react-cheminfo 0.39.1 → 0.40.0

package/lib/molstar/core/hover.d.ts

@@ -0,0 +1,49 @@
+/**
+ * What the pointer rests on, as a line of text.
+ *
+ * Every drawing our sites make carries a label already — `C1 sp³ σ to H5 (+)`,
+ * `C3 along [111]` — but molstar's own UI is not mounted, so nothing shows
+ * them. This turns the plugin's hover behaviour into that one string, which the
+ * canvas renders itself.
+ */
+import type { Loci } from 'molstar/lib/mol-model/loci.js';
+import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
+/**
+ * Report whatever the pointer rests on.
+ * @param plugin - The molstar context.
+ * @param listener - Called with the loci, or `null` when the pointer is over
+ * nothing. The pointer over the background reports an empty loci, whose label
+ * is the word "Nothing" — a sentence, not an absence — so it arrives as `null`.
+ * @returns The unsubscribe function.
+ */
+export declare function subscribeHover(plugin: PluginContext, listener: (loci: Loci | null) => void): () => void;
+/**
+ * The one line a loci is worth, in molstar's own words.
+ * @param loci - What the pointer is over.
+ * @returns The label, stripped of the markup molstar writes into it, or `null`
+ * when there is nothing to say.
+ */
+export declare function lociText(loci: Loci): string | null;
+/**
+ * The atoms a loci holds, in words a reader wants.
+ *
+ * molstar names one after the row it parsed — `xyz | Model 0 | Instance 1_555 |
+ * A | MOL 1 | O [idx 1]` — which is the address of a line in a file we wrote to
+ * hand it the atoms, and says nothing a student wants. The element and which
+ * atom of the scene it is do: the two hydrogens of water can then be told apart.
+ * @param loci - What the pointer rests on: an atom, or the two ends of a bond.
+ * @returns `O 1`, `Si 4 — O 8`, or `null` when the loci holds no atom.
+ */
+export declare function atomText(loci: Loci): string | null;
+/**
+ * What a site calls one atom of its scene.
+ *
+ * molstar upper-cases an element symbol on its way in, so the atom it hands
+ * back from an `Si` it was given is an `SI`, which is not how anybody writes
+ * silicon. The number is which atom of the scene it is, counting from one.
+ * @param element - Its element symbol, in any case.
+ * @param index - Its place in the file the viewer was handed, from zero.
+ * @returns `O 1`, `Si 4`.
+ */
+export declare function atomName(element: string, index: number): string;
+//# sourceMappingURL=hover.d.ts.map

package/lib/molstar/core/hover.d.ts.map

@@ -0,0 +1 @@
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package/lib/molstar/core/hover.js

@@ -0,0 +1,91 @@
+/**
+ * What the pointer rests on, as a line of text.
+ *
+ * Every drawing our sites make carries a label already — `C1 sp³ σ to H5 (+)`,
+ * `C3 along [111]` — but molstar's own UI is not mounted, so nothing shows
+ * them. This turns the plugin's hover behaviour into that one string, which the
+ * canvas renders itself.
+ */
+import { isEmptyLoci, isEveryLoci } from 'molstar/lib/mol-model/loci.js';
+import { Bond, StructureElement, StructureProperties, } from 'molstar/lib/mol-model/structure.js';
+import { lociLabel } from 'molstar/lib/mol-theme/label.js';
+/**
+ * Report whatever the pointer rests on.
+ * @param plugin - The molstar context.
+ * @param listener - Called with the loci, or `null` when the pointer is over
+ * nothing. The pointer over the background reports an empty loci, whose label
+ * is the word "Nothing" — a sentence, not an absence — so it arrives as `null`.
+ * @returns The unsubscribe function.
+ */
+export function subscribeHover(plugin, listener) {
+    const subscription = plugin.behaviors.interaction.hover.subscribe((event) => {
+        const { loci } = event.current;
+        listener(isEmptyLoci(loci) || isEveryLoci(loci) ? null : loci);
+    });
+    return () => {
+        subscription.unsubscribe();
+    };
+}
+/**
+ * The one line a loci is worth, in molstar's own words.
+ * @param loci - What the pointer is over.
+ * @returns The label, stripped of the markup molstar writes into it, or `null`
+ * when there is nothing to say.
+ */
+export function lociText(loci) {
+    if (isEmptyLoci(loci) || isEveryLoci(loci))
+        return null;
+    const label = stripMarkup(lociLabel(loci, { granularity: 'element' }));
+    return label === '' ? null : label;
+}
+/**
+ * The atoms a loci holds, in words a reader wants.
+ *
+ * molstar names one after the row it parsed — `xyz | Model 0 | Instance 1_555 |
+ * A | MOL 1 | O [idx 1]` — which is the address of a line in a file we wrote to
+ * hand it the atoms, and says nothing a student wants. The element and which
+ * atom of the scene it is do: the two hydrogens of water can then be told apart.
+ * @param loci - What the pointer rests on: an atom, or the two ends of a bond.
+ * @returns `O 1`, `Si 4 — O 8`, or `null` when the loci holds no atom.
+ */
+export function atomText(loci) {
+    const atoms = StructureElement.Loci.is(loci)
+        ? loci
+        : Bond.isLoci(loci)
+            ? Bond.toStructureElementLoci(loci)
+            : null;
+    if (atoms === null)
+        return null;
+    const names = [];
+    StructureElement.Loci.forEachLocation(atoms, (location) => {
+        names.push(atomName(String(StructureProperties.atom.type_symbol(location)), StructureProperties.atom.sourceIndex(location)));
+    });
+    return names.length === 0 ? null : names.join(' — ');
+}
+/**
+ * What a site calls one atom of its scene.
+ *
+ * molstar upper-cases an element symbol on its way in, so the atom it hands
+ * back from an `Si` it was given is an `SI`, which is not how anybody writes
+ * silicon. The number is which atom of the scene it is, counting from one.
+ * @param element - Its element symbol, in any case.
+ * @param index - Its place in the file the viewer was handed, from zero.
+ * @returns `O 1`, `Si 4`.
+ */
+export function atomName(element, index) {
+    const symbol = element.charAt(0).toUpperCase() + element.slice(1).toLowerCase();
+    return `${symbol} ${index + 1}`;
+}
+/**
+ * Molstar's label providers return HTML, and a readout is plain text.
+ * @param label
+ */
+function stripMarkup(label) {
+    return label
+        .replaceAll(/<[^>]*>/g, ' ')
+        .replaceAll('&nbsp;', ' ')
+        .replaceAll('&amp;', '&')
+        .replaceAll(/\s+/g, ' ')
+        .trim();
+}
+//# sourceMappingURL=hover.js.map

package/lib/molstar/core/hover.js.map

@@ -0,0 +1 @@
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package/lib/molstar/core/index.d.ts

@@ -0,0 +1,7 @@
+export type { CameraPose, CameraReference, PoseOptions } from './cameraPose.ts';
+export { cameraToPose, poseToCamera } from './cameraPose.ts';
+export { DEFAULT_CAMERA_DURATION, DEFAULT_SPIN_SPEED, FRAMING_MARGIN, MINIMUM_FRAMING_RADIUS, framedRadius, setSpin, } from './camera.ts';
+export { atomName, atomText, lociText, subscribeHover } from './hover.ts';
+export type { MolstarPluginOptions } from './plugin.ts';
+export { MolstarPlugin } from './plugin.ts';
+//# sourceMappingURL=index.d.ts.map

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

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

@@ -0,0 +1,5 @@
+export { cameraToPose, poseToCamera } from "./cameraPose.js";
+export { DEFAULT_CAMERA_DURATION, DEFAULT_SPIN_SPEED, FRAMING_MARGIN, MINIMUM_FRAMING_RADIUS, framedRadius, setSpin, } from "./camera.js";
+export { atomName, atomText, lociText, subscribeHover } from "./hover.js";
+export { MolstarPlugin } from "./plugin.js";
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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package/lib/molstar/core/plugin.d.ts

@@ -0,0 +1,80 @@
+/**
+ * Lifecycle of one headless molstar canvas: created now, disposed whenever,
+ * every call queued behind initialisation.
+ *
+ * The constructor is **synchronous** on purpose. React 19 runs an effect, its
+ * cleanup and the effect again on every mount in development, so an `await`ed
+ * constructor hands the cleanup nothing to dispose and leaks a WebGL context
+ * per mount — browsers drop the oldest after about sixteen, and the viewer
+ * silently goes blank. Returning the handle immediately means `dispose()` can
+ * always be called, even before initialisation has finished; the work is queued
+ * behind `ready`.
+ *
+ * molstar's own UI is never mounted: every control on our sites is ours.
+ */
+import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
+import type { PluginSpec } from 'molstar/lib/mol-plugin/spec.js';
+/** Settings fixed for the life of a plugin. */
+export interface MolstarPluginOptions {
+    /**
+     * Scene background, as `#rrggbb`. A WebGL clear colour, so it cannot be a CSS
+     * custom property.
+     * @default '#ffffff'
+     */
+    background?: string;
+    /**
+     * How long molstar animates a reframe it decided on itself; 0 jumps.
+     *
+     * Replacing a scene commits several times — the old drawing is deleted, the
+     * new one added — and molstar glides the camera on each, so the model appears
+     * to drift into place. Reframing is right; animating it between two unrelated
+     * scenes is not.
+     * @default molstar's own 250 ms
+     */
+    cameraResetDurationMilliseconds?: number;
+    /**
+     * The last word on the spec, applied over everything above: a site that needs
+     * a behaviour dropped, a marking colour or a renderer setting of its own
+     * passes it here rather than mounting its own view model.
+     */
+    spec?: (spec: PluginSpec) => PluginSpec;
+}
+/** One molstar canvas, and the queue everything drawn on it goes through. */
+export declare class MolstarPlugin {
+    #private;
+    /** Resolves once the canvas exists; every call awaits it internally. */
+    readonly ready: Promise<void>;
+    /**
+     * Mount a canvas in `container` and start initialising it.
+     * @param container - An element with `position: relative`; molstar inserts
+     * its own canvas into it.
+     * @param options - See {@link MolstarPluginOptions}.
+     */
+    constructor(container: HTMLElement, options?: MolstarPluginOptions);
+    /** Whether {@link dispose} has been called. */
+    get disposed(): boolean;
+    /**
+     * Wait for initialisation, then run `action` on the plugin.
+     * @param action - What to do with the molstar context.
+     * @returns What `action` returned, or `undefined` once the plugin has been
+     * disposed — before the call or while `action` was still running. An
+     * initialisation failure, and anything `action` throws while the plugin is
+     * alive, still reach the caller.
+     */
+    run<Result>(action: (plugin: PluginContext) => Result | Promise<Result>): Promise<Result | undefined>;
+    /**
+     * Start a subscription once the plugin exists.
+     * @param start - Subscribes, and returns its own unsubscribe function.
+     * @returns A function that stops the subscription, or stops it from ever
+     * starting; safe to call at any time.
+     */
+    subscribe(start: (plugin: PluginContext) => () => void): () => void;
+    /** Re-read the container's size. Call from a `ResizeObserver`. */
+    handleResize(): void;
+    /**
+     * Tear the canvas down and release its WebGL context. Idempotent, and safe to
+     * call before initialisation has finished.
+     */
+    dispose(): void;
+}
+//# sourceMappingURL=plugin.d.ts.map

package/lib/molstar/core/plugin.d.ts.map

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package/lib/molstar/core/plugin.js

@@ -0,0 +1,125 @@
+/**
+ * Lifecycle of one headless molstar canvas: created now, disposed whenever,
+ * every call queued behind initialisation.
+ *
+ * The constructor is **synchronous** on purpose. React 19 runs an effect, its
+ * cleanup and the effect again on every mount in development, so an `await`ed
+ * constructor hands the cleanup nothing to dispose and leaks a WebGL context
+ * per mount — browsers drop the oldest after about sixteen, and the viewer
+ * silently goes blank. Returning the handle immediately means `dispose()` can
+ * always be called, even before initialisation has finished; the work is queued
+ * behind `ready`.
+ *
+ * molstar's own UI is never mounted: every control on our sites is ours.
+ */
+import { PluginViewModel } from 'molstar/lib/extensions/plugin/view-model.js';
+// Lowercased on import: it is a factory, not a constructor.
+import { DefaultPluginSpec as defaultPluginSpec } from 'molstar/lib/mol-plugin/spec.js';
+import { Color } from 'molstar/lib/mol-util/color/color.js';
+/** One molstar canvas, and the queue everything drawn on it goes through. */
+export class MolstarPlugin {
+    #model;
+    #disposed = false;
+    /** Resolves once the canvas exists; every call awaits it internally. */
+    ready;
+    /**
+     * Mount a canvas in `container` and start initialising it.
+     * @param container - An element with `position: relative`; molstar inserts
+     * its own canvas into it.
+     * @param options - See {@link MolstarPluginOptions}.
+     */
+    constructor(container, options = {}) {
+        const { background = '#ffffff', // tokens-ok: a WebGL clear colour
+        cameraResetDurationMilliseconds, spec: refine, } = options;
+        const base = defaultPluginSpec();
+        const spec = {
+            ...base,
+            canvas3d: {
+                ...base.canvas3d,
+                renderer: { backgroundColor: Color.fromHexStyle(background) },
+                // A scene is read from its own shape, never from the world axes.
+                camera: { helper: { axes: { name: 'off', params: {} } } },
+                ...(cameraResetDurationMilliseconds === undefined
+                    ? {}
+                    : { cameraResetDurationMs: cameraResetDurationMilliseconds }),
+            },
+        };
+        this.#model = new PluginViewModel({
+            spec: refine === undefined ? spec : refine(spec),
+        });
+        this.#model.mount(container);
+        this.ready = this.#model.initialized;
+    }
+    /** Whether {@link dispose} has been called. */
+    get disposed() {
+        return this.#disposed;
+    }
+    /**
+     * Wait for initialisation, then run `action` on the plugin.
+     * @param action - What to do with the molstar context.
+     * @returns What `action` returned, or `undefined` once the plugin has been
+     * disposed — before the call or while `action` was still running. An
+     * initialisation failure, and anything `action` throws while the plugin is
+     * alive, still reach the caller.
+     */
+    async run(action) {
+        if (this.#disposed)
+            return undefined;
+        await this.ready;
+        if (this.#disposed)
+            return undefined;
+        try {
+            return await action(this.#model.plugin);
+        }
+        catch (error) {
+            if (this.#disposed)
+                return undefined;
+            throw error;
+        }
+    }
+    /**
+     * Start a subscription once the plugin exists.
+     * @param start - Subscribes, and returns its own unsubscribe function.
+     * @returns A function that stops the subscription, or stops it from ever
+     * starting; safe to call at any time.
+     */
+    subscribe(start) {
+        let stop = null;
+        let cancelled = false;
+        void this.run((plugin) => {
+            if (cancelled)
+                return;
+            stop = start(plugin);
+        });
+        return () => {
+            cancelled = true;
+            stop?.();
+            stop = null;
+        };
+    }
+    /** Re-read the container's size. Call from a `ResizeObserver`. */
+    handleResize() {
+        if (this.#disposed)
+            return;
+        this.#model.plugin.handleResize();
+    }
+    /**
+     * Tear the canvas down and release its WebGL context. Idempotent, and safe to
+     * call before initialisation has finished.
+     */
+    dispose() {
+        if (this.#disposed)
+            return;
+        this.#disposed = true;
+        // `mount` creates the canvas synchronously, so the context exists even when
+        // initialisation went on to fail; releasing it is what stops the browser
+        // dropping an older viewer's. A rejected `ready` must not escape here
+        // either — nobody is left to handle it.
+        void this.ready
+            .catch(() => undefined)
+            .then(() => {
+            this.#model.plugin.dispose();
+        });
+    }
+}
+//# sourceMappingURL=plugin.js.map

package/lib/molstar/core/plugin.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"plugin.js","sourceRoot":"","sources":["../../../src/molstar/core/plugin.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAE,eAAe,EAAE,MAAM,6CAA6C,CAAC;AAG9E,4DAA4D;AAC5D,OAAO,EAAE,iBAAiB,IAAI,iBAAiB,EAAE,MAAM,gCAAgC,CAAC;AACxF,OAAO,EAAE,KAAK,EAAE,MAAM,qCAAqC,CAAC;AA4B5D,6EAA6E;AAC7E,MAAM,OAAO,aAAa;IACf,MAAM,CAAkB;IACjC,SAAS,GAAG,KAAK,CAAC;IAElB,wEAAwE;IAC/D,KAAK,CAAgB;IAE9B;;;;;OAKG;IACH,YAAY,SAAsB,EAAE,UAAgC,EAAE;QACpE,MAAM,EACJ,UAAU,GAAG,SAAS,EAAE,kCAAkC;QAC1D,+BAA+B,EAC/B,IAAI,EAAE,MAAM,GACb,GAAG,OAAO,CAAC;QACZ,MAAM,IAAI,GAAG,iBAAiB,EAAE,CAAC;QACjC,MAAM,IAAI,GAAe;YACvB,GAAG,IAAI;YACP,QAAQ,EAAE;gBACR,GAAG,IAAI,CAAC,QAAQ;gBAChB,QAAQ,EAAE,EAAE,eAAe,EAAE,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,EAAE;gBAC7D,iEAAiE;gBACjE,MAAM,EAAE,EAAE,MAAM,EAAE,EAAE,IAAI,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE;gBACzD,GAAG,CAAC,+BAA+B,KAAK,SAAS;oBAC/C,CAAC,CAAC,EAAE;oBACJ,CAAC,CAAC,EAAE,qBAAqB,EAAE,+BAA+B,EAAE,CAAC;aAChE;SACF,CAAC;QACF,IAAI,CAAC,MAAM,GAAG,IAAI,eAAe,CAAC;YAChC,IAAI,EAAE,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC;SACjD,CAAC,CAAC;QACH,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;QAC7B,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC;IACvC,CAAC;IAED,+CAA+C;IAC/C,IAAI,QAAQ;QACV,OAAO,IAAI,CAAC,SAAS,CAAC;IACxB,CAAC;IAED;;;;;;;OAOG;IACH,KAAK,CAAC,GAAG,CACP,MAA2D;QAE3D,IAAI,IAAI,CAAC,SAAS;YAAE,OAAO,SAAS,CAAC;QACrC,MAAM,IAAI,CAAC,KAAK,CAAC;QACjB,IAAI,IAAI,CAAC,SAAS;YAAE,OAAO,SAAS,CAAC;QACrC,IAAI,CAAC;YACH,OAAO,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAC1C,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,IAAI,IAAI,CAAC,SAAS;gBAAE,OAAO,SAAS,CAAC;YACrC,MAAM,KAAK,CAAC;QACd,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,SAAS,CAAC,KAA4C;QACpD,IAAI,IAAI,GAAwB,IAAI,CAAC;QACrC,IAAI,SAAS,GAAG,KAAK,CAAC;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;YACvB,IAAI,SAAS;gBAAE,OAAO;YACtB,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC;QACvB,CAAC,CAAC,CAAC;QACH,OAAO,GAAG,EAAE;YACV,SAAS,GAAG,IAAI,CAAC;YACjB,IAAI,EAAE,EAAE,CAAC;YACT,IAAI,GAAG,IAAI,CAAC;QACd,CAAC,CAAC;IACJ,CAAC;IAED,kEAAkE;IAClE,YAAY;QACV,IAAI,IAAI,CAAC,SAAS;YAAE,OAAO;QAC3B,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC;IACpC,CAAC;IAED;;;OAGG;IACH,OAAO;QACL,IAAI,IAAI,CAAC,SAAS;YAAE,OAAO;QAC3B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC;QACtB,4EAA4E;QAC5E,yEAAyE;QACzE,sEAAsE;QACtE,wCAAwC;QACxC,KAAK,IAAI,CAAC,KAAK;aACZ,KAAK,CAAC,GAAG,EAAE,CAAC,SAAS,CAAC;aACtB,IAAI,CAAC,GAAG,EAAE;YACT,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;QAC/B,CAAC,CAAC,CAAC;IACP,CAAC;CACF"}

package/lib/molstar.d.ts

@@ -0,0 +1,18 @@
+/**
+ * The molstar layer under the 3D views: the plugin lifecycle, the camera, the
+ * hover labels, the measurements and the picture of a scene.
+ *
+ * Three of our sites mount a headless molstar canvas — the molecule viewer
+ * here, lcao's orbitals and symmetry's crystals — and each of them had its own
+ * copy of the lifecycle, the spec and the spin. This is that one copy; what
+ * stays in a site is the scene it draws.
+ *
+ * **Importing this pulls molstar in statically.** A site that only wants
+ * `<MoleculeViewer3D>` imports `react-cheminfo/molecule3d`, whose canvas is
+ * lazy.
+ */
+export * from './molstar/core/index.ts';
+export { captureScene } from './molecule3d/ui/captureScene.ts';
+export type { MoleculeStructureSource } from './molecule3d/ui/measurements.ts';
+export { atomReferenceOf, clearMeasurements, renderMeasurements, } from './molecule3d/ui/measurements.ts';
+//# sourceMappingURL=molstar.d.ts.map

package/lib/molstar.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"molstar.d.ts","sourceRoot":"","sources":["../src/molstar.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,cAAc,yBAAyB,CAAC;AACxC,OAAO,EAAE,YAAY,EAAE,MAAM,iCAAiC,CAAC;AAC/D,YAAY,EAAE,uBAAuB,EAAE,MAAM,iCAAiC,CAAC;AAC/E,OAAO,EACL,eAAe,EACf,iBAAiB,EACjB,kBAAkB,GACnB,MAAM,iCAAiC,CAAC"}

package/lib/molstar.js

@@ -0,0 +1,17 @@
+/**
+ * The molstar layer under the 3D views: the plugin lifecycle, the camera, the
+ * hover labels, the measurements and the picture of a scene.
+ *
+ * Three of our sites mount a headless molstar canvas — the molecule viewer
+ * here, lcao's orbitals and symmetry's crystals — and each of them had its own
+ * copy of the lifecycle, the spec and the spin. This is that one copy; what
+ * stays in a site is the scene it draws.
+ *
+ * **Importing this pulls molstar in statically.** A site that only wants
+ * `<MoleculeViewer3D>` imports `react-cheminfo/molecule3d`, whose canvas is
+ * lazy.
+ */
+export * from "./molstar/core/index.js";
+export { captureScene } from "./molecule3d/ui/captureScene.js";
+export { atomReferenceOf, clearMeasurements, renderMeasurements, } from "./molecule3d/ui/measurements.js";
+//# sourceMappingURL=molstar.js.map

package/lib/molstar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"molstar.js","sourceRoot":"","sources":["../src/molstar.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,cAAc,yBAAyB,CAAC;AACxC,OAAO,EAAE,YAAY,EAAE,MAAM,iCAAiC,CAAC;AAE/D,OAAO,EACL,eAAe,EACf,iBAAiB,EACjB,kBAAkB,GACnB,MAAM,iCAAiC,CAAC"}

package/lib/structure/ui/ConformerTable.d.ts

@@ -59,6 +59,14 @@ export interface ConformerTableProps {
      * @default undefined — every column keeps its own
      */
     columnLabels?: Partial<Record<ConformerColumn, string>>;
+    /**
+     * Whether the energies on screen are expected to be replaced — a force
+     * field's numbers while a better method is still working on the set. They
+     * are then drawn muted, so a reader can tell at a glance which of the two
+     * rankings they are looking at.
+     * @default false
+     */
+    provisional?: boolean;
 }
 /**
  * The conformers of a set, as a selectable table.

package/lib/structure/ui/ConformerTable.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ConformerTable.d.ts","sourceRoot":"","sources":["../../../src/structure/ui/ConformerTable.tsx"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAGH,OAAO,KAAK,EAAgC,YAAY,EAAE,MAAM,OAAO,CAAC;AAUxE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAC;AAE/D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAO7D,uCAAuC;AACvC,MAAM,WAAW,mBAAmB;IAClC,kDAAkD;IAClD,UAAU,EAAE,SAAS,YAAY,EAAE,CAAC;IACpC;;;OAGG;IACH,OAAO,CAAC,EAAE,SAAS,eAAe,EAAE,CAAC;IACrC;;;OAGG;IACH,OAAO,CAAC,EAAE,gBAAgB,CAAC;IAC3B;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,uDAAuD;IACvD,QAAQ,CAAC,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,IAAI,CAAC;IAChC;;;OAGG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;;;OAGG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;IACf;;;;OAIG;IACH,OAAO,CAAC,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,MAAM,CAAC;IACjC;;;OAGG;IACH,YAAY,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,eAAe,EAAE,MAAM,CAAC,CAAC,CAAC;CACzD;AAED;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,KAAK,EAAE,mBAAmB,GACzB,YAAY,GAAG,IAAI,CA4IrB"}
+{"version":3,"file":"ConformerTable.d.ts","sourceRoot":"","sources":["../../../src/structure/ui/ConformerTable.tsx"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAGH,OAAO,KAAK,EAAgC,YAAY,EAAE,MAAM,OAAO,CAAC;AAUxE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAC;AAE/D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAO7D,uCAAuC;AACvC,MAAM,WAAW,mBAAmB;IAClC,kDAAkD;IAClD,UAAU,EAAE,SAAS,YAAY,EAAE,CAAC;IACpC;;;OAGG;IACH,OAAO,CAAC,EAAE,SAAS,eAAe,EAAE,CAAC;IACrC;;;OAGG;IACH,OAAO,CAAC,EAAE,gBAAgB,CAAC;IAC3B;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,uDAAuD;IACvD,QAAQ,CAAC,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,IAAI,CAAC;IAChC;;;OAGG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;;;OAGG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC;IACf;;;;OAIG;IACH,OAAO,CAAC,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,MAAM,CAAC;IACjC;;;OAGG;IACH,YAAY,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,eAAe,EAAE,MAAM,CAAC,CAAC,CAAC;IACxD;;;;;;OAMG;IACH,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,KAAK,EAAE,mBAAmB,GACzB,YAAY,GAAG,IAAI,CA6IrB"}

package/lib/structure/ui/ConformerTable.js

@@ -32,7 +32,7 @@ import { CONFORMER_COLUMN_LABELS, NUMERIC_CONFORMER_COLUMNS, PICKER_COLUMNS, } f
  * @returns The table, or `null` when there is nothing to show.
  */
 export function ConformerTable(props) {
-    const { conformers, columns = PICKER_COLUMNS, ranking = 'force-field', selectedId = null, onSelect, temperature = ROOM_TEMPERATURE, label = 'Conformers, most stable first', rowName = String, columnLabels, } = props;
+    const { conformers, columns = PICKER_COLUMNS, ranking = 'force-field', selectedId = null, onSelect, temperature = ROOM_TEMPERATURE, label = 'Conformers, most stable first', rowName = String, columnLabels, provisional = false, } = props;
     const bodyRef = useRef(null);
     const shares = useMemo(() => {
         if (!columns.includes('population'))
@@ -93,7 +93,7 @@ export function ConformerTable(props) {
                             return copyableHere &&
                                 COPY_LABELS[column] !== undefined &&
                                 typeof content === 'string' &&
-                                content !== '—' ? (_jsx(ClickToCopy, { as: "td", style: cellStyle(column), value: content, label: COPY_LABELS[column], testId: CELL_TEST_IDS[column], children: content }, column)) : (_jsx("td", { style: cellStyle(column), "data-testid": CELL_TEST_IDS[column], children: content }, column));
+                                content !== '—' ? (_jsx(ClickToCopy, { as: "td", style: cellStyle(column, provisional), value: content, label: COPY_LABELS[column], testId: CELL_TEST_IDS[column], children: content }, column)) : (_jsx("td", { style: cellStyle(column, provisional), "data-testid": CELL_TEST_IDS[column], children: content }, column));
                         }) }, conformer.id));
                 }) })] }));
 }
@@ -200,14 +200,34 @@ const ENERGY_RESOLUTION = 0.005;
 function headerStyle(column) {
     return NUMERIC_CONFORMER_COLUMNS.has(column) ? numericStyle : undefined;
 }
-function cellStyle(column) {
-    return NUMERIC_CONFORMER_COLUMNS.has(column) ? numericStyle : undefined;
+/**
+ * A cell's own style: numbers are right-aligned and tabular, and every cell a
+ * better method will restate is muted while it works. The rank is not one of
+ * them — it names the row rather than measuring it, and it is what a reader
+ * follows as the order changes under them.
+ * @param column - The column the cell is in.
+ * @param provisional - Whether the energies are still expected to change.
+ * @returns The cell's inline style, or `undefined` when it needs none.
+ */
+function cellStyle(column, provisional) {
+    const numeric = NUMERIC_CONFORMER_COLUMNS.has(column);
+    if (!provisional || column === 'id') {
+        return numeric ? numericStyle : undefined;
+    }
+    return numeric ? provisionalNumericStyle : provisionalStyle;
 }
 const tableStyle = { width: '100%' };
 const numericStyle = {
     textAlign: 'right',
     fontVariantNumeric: 'tabular-nums',
 };
+const provisionalStyle = {
+    color: 'var(--text-muted)',
+};
+const provisionalNumericStyle = {
+    ...numericStyle,
+    ...provisionalStyle,
+};
 /**
  * The selected row is tinted with the site's own accent, so the table belongs
  * to whichever site draws it; a row is a pointer only where a click does

package/lib/structure/ui/ConformerTable.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-cheminfo",
-  "version": "0.39.1",
+  "version": "0.40.0",
   "license": "MIT",
   "description": "React components, hooks and framework-free helpers shared by the cheminfo sites: site chrome, citations, sharing, routing, pedagogy, charts, and the structure, orbital and 3D molecule viewers",
   "author": "Luc Patiny",
@@ -20,6 +20,7 @@
     "./core": "./lib/core.js",
     "./ir": "./lib/ir.js",
     "./molecule3d": "./lib/molecule3d.js",
+    "./molstar": "./lib/molstar.js",
     "./orbital": "./lib/orbital.js",
     "./slides": "./lib/slides.js",
     "./spectra": "./lib/spectra.js",

package/src/deploy/core/checkDeploy.ts

@@ -1,6 +1,11 @@
 import { readComposeFile } from './composeFile.ts';
 import { readEnvExample } from './envExample.ts';
 import { readPageCache } from './pageCache.ts';
+import {
+  DOCKER_IMAGE_WORKFLOW,
+  readInstallRetries,
+  readPublishedImage,
+} from './publishedImage.ts';
 import type { CheckDeployOptions, DeployFile, DeployProblem } from './types.ts';
 import { DEPLOY_COMPOSE_FILES } from './types.ts';
 
@@ -13,7 +18,9 @@ import { DEPLOY_COMPOSE_FILES } from './types.ts';
  * reports it healthy. So a repository has to hand it a selectable tag on every
  * image we build, an `IMAGE_NAME` that names the package our own workflow
  * publishes, a compose file that parses on a checkout with no `.env` yet, and a
- * health probe to read. It also has to hand the browser a page the browser will
+ * health probe to read. It also has to publish that image in the first place:
+ * with no `latest` to pull the script builds from source on the deploy host,
+ * and the install that follows must survive a blip in the registry. It also has to hand the browser a page the browser will
  * not keep, or the next deploy leaves returning visitors on a blank one. Each
  * of those is invisible until a deploy, which is the
  * worst moment to discover it — an `env_file` without `required: false` fails
@@ -72,7 +79,12 @@ export function findDeployProblems(
   }
 
   const dockerfile = byPath.get('Dockerfile');
-  if (dockerfile !== undefined) readPageCache(dockerfile, byPath, problems);
+  if (dockerfile !== undefined) {
+    readPageCache(dockerfile, byPath, problems);
+    readInstallRetries(dockerfile, problems);
+  }
+
+  readPublishedImage(byPath.get(DOCKER_IMAGE_WORKFLOW), problems);
 
   const gitignore = byPath.get('.gitignore');
   if (gitignore === undefined || !/^\s*\/?\.deploy\/?\s*$/m.test(gitignore)) {

package/src/deploy/core/index.ts

@@ -6,4 +6,9 @@ export type {
   DeployProblemKind,
 } from './types.ts';
 export { NGINX_CONFIG, PAGE_CACHE_CONFIG } from './pageCache.ts';
+export {
+  DOCKER_IMAGE_WORKFLOW,
+  readInstallRetries,
+  readPublishedImage,
+} from './publishedImage.ts';
 export { DEPLOY_COMPOSE_FILES } from './types.ts';