react-cheminfo 0.63.1 → 0.64.1

package/lib/molecule3d/ui/sceneDrawer.js

@@ -0,0 +1,103 @@
+/**
+ * What one canvas shows, what it is asked to show next, and the least work
+ * between the two.
+ *
+ * The measurements are drawn over the model, not into it: a change of them
+ * alone replaces their own representations and leaves the model, its surface,
+ * its highlights and the camera as they are. Only another molecule, or another
+ * style for it, draws the scene again, and only another molecule frames the
+ * camera. Draws run one after another, so a measurement never lands on a model
+ * that is half built, and the last request asked is the one drawn.
+ */
+import { sameMeasurements } from "../core/measurement.js";
+import { sameMolecule3DSettings } from "../core/settings.js";
+import { drawScene } from "./drawScene.js";
+/** Keeps one viewer showing the last scene it was asked for. */
+export class SceneDrawer {
+    /** The viewer drawn on. */
+    viewer;
+    #takeLinkedCamera;
+    #asked = null;
+    // The model on screen, or `null` when the next request must draw it again.
+    #drawn = null;
+    // The measurements on screen, or `null` when the next request must draw them.
+    #measured = [];
+    // The molecule the camera was last framed on, so another one is told apart.
+    #framed = null;
+    #queue = Promise.resolve();
+    /**
+     * Start drawing on `viewer`, whose scene is empty.
+     * @param viewer - The viewer to draw on.
+     * @param takeLinkedCamera - Asked when a molecule is new: a camera to stand
+     * at instead of framing it, or `null`.
+     */
+    constructor(viewer, takeLinkedCamera) {
+        this.viewer = viewer;
+        this.#takeLinkedCamera = takeLinkedCamera;
+    }
+    /**
+     * Bring the canvas to `request`, once whatever was asked before is drawn.
+     * @param request - The scene to show; replaces any request still waiting.
+     * @returns Nothing; resolves once the canvas shows the last request asked,
+     * and rejects with what stopped it from being drawn.
+     */
+    draw(request) {
+        this.#asked = request;
+        const drawn = this.#queue.then(() => this.#catchUp());
+        this.#queue = drawn.catch(ignore);
+        return drawn;
+    }
+    async #catchUp() {
+        const request = this.#asked;
+        if (request === null)
+            return;
+        const drawn = this.#drawn;
+        if (drawn !== null &&
+            sameFile(drawn.molfile, request.molfile) &&
+            sameMolecule3DSettings(drawn.settings, request.settings)) {
+            await this.#measure(request);
+            return;
+        }
+        await this.#redraw(request);
+    }
+    // The model stays: only the measurements over it can have changed.
+    async #measure(request) {
+        const { molfile, measurements } = request;
+        const measured = this.#measured;
+        if (measured !== null && sameMeasurements(measured, measurements))
+            return;
+        // As for the model: a list that fails partway is drawn again next time.
+        this.#measured = null;
+        // An empty scene has nothing to measure; the list waits for a molecule.
+        if (molfile !== null)
+            await this.viewer.showMeasurements(measurements);
+        this.#measured = measurements;
+    }
+    async #redraw(request) {
+        const { molfile, settings, measurements, frameNewMolecule } = request;
+        const isNew = molfile !== null &&
+            (this.#framed === null || !sameFile(this.#framed, molfile));
+        this.#framed = molfile;
+        // A link's camera is spent on the first molecule framed; afterwards the
+        // camera is the reader's and a new molecule is framed as usual.
+        const linked = isNew ? this.#takeLinkedCamera() : null;
+        const frameCamera = isNew && linked === null ? frameNewMolecule : 'none';
+        // Kept only once drawn: a draw that fails is drawn again by the next
+        // request, whatever that one changes.
+        this.#drawn = null;
+        await drawScene(this.viewer, molfile, settings, measurements, frameCamera);
+        this.#drawn = { molfile, settings };
+        this.#measured = measurements;
+        if (linked !== null)
+            await this.viewer.setCamera(linked);
+    }
+}
+function sameFile(first, second) {
+    if (first === null || second === null)
+        return first === second;
+    return first.format === second.format && first.data === second.data;
+}
+function ignore() {
+    // A failure reached the caller of `draw`; the next draw still runs.
+}
+//# sourceMappingURL=sceneDrawer.js.map

package/lib/molecule3d/ui/sceneDrawer.js.map

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/useMoleculeScene.d.ts

@@ -5,7 +5,8 @@
  * The draw is coalesced into one animation frame, so dragging a slider costs
  * one rebuild rather than one per pixel, and the camera is framed only when the
  * molecule is new — a restyle that snapped the view back would undo the
- * reader's orientation.
+ * reader's orientation. What each draw rebuilds is the scene drawer's call: a
+ * change of the measurements alone redraws them and nothing else.
  */
 import type { RefObject } from 'react';
 import type { Measurement } from '../core/measurement.ts';

package/lib/molecule3d/ui/useMoleculeScene.d.ts.map

@@ -1 +1 @@
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package/lib/molecule3d/ui/useMoleculeScene.js

@@ -5,10 +5,11 @@
  * The draw is coalesced into one animation frame, so dragging a slider costs
  * one rebuild rather than one per pixel, and the camera is framed only when the
  * molecule is new — a restyle that snapped the view back would undo the
- * reader's orientation.
+ * reader's orientation. What each draw rebuilds is the scene drawer's call: a
+ * change of the measurements alone redraws them and nothing else.
  */
 import { useCallback, useEffect, useRef } from 'react';
-import { drawScene } from "./drawScene.js";
+import { SceneDrawer } from "./sceneDrawer.js";
 import { DEFAULT_CAMERA_SETTLE_DELAY, useSharedCamera, } from "./useSharedCamera.js";
 /**
  * Draw the scene the options describe, and keep it drawn.
@@ -17,7 +18,7 @@ import { DEFAULT_CAMERA_SETTLE_DELAY, useSharedCamera, } from "./useSharedCamera
  */
 export function useMoleculeScene(options) {
     const { container, viewerRef, molfile, frameNewMolecule, settings, measurements, spinning, onFailureChange, camera: cameraProps, } = options;
-    const framedRef = useRef(null);
+    const drawerRef = useRef(null);
     const reportFailure = useRef(onFailureChange);
     useEffect(() => {
         reportFailure.current = onFailureChange;
@@ -34,27 +35,17 @@ export function useMoleculeScene(options) {
         const viewer = viewerRef.current;
         if (container === null || viewer === null)
             return;
+        // A new viewer starts from an empty scene, so it gets a drawer of its own.
+        if (drawerRef.current?.viewer !== viewer) {
+            drawerRef.current = new SceneDrawer(viewer, camera.takeLinkedCamera);
+        }
+        const drawer = drawerRef.current;
         let cancelled = false;
         const frame = requestAnimationFrame(() => {
-            const framed = framedRef.current;
-            const isNew = molfile !== null &&
-                (framed?.molfile !== molfile || framed.viewer !== viewer);
-            framedRef.current = molfile === null ? null : { molfile, viewer };
-            // The link's camera is spent on the first molecule framed; afterwards the
-            // camera is the reader's and a new molecule is framed as usual.
-            const linked = isNew
-                ? camera.takeLinkedCamera()
-                : null;
-            const frameCamera = isNew && linked === null ? frameNewMolecule : 'none';
-            void drawScene(viewer, molfile, settings, measurements, frameCamera)
-                .then(() => {
-                if (cancelled)
-                    return;
-                if (linked !== null)
-                    void viewer.setCamera(linked);
-                reportFailure.current(null);
-            })
-                .catch((error) => {
+            drawer.draw({ molfile, settings, measurements, frameNewMolecule }).then(() => {
+                if (!cancelled)
+                    reportFailure.current(null);
+            }, (error) => {
                 if (cancelled)
                     return;
                 reportFailure.current(error instanceof Error ? error.message : String(error));

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+{"version":3,"file":"useMoleculeScene.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/useMoleculeScene.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,EAAE,WAAW,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAC;AAMvD,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAC/C,OAAO,EACL,2BAA2B,EAC3B,eAAe,GAChB,MAAM,sBAAsB,CAAC;AAkC9B;;;;GAIG;AACH,MAAM,UAAU,gBAAgB,CAAC,OAA6B;IAC5D,MAAM,EACJ,SAAS,EACT,SAAS,EACT,OAAO,EACP,gBAAgB,EAChB,QAAQ,EACR,YAAY,EACZ,QAAQ,EACR,eAAe,EACf,MAAM,EAAE,WAAW,GACpB,GAAG,OAAO,CAAC;IACZ,MAAM,SAAS,GAAG,MAAM,CAAqB,IAAI,CAAC,CAAC;IACnD,MAAM,aAAa,GAAG,MAAM,CAAC,eAAe,CAAC,CAAC;IAC9C,SAAS,CAAC,GAAG,EAAE;QACb,aAAa,CAAC,OAAO,GAAG,eAAe,CAAC;IAC1C,CAAC,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,eAAe,CAAC;QAC7B,SAAS;QACT,SAAS;QACT,QAAQ;QACR,aAAa,EAAE,WAAW,CAAC,aAAa,IAAI,IAAI;QAChD,cAAc,EAAE,WAAW,CAAC,cAAc;QAC1C,WAAW,EAAE,WAAW,CAAC,iBAAiB,IAAI,2BAA2B;KAC1E,CAAC,CAAC;IAEH,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC;QACjC,IAAI,SAAS,KAAK,IAAI,IAAI,MAAM,KAAK,IAAI;YAAE,OAAO;QAClD,2EAA2E;QAC3E,IAAI,SAAS,CAAC,OAAO,EAAE,MAAM,KAAK,MAAM,EAAE,CAAC;YACzC,SAAS,CAAC,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,gBAAgB,CAAC,CAAC;QACvE,CAAC;QACD,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC;QACjC,IAAI,SAAS,GAAG,KAAK,CAAC;QACtB,MAAM,KAAK,GAAG,qBAAqB,CAAC,GAAG,EAAE;YACvC,MAAM,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,gBAAgB,EAAE,CAAC,CAAC,IAAI,CACrE,GAAG,EAAE;gBACH,IAAI,CAAC,SAAS;oBAAE,aAAa,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;YAC9C,CAAC,EACD,CAAC,KAAc,EAAE,EAAE;gBACjB,IAAI,SAAS;oBAAE,OAAO;gBACtB,aAAa,CAAC,OAAO,CACnB,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CACvD,CAAC;YACJ,CAAC,CACF,CAAC;QACJ,CAAC,CAAC,CAAC;QACH,OAAO,GAAG,EAAE;YACV,SAAS,GAAG,IAAI,CAAC;YACjB,oBAAoB,CAAC,KAAK,CAAC,CAAC;QAC9B,CAAC,CAAC;IACJ,CAAC,EAAE;QACD,SAAS;QACT,SAAS;QACT,OAAO;QACP,gBAAgB;QAChB,QAAQ;QACR,YAAY;QACZ,MAAM;KACP,CAAC,CAAC;IAEH,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,EAAE;QACjC,MAAM,CAAC,QAAQ,EAAE,CAAC;QAClB,KAAK,SAAS,CAAC,OAAO,EAAE,WAAW,EAAE,CAAC;IACxC,CAAC,EAAE,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC,CAAC;IAExB,OAAO,EAAE,SAAS,EAAE,CAAC;AACvB,CAAC"}

package/lib/molecule3d/ui/useSharedCamera.d.ts

@@ -29,9 +29,7 @@ export interface SharedCameraOptions {
 }
 /**
  * What {@link useSharedCamera} answers. The same object on every render: the
- * draw effect keys on it, and a fresh one would tear the scene down and build
- * it again — which makes molstar frame the model afresh and loses the camera a
- * link had just restored.
+ * draw effect keys on it, and a fresh one would run it again for nothing.
  */
 export interface SharedCamera {
     /**

package/lib/molecule3d/ui/useSharedCamera.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"useSharedCamera.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/useSharedCamera.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAGvC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAG1D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAEpD,iFAAiF;AACjF,eAAO,MAAM,2BAA2B,MAAM,CAAC;AAE/C,6CAA6C;AAC7C,MAAM,WAAW,mBAAmB;IAClC,gEAAgE;IAChE,SAAS,EAAE,WAAW,GAAG,IAAI,CAAC;IAC9B,gCAAgC;IAChC,SAAS,EAAE,SAAS,CAAC,gBAAgB,GAAG,IAAI,CAAC,CAAC;IAC9C,iEAAiE;IACjE,aAAa,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACvC,2DAA2D;IAC3D,cAAc,CAAC,EAAE,CAAC,MAAM,EAAE,gBAAgB,KAAK,IAAI,CAAC;IACpD,8DAA8D;IAC9D,QAAQ,EAAE,OAAO,CAAC;IAClB,mEAAmE;IACnE,WAAW,EAAE,MAAM,CAAC;CACrB;AAED;;;GAGG;AACH,MAAM,WAAW,YAAY;IAC3B;;;;OAIG;IACH,gBAAgB,EAAE,MAAM,gBAAgB,GAAG,IAAI,CAAC;IAChD,mEAAmE;IACnE,QAAQ,EAAE,MAAM,IAAI,CAAC;CACtB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB,GAAG,YAAY,CA6D1E"}

package/lib/molecule3d/ui/useSharedCamera.js.map

@@ -1 +1 @@
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+{"version":3,"file":"useSharedCamera.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/useSharedCamera.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAGH,OAAO,EAAE,WAAW,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,OAAO,CAAC;AAGhE,OAAO,EAAE,sBAAsB,EAAE,MAAM,mBAAmB,CAAC;AAI3D,iFAAiF;AACjF,MAAM,CAAC,MAAM,2BAA2B,GAAG,GAAG,CAAC;AAiC/C;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAAC,OAA4B;IAC1D,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,OAAO,CAAC;IACtD,sCAAsC;IACtC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAChC,4EAA4E;IAC5E,4DAA4D;IAC5D,MAAM,WAAW,GAAG,MAAM,CAAgB,IAAI,CAAC,CAAC;IAChD,6EAA6E;IAC7E,MAAM,QAAQ,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;IAC/B,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;IAC3B,CAAC,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,EAAE;QAChC,QAAQ,CAAC,OAAO,GAAG,IAAI,CAAC;IAC1B,CAAC,EAAE,EAAE,CAAC,CAAC;IAEP,MAAM,gBAAgB,GAAG,WAAW,CAAC,GAAG,EAAE;QACxC,IAAI,SAAS,CAAC,OAAO;YAAE,OAAO,IAAI,CAAC;QACnC,SAAS,CAAC,OAAO,GAAG,IAAI,CAAC;QACzB,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,aAAa,CAAC;QAC5C,IAAI,MAAM,KAAK,IAAI;YAAE,WAAW,CAAC,OAAO,GAAG,sBAAsB,CAAC,MAAM,CAAC,CAAC;QAC1E,OAAO,MAAM,CAAC;IAChB,CAAC,EAAE,EAAE,CAAC,CAAC;IAEP,6EAA6E;IAC7E,yEAAyE;IACzE,4EAA4E;IAC5E,wDAAwD;IACxD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC;QACjC,IAAI,SAAS,KAAK,IAAI,IAAI,MAAM,KAAK,IAAI;YAAE,OAAO;QAClD,IAAI,KAAK,GAAyC,IAAI,CAAC;QACvD,SAAS,CAAC,gBAAgB,CAAC,aAAa,EAAE,QAAQ,CAAC,CAAC;QACpD,SAAS,CAAC,gBAAgB,CAAC,OAAO,EAAE,QAAQ,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC;QACjE,MAAM,YAAY,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,MAAM,EAAE,EAAE;YACjD,IAAI,MAAM,KAAK,IAAI;gBAAE,OAAO;YAC5B,IAAI,KAAK,KAAK,IAAI;gBAAE,YAAY,CAAC,KAAK,CAAC,CAAC;YACxC,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE;gBACtB,KAAK,GAAG,IAAI,CAAC;gBACb,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC;gBAC/B,IAAI,OAAO,CAAC,QAAQ,IAAI,CAAC,QAAQ,CAAC,OAAO;oBAAE,OAAO;gBAClD,MAAM,IAAI,GAAG,sBAAsB,CAAC,MAAM,CAAC,CAAC;gBAC5C,IAAI,IAAI,KAAK,WAAW,CAAC,OAAO;oBAAE,OAAO;gBACzC,WAAW,CAAC,OAAO,GAAG,IAAI,CAAC;gBAC3B,OAAO,CAAC,cAAc,EAAE,CAAC,MAAM,CAAC,CAAC;YACnC,CAAC,EAAE,WAAW,CAAC,CAAC;QAClB,CAAC,CAAC,CAAC;QACH,OAAO,GAAG,EAAE;YACV,IAAI,KAAK,KAAK,IAAI;gBAAE,YAAY,CAAC,KAAK,CAAC,CAAC;YACxC,SAAS,CAAC,mBAAmB,CAAC,aAAa,EAAE,QAAQ,CAAC,CAAC;YACvD,SAAS,CAAC,mBAAmB,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,CAAC;QACjB,CAAC,CAAC;IACJ,CAAC,EAAE,CAAC,SAAS,EAAE,SAAS,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC;IAElD,OAAO,OAAO,CACZ,GAAG,EAAE,CAAC,CAAC,EAAE,gBAAgB,EAAE,QAAQ,EAAE,CAAC,EACtC,CAAC,gBAAgB,EAAE,QAAQ,CAAC,CAC7B,CAAC;AACJ,CAAC"}

package/lib/molecule3d/ui/viewer.d.ts

@@ -9,6 +9,7 @@
  */
 import type { Molecule3DCamera } from '../core/camera.ts';
 import type { ImageSize } from '../core/exportImage.ts';
+import type { Molecule3DHighlight } from '../core/highlight.ts';
 import type { Measurement, MeasurementKind } from '../core/measurement.ts';
 import type { Molecule3DFile } from '../core/settings.ts';
 import type { Molecule3DViewerOptions, MoleculeStyle, SurfaceStyle } from './viewerTypes.ts';
@@ -56,6 +57,14 @@ export declare class Molecule3DViewer {
      * @returns Nothing; resolves once the labels are on screen.
      */
     showMeasurements(measurements: readonly Measurement[]): Promise<void>;
+    /**
+     * Emphasise exactly these paths of atoms on the model — this one and every
+     * one drawn after it — without redrawing the scene or moving the camera.
+     * @param highlights - Replaces what is emphasised; empty restores the model.
+     * @param color - What they are painted in, as `#rrggbb`.
+     * @returns Nothing; resolves once the model is repainted.
+     */
+    setHighlights(highlights: readonly Molecule3DHighlight[], color: string): Promise<void>;
     /**
      * Make clicks on atoms build a measurement, or give them back to the camera.
      * @param kind - The measurement to build, or `null`.

package/lib/molecule3d/ui/viewer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAcH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,KAAK,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AAC3E,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAS1D,OAAO,KAAK,EACV,uBAAuB,EACvB,aAAa,EACb,YAAY,EACb,MAAM,kBAAkB,CAAC;AAE1B;;;GAGG;AACH,qBAAa,gBAAgB;;IAI3B,0EAA0E;IAC1E,QAAQ,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;IAE9B;;;;OAIG;gBACS,SAAS,EAAE,WAAW,EAAE,OAAO,GAAE,uBAA4B;IAgBzE;;;;;;OAMG;IACH,YAAY,CAAC,OAAO,EAAE,cAAc,EAAE,KAAK,CAAC,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC;IAO3E;;;OAGG;IACH,YAAY,IAAI,OAAO,CAAC,IAAI,CAAC;IAO7B;;;;OAIG;IACH,WAAW,CAAC,KAAK,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC;IAIhD;;;OAGG;IACH,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC;IAI5B;;;;OAIG;IACH,gBAAgB,CAAC,YAAY,EAAE,SAAS,WAAW,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAMrE;;;;OAIG;IACH,cAAc,CAAC,IAAI,EAAE,eAAe,GAAG,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAM3D;;;;;;OAMG;IACH,YAAY,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC;IAI1D;;;;;OAKG;IACH,WAAW,CACT,oBAAoB,SAA0B,EAC9C,SAAS,UAAQ,GAChB,OAAO,CAAC,IAAI,CAAC;IAMhB;;;;;OAKG;IACH,SAAS,CAAC,MAAM,EAAE,gBAAgB,EAAE,oBAAoB,SAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAM5E;;;;;OAKG;IACH,WAAW,CAAC,QAAQ,EAAE,CAAC,MAAM,EAAE,gBAAgB,GAAG,IAAI,KAAK,IAAI,GAAG,MAAM,IAAI;IAI5E;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,KAAK,SAAqB,GAAG,OAAO,CAAC,IAAI,CAAC;IAMrE,kEAAkE;IAClE,YAAY,IAAI,IAAI;IAIpB,sEAAsE;IACtE,OAAO,IAAI,IAAI;CAUhB"}
+{"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAgBH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAC;AAChE,OAAO,KAAK,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AAC3E,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAU1D,OAAO,KAAK,EACV,uBAAuB,EACvB,aAAa,EACb,YAAY,EACb,MAAM,kBAAkB,CAAC;AAE1B;;;GAGG;AACH,qBAAa,gBAAgB;;IAK3B,0EAA0E;IAC1E,QAAQ,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;IAE9B;;;;OAIG;gBACS,SAAS,EAAE,WAAW,EAAE,OAAO,GAAE,uBAA4B;IAiBzE;;;;;;OAMG;IACH,YAAY,CAAC,OAAO,EAAE,cAAc,EAAE,KAAK,CAAC,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC;IAO3E;;;OAGG;IACH,YAAY,IAAI,OAAO,CAAC,IAAI,CAAC;IAO7B;;;;OAIG;IACH,WAAW,CAAC,KAAK,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC;IAIhD;;;OAGG;IACH,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC;IAI5B;;;;OAIG;IACH,gBAAgB,CAAC,YAAY,EAAE,SAAS,WAAW,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAMrE;;;;;;OAMG;IACH,aAAa,CACX,UAAU,EAAE,SAAS,mBAAmB,EAAE,EAC1C,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC,IAAI,CAAC;IAMhB;;;;OAIG;IACH,cAAc,CAAC,IAAI,EAAE,eAAe,GAAG,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAM3D;;;;;;OAMG;IACH,YAAY,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC;IAI1D;;;;;OAKG;IACH,WAAW,CACT,oBAAoB,SAA0B,EAC9C,SAAS,UAAQ,GAChB,OAAO,CAAC,IAAI,CAAC;IAMhB;;;;;OAKG;IACH,SAAS,CAAC,MAAM,EAAE,gBAAgB,EAAE,oBAAoB,SAAI,GAAG,OAAO,CAAC,IAAI,CAAC;IAM5E;;;;;OAKG;IACH,WAAW,CAAC,QAAQ,EAAE,CAAC,MAAM,EAAE,gBAAgB,GAAG,IAAI,KAAK,IAAI,GAAG,MAAM,IAAI;IAI5E;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,KAAK,SAAqB,GAAG,OAAO,CAAC,IAAI,CAAC;IAMrE,kEAAkE;IAClE,YAAY,IAAI,IAAI;IAIpB,sEAAsE;IACtE,OAAO,IAAI,IAAI;CAWhB"}

package/lib/molecule3d/ui/viewer.js

@@ -7,9 +7,10 @@
  * the viewer has been disposed. molstar's own UI is not mounted: every control
  * is the component's.
  */
-import { DEFAULT_CAMERA_DURATION, DEFAULT_SPIN_SPEED, MeasurementPicker, MolstarPlugin, captureScene, clearMeasurements, renderMeasurements, setSpin, } from "../../molstar/core/index.js";
+import { Color } from 'molstar/lib/mol-util/color/color.js';
+import { DEFAULT_CAMERA_DURATION, DEFAULT_SPIN_SPEED, HighlightPainter, MeasurementPicker, MolstarPlugin, captureScene, clearMeasurements, renderMeasurements, setSpin, } from "../../molstar/core/index.js";
 import { applyCamera, resetCamera, watchCamera } from "./camera.js";
-import { clearMolecule, moleculeStructure, renderMolecule, } from "./renderMolecule.js";
+import { MODEL_REPRESENTATION_REF, clearMolecule, moleculeStructure, renderMolecule, } from "./renderMolecule.js";
 import { clearSurface, renderSurface } from "./renderSurface.js";
 /**
  * One molstar canvas, and every operation the component performs on it. Every
@@ -18,6 +19,7 @@ import { clearSurface, renderSurface } from "./renderSurface.js";
 export class Molecule3DViewer {
     #plugin;
     #picker;
+    #painter;
     /** Resolves once the canvas exists; every method awaits it internally. */
     ready;
     /**
@@ -33,6 +35,7 @@ export class Molecule3DViewer {
         void this.#plugin
             .run((plugin) => {
             this.#picker = new MeasurementPicker(plugin, onMeasure, moleculeStructure);
+            this.#painter = new HighlightPainter(plugin, MODEL_REPRESENTATION_REF);
         })
             .catch(ignore);
     }
@@ -82,6 +85,18 @@ export class Molecule3DViewer {
     showMeasurements(measurements) {
         return this.#run((plugin) => renderMeasurements(plugin, measurements, moleculeStructure));
     }
+    /**
+     * Emphasise exactly these paths of atoms on the model — this one and every
+     * one drawn after it — without redrawing the scene or moving the camera.
+     * @param highlights - Replaces what is emphasised; empty restores the model.
+     * @param color - What they are painted in, as `#rrggbb`.
+     * @returns Nothing; resolves once the model is repainted.
+     */
+    setHighlights(highlights, color) {
+        return this.#run(() => {
+            this.#painter?.set(highlights, Color.fromHexStyle(color));
+        });
+    }
     /**
      * Make clicks on atoms build a measurement, or give them back to the camera.
      * @param kind - The measurement to build, or `null`.
@@ -151,6 +166,7 @@ export class Molecule3DViewer {
     /** Tear the viewer down and release its WebGL context. Idempotent. */
     dispose() {
         this.#picker?.dispose();
+        this.#painter?.dispose();
         this.#plugin.dispose();
     }
     #run(action) {

package/lib/molecule3d/ui/viewer.js.map

@@ -1 +1 @@
-{"version":3,"file":"viewer.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAIH,OAAO,EACL,uBAAuB,EACvB,kBAAkB,EAClB,iBAAiB,EACjB,aAAa,EACb,YAAY,EACZ,iBAAiB,EACjB,kBAAkB,EAClB,OAAO,GACR,MAAM,6BAA6B,CAAC;AAMrC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AACpE,OAAO,EACL,aAAa,EACb,iBAAiB,EACjB,cAAc,GACf,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAOjE;;;GAGG;AACH,MAAM,OAAO,gBAAgB;IAClB,OAAO,CAAgB;IAChC,OAAO,CAAgC;IAEvC,0EAA0E;IACjE,KAAK,CAAgB;IAE9B;;;;OAIG;IACH,YAAY,SAAsB,EAAE,UAAmC,EAAE;QACvE,MAAM,EAAE,UAAU,EAAE,SAAS,GAAG,MAAM,EAAE,GAAG,OAAO,CAAC;QACnD,IAAI,CAAC,OAAO,GAAG,IAAI,aAAa,CAAC,SAAS,EAAE,EAAE,UAAU,EAAE,CAAC,CAAC;QAC5D,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC;QAChC,2EAA2E;QAC3E,KAAK,IAAI,CAAC,OAAO;aACd,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;YACd,IAAI,CAAC,OAAO,GAAG,IAAI,iBAAiB,CAClC,MAAM,EACN,SAAS,EACT,iBAAiB,CAClB,CAAC;QACJ,CAAC,CAAC;aACD,KAAK,CAAC,MAAM,CAAC,CAAC;IACnB,CAAC;IAED;;;;;;OAMG;IACH,YAAY,CAAC,OAAuB,EAAE,KAAqB;QACzD,OAAO,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YAChC,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAChC,MAAM,cAAc,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC;QAC/C,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;OAGG;IACH,YAAY;QACV,OAAO,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YAChC,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAChC,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;QAC9B,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,KAAoB;QAC9B,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,aAAa,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC;IAC7D,CAAC;IAED;;;OAGG;IACH,WAAW;QACT,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC;IACrD,CAAC;IAED;;;;OAIG;IACH,gBAAgB,CAAC,YAAoC;QACnD,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAC1B,kBAAkB,CAAC,MAAM,EAAE,YAAY,EAAE,iBAAiB,CAAC,CAC5D,CAAC;IACJ,CAAC;IAED;;;;OAIG;IACH,cAAc,CAAC,IAA4B;QACzC,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACpB,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;QAC9B,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;;OAMG;IACH,YAAY,CAAC,IAAe;QAC1B,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,CAAC;IAC3D,CAAC;IAED;;;;;OAKG;IACH,WAAW,CACT,oBAAoB,GAAG,uBAAuB,EAC9C,SAAS,GAAG,KAAK;QAEjB,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,WAAW,CAAC,MAAM,EAAE,oBAAoB,EAAE,SAAS,CAAC,CAAC;QACvD,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACH,SAAS,CAAC,MAAwB,EAAE,oBAAoB,GAAG,CAAC;QAC1D,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,oBAAoB,CAAC,CAAC;QACpD,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACH,WAAW,CAAC,QAAmD;QAC7D,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC;IAC3E,CAAC;IAED;;;;;OAKG;IACH,OAAO,CAAC,QAAiB,EAAE,KAAK,GAAG,kBAAkB;QACnD,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,OAAO,CAAC,MAAM,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;QACnC,CAAC,CAAC,CAAC;IACL,CAAC;IAED,kEAAkE;IAClE,YAAY;QACV,IAAI,CAAC,OAAO,CAAC,YAAY,EAAE,CAAC;IAC9B,CAAC;IAED,sEAAsE;IACtE,OAAO;QACL,IAAI,CAAC,OAAO,EAAE,OAAO,EAAE,CAAC;QACxB,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;IACzB,CAAC;IAED,IAAI,CACF,MAA2D;QAE3D,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAClC,CAAC;CACF;AAED,SAAS,MAAM;IACb,iBAAiB;AACnB,CAAC"}
+{"version":3,"file":"viewer.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAGH,OAAO,EAAE,KAAK,EAAE,MAAM,qCAAqC,CAAC;AAE5D,OAAO,EACL,uBAAuB,EACvB,kBAAkB,EAClB,gBAAgB,EAChB,iBAAiB,EACjB,aAAa,EACb,YAAY,EACZ,iBAAiB,EACjB,kBAAkB,EAClB,OAAO,GACR,MAAM,6BAA6B,CAAC;AAOrC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AACpE,OAAO,EACL,wBAAwB,EACxB,aAAa,EACb,iBAAiB,EACjB,cAAc,GACf,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAOjE;;;GAGG;AACH,MAAM,OAAO,gBAAgB;IAClB,OAAO,CAAgB;IAChC,OAAO,CAAgC;IACvC,QAAQ,CAA+B;IAEvC,0EAA0E;IACjE,KAAK,CAAgB;IAE9B;;;;OAIG;IACH,YAAY,SAAsB,EAAE,UAAmC,EAAE;QACvE,MAAM,EAAE,UAAU,EAAE,SAAS,GAAG,MAAM,EAAE,GAAG,OAAO,CAAC;QACnD,IAAI,CAAC,OAAO,GAAG,IAAI,aAAa,CAAC,SAAS,EAAE,EAAE,UAAU,EAAE,CAAC,CAAC;QAC5D,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC;QAChC,2EAA2E;QAC3E,KAAK,IAAI,CAAC,OAAO;aACd,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;YACd,IAAI,CAAC,OAAO,GAAG,IAAI,iBAAiB,CAClC,MAAM,EACN,SAAS,EACT,iBAAiB,CAClB,CAAC;YACF,IAAI,CAAC,QAAQ,GAAG,IAAI,gBAAgB,CAAC,MAAM,EAAE,wBAAwB,CAAC,CAAC;QACzE,CAAC,CAAC;aACD,KAAK,CAAC,MAAM,CAAC,CAAC;IACnB,CAAC;IAED;;;;;;OAMG;IACH,YAAY,CAAC,OAAuB,EAAE,KAAqB;QACzD,OAAO,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YAChC,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAChC,MAAM,cAAc,CAAC,MAAM,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC;QAC/C,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;OAGG;IACH,YAAY;QACV,OAAO,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;YAChC,MAAM,iBAAiB,CAAC,MAAM,CAAC,CAAC;YAChC,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;QAC9B,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,KAAoB;QAC9B,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,aAAa,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC;IAC7D,CAAC;IAED;;;OAGG;IACH,WAAW;QACT,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC;IACrD,CAAC;IAED;;;;OAIG;IACH,gBAAgB,CAAC,YAAoC;QACnD,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAC1B,kBAAkB,CAAC,MAAM,EAAE,YAAY,EAAE,iBAAiB,CAAC,CAC5D,CAAC;IACJ,CAAC;IAED;;;;;;OAMG;IACH,aAAa,CACX,UAA0C,EAC1C,KAAa;QAEb,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACpB,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC;QAC5D,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;OAIG;IACH,cAAc,CAAC,IAA4B;QACzC,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACpB,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;QAC9B,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;;OAMG;IACH,YAAY,CAAC,IAAe;QAC1B,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,CAAC;IAC3D,CAAC;IAED;;;;;OAKG;IACH,WAAW,CACT,oBAAoB,GAAG,uBAAuB,EAC9C,SAAS,GAAG,KAAK;QAEjB,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,WAAW,CAAC,MAAM,EAAE,oBAAoB,EAAE,SAAS,CAAC,CAAC;QACvD,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACH,SAAS,CAAC,MAAwB,EAAE,oBAAoB,GAAG,CAAC;QAC1D,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,oBAAoB,CAAC,CAAC;QACpD,CAAC,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACH,WAAW,CAAC,QAAmD;QAC7D,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC;IAC3E,CAAC;IAED;;;;;OAKG;IACH,OAAO,CAAC,QAAiB,EAAE,KAAK,GAAG,kBAAkB;QACnD,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE;YAC1B,OAAO,CAAC,MAAM,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;QACnC,CAAC,CAAC,CAAC;IACL,CAAC;IAED,kEAAkE;IAClE,YAAY;QACV,IAAI,CAAC,OAAO,CAAC,YAAY,EAAE,CAAC;IAC9B,CAAC;IAED,sEAAsE;IACtE,OAAO;QACL,IAAI,CAAC,OAAO,EAAE,OAAO,EAAE,CAAC;QACxB,IAAI,CAAC,QAAQ,EAAE,OAAO,EAAE,CAAC;QACzB,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;IACzB,CAAC;IAED,IAAI,CACF,MAA2D;QAE3D,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAClC,CAAC;CACF;AAED,SAAS,MAAM;IACb,iBAAiB;AACnB,CAAC"}

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

@@ -0,0 +1,57 @@
+/**
+ * Atoms and bonds of the displayed molecule emphasised in one colour, for as
+ * long as a site keeps pointing at them.
+ *
+ * Neither of molstar's own markings fits: its hover highlight is erased by the
+ * next move of the pointer, and its selection belongs to the measuring tools.
+ * This is an overpaint of the model's own representation instead, so it
+ * follows the model in every style, survives the hover, and leaves the camera
+ * and every other drawing alone.
+ *
+ * molstar paints an atom and every half-bond leaving it from one element loci,
+ * which would tint the C–C bonds of a row that names only C–H ones. So the
+ * overpaint has three layers: the atoms, then those half-bonds cleared again,
+ * then exactly the bonds the paths name, as bond loci.
+ */
+import type { Structure } from 'molstar/lib/mol-model/structure.js';
+import { Bond, StructureElement } from 'molstar/lib/mol-model/structure.js';
+import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
+import { Overpaint } from 'molstar/lib/mol-theme/overpaint.js';
+import type { Color } from 'molstar/lib/mol-util/color/color.js';
+import type { Molecule3DHighlight } from '../../molecule3d/core/highlight.ts';
+/** The loci an overpaint layer of {@link highlightOverpaint} holds. */
+type HighlightLoci = StructureElement.Loci | Bond.Loci;
+/**
+ * The overpaint that emphasises `highlights` on a representation of
+ * `structure`: their atoms, and exactly the bonds between consecutive atoms of
+ * each path.
+ * @param structure - The structure the representation is drawn from.
+ * @param highlights - The paths; an atom the structure lacks is skipped.
+ * @param color - What they are painted in.
+ * @returns The overpaint, empty when no atom is left to paint.
+ */
+export declare function highlightOverpaint(structure: Structure, highlights: readonly Molecule3DHighlight[], color: Color): Overpaint<HighlightLoci>;
+/**
+ * Keeps one representation of the state tree painted with the highlights a
+ * site asks for: the one there now, and every one built under the same ref
+ * afterwards, so a restyled model or a new conformer comes up already painted.
+ */
+export declare class HighlightPainter {
+    #private;
+    /**
+     * Start following the representation at `representationRef`.
+     * @param plugin - The molstar context.
+     * @param representationRef - State-tree ref of the representation to paint.
+     */
+    constructor(plugin: PluginContext, representationRef: string);
+    /**
+     * Paint exactly these highlights, in place of the ones painted.
+     * @param highlights - The paths; an empty list restores the plain model.
+     * @param color - What they are painted in.
+     */
+    set(highlights: readonly Molecule3DHighlight[], color: Color): void;
+    /** Stop following the representation. */
+    dispose(): void;
+}
+export {};
+//# sourceMappingURL=highlights.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"highlights.d.ts","sourceRoot":"","sources":["../../../src/molstar/core/highlights.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAIH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,EACL,IAAI,EACJ,gBAAgB,EAEjB,MAAM,oCAAoC,CAAC;AAC5C,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAC;AAGvE,OAAO,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AAC/D,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,qCAAqC,CAAC;AAEjE,OAAO,KAAK,EAEV,mBAAmB,EACpB,MAAM,oCAAoC,CAAC;AAY5C,uEAAuE;AACvE,KAAK,aAAa,GAAG,gBAAgB,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC;AAEvD;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,CAChC,SAAS,EAAE,SAAS,EACpB,UAAU,EAAE,SAAS,mBAAmB,EAAE,EAC1C,KAAK,EAAE,KAAK,GACX,SAAS,CAAC,aAAa,CAAC,CAgB1B;AAED;;;;GAIG;AACH,qBAAa,gBAAgB;;IAO3B;;;;OAIG;gBACS,MAAM,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM;IAgB5D;;;;OAIG;IACH,GAAG,CAAC,UAAU,EAAE,SAAS,mBAAmB,EAAE,EAAE,KAAK,EAAE,KAAK,GAAG,IAAI;IASnE,yCAAyC;IACzC,OAAO,IAAI,IAAI;CAwBhB"}

package/lib/molstar/core/highlights.js

@@ -0,0 +1,178 @@
+/**
+ * Atoms and bonds of the displayed molecule emphasised in one colour, for as
+ * long as a site keeps pointing at them.
+ *
+ * Neither of molstar's own markings fits: its hover highlight is erased by the
+ * next move of the pointer, and its selection belongs to the measuring tools.
+ * This is an overpaint of the model's own representation instead, so it
+ * follows the model in every style, survives the hover, and leaves the camera
+ * and every other drawing alone.
+ *
+ * molstar paints an atom and every half-bond leaving it from one element loci,
+ * which would tint the C–C bonds of a row that names only C–H ones. So the
+ * overpaint has three layers: the atoms, then those half-bonds cleared again,
+ * then exactly the bonds the paths name, as bond loci.
+ */
+import { OrderedSet, SortedArray } from 'molstar/lib/mol-data/int.js';
+import { Bond, StructureElement, Unit, } from 'molstar/lib/mol-model/structure.js';
+import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects.js';
+import { Overpaint } from 'molstar/lib/mol-theme/overpaint.js';
+import { highlightedParts, sameHighlights, } from "../../molecule3d/core/highlight.js";
+// Lowercased: they are factories, not constructors.
+const elementLoci = StructureElement.Loci;
+const bondLoci = Bond.Loci;
+const bondLocation = Bond.Location;
+/**
+ * The overpaint that emphasises `highlights` on a representation of
+ * `structure`: their atoms, and exactly the bonds between consecutive atoms of
+ * each path.
+ * @param structure - The structure the representation is drawn from.
+ * @param highlights - The paths; an atom the structure lacks is skipped.
+ * @param color - What they are painted in.
+ * @returns The overpaint, empty when no atom is left to paint.
+ */
+export function highlightOverpaint(structure, highlights, color) {
+    const { atoms, bonds } = highlightedParts(highlights, (atom) => unitOf(structure, atom) !== undefined);
+    if (atoms.length === 0)
+        return { kind: 'bond-loci', layers: [] };
+    const layers = [
+        { loci: atomsLoci(structure, atoms), color, clear: false },
+        { loci: leavingBondsLoci(structure, atoms), color, clear: true },
+    ];
+    if (bonds.length > 0) {
+        layers.push({ loci: pathBondsLoci(structure, bonds), color, clear: false });
+    }
+    // Not `element-loci`, which molstar would remap layer by layer as atoms, and
+    // a bond loci read as atoms is a crash.
+    return { kind: 'bond-loci', layers };
+}
+/**
+ * Keeps one representation of the state tree painted with the highlights a
+ * site asks for: the one there now, and every one built under the same ref
+ * afterwards, so a restyled model or a new conformer comes up already painted.
+ */
+export class HighlightPainter {
+    #plugin;
+    #ref;
+    #unsubscribe;
+    #highlights = [];
+    #color;
+    /**
+     * Start following the representation at `representationRef`.
+     * @param plugin - The molstar context.
+     * @param representationRef - State-tree ref of the representation to paint.
+     */
+    constructor(plugin, representationRef) {
+        this.#plugin = plugin;
+        this.#ref = representationRef;
+        const repaint = (event) => {
+            if (event.ref === this.#ref)
+                this.#paint(event.obj);
+        };
+        const { created, updated } = plugin.state.data.events.object;
+        const subscriptions = [
+            created.subscribe(repaint),
+            updated.subscribe(repaint),
+        ];
+        this.#unsubscribe = () => {
+            for (const subscription of subscriptions)
+                subscription.unsubscribe();
+        };
+    }
+    /**
+     * Paint exactly these highlights, in place of the ones painted.
+     * @param highlights - The paths; an empty list restores the plain model.
+     * @param color - What they are painted in.
+     */
+    set(highlights, color) {
+        if (color === this.#color && sameHighlights(highlights, this.#highlights)) {
+            return;
+        }
+        this.#highlights = highlights;
+        this.#color = color;
+        this.#paint(this.#plugin.state.data.cells.get(this.#ref)?.obj);
+    }
+    /** Stop following the representation. */
+    dispose() {
+        this.#unsubscribe();
+    }
+    #paint(object) {
+        if (!PluginStateObject.Molecule.Structure.Representation3D.is(object)) {
+            return;
+        }
+        const { repr, sourceData } = object.data;
+        const color = this.#color;
+        const overpaint = color === undefined
+            ? Overpaint.Empty
+            : highlightOverpaint(sourceData, this.#highlights, color);
+        if (Overpaint.isEmpty(overpaint) &&
+            Overpaint.isEmpty(repr.state.overpaint)) {
+            return;
+        }
+        repr.setState({ overpaint });
+        // No commit: the scene keeps its bounds, so the camera is never reframed.
+        this.#plugin.canvas3d?.update(repr, true);
+    }
+}
+function unitOf(structure, atom) {
+    const unit = structure.units[atom.unit];
+    if (unit === undefined || atom.element >= unit.elements.length) {
+        return undefined;
+    }
+    return unit;
+}
+function atomsLoci(structure, atoms) {
+    const elements = [];
+    for (let index = 0; index < structure.units.length; index++) {
+        const unit = structure.units[index];
+        const indices = [];
+        for (const atom of atoms) {
+            if (atom.unit === index)
+                indices.push(atom.element);
+        }
+        if (unit === undefined || indices.length === 0)
+            continue;
+        const sorted = SortedArray.ofUnsortedArray(indices);
+        elements.push({ unit, indices: OrderedSet.ofSortedArray(sorted) });
+    }
+    return elementLoci(structure, elements);
+}
+// Every half-bond leaving the atoms, which an element loci paints as well.
+function leavingBondsLoci(structure, atoms) {
+    const locations = [];
+    const iterator = new Bond.ElementBondIterator();
+    for (const atom of atoms) {
+        const unit = unitOf(structure, atom);
+        if (unit === undefined || !Unit.isAtomic(unit))
+            continue;
+        const index = atom.element;
+        iterator.setElement(structure, unit, index);
+        while (iterator.hasNext) {
+            const { otherUnit, otherIndex } = iterator.move();
+            locations.push(bondLocation(structure, unit, index, structure, otherUnit, otherIndex));
+        }
+    }
+    return bondLoci(structure, locations);
+}
+// molstar draws a bond as two halves, one from each atom.
+function pathBondsLoci(structure, bonds) {
+    const locations = [];
+    for (const [first, second] of bonds) {
+        const forward = halfBond(structure, first, second);
+        const backward = halfBond(structure, second, first);
+        if (forward !== undefined && backward !== undefined) {
+            locations.push(forward, backward);
+        }
+    }
+    return bondLoci(structure, locations);
+}
+function halfBond(structure, from, to) {
+    const fromUnit = unitOf(structure, from);
+    const toUnit = unitOf(structure, to);
+    if (fromUnit === undefined || toUnit === undefined)
+        return undefined;
+    const fromIndex = from.element;
+    const toIndex = to.element;
+    return bondLocation(structure, fromUnit, fromIndex, structure, toUnit, toIndex);
+}
+//# sourceMappingURL=highlights.js.map

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

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

@@ -1,6 +1,6 @@
 /**
  * The molstar layer under the 3D views: the plugin lifecycle, the camera, the
- * hover labels, the measurements and the picture of a scene.
+ * hover labels, the measurements, the highlights 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
@@ -17,6 +17,7 @@
 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 { HighlightPainter, highlightOverpaint } from './highlights.ts';
 export { atomName, atomText, lociText, subscribeHover } from './hover.ts';
 export type { MolstarPluginOptions } from './plugin.ts';
 export { MolstarPlugin } from './plugin.ts';

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

@@ -1 +1 @@
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