n * A coil stays round (width equals thickness), which is the other half of the\n * statement: a loop has no face to turn, so giving it one would claim a\n * structure the file did not annotate.\n */\nconst SECTION: Readonly<\n  Record<SecondaryStructure, { width: number; thickness: number }>\n> = {\n  helix: { width: 2.4, thickness: 0.5 },\n  sheet: { width: 2.6, thickness: 0.45 },\n  coil: { width: 1, thickness: 1 },\n}\n\n/** How wide a strand's arrowhead is at its base, in the same multiples. */\nconst ARROW_WIDTH = 4.4\n\n/**\n * How many residues at the C-terminal end of a strand the arrowhead occupies.\n *\n * Residues rather than a fraction of the span, because an arrowhead is a fixed\n * *shape* — the same barb whether the strand is five residues or fifteen. A\n * fraction would draw a stubby wedge on a short strand and a long spike on a\n * β-hairpin's arm. Capped below at a third of the span so a three-residue\n * strand is still a strand with a point on it rather than one long taper.\n */\nconst ARROW_RESIDUES = 2.4\n\n/** What a strand's arrow narrows to at its tip, so the point is a point. */\nconst ARROW_TIP = 0.08\n\n/**\n * How many samples each residue-to-residue step is drawn with.\n *\n * The curve is the picture here. Consecutive α-carbons are 3.8 Å apart and a\n * helix turns fully in 3.6 of them, so a ribbon drawn straight between residues\n * is a polygon with about five sides per turn — which is exactly the faceted,\n * angular look that separates a rendering nobody trusts from one that reads as\n * a molecule. Tied to the node's mesh detail so the same control that coarsens\n * the spheres coarsens this.\n */\nfunction subdivisionsFor(quality: number): number {\n  return Math.min(10, Math.max(3, Math.round(quality / 2)))\n}\n\n/**\n * Splits a chain's trace into the spans a cartoon is built from — one per\n * unbroken stretch of the same secondary structure.\n *\n * Consecutive spans overlap by one point, for the reason `backboneRuns`'\n * consecutive runs do: the shared residue is the last sample of one sweep and\n * the first of the next, so the two meshes butt up rather than leaving a hole\n * at every helix-to-loop transition.\n */\nexport function cartoonSpans(\n  chain: ProteinChain,\n  colors: string[]\n): CartoonSpan[] {\n  const spans: CartoonSpan[] = []\n\n  chain.trace.forEach((point, index) => {\n    const color = colors[index] ?? colors[0] ?? \"#ffffff\"\n    let current = spans[spans.length - 1]\n\n    if (!current || current.secondary !== point.secondary) {\n      const previous = current\n      current = { secondary: point.secondary, points: [], colors: [] }\n      // Carry the previous span's last residue in as this one's first.\n      if (previous) {\n        current.points.push(previous.points[previous.points.length - 1]!)\n        current.colors.push(previous.colors[previous.colors.length - 1]!)\n      }\n      spans.push(current)\n    }\n\n    current.points.push(point)\n    current.colors.push(color)\n  })\n\n  // A lone point is not a curve: there is no direction to sweep along and no\n  // tangent to build a frame from. Only ever the first span, since every later\n  // one is seeded with its predecessor's last point.\n  return spans.filter((span) => span.points.length > 1)\n}\n\n/**\n * One span, as a mesh.\n *\n * `null` when there is nothing to sweep, so the caller can skip the op rather\n * than hand the renderer an empty buffer.\n *\n * The arrays are freshly allocated and never mutated afterwards, which is what\n * makes `staticData` honest: the renderer then compares them by identity and\n * uploads each exactly once, where re-deriving them per frame would re-upload\n * the whole fold sixty times a second to spin the camera.\n */\nexport function cartoonGeometry(\n  span: CartoonSpan,\n  options: { radius: number; quality: number }\n): BufferGeometry3D | null {\n  const samples = sampleSpan(span, options)\n  if (samples.length < 2) return null\n  return sweep(samples, profileFor(span.secondary, options.quality))\n}\n\n// --- Sampling --------------------------------------------------------------\n\n/** One cross-section of the sweep: where it is, how it is turned, how big. */\ninterface Sample {\n  position: Vector3\n  /** Unit tangent — the direction the sweep is travelling. */\n  tangent: Vector3\n  /** Unit **wide** direction: the ribbon's face turns with this. */\n  normal: Vector3\n  /** Unit binormal, completing the frame. */\n  binormal: Vector3\n  halfWidth: number\n  halfThickness: number\n  /** Linear RGB, as a vertex colour attribute holds it. */\n  color: [number, number, number]\n}\n\n/**\n * The span, resampled onto a smooth curve with a frame and a size at every\n * sample.\n *\n * Three things happen here that each fix something visible:\n *\n * **Catmull-Rom through the residues**, so the ribbon is a curve rather than a\n * five-sided polygon per helical turn — see {@link subdivisionsFor}.\n *\n * **The frames are made continuous before anything is interpolated.** A\n * β-strand's carbonyls point alternately to one side and the other, which is\n * chemistry rather than noise: hydrogen bonds go to the neighbouring strand on\n * both sides. Swept as given, the ribbon would flip 180° at every residue and\n * come out as a chain of triangles. Flipping each frame to agree with its\n * predecessor is what every viewer does and what makes a strand flat.\n *\n * **The arrow is measured in residues from the C-terminal end**, before\n * subdivision, so it is the same barb on a long strand and a short one.\n */\nfunction sampleSpan(\n  span: CartoonSpan,\n  options: { radius: number; quality: number }\n): Sample[] {\n  const points = span.points\n  const count = points.length\n  const section = SECTION[span.secondary]\n  const radius = Math.max(0.01, options.radius)\n\n  const frames = continuousFrames(points)\n  const tints = span.colors.map((color) => linearRgb(color))\n\n  // Where the arrowhead starts, as a position along the span in *residues*.\n  // A strand shorter than the barb gives up a third of itself to it rather than\n  // becoming one long taper.\n  const arrow =\n    span.secondary === \"sheet\"\n      ? Math.max(count - 1 - ARROW_RESIDUES, (count - 1) * (2 / 3))\n      : Infinity\n\n  const steps = subdivisionsFor(options.quality)\n  const samples: Sample[] = []\n\n  // Positions first, frames second: a tangent is a finite difference over the\n  // *sampled* curve, so every position has to exist before any of them can be\n  // taken. Doing it in one pass would take each tangent from the residues\n  // instead, which is the polyline this subdivision exists to get away from.\n  const curve: Vector3[] = []\n  const carried: Vector3[] = []\n  const colors: [number, number, number][] = []\n  const positions: number[] = []\n\n  for (let i = 0; i < count - 1; i++) {\n    // The last segment emits its endpoint too, so the sweep reaches the final\n    // residue rather than stopping one sample short of it.\n    const last = i === count - 2\n    for (let s = 0; s < steps + (last ? 1 : 0); s++) {\n      const t = s / steps\n      curve.push(\n        catmullRom(\n          points[i - 1] ?? points[i]!,\n          points[i]!,\n          points[i + 1]!,\n          points[i + 2] ?? points[i + 1]!,\n          t\n        )\n      )\n      carried.push(lerpVector(frames[i]!, frames[i + 1]!, t))\n      colors.push(lerpRgb(tints[i]!, tints[i + 1]!, t))\n      positions.push(i + t)\n    }\n  }\n\n  for (let i = 0; i < curve.length; i++) {\n    const position = curve[i]!\n    const tangent = normalize(\n      subtract(\n        curve[Math.min(curve.length - 1, i + 1)]!,\n        curve[Math.max(0, i - 1)]!\n      )\n    )\n    // Squared against the tangent, so the frame is orthonormal even though the\n    // carbonyl it came from is not perpendicular to the chain.\n    const normal = perpendicular(carried[i]!, tangent)\n    const binormal = normalize(cross(tangent, normal))\n\n    const along = positions[i]!\n    const width =\n      along <= arrow\n        ? section.width\n        : // Linear from the barb's base to its point. The base is *wider* than\n          // the strand, which is what makes an arrowhead read as one rather\n          // than as the strand simply stopping.\n          ARROW_WIDTH +\n          (ARROW_TIP - ARROW_WIDTH) *\n            clamp01((along - arrow) / Math.max(1e-6, count - 1 - arrow))\n\n    samples.push({\n      position,\n      tangent,\n      normal,\n      binormal,\n      halfWidth: radius * width,\n      halfThickness: radius * section.thickness,\n      color: colors[i]!,\n    })\n  }\n\n  return samples\n}\n\n/**\n * Each residue's ribbon direction, made to agree with its predecessor.\n *\n * Falls back to the curve's own binormal — the axis its turn is about — where\n * the file gives no carbonyl. That is the right stand-in rather than an\n * arbitrary perpendicular: in a helix the carbonyl points very nearly along the\n * helix axis, and so does the binormal of the curve the α-carbons trace, so a\n * Cα-only model comes out with its bands lying the same way a complete file's\n * do.\n */\nfunction continuousFrames(points: TracePoint[]): Vector3[] {\n  const frames: Vector3[] = []\n\n  for (let i = 0; i < points.length; i++) {\n    const point = points[i]!\n    let direction = point.normal ?? binormalAt(points, i)\n    // Degenerate — three collinear residues with no carbonyl. Any perpendicular\n    // will do, and the frame is squared against the tangent anyway.\n    if (lengthOf(direction) < 1e-6) direction = { x: 0, y: 0, z: 1 }\n\n    const previous = frames[i - 1]\n    // The 180° flip a β-strand's alternating carbonyls would otherwise put into\n    // the sweep. See {@link sampleSpan}.\n    if (previous && dot(previous, direction) < 0) direction = negate(direction)\n    frames.push(normalize(direction))\n  }\n\n  return frames\n}\n\n/** The curve's binormal at a residue — the axis its local turn is about. */\nfunction binormalAt(points: TracePoint[], index: number): Vector3 {\n  const before = points[Math.max(0, index - 1)]!\n  const here = points[index]!\n  const after = points[Math.min(points.length - 1, index + 1)]!\n  return cross(subtract(here, before), subtract(after, here))\n}\n\n// --- Sweeping --------------------------------------------------------------\n\n/**\n * One vertex of a cross-section: where it sits in the frame's `(wide, thick)`\n * plane, and which way the surface faces there.\n *\n * A hard edge is **two entries at the same place with different normals**,\n * which is what gives a ribbon the crisp corner a cartoon has rather than the\n * chamfered one a shared-vertex mesh with averaged normals would. It is also\n * why the normals are stated rather than derived: `computeNormals` averages\n * across whatever shares a vertex, and averaging is exactly what a corner must\n * not do.\n */\ninterface ProfileVertex {\n  /** Position along the ribbon's width, in `[-1, 1]`. */\n  u: number\n  /** Position along its thickness, in `[-1, 1]`. */\n  v: number\n  /** Surface direction at that vertex, in the same plane. */\n  nu: number\n  nv: number\n}\n\n/**\n * The cross-section a secondary structure is swept with.\n *\n * A loop is a round cord and a helix or a strand is a flat band — the whole\n * distinction the convention rests on, and the one a radius could not express.\n * The band is a rectangle rather than an ellipse because its *edge* is what the\n * eye reads a twist by: an ellipse turning through 90° goes smoothly from wide\n * to narrow and reads as a tube pinching, where a rectangle's corner catches the\n * light and reads as a face turning over.\n */\nfunction profileFor(\n  secondary: SecondaryStructure,\n  quality: number\n): ProfileVertex[] {\n  if (secondary === \"coil\") {\n    const sides = Math.min(16, Math.max(5, Math.round(quality / 2)))\n    const profile: ProfileVertex[] = []\n    for (let i = 0; i < sides; i++) {\n      const angle = (i / sides) * Math.PI * 2\n      const u = Math.cos(angle)\n      const v = Math.sin(angle)\n      // Smooth: one vertex per side, its normal radial, so a cord reads as\n      // round rather than as a faceted prism.\n      profile.push({ u, v, nu: u, nv: v })\n    }\n    return profile\n  }\n\n  // Four faces, each with its own pair of corners, walked so consecutive\n  // entries are consecutive around the section.\n  return [\n    { u: 1, v: 1, nu: 0, nv: 1 },\n    { u: -1, v: 1, nu: 0, nv: 1 },\n    { u: -1, v: 1, nu: -1, nv: 0 },\n    { u: -1, v: -1, nu: -1, nv: 0 },\n    { u: -1, v: -1, nu: 0, nv: -1 },\n    { u: 1, v: -1, nu: 0, nv: -1 },\n    { u: 1, v: -1, nu: 1, nv: 0 },\n    { u: 1, v: 1, nu: 1, nv: 0 },\n  ]\n}\n\n/**\n * The samples and the profile, as one indexed mesh.\n *\n * Ends are **capped**: a ribbon is a solid band and an open end shows the\n * inside of the far face, which at a helix-to-loop transition would be a\n * visible hole rather than a join. Cheap — one fan per end — and it is what\n * lets a span be drawn as its own mesh at all.\n */\nfunction sweep(samples: Sample[], profile: ProfileVertex[]): BufferGeometry3D {\n  const ring = profile.length\n  const position: number[] = []\n  const normal: number[] = []\n  const color: number[] = []\n  const index: number[] = []\n\n  for (const sample of samples) {\n    for (const vertex of profile) {\n      const u = vertex.u * sample.halfWidth\n      const v = vertex.v * sample.halfThickness\n      position.push(\n        sample.position.x + sample.normal.x * u + sample.binormal.x * v,\n        sample.position.y + sample.normal.y * u + sample.binormal.y * v,\n        sample.position.z + sample.normal.z * u + sample.binormal.z * v\n      )\n      // A normal does not survive a non-uniform scale the way a position does:\n      // squashing a circle to a 5:1 ellipse tips every one of its normals\n      // toward the wide axis. Dividing by the half-extents is the inverse\n      // transpose of that scale, written out for two dimensions.\n      const n = normalize2(\n        vertex.nu / sample.halfWidth,\n        vertex.nv / sample.halfThickness\n      )\n      normal.push(\n        sample.normal.x * n[0] + sample.binormal.x * n[1],\n        sample.normal.y * n[0] + sample.binormal.y * n[1],\n        sample.normal.z * n[0] + sample.binormal.z * n[1]\n      )\n      color.push(sample.color[0], sample.color[1], sample.color[2])\n    }\n  }\n\n  for (let i = 0; i < samples.length - 1; i++) {\n    for (let j = 0; j < ring; j++) {\n      const next = (j + 1) % ring\n      const a = profile[j]!\n      const b = profile[next]!\n      // The two halves of a hard corner sit in the same place, so the quad\n      // between them has no area. Skipping it keeps the index buffer honest\n      // rather than filling it with degenerate triangles.\n      if (a.u === b.u && a.v === b.v) continue\n      const i0 = i * ring + j\n      const i1 = i * ring + next\n      const i2 = (i + 1) * ring + next\n      const i3 = (i + 1) * ring + j\n      index.push(i0, i1, i2, i0, i2, i3)\n    }\n  }\n\n  capEnd(samples[0]!, profile, position, normal, color, index, false)\n  capEnd(\n    samples[samples.length - 1]!,\n    profile,\n    position,\n    normal,\n    color,\n    index,\n    true\n  )\n\n  return {\n    type: \"buffer\",\n    position: new Float32Array(position),\n    normal: new Float32Array(normal),\n    color: new Float32Array(color),\n    index: new Uint32Array(index),\n    // Built once per structure and cached by the node; nothing mutates these\n    // arrays afterwards, so the renderer may compare them by identity alone.\n    staticData: true,\n  }\n}\n\n/** A triangle fan closing one end of the sweep, facing along the tangent. */\nfunction capEnd(\n  sample: Sample,\n  profile: ProfileVertex[],\n  position: number[],\n  normal: number[],\n  color: number[],\n  index: number[],\n  forward: boolean\n): void {\n  const sign = forward ? 1 : -1\n  const nx = sample.tangent.x * sign\n  const ny = sample.tangent.y * sign\n  const nz = sample.tangent.z * sign\n\n  const center = position.length / 3\n  position.push(sample.position.x, sample.position.y, sample.position.z)\n  normal.push(nx, ny, nz)\n  color.push(sample.color[0], sample.color[1], sample.color[2])\n\n  const first = position.length / 3\n  for (const vertex of profile) {\n    const u = vertex.u * sample.halfWidth\n    const v = vertex.v * sample.halfThickness\n    position.push(\n      sample.position.x + sample.normal.x * u + sample.binormal.x * v,\n      sample.position.y + sample.normal.y * u + sample.binormal.y * v,\n      sample.position.z + sample.normal.z * u + sample.binormal.z * v\n    )\n    normal.push(nx, ny, nz)\n    color.push(sample.color[0], sample.color[1], sample.color[2])\n  }\n\n  for (let j = 0; j < profile.length; j++) {\n    const next = (j + 1) % profile.length\n    // Wound the opposite way at the two ends, so both caps face outward.\n    if (forward) index.push(center, first + j, first + next)\n    else index.push(center, first + next, first + j)\n  }\n}\n\n// --- Small vector maths ----------------------------------------------------\n//\n// Written out rather than reached for, on the same terms as `chemistry.ts`:\n// this package has to stay loadable in a bare Node process, and none of it is\n// more than a few lines.\n\nfunction catmullRom(\n  p0: { x: number; y: number; z: number },\n  p1: { x: number; y: number; z: number },\n  p2: { x: number; y: number; z: number },\n  p3: { x: number; y: number; z: number },\n  t: number\n): Vector3 {\n  const t2 = t * t\n  const t3 = t2 * t\n  const a = -0.5 * t3 + t2 - 0.5 * t\n  const b = 1.5 * t3 - 2.5 * t2 + 1\n  const c = -1.5 * t3 + 2 * t2 + 0.5 * t\n  const d = 0.5 * t3 - 0.5 * t2\n  return {\n    x: p0.x * a + p1.x * b + p2.x * c + p3.x * d,\n    y: p0.y * a + p1.y * b + p2.y * c + p3.y * d,\n    z: p0.z * a + p1.z * b + p2.z * c + p3.z * d,\n  }\n}\n\nfunction subtract(\n  a: { x: number; y: number; z: number },\n  b: { x: number; y: number; z: number }\n): Vector3 {\n  return { x: a.x - b.x, y: a.y - b.y, z: a.z - b.z }\n}\n\nfunction cross(a: Vector3, b: Vector3): Vector3 {\n  return {\n    x: a.y * b.z - a.z * b.y,\n    y: a.z * b.x - a.x * b.z,\n    z: a.x * b.y - a.y * b.x,\n  }\n}\n\nfunction dot(a: Vector3, b: Vector3): number {\n  return a.x * b.x + a.y * b.y + a.z * b.z\n}\n\nfunction negate(v: Vector3): Vector3 {\n  return { x: -v.x, y: -v.y, z: -v.z }\n}\n\nfunction lengthOf(v: Vector3): number {\n  return Math.hypot(v.x, v.y, v.z)\n}\n\nfunction normalize(v: Vector3): Vector3 {\n  const length = lengthOf(v)\n  if (length < 1e-9) return { x: 0, y: 0, z: 1 }\n  return { x: v.x / length, y: v.y / length, z: v.z / length }\n}\n\nfunction normalize2(u: number, v: number): [number, number] {\n  const length = Math.hypot(u, v)\n  if (length < 1e-9) return [1, 0]\n  return [u / length, v / length]\n}\n\n/** `v` with everything along `axis` taken out of it, normalized. */\nfunction perpendicular(v: Vector3, axis: Vector3): Vector3 {\n  const along = dot(v, axis)\n  const out = {\n    x: v.x - axis.x * along,\n    y: v.y - axis.y * along,\n    z: v.z - axis.z * along,\n  }\n  // The carbonyl parallel to the chain — vanishingly rare, but it would leave\n  // no frame at all. Any perpendicular is correct; take one from the axis.\n  if (lengthOf(out) < 1e-6) {\n    const fallback =\n      Math.abs(axis.x) < 0.9 ? { x: 1, y: 0, z: 0 } : { x: 0, y: 1, z: 0 }\n    return normalize(cross(axis, fallback))\n  }\n  return normalize(out)\n}\n\nfunction lerpVector(\n  a: { x: number; y: number; z: number },\n  b: { x: number; y: number; z: number },\n  t: number\n): Vector3 {\n  return {\n    x: a.x + (b.x - a.x) * t,\n    y: a.y + (b.y - a.y) * t,\n    z: a.z + (b.z - a.z) * t,\n  }\n}\n\nfunction lerpRgb(\n  a: [number, number, number],\n  b: [number, number, number],\n  t: number\n): [number, number, number] {\n  return [\n    a[0] + (b[0] - a[0]) * t,\n    a[1] + (b[1] - a[1]) * t,\n    a[2] + (b[2] - a[2]) * t,\n  ]\n}\n\nfunction clamp01(value: number): number {\n  return Math.min(1, Math.max(0, value))\n}\n\n/**\n * A colour as the **linear** RGB triple a vertex attribute holds.\n *\n * The same conversion `grid3d.ts` documents and for the same reason: three\n * reads vertex colours as linear, so an sRGB channel uploaded raw paints far\n * too bright. Skipping it here would wash every ribbon out against the atoms\n * beside it, which take their colour through the material instead.\n */\nfunction linearRgb(value: Color): [number, number, number] {\n  const [r, g, b] = resolveColor3D(value)\n  return [srgbToLinear(r), srgbToLinear(g), srgbToLinear(b)]\n}\n\n/** The sRGB transfer function, inverted. three's own `SRGBToLinear`. */\nfunction srgbToLinear(channel: number): number {\n  return channel < 0.04045\n    ? channel * 0.0773993808\n    : Math.pow(channel * 0.9478672986 + 0.0521327014, 2.4)\n}\n"]}