react-cheminfo 0.3.0 → 0.4.1

package/lib/orbital/ui/AtomicOrbitalCanvas.js

@@ -15,7 +15,7 @@ export function AtomicOrbitalCanvas(props) {
     const [drawn, setDrawn] = useState(null);
     // What the canvas is being asked to show. Comparing it with what it *is*
     // showing gives the progress note without a state write on every prop change.
-    const wanted = `${atomicNumber}|${orbitalId}|${resolution}|${palette.id}`;
+    const wanted = `${atomicNumber}|${orbitalId}|${resolutionKey(resolution)}|${palette.id}`;
     const busy = drawn !== wanted;
     // Callbacks are read through refs so a caller passing an inline arrow does
     // not re-sample the orbital on every render of its parent.
@@ -52,7 +52,7 @@ export function AtomicOrbitalCanvas(props) {
             if (cancelled)
                 return;
             callbacks.current.onNodeRadii?.(result.nodeRadii);
-            const reach = await viewer.showOrbital(result.grid, {
+            const reach = await viewer.showOrbital(result.grid, result.contour, {
                 positiveColour: palette.positive,
                 negativeColour: palette.negative,
             });
@@ -76,6 +76,16 @@ export function AtomicOrbitalCanvas(props) {
 }
 /** Samples per edge; 56 resolves the radial node of a 3s in about 25 ms. */
 const DEFAULT_RESOLUTION = 56;
+/**
+ * A stable identity for either shape the resolution prop can take.
+ * @param resolution - A fixed sample count, or the limits it may vary between.
+ * @returns A string that changes exactly when the sampling would.
+ */
+function resolutionKey(resolution) {
+    return typeof resolution === 'number'
+        ? String(resolution)
+        : `${resolution.floor}-${resolution.cap}`;
+}
 /**
  * A square, centred stage: an atomic orbital is as tall as it is wide, so a
  * square wastes the least of the frame and keeps the lobes the same size when

package/lib/orbital/ui/AtomicOrbitalCanvas.js.map

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package/lib/orbital/ui/AtomicOrbitalViewer.d.ts

@@ -15,6 +15,7 @@
  * ```
  */
 import type { ReactElement, ReactNode } from 'react';
+import type { ResolutionLimits } from '../core/atomicGrid.ts';
 import type { PhasePalette } from '../core/palette.ts';
 import type { AtomicSampler } from '../core/sample.ts';
 import type { ViewerCapability } from './capability.ts';
@@ -31,9 +32,12 @@ export interface AtomicOrbitalViewerProps {
     palette?: PhasePalette;
     /**
      * Samples along each edge of the cube; the cost is the cube of it.
+     *
+     * A number fixes it. A {@link ResolutionLimits} pair lets each orbital's own
+     * shape pick a resolution between the two.
      * @default 56
      */
-    resolution?: number;
+    resolution?: number | ResolutionLimits;
     /**
      * Whether the scene turns on its own.
      * @default false

package/lib/orbital/ui/AtomicOrbitalViewer.d.ts.map

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package/lib/orbital/ui/AtomicOrbitalViewer.js.map

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+{"version":3,"file":"AtomicOrbitalViewer.js","sourceRoot":"","sources":["../../../src/orbital/ui/AtomicOrbitalViewer.tsx"],"names":[],"mappings":";AAkBA,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAC;AASjD,OAAO,EAAE,qBAAqB,EAAE,MAAM,iBAAiB,CAAC;AAExD,MAAM,mBAAmB,GAAG,IAAI,CAAC,KAAK,IAAI,EAAE;IAC1C,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,0BAA2B,CAAC,CAAC;IACzD,OAAO,EAAE,OAAO,EAAE,MAAM,CAAC,mBAAmB,EAAE,CAAC;AACjD,CAAC,CAAC,CAAC;AAoDH;;;;GAIG;AACH,MAAM,UAAU,mBAAmB,CACjC,KAA+B;IAE/B,MAAM,EACJ,QAAQ,GAAG,wBAAwB,EACnC,iBAAiB,EACjB,GAAG,MAAM,EACV,GAAG,KAAK,CAAC;IACV,MAAM,CAAC,UAAU,CAAC,GAAG,QAAQ,CAAC,qBAAqB,CAAC,CAAC;IACrD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAgB,IAAI,CAAC,CAAC;IAE5D,IAAI,CAAC,UAAU,CAAC,SAAS,EAAE,CAAC;QAC1B,OAAO,CACL,cAAK,KAAK,EAAE,UAAU,YACnB,iBAAiB,EAAE,CAAC,UAAU,CAAC,IAAI,UAAU,CAAC,OAAO,GAClD,CACP,CAAC;IACJ,CAAC;IAED,OAAO,CACL,eAAK,KAAK,EAAE,UAAU,aACpB,KAAC,QAAQ,IAAC,QAAQ,EAAE,cAAK,KAAK,EAAE,UAAU,YAAG,QAAQ,GAAO,YAC1D,KAAC,mBAAmB,OACd,MAAM,EACV,OAAO,EAAE,CAAC,OAAO,EAAE,EAAE;wBACnB,UAAU,CAAC,OAAO,CAAC,CAAC;oBACtB,CAAC,GACD,GACO,EACV,OAAO,KAAK,IAAI,IAAI,CACnB,eAAK,KAAK,EAAE,aAAa,kDACW,OAAO,IACrC,CACP,IACG,CACP,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,GAAkB;IAChC,OAAO,EAAE,MAAM;IACf,aAAa,EAAE,QAAQ;IACvB,GAAG,EAAE,CAAC;IACN,QAAQ,EAAE,CAAC;CACZ,CAAC;AAEF,MAAM,UAAU,GAAkB;IAChC,OAAO,EAAE,MAAM;IACf,UAAU,EAAE,QAAQ;IACpB,cAAc,EAAE,QAAQ;IACxB,SAAS,EAAE,GAAG;IACd,OAAO,EAAE,EAAE;IACX,YAAY,EAAE,CAAC;IACf,UAAU,EAAE,kBAAkB;IAC9B,KAAK,EAAE,SAAS;IAChB,QAAQ,EAAE,EAAE;IACZ,SAAS,EAAE,QAAQ;CACpB,CAAC;AAEF,MAAM,aAAa,GAAkB;IACnC,OAAO,EAAE,SAAS;IAClB,YAAY,EAAE,CAAC;IACf,UAAU,EAAE,SAAS;IACrB,KAAK,EAAE,SAAS;IAChB,QAAQ,EAAE,EAAE;CACb,CAAC"}

package/lib/orbital/ui/renderVolume.d.ts

@@ -15,6 +15,7 @@
  */
 import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
 import type { OrbitalGrid } from '../core/grid.ts';
+import type { OrbitalContour } from '../core/isovalue.ts';
 /** Colours and opacity of one signed isosurface pair. */
 export interface VolumeStyle {
     /**
@@ -28,8 +29,8 @@ export interface VolumeStyle {
      */
     negativeColour?: string;
     /**
-     * Isovalue as a multiple of the one enclosing `ENCLOSED_WEIGHT` of the
-     * orbital's weight. Larger means a tighter, smaller surface.
+     * Isovalue as a multiple of the contour's own cutoff. Larger means a
+     * tighter, smaller surface.
      * @default 1
      */
     relativeIsovalue?: number;
@@ -43,12 +44,14 @@ export interface VolumeStyle {
  * Replace the isosurface pair drawn from a sampled field.
  * @param plugin - The molstar context.
  * @param field - The field, as `sampleAtomicOrbital` produced it.
+ * @param contour - The isovalue and reach measured on that field, as
+ * `runAtomicSample` returned them.
  * @param style - See {@link VolumeStyle}.
  * @returns How far the drawn surface reaches from the centre of the box,
  * ångström — what a camera has to frame to fill the viewport with it.
  * @throws {Error} When the canvas is not ready.
  */
-export declare function renderSampledVolume(plugin: PluginContext, field: OrbitalGrid, style?: VolumeStyle): Promise<number>;
+export declare function renderSampledVolume(plugin: PluginContext, field: OrbitalGrid, contour: OrbitalContour, style?: VolumeStyle): Promise<number>;
 /**
  * Remove the sampled isosurfaces, leaving anything else on the canvas.
  * @param plugin - The molstar context.

package/lib/orbital/ui/renderVolume.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"renderVolume.d.ts","sourceRoot":"","sources":["../../../src/orbital/ui/renderVolume.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAGH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAC;AAMvE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAI1D,yDAAyD;AACzD,MAAM,WAAW,WAAW;IAC1B;;;OAGG;IACH,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;;;OAGG;IACH,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;;;;OAIG;IACH,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B;;;OAGG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,MAAM,EAAE,aAAa,EACrB,KAAK,EAAE,WAAW,EAClB,OAAO,EAAE,cAAc,EACvB,KAAK,GAAE,WAAgB,GACtB,OAAO,CAAC,MAAM,CAAC,CA8CjB;AAED;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,aAAa,GAAG,IAAI,CAQ9D"}

package/lib/orbital/ui/renderVolume.js

@@ -13,47 +13,40 @@
  * tree and are tracked per plugin, because every change of orbital replaces
  * them wholesale.
  */
-import { computeOrbitalIsocontourValues } from 'molstar/lib/extensions/alpha-orbitals/orbitals.js';
 import { createVolumeRepresentationParams } from 'molstar/lib/mol-plugin-state/helpers/volume-representation-params.js';
 import { Theme } from 'molstar/lib/mol-theme/theme.js';
 import { Color } from 'molstar/lib/mol-util/color/color.js';
-import { ENCLOSED_WEIGHT } from "../core/constants.js";
-import { DISPLAY_REACH, surfaceReach, toVolume } from "./volumeField.js";
+import { DISPLAY_REACH, toVolume } from "./volumeField.js";
 /**
  * Replace the isosurface pair drawn from a sampled field.
  * @param plugin - The molstar context.
  * @param field - The field, as `sampleAtomicOrbital` produced it.
+ * @param contour - The isovalue and reach measured on that field, as
+ * `runAtomicSample` returned them.
  * @param style - See {@link VolumeStyle}.
  * @returns How far the drawn surface reaches from the centre of the box,
  * ångström — what a camera has to frame to fill the viewport with it.
  * @throws {Error} When the canvas is not ready.
  */
-export async function renderSampledVolume(plugin, field, style = {}) {
+export async function renderSampledVolume(plugin, field, contour, style = {}) {
     const canvas3d = plugin.canvas3d;
     if (canvas3d === undefined) {
         throw new Error('renderSampledVolume: the molstar canvas is not ready.');
     }
     const { positiveColour = '#2563eb', negativeColour = '#dc2626', relativeIsovalue = 1, alpha = 0.72, } = style;
     clearSampledVolume(plugin);
-    const isovalues = computeOrbitalIsocontourValues(field.data, ENCLOSED_WEIGHT);
+    const { cutoff, reach } = contour;
     // Molstar's camera clamps both its target distance and its near plane, so it
     // cannot get close to a small object: uranium's 4f reaches 0.35 Å and would
     // stay a dot in the corner whatever the camera is asked to frame. Every
     // orbital is therefore drawn at one canonical size, and the true extent is
     // reported as ⟨r⟩ and on the radial plot instead of by the picture's scale.
-    const reach = surfaceReach(field, isovalues);
     const volume = toVolume(field, reach > 0 ? DISPLAY_REACH / reach : 1);
     // A nodeless orbital — every 1s — has no negative lobe at all, and asking for
     // its isosurface would draw an empty mesh at value 0.
     const surfaces = await Promise.all([
-        maybeSurface(plugin, volume, isovalues.positive, relativeIsovalue, {
-            colour: positiveColour,
-            alpha,
-        }),
-        maybeSurface(plugin, volume, isovalues.negative, relativeIsovalue, {
-            colour: negativeColour,
-            alpha,
-        }),
+        maybeSurface(plugin, volume, field.max >= cutoff ? cutoff : undefined, relativeIsovalue, { colour: positiveColour, alpha }),
+        maybeSurface(plugin, volume, field.min <= -cutoff ? -cutoff : undefined, relativeIsovalue, { colour: negativeColour, alpha }),
     ]);
     const drawn = surfaces.filter((surface) => surface !== null);
     representations.set(plugin, drawn);
@@ -100,7 +93,13 @@ async function createSurface(plugin, volume, isovalue, colour, alpha) {
             isoValue: { kind: 'absolute', absoluteValue: isovalue },
             alpha,
             xrayShaded: true,
-            tryUseGpu: true,
+            // Molstar's GPU marching cubes pits the outer lobe of a diffuse orbital
+            // with voxel-sized dimples — caesium's 6s and every 7s, 6d and 7p above
+            // it — and quantises the field to 255 steps on upload unless told
+            // otherwise, which terraces xenon's 4p. The surface is a thin shell
+            // whatever the box holds, so the CPU path costs 13–44 ms and returns
+            // 27 k vertices even on the 152³ grid the highest quality asks for.
+            tryUseGpu: false,
         },
         color: 'uniform',
         colorParams: { value: Color.fromHexStyle(colour) },

package/lib/orbital/ui/renderVolume.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderVolume.js","sourceRoot":"","sources":["../../../src/orbital/ui/renderVolume.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAIH,OAAO,EAAE,gCAAgC,EAAE,MAAM,sEAAsE,CAAC;AAExH,OAAO,EAAE,KAAK,EAAE,MAAM,gCAAgC,CAAC;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,qCAAqC,CAAC;AAK5D,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AA2B3D;;;;;;;;;;GAUG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,MAAqB,EACrB,KAAkB,EAClB,OAAuB,EACvB,QAAqB,EAAE;IAEvB,MAAM,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;IACjC,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAC;IAC3E,CAAC;IACD,MAAM,EACJ,cAAc,GAAG,SAAS,EAC1B,cAAc,GAAG,SAAS,EAC1B,gBAAgB,GAAG,CAAC,EACpB,KAAK,GAAG,IAAI,GACb,GAAG,KAAK,CAAC;IACV,kBAAkB,CAAC,MAAM,CAAC,CAAC;IAE3B,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAClC,6EAA6E;IAC7E,4EAA4E;IAC5E,wEAAwE;IACxE,2EAA2E;IAC3E,4EAA4E;IAC5E,MAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACtE,8EAA8E;IAC9E,sDAAsD;IACtD,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QACjC,YAAY,CACV,MAAM,EACN,MAAM,EACN,KAAK,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EACxC,gBAAgB,EAChB,EAAE,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,CAClC;QACD,YAAY,CACV,MAAM,EACN,MAAM,EACN,KAAK,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EAC1C,gBAAgB,EAChB,EAAE,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,CAClC;KACF,CAAC,CAAC;IACH,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAC3B,CAAC,OAAO,EAAiC,EAAE,CAAC,OAAO,KAAK,IAAI,CAC7D,CAAC;IACF,eAAe,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACnC,KAAK,MAAM,cAAc,IAAI,KAAK;QAAE,QAAQ,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;IACjE,mEAAmE;IACnE,QAAQ,CAAC,MAAM,EAAE,CAAC;IAClB,OAAO,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC;AACvC,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,kBAAkB,CAAC,MAAqB;IACtD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC7C,IAAI,QAAQ,KAAK,SAAS;QAAE,OAAO;IACnC,eAAe,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC/B,KAAK,MAAM,cAAc,IAAI,QAAQ,EAAE,CAAC;QACtC,MAAM,CAAC,QAAQ,EAAE,MAAM,CAAC,cAAc,CAAC,CAAC;IAC1C,CAAC;IACD,MAAM,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC;AAC5B,CAAC;AAED;;;;;;;;;;GAUG;AACH,KAAK,UAAU,YAAY,CACzB,MAAqB,EACrB,MAAc,EACd,QAA4B,EAC5B,gBAAwB,EACxB,KAAwC;IAExC,IAAI,QAAQ,KAAK,SAAS,IAAI,QAAQ,KAAK,CAAC;QAAE,OAAO,IAAI,CAAC;IAC1D,OAAO,aAAa,CAClB,MAAM,EACN,MAAM,EACN,QAAQ,GAAG,gBAAgB,EAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,KAAK,CACZ,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,MAAqB,EACrB,MAAc,EACd,QAAgB,EAChB,MAAc,EACd,KAAa;IAEb,MAAM,MAAM,GAAG,gCAAgC,CAAC,MAAM,EAAE,MAAM,EAAE;QAC9D,IAAI,EAAE,YAAY;QAClB,UAAU,EAAE;YACV,QAAQ,EAAE,EAAE,IAAI,EAAE,UAAU,EAAE,aAAa,EAAE,QAAQ,EAAE;YACvD,KAAK;YACL,UAAU,EAAE,IAAI;YAChB,wEAAwE;YACxE,wEAAwE;YACxE,kEAAkE;YAClE,oEAAoE;YACpE,qEAAqE;YACrE,oEAAoE;YACpE,SAAS,EAAE,KAAK;SACjB;QACD,KAAK,EAAE,SAAS;QAChB,WAAW,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE;KACnD,CAAC,CAAC;IACH,MAAM,QAAQ,GAAG,MAAM,CAAC,cAAc,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC7E,MAAM,cAAc,GAAG,QAAQ,CAAC,OAAO,CACrC,EAAE,KAAK,EAAE,MAAM,CAAC,QAAQ,EAAE,KAAK,EAAE,GAAG,MAAM,CAAC,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,EACzE,QAAQ,CAAC,SAAS,CACnB,CAAC;IACF,cAAc,CAAC,QAAQ,CACrB,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,cAAc,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,CACtE,CAAC;IACF,MAAM,MAAM,CAAC,OAAO,CAClB,cAAc,CAAC,cAAc,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,IAAI,EAAE,EAAE,MAAM,CAAC,CAChE,CAAC;IACF,cAAc,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAC,CAAC;IAC7C,OAAO,cAAc,CAAC;AACxB,CAAC;AAED;;;GAGG;AACH,MAAM,eAAe,GAAG,IAAI,OAAO,EAAuC,CAAC"}

package/lib/orbital/ui/viewer.d.ts

@@ -13,6 +13,7 @@
  * molstar's own UI is not mounted: the surrounding site owns every control.
  */
 import type { OrbitalGrid } from '../core/grid.ts';
+import type { OrbitalContour } from '../core/isovalue.ts';
 import type { VolumeStyle } from './renderVolume.ts';
 /** Settings fixed for the life of a viewer. */
 export interface OrbitalViewerOptions {
@@ -49,11 +50,12 @@ export declare class OrbitalViewer {
     /**
      * Replace the isosurface pair with one drawn from a sampled field.
      * @param field - The sampled wavefunction, in ångström.
+     * @param contour - The isovalue and reach measured on that field.
      * @param style - See {@link VolumeStyle}.
      * @returns How far the drawn surface reaches, in scene units, for the camera
      * to frame; `undefined` once the viewer has been disposed.
      */
-    showOrbital(field: OrbitalGrid, style?: VolumeStyle): Promise<number | undefined>;
+    showOrbital(field: OrbitalGrid, contour: OrbitalContour, style?: VolumeStyle): Promise<number | undefined>;
     /**
      * Remove the isosurface pair.
      * @returns Nothing, once the surfaces are gone.

package/lib/orbital/ui/viewer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["../../../src/orbital/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAQH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAGnD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAGrD,+CAA+C;AAC/C,MAAM,WAAW,oBAAoB;IACnC;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CACjC,SAAS,EAAE,WAAW,EACtB,OAAO,GAAE,oBAAyB,GACjC,aAAa,CAEf;AAED;;;;;GAKG;AACH,qBAAa,aAAa;;IAIxB,0EAA0E;IAC1E,QAAQ,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;gBAElB,SAAS,EAAE,WAAW,EAAE,OAAO,GAAE,oBAAyB;IAiBtE;;;OAGG;IACH,IAAI,QAAQ,IAAI,OAAO,CAEtB;IAED;;;;;;OAMG;IACH,WAAW,CACT,KAAK,EAAE,WAAW,EAClB,KAAK,CAAC,EAAE,WAAW,GAClB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC;IAI9B;;;OAGG;IACH,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC;IAM5B;;;;;;;OAOG;IACH,KAAK,CACH,aAAa,CAAC,EAAE,MAAM,EACtB,UAAU,SAA0B,GACnC,OAAO,CAAC,IAAI,CAAC;IAMhB;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,KAAK,SAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAMpD,kEAAkE;IAClE,YAAY,IAAI,IAAI;IAKpB;;;OAGG;IACH,OAAO,IAAI,IAAI;CAkChB"}
+{"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["../../../src/orbital/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAQH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAG1D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAGrD,+CAA+C;AAC/C,MAAM,WAAW,oBAAoB;IACnC;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CACjC,SAAS,EAAE,WAAW,EACtB,OAAO,GAAE,oBAAyB,GACjC,aAAa,CAEf;AAED;;;;;GAKG;AACH,qBAAa,aAAa;;IAIxB,0EAA0E;IAC1E,QAAQ,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;gBAElB,SAAS,EAAE,WAAW,EAAE,OAAO,GAAE,oBAAyB;IAiBtE;;;OAGG;IACH,IAAI,QAAQ,IAAI,OAAO,CAEtB;IAED;;;;;;;OAOG;IACH,WAAW,CACT,KAAK,EAAE,WAAW,EAClB,OAAO,EAAE,cAAc,EACvB,KAAK,CAAC,EAAE,WAAW,GAClB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC;IAM9B;;;OAGG;IACH,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC;IAM5B;;;;;;;OAOG;IACH,KAAK,CACH,aAAa,CAAC,EAAE,MAAM,EACtB,UAAU,SAA0B,GACnC,OAAO,CAAC,IAAI,CAAC;IAMhB;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,KAAK,SAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAMpD,kEAAkE;IAClE,YAAY,IAAI,IAAI;IAKpB;;;OAGG;IACH,OAAO,IAAI,IAAI;CAkChB"}

package/lib/orbital/ui/viewer.js

@@ -65,12 +65,13 @@ export class OrbitalViewer {
     /**
      * Replace the isosurface pair with one drawn from a sampled field.
      * @param field - The sampled wavefunction, in ångström.
+     * @param contour - The isovalue and reach measured on that field.
      * @param style - See {@link VolumeStyle}.
      * @returns How far the drawn surface reaches, in scene units, for the camera
      * to frame; `undefined` once the viewer has been disposed.
      */
-    showOrbital(field, style) {
-        return this.#run((plugin) => renderSampledVolume(plugin, field, style));
+    showOrbital(field, contour, style) {
+        return this.#run((plugin) => renderSampledVolume(plugin, field, contour, style));
     }
     /**
      * Remove the isosurface pair.

package/lib/orbital/ui/viewer.js.map

@@ -1 +1 @@
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package/lib/orbital/ui/volumeField.d.ts

@@ -1,9 +1,11 @@
 /**
  * Turning a field the caller sampled into the `Volume` molstar's isosurface
- * renderer wants, and measuring how far the surface inside it actually reaches.
+ * renderer wants.
  *
- * Both halves are arithmetic over the samples, which is why they are here
- * rather than in `renderVolume.ts` — that module is about representations.
+ * It is arithmetic over the samples, which is why it is here rather than in
+ * `renderVolume.ts` — that module is about representations. How far the
+ * surface inside the box reaches is measured in `core/isovalue.ts`, beside the
+ * isovalue it is measured against.
  */
 import type { Volume } from 'molstar/lib/mol-model/volume.js';
 import type { OrbitalGrid } from '../core/grid.ts';
@@ -15,24 +17,6 @@ import type { OrbitalGrid } from '../core/grid.ts';
  * impossible to fill the frame with.
  */
 export declare const DISPLAY_REACH = 12;
-/**
- * How far from the centre of the box the drawn surface actually reaches.
- *
- * Molstar sizes a volume representation's bounding sphere from the whole
- * sampled box, which is deliberately much larger than the isosurface inside it,
- * so a camera framing that sphere leaves the orbital a quarter of the frame
- * wide. Measuring the samples that are actually enclosed gives the camera the
- * real extent, and does it here because this is where the isovalue is known.
- * @param field - The sampled field.
- * @param isovalues - The two isovalues the surfaces were drawn at.
- * @param isovalues.negative - Isovalue the negative lobe was drawn at, if any.
- * @param isovalues.positive - Isovalue the positive lobe was drawn at, if any.
- * @returns The reach in ångström, or 0 when nothing was drawn.
- */
-export declare function surfaceReach(field: OrbitalGrid, isovalues: {
-    negative?: number | undefined;
-    positive?: number | undefined;
-}): number;
 /**
  * Wrap a sampled field in molstar's `Volume`.
  *

package/lib/orbital/ui/volumeField.d.ts.map

@@ -1 +1 @@
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package/lib/orbital/ui/volumeField.js

@@ -1,9 +1,11 @@
 /**
  * Turning a field the caller sampled into the `Volume` molstar's isosurface
- * renderer wants, and measuring how far the surface inside it actually reaches.
+ * renderer wants.
  *
- * Both halves are arithmetic over the samples, which is why they are here
- * rather than in `renderVolume.ts` — that module is about representations.
+ * It is arithmetic over the samples, which is why it is here rather than in
+ * `renderVolume.ts` — that module is about representations. How far the
+ * surface inside the box reaches is measured in `core/isovalue.ts`, beside the
+ * isovalue it is measured against.
  */
 import { Mat4, Tensor, Vec3 } from 'molstar/lib/mol-math/linear-algebra.js';
 import { CustomProperties } from 'molstar/lib/mol-model/custom-property.js';
@@ -17,48 +19,6 @@ const { Space: createTensorSpace, Data1: asTensorData } = Tensor;
  * impossible to fill the frame with.
  */
 export const DISPLAY_REACH = 12;
-/**
- * How far from the centre of the box the drawn surface actually reaches.
- *
- * Molstar sizes a volume representation's bounding sphere from the whole
- * sampled box, which is deliberately much larger than the isosurface inside it,
- * so a camera framing that sphere leaves the orbital a quarter of the frame
- * wide. Measuring the samples that are actually enclosed gives the camera the
- * real extent, and does it here because this is where the isovalue is known.
- * @param field - The sampled field.
- * @param isovalues - The two isovalues the surfaces were drawn at.
- * @param isovalues.negative - Isovalue the negative lobe was drawn at, if any.
- * @param isovalues.positive - Isovalue the positive lobe was drawn at, if any.
- * @returns The reach in ångström, or 0 when nothing was drawn.
- */
-export function surfaceReach(field, isovalues) {
-    const cutoff = Math.min(Math.abs(isovalues.positive ?? Infinity), Math.abs(isovalues.negative ?? Infinity));
-    if (!Number.isFinite(cutoff) || cutoff <= 0)
-        return 0;
-    const { data, dimensions, origin, spacing } = field;
-    const [countX, countY, countZ] = dimensions;
-    const centreX = origin.x + ((countX - 1) * spacing) / 2;
-    const centreY = origin.y + ((countY - 1) * spacing) / 2;
-    const centreZ = origin.z + ((countZ - 1) * spacing) / 2;
-    let furthest = 0;
-    let index = 0;
-    for (let indexX = 0; indexX < countX; indexX++) {
-        const dx = origin.x + indexX * spacing - centreX;
-        for (let indexY = 0; indexY < countY; indexY++) {
-            const dy = origin.y + indexY * spacing - centreY;
-            for (let indexZ = 0; indexZ < countZ; indexZ++) {
-                const value = data[index++];
-                if (value < cutoff && value > -cutoff)
-                    continue;
-                const dz = origin.z + indexZ * spacing - centreZ;
-                const squared = dx * dx + dy * dy + dz * dz;
-                if (squared > furthest)
-                    furthest = squared;
-            }
-        }
-    }
-    return Math.sqrt(furthest);
-}
 /**
  * Wrap a sampled field in molstar's `Volume`.
  *

package/lib/orbital/ui/volumeField.js.map

@@ -1 +1 @@
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package/lib/pedagogy/core/glossary.d.ts

@@ -0,0 +1,79 @@
+/**
+ * The `[[term]]` marker language, parsed without a DOM.
+ *
+ * Authored prose — tutorial steps, exercise descriptions, hints — links its
+ * jargon by wrapping it in `[[double brackets]]`. A marker may be written
+ * `[[term|displayed text]]` when the sentence needs a different wording than
+ * the glossary key. Parsing and resolution live here, in plain TypeScript, so
+ * both are unit-tested without rendering anything.
+ */
+/** One worked example inside a glossary entry. */
+export interface GlossaryExample {
+    /** The construct itself: a pattern, a SMILES, a LaTeX fragment, a layer. */
+    code: string;
+    /**
+     * What the construct is shown working on, for a term whose examples take an
+     * input. Left out when the example is about notation only.
+     * @default undefined
+     */
+    input?: string;
+    /**
+     * What this example demonstrates, in one line.
+     * @default undefined
+     */
+    note?: string;
+}
+/** One glossary term, shown wherever a `[[marker]]` names it. */
+export interface GlossaryEntry {
+    /** The term, spelled out as the heading of the tooltip. */
+    title: string;
+    /** One short paragraph — the whole definition. */
+    summary: string;
+    /** Worked examples, shown under the summary. */
+    examples: GlossaryExample[];
+}
+/**
+ * Every term a site defines, keyed by the lowercased text inside a `[[...]]`.
+ *
+ * A key that no marker names is simply never shown, and a marker naming no key
+ * renders as plain prose — so the two sides may be written in either order.
+ */
+export type Glossary = Record<string, GlossaryEntry>;
+/**
+ * One piece of parsed prose: either a run of text, or one marker.
+ *
+ * `start` is the offset of the piece in the source string, which makes it a
+ * stable and unique React key — an array index is neither.
+ */
+export type GlossarySegment = {
+    kind: 'text';
+    start: number;
+    text: string;
+} | {
+    kind: 'term';
+    start: number;
+    term: string;
+    text: string;
+};
+/**
+ * Split authored prose into prose runs and markers.
+ *
+ * A marker yields the lowercased lookup `term` and the `text` to display, which
+ * are the same thing unless the marker used the `term|text` form. The term is
+ * never checked against any glossary here: an unknown term still produces a
+ * `term` segment, and the renderer falls back to showing its text as plain
+ * prose — an author may link a term months before it is written, and the page
+ * must never show the brackets. Text that never closes its brackets (`[[foo`)
+ * is not a marker at all and comes back verbatim inside a `text` segment.
+ * @param text - Authored prose, with or without markers.
+ * @returns The segments, in order, with no empty run between adjacent markers.
+ */
+export declare function parseGlossaryMarkers(text: string): GlossarySegment[];
+/**
+ * Resolve a marker term against a glossary, case-insensitively.
+ * @param glossary - The terms the site defines.
+ * @param term - The text before the pipe of a `[[marker]]`, in any case.
+ * @returns The entry, or `undefined` when no such term has been written yet.
+ */
+export declare function lookupGlossaryTerm(glossary: Glossary, term: string): GlossaryEntry | undefined;
+//# sourceMappingURL=glossary.d.ts.map

package/lib/pedagogy/core/glossary.d.ts.map

@@ -0,0 +1 @@
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package/lib/pedagogy/core/glossary.js

@@ -0,0 +1,71 @@
+/**
+ * The `[[term]]` marker language, parsed without a DOM.
+ *
+ * Authored prose — tutorial steps, exercise descriptions, hints — links its
+ * jargon by wrapping it in `[[double brackets]]`. A marker may be written
+ * `[[term|displayed text]]` when the sentence needs a different wording than
+ * the glossary key. Parsing and resolution live here, in plain TypeScript, so
+ * both are unit-tested without rendering anything.
+ */
+/**
+ * Split authored prose into prose runs and markers.
+ *
+ * A marker yields the lowercased lookup `term` and the `text` to display, which
+ * are the same thing unless the marker used the `term|text` form. The term is
+ * never checked against any glossary here: an unknown term still produces a
+ * `term` segment, and the renderer falls back to showing its text as plain
+ * prose — an author may link a term months before it is written, and the page
+ * must never show the brackets. Text that never closes its brackets (`[[foo`)
+ * is not a marker at all and comes back verbatim inside a `text` segment.
+ * @param text - Authored prose, with or without markers.
+ * @returns The segments, in order, with no empty run between adjacent markers.
+ */
+export function parseGlossaryMarkers(text) {
+    const segments = [];
+    // A fresh regexp per call: a /g/ literal carries `lastIndex` between calls.
+    const marker = new RegExp(MARKER_SOURCE, 'g');
+    let cursor = 0;
+    let match = marker.exec(text);
+    while (match !== null) {
+        if (match.index > cursor) {
+            segments.push({
+                kind: 'text',
+                start: cursor,
+                text: text.slice(cursor, match.index),
+            });
+        }
+        segments.push(toTermSegment(match.groups?.term ?? '', match.index));
+        cursor = match.index + match[0].length;
+        match = marker.exec(text);
+    }
+    if (cursor < text.length) {
+        segments.push({ kind: 'text', start: cursor, text: text.slice(cursor) });
+    }
+    return segments;
+}
+/**
+ * Resolve a marker term against a glossary, case-insensitively.
+ * @param glossary - The terms the site defines.
+ * @param term - The text before the pipe of a `[[marker]]`, in any case.
+ * @returns The entry, or `undefined` when no such term has been written yet.
+ */
+export function lookupGlossaryTerm(glossary, term) {
+    const key = term.trim().toLowerCase();
+    // `[[constructor]]` and `[[tostring]]` are prose, not inherited members.
+    return Object.hasOwn(glossary, key) ? glossary[key] : undefined;
+}
+const MARKER_SOURCE = String.raw `\[\[(?<term>[^\]]+)\]\]`;
+function toTermSegment(inner, start) {
+    const pipe = inner.indexOf('|');
+    const rawTerm = pipe === -1 ? inner : inner.slice(0, pipe);
+    const rawText = pipe === -1 ? inner : inner.slice(pipe + 1);
+    const term = rawTerm.trim().toLowerCase();
+    const text = rawText.trim();
+    return {
+        kind: 'term',
+        start,
+        term,
+        text: text === '' ? rawTerm.trim() : text,
+    };
+}
+//# sourceMappingURL=glossary.js.map

package/lib/pedagogy/core/glossary.js.map

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package/lib/pedagogy/core/index.d.ts

@@ -0,0 +1,8 @@
+export type { Glossary, GlossaryEntry, GlossaryExample, GlossarySegment, } from './glossary.ts';
+export { parseGlossaryMarkers } from './glossary.ts';
+export type { ExerciseProgress, LocalStorageProgressStoreOptions, ProgressRecords, ProgressStore, ProgressSummary, } from './progress.ts';
+export { localStorageProgressStore, progressSummary } from './progress.ts';
+export type { BaseExercise, ExerciseLevel, ExerciseSet, ExerciseStatus, TutorialStep, } from './types.ts';
+export type { FinishValidationOptions, TestCaseResult, ValidationResult, } from './validation.ts';
+export { failedValidation, finishValidation } from './validation.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/pedagogy/core/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/pedagogy/core/index.js

@@ -0,0 +1,4 @@
+export { parseGlossaryMarkers } from "./glossary.js";
+export { localStorageProgressStore, progressSummary } from "./progress.js";
+export { failedValidation, finishValidation } from "./validation.js";
+//# sourceMappingURL=index.js.map

package/lib/pedagogy/core/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/pedagogy/core/index.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AAQrD,OAAO,EAAE,yBAAyB,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAa3E,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC"}

package/lib/pedagogy/core/jsonStorage.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Best-effort JSON access to `localStorage`.
+ *
+ * A page framed in a course may have no storage at all — third-party storage is
+ * partitioned in Chrome and blocked in Safari — and a full quota must never
+ * take the page down with it. So both calls swallow everything: an unreadable
+ * entry reads as nothing stored, and a refused write is simply lost.
+ */
+/**
+ * Read one entry back as JSON.
+ * @param key - The storage key.
+ * @returns What was parsed, or `undefined` when there is nothing readable.
+ */
+export declare function readJsonEntry(key: string): unknown;
+/**
+ * Write one entry as JSON.
+ * @param key - The storage key.
+ * @param value - What to store.
+ */
+export declare function writeJsonEntry(key: string, value: unknown): void;
+//# sourceMappingURL=jsonStorage.d.ts.map