react-cheminfo 0.63.1 → 0.64.0

package/lib/molecule3d/core/highlight.d.ts

@@ -0,0 +1,53 @@
+/**
+ * What a highlight on a 3D molecule is, without React and without molstar: a
+ * bonded path of atoms a site points at — the two atoms of a bond, the three of
+ * an angle, the four of a dihedral — for the model to emphasise.
+ *
+ * Atoms are named by position, as measurements name them, so a row of a table
+ * read off one conformer lands on the same atoms of every other conformer of
+ * the same molecule.
+ */
+import type { AtomReference } from './measurement.ts';
+/** One bonded path of atoms to emphasise on the model. */
+export interface Molecule3DHighlight {
+    /**
+     * The atoms in the order they are bonded: two for a bond, three for the two
+     * bonds of an angle, four for the three bonds of a dihedral. One atom
+     * emphasises that atom alone.
+     */
+    atoms: readonly AtomReference[];
+}
+/** Two consecutive atoms of a path: the bond a highlight emphasises. */
+export type HighlightedBond = readonly [AtomReference, AtomReference];
+/** Everything a list of highlights emphasises, each atom and bond once. */
+export interface HighlightedParts {
+    /** Every atom of every path, in the order the paths first name them. */
+    atoms: readonly AtomReference[];
+    /** Every pair of consecutive atoms, in the order the paths first name them. */
+    bonds: readonly HighlightedBond[];
+}
+/**
+ * The atoms and the bonds a list of highlights emphasises.
+ *
+ * A bond is a pair of consecutive atoms of one path, and nothing else: two
+ * atoms that are both highlighted, but by different paths or not next to each
+ * other in one, are not a bond of the highlight — so six C–H paths never
+ * emphasise the C–C bond between two of their carbons. An atom the structure
+ * lacks is left out, with the two pairs it stands in; the atoms on either side
+ * of it are not joined in its place.
+ * @param highlights - The paths, as a site passes them.
+ * @param hasAtom - Whether the structure on screen has an atom; asked only of
+ * references whose two numbers are whole and not negative.
+ * @default () => true
+ * @returns The atoms and the bonds, each once, in the order first named.
+ */
+export declare function highlightedParts(highlights: readonly Molecule3DHighlight[], hasAtom?: (atom: AtomReference) => boolean): HighlightedParts;
+/**
+ * Whether two lists of highlights name the same atoms, in the same paths and
+ * the same order — what decides that the model needs no repainting.
+ * @param first - One list.
+ * @param second - The other.
+ * @returns True when every path of one is the path of the other at its place.
+ */
+export declare function sameHighlights(first: readonly Molecule3DHighlight[], second: readonly Molecule3DHighlight[]): boolean;
+//# sourceMappingURL=highlight.d.ts.map

package/lib/molecule3d/core/highlight.d.ts.map

@@ -0,0 +1 @@
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package/lib/molecule3d/core/highlight.js

@@ -0,0 +1,102 @@
+/**
+ * What a highlight on a 3D molecule is, without React and without molstar: a
+ * bonded path of atoms a site points at — the two atoms of a bond, the three of
+ * an angle, the four of a dihedral — for the model to emphasise.
+ *
+ * Atoms are named by position, as measurements name them, so a row of a table
+ * read off one conformer lands on the same atoms of every other conformer of
+ * the same molecule.
+ */
+/**
+ * The atoms and the bonds a list of highlights emphasises.
+ *
+ * A bond is a pair of consecutive atoms of one path, and nothing else: two
+ * atoms that are both highlighted, but by different paths or not next to each
+ * other in one, are not a bond of the highlight — so six C–H paths never
+ * emphasise the C–C bond between two of their carbons. An atom the structure
+ * lacks is left out, with the two pairs it stands in; the atoms on either side
+ * of it are not joined in its place.
+ * @param highlights - The paths, as a site passes them.
+ * @param hasAtom - Whether the structure on screen has an atom; asked only of
+ * references whose two numbers are whole and not negative.
+ * @default () => true
+ * @returns The atoms and the bonds, each once, in the order first named.
+ */
+export function highlightedParts(highlights, hasAtom = isAnyAtom) {
+    const atoms = [];
+    const bonds = [];
+    const atomKeys = new Set();
+    const bondKeys = new Set();
+    for (const highlight of highlights) {
+        let previous;
+        for (const atom of highlight.atoms) {
+            const present = isAtomReference(atom) && hasAtom(atom);
+            if (present && !atomKeys.has(atomKey(atom))) {
+                atomKeys.add(atomKey(atom));
+                atoms.push({ unit: atom.unit, element: atom.element });
+            }
+            if (present && previous !== undefined) {
+                const key = bondKey(previous, atom);
+                if (key !== null && !bondKeys.has(key)) {
+                    bondKeys.add(key);
+                    bonds.push([
+                        { unit: previous.unit, element: previous.element },
+                        { unit: atom.unit, element: atom.element },
+                    ]);
+                }
+            }
+            previous = present ? atom : undefined;
+        }
+    }
+    return { atoms, bonds };
+}
+/**
+ * Whether two lists of highlights name the same atoms, in the same paths and
+ * the same order — what decides that the model needs no repainting.
+ * @param first - One list.
+ * @param second - The other.
+ * @returns True when every path of one is the path of the other at its place.
+ */
+export function sameHighlights(first, second) {
+    if (first === second)
+        return true;
+    if (first.length !== second.length)
+        return false;
+    for (let index = 0; index < first.length; index++) {
+        const one = first[index]?.atoms;
+        const other = second[index]?.atoms;
+        if (one === undefined || other === undefined)
+            return false;
+        if (one.length !== other.length)
+            return false;
+        for (let position = 0; position < one.length; position++) {
+            const atom = one[position];
+            const match = other[position];
+            if (atom?.unit !== match?.unit || atom?.element !== match?.element) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
+function isAnyAtom() {
+    return true;
+}
+function isAtomReference(atom) {
+    return (Number.isInteger(atom.unit) &&
+        atom.unit >= 0 &&
+        Number.isInteger(atom.element) &&
+        atom.element >= 0);
+}
+function atomKey(atom) {
+    return `${atom.unit}:${atom.element}`;
+}
+// One key for a pair whichever way round, and none for an atom with itself.
+function bondKey(first, second) {
+    const one = atomKey(first);
+    const other = atomKey(second);
+    if (one === other)
+        return null;
+    return one < other ? `${one}-${other}` : `${other}-${one}`;
+}
+//# sourceMappingURL=highlight.js.map

package/lib/molecule3d/core/highlight.js.map

@@ -0,0 +1 @@
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package/lib/molecule3d/core/index.d.ts

@@ -4,6 +4,8 @@ export type { ImageSize } from './exportImage.ts';
 export { dataUriBytes, rasterSvgMarkup } from './exportImage.ts';
 export type { Molecule3DGesture, Molecule3DGestureKey } from './gestures.ts';
 export { MOLECULE_3D_GESTURES } from './gestures.ts';
+export type { HighlightedBond, HighlightedParts, Molecule3DHighlight, } from './highlight.ts';
+export { highlightedParts, sameHighlights } from './highlight.ts';
 export type { AtomReference, Measurement, MeasurementKind, } from './measurement.ts';
 export { MEASUREMENT_ATOM_COUNTS, MEASUREMENT_KINDS, MEASUREMENT_LABELS, } from './measurement.ts';
 export type { Molecule3DFile, Molecule3DSettings, Molecule3DTools, RepresentationId, SurfaceColoringId, } from './settings.ts';

package/lib/molecule3d/core/index.d.ts.map

@@ -1 +1 @@
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package/lib/molecule3d/core/index.js

@@ -1,6 +1,7 @@
 export { DEFAULT_MOLECULE_3D_CAMERA, MOLECULE_3D_ZOOM_RANGE, formatMolecule3DCamera, molecule3DCameraParam, normalizeMolecule3DCamera, parseMolecule3DCamera, sameMolecule3DCamera, } from "./camera.js";
 export { dataUriBytes, rasterSvgMarkup } from "./exportImage.js";
 export { MOLECULE_3D_GESTURES } from "./gestures.js";
+export { highlightedParts, sameHighlights } from "./highlight.js";
 export { MEASUREMENT_ATOM_COUNTS, MEASUREMENT_KINDS, MEASUREMENT_LABELS, } from "./measurement.js";
 export { DEFAULT_MOLECULE_3D_SETTINGS, DEFAULT_MOLECULE_3D_TOOLS, MOLECULE_3D_RANGES, REPRESENTATIONS, REPRESENTATION_LABELS, SURFACE_CHARGE_COLORS, SURFACE_COLORINGS, SURFACE_COLORING_LABELS, isRepresentationId, isSurfaceColoringId, normalizeMolecule3DSettings, resetMolecule3DSettings, resolveMolecule3DTools, sameMolecule3DSettings, } from "./settings.js";
 //# sourceMappingURL=index.js.map

package/lib/molecule3d/core/index.js.map

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package/lib/molecule3d/ui/MoleculeCanvas3D.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"MoleculeCanvas3D.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/MoleculeCanvas3D.tsx"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAiB,YAAY,EAAE,MAAM,OAAO,CAAC;AAiBzD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AAOxE,yCAAyC;AACzC,MAAM,WAAW,qBAAsB,SAAQ,IAAI,CACjD,qBAAqB,EACrB,UAAU,GAAG,mBAAmB,CACjC;IACC,2EAA2E;IAC3E,eAAe,EAAE,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,KAAK,IAAI,CAAC;CACnD;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,qBAAqB,GAAG,YAAY,CAuK3E"}

package/lib/molecule3d/ui/MoleculeCanvas3D.js

@@ -7,6 +7,7 @@ import { Molecule3DOptions } from "./Molecule3DOptions.js";
 import { Molecule3DStage } from "./Molecule3DStage.js";
 import { Molecule3DToolbar } from "./Molecule3DToolbar.js";
 import { createMolecule3DViewer } from "./createViewer.js";
+import { highlightColorOf } from "./highlightColor.js";
 import { useControlledState } from "./useControlledState.js";
 import { useImageExport } from "./useImageExport.js";
 import { useMoleculeScene } from "./useMoleculeScene.js";
@@ -17,7 +18,7 @@ import { usePolarSurfaceArea } from "./usePolarSurfaceArea.js";
  * @returns The canvas with its toolbars.
  */
 export function MoleculeCanvas3D(props) {
-    const { molfile, frameNewMolecule = 'keep', tools: toolsProp, settings: settingsProp, defaultSettings, onSettingsChange, spinning: spinningProp, defaultSpinning = false, onSpinningChange, spinSpeed = DEFAULT_SPIN_SPEED, measurements: measurementsProp, onMeasurementsChange, fileName = 'molecule', background, minHeight = 320, onFailureChange, } = props;
+    const { molfile, frameNewMolecule = 'keep', tools: toolsProp, settings: settingsProp, defaultSettings, onSettingsChange, spinning: spinningProp, defaultSpinning = false, onSpinningChange, spinSpeed = DEFAULT_SPIN_SPEED, measurements: measurementsProp, onMeasurementsChange, highlights = NO_HIGHLIGHTS, fileName = 'molecule', background, minHeight = 320, onFailureChange, } = props;
     const tools = resolveMolecule3DTools(toolsProp);
     const [initialSettings] = useState(() => normalizeMolecule3DSettings(defaultSettings));
     const [settings, setSettings] = useControlledState(settingsProp, initialSettings, onSettingsChange);
@@ -71,6 +72,10 @@ export function MoleculeCanvas3D(props) {
     useEffect(() => {
         void viewerRef.current?.setMeasureKind(measureKind);
     }, [container, measureKind]);
+    // Kept out of the scene: a new highlight repaints the model, never redraws it.
+    useEffect(() => {
+        void viewerRef.current?.setHighlights(highlights, highlightColorOf(container));
+    }, [container, highlights]);
     const { resetView } = useMoleculeScene({
         container,
         viewerRef,
@@ -90,6 +95,7 @@ export function MoleculeCanvas3D(props) {
                         }, onResetView: resetView, options: _jsx(Molecule3DOptions, { settings: settings, onChange: setSettings, polarSurfaceArea: polarSurfaceArea, defaults: initialSettings }), exportPanel: _jsx(Molecule3DExport, { getSize: canvasSize, onExport: exportImage, onCopy: copyImage }) }) }))] })) }));
 }
 const NO_MEASUREMENTS = [];
+const NO_HIGHLIGHTS = [];
 const STAGE_STYLE = {
     position: 'relative',
     flex: '1 0 auto',

package/lib/molecule3d/ui/MoleculeCanvas3D.js.map

@@ -1 +1 @@
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package/lib/molecule3d/ui/highlightColor.d.ts

@@ -0,0 +1,18 @@
+/**
+ * The colour the 3D view emphasises in, read off the page it sits on.
+ *
+ * A WebGL colour cannot be a custom property, and the family's accent is the
+ * one colour a site owns, so it cannot be written into a shared library either:
+ * the view asks the browser what `--accent` resolved to where it is drawn, as
+ * the parallel coordinates do, and hands molstar the answer.
+ */
+/**
+ * What `--accent` resolved to on an element of the view.
+ * @param element - An element of the view, once it is on the page, or `null`
+ * before it is.
+ * @returns The accent as `#rrggbb`. A site that declares none emphasises in its
+ * text colour, and a page that declares neither, or no page yet, in the
+ * family's.
+ */
+export declare function highlightColorOf(element: Element | null): string;
+//# sourceMappingURL=highlightColor.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"highlightColor.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/highlightColor.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAKH;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,GAAG,MAAM,CAMhE"}

package/lib/molecule3d/ui/highlightColor.js

@@ -0,0 +1,31 @@
+/**
+ * The colour the 3D view emphasises in, read off the page it sits on.
+ *
+ * A WebGL colour cannot be a custom property, and the family's accent is the
+ * one colour a site owns, so it cannot be written into a shared library either:
+ * the view asks the browser what `--accent` resolved to where it is drawn, as
+ * the parallel coordinates do, and hands molstar the answer.
+ */
+import { normalizeColor } from "../../tokens/core/colors.js";
+import { FAMILY_TOKEN_VALUES } from "../../tokens/core/familyTokens.js";
+/**
+ * What `--accent` resolved to on an element of the view.
+ * @param element - An element of the view, once it is on the page, or `null`
+ * before it is.
+ * @returns The accent as `#rrggbb`. A site that declares none emphasises in its
+ * text colour, and a page that declares neither, or no page yet, in the
+ * family's.
+ */
+export function highlightColorOf(element) {
+    return (tokenColor(element, '--accent') ??
+        tokenColor(element, '--text') ??
+        FAMILY_TOKEN_VALUES['--text']);
+}
+function tokenColor(element, name) {
+    const resolve = globalThis.getComputedStyle;
+    if (element === null || typeof resolve !== 'function')
+        return undefined;
+    const color = normalizeColor(resolve(element).getPropertyValue(name));
+    return color === null ? undefined : `#${color}`;
+}
+//# sourceMappingURL=highlightColor.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"highlightColor.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/highlightColor.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,mBAAmB,EAAE,MAAM,mCAAmC,CAAC;AAExE;;;;;;;GAOG;AACH,MAAM,UAAU,gBAAgB,CAAC,OAAuB;IACtD,OAAO,CACL,UAAU,CAAC,OAAO,EAAE,UAAU,CAAC;QAC/B,UAAU,CAAC,OAAO,EAAE,QAAQ,CAAC;QAC7B,mBAAmB,CAAC,QAAQ,CAAC,CAC9B,CAAC;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,OAAuB,EAAE,IAAY;IACvD,MAAM,OAAO,GAAG,UAAU,CAAC,gBAAgB,CAAC;IAC5C,IAAI,OAAO,KAAK,IAAI,IAAI,OAAO,OAAO,KAAK,UAAU;QAAE,OAAO,SAAS,CAAC;IACxE,MAAM,KAAK,GAAG,cAAc,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC;IACtE,OAAO,KAAK,KAAK,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,KAAK,EAAE,CAAC;AAClD,CAAC"}

package/lib/molecule3d/ui/moleculeViewer3DProps.d.ts

@@ -1,6 +1,7 @@
 import type { ReactNode } from 'react';
 import type { ViewerCapability } from '../../orbital/ui/capability.ts';
 import type { Molecule3DCamera } from '../core/camera.ts';
+import type { Molecule3DHighlight } from '../core/highlight.ts';
 import type { Measurement } from '../core/measurement.ts';
 import type { Molecule3DFile, Molecule3DSettings, Molecule3DTools } from '../core/settings.ts';
 /**
@@ -74,6 +75,18 @@ export interface MoleculeViewer3DProps {
      * @default undefined
      */
     onMeasurementsChange?: (measurements: readonly Measurement[]) => void;
+    /**
+     * The parts of the model to emphasise in the site's accent colour, each a
+     * bonded path of atoms named as measurements name them: two atoms are that
+     * bond, three the two bonds of an angle, four the three bonds of a dihedral,
+     * and one atom is that atom alone. Only the bonds between consecutive atoms
+     * of one path are emphasised, never another bond between two highlighted
+     * atoms, and an atom the structure lacks is skipped. Changing them repaints
+     * the model and nothing else: the camera, the measurements and the hover are
+     * left as they are.
+     * @default [] — nothing is emphasised
+     */
+    highlights?: readonly Molecule3DHighlight[];
     /**
      * Where the camera stands when the first molecule is framed — what a shared
      * link carries. The camera belongs to whoever is dragging it afterwards, so

package/lib/molecule3d/ui/moleculeViewer3DProps.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"moleculeViewer3DProps.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/moleculeViewer3DProps.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAEvC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AACvE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EAChB,MAAM,qBAAqB,CAAC;AAE7B;;;;;;GAMG;AACH,MAAM,WAAW,qBAAqB;IACpC,qEAAqE;IACrE,OAAO,EAAE,cAAc,GAAG,IAAI,CAAC;IAC/B;;;;;;OAMG;IACH,gBAAgB,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IACpC;;;OAGG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC,eAAe,CAAC,CAAC;IACjC;;;OAGG;IACH,QAAQ,CAAC,EAAE,kBAAkB,CAAC;IAC9B;;;;OAIG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC9C;;;OAGG;IACH,gBAAgB,CAAC,EAAE,CAAC,QAAQ,EAAE,kBAAkB,KAAK,IAAI,CAAC;IAC1D;;;OAGG;IACH,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B;;;OAGG;IACH,gBAAgB,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,KAAK,IAAI,CAAC;IAC/C;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;;OAKG;IACH,YAAY,CAAC,EAAE,SAAS,WAAW,EAAE,CAAC;IACtC;;;OAGG;IACH,oBAAoB,CAAC,EAAE,CAAC,YAAY,EAAE,SAAS,WAAW,EAAE,KAAK,IAAI,CAAC;IACtE;;;;;;OAMG;IACH,aAAa,CAAC,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACxC;;;;OAIG;IACH,cAAc,CAAC,EAAE,CAAC,MAAM,EAAE,gBAAgB,KAAK,IAAI,CAAC;IACpD;;;;OAIG;IACH,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B;;;OAGG;IACH,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;OAGG;IACH,QAAQ,CAAC,EAAE,SAAS,CAAC;IACrB;;;OAGG;IACH,iBAAiB,CAAC,EAAE,CAAC,UAAU,EAAE,gBAAgB,KAAK,SAAS,CAAC;CACjE"}
+{"version":3,"file":"moleculeViewer3DProps.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/moleculeViewer3DProps.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAEvC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AACvE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AAC1D,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAC;AAChE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EAChB,MAAM,qBAAqB,CAAC;AAE7B;;;;;;GAMG;AACH,MAAM,WAAW,qBAAqB;IACpC,qEAAqE;IACrE,OAAO,EAAE,cAAc,GAAG,IAAI,CAAC;IAC/B;;;;;;OAMG;IACH,gBAAgB,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IACpC;;;OAGG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC,eAAe,CAAC,CAAC;IACjC;;;OAGG;IACH,QAAQ,CAAC,EAAE,kBAAkB,CAAC;IAC9B;;;;OAIG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAC;IAC9C;;;OAGG;IACH,gBAAgB,CAAC,EAAE,CAAC,QAAQ,EAAE,kBAAkB,KAAK,IAAI,CAAC;IAC1D;;;OAGG;IACH,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B;;;OAGG;IACH,gBAAgB,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,KAAK,IAAI,CAAC;IAC/C;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;;OAKG;IACH,YAAY,CAAC,EAAE,SAAS,WAAW,EAAE,CAAC;IACtC;;;OAGG;IACH,oBAAoB,CAAC,EAAE,CAAC,YAAY,EAAE,SAAS,WAAW,EAAE,KAAK,IAAI,CAAC;IACtE;;;;;;;;;;OAUG;IACH,UAAU,CAAC,EAAE,SAAS,mBAAmB,EAAE,CAAC;IAC5C;;;;;;OAMG;IACH,aAAa,CAAC,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACxC;;;;OAIG;IACH,cAAc,CAAC,EAAE,CAAC,MAAM,EAAE,gBAAgB,KAAK,IAAI,CAAC;IACpD;;;;OAIG;IACH,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B;;;OAGG;IACH,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB;;;OAGG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB;;;OAGG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;OAGG;IACH,QAAQ,CAAC,EAAE,SAAS,CAAC;IACrB;;;OAGG;IACH,iBAAiB,CAAC,EAAE,CAAC,UAAU,EAAE,gBAAgB,KAAK,SAAS,CAAC;CACjE"}

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

@@ -12,6 +12,8 @@ import type { Molecule3DFile } from '../core/settings.ts';
 import type { MoleculeStyle } from './viewerTypes.ts';
 /** State-tree ref of the structure every representation hangs off. */
 export declare const MOLECULE_STRUCTURE_REF = "molecule3d-structure";
+/** The drawn model, replaced in place whenever the style changes. */
+export declare const MODEL_REPRESENTATION_REF = "molecule3d-model";
 /**
  * Replace the displayed molecule. Everything already on screen goes first.
  * @param plugin - The molstar context.

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

@@ -1 +1 @@
-{"version":3,"file":"renderMolecule.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/renderMolecule.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAC;AAOvE,OAAO,KAAK,EAAE,cAAc,EAAoB,MAAM,qBAAqB,CAAC;AAE5E,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEtD,sEAAsE;AACtE,eAAO,MAAM,sBAAsB,yBAAyB,CAAC;AAuB7D;;;;;;;;;GASG;AACH,wBAAsB,cAAc,CAClC,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE,cAAc,EACvB,KAAK,GAAE,aAAkB,GACxB,OAAO,CAAC,IAAI,CAAC,CA0Cf;AAED;;;;GAIG;AACH,wBAAsB,aAAa,CAAC,MAAM,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAGxE;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,aAAa,GACpB,SAAS,GAAG,SAAS,CAIvB"}
+{"version":3,"file":"renderMolecule.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/renderMolecule.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAC;AAOvE,OAAO,KAAK,EAAE,cAAc,EAAoB,MAAM,qBAAqB,CAAC;AAE5E,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEtD,sEAAsE;AACtE,eAAO,MAAM,sBAAsB,yBAAyB,CAAC;AAK7D,qEAAqE;AACrE,eAAO,MAAM,wBAAwB,qBAAqB,CAAC;AAiB3D;;;;;;;;;GASG;AACH,wBAAsB,cAAc,CAClC,MAAM,EAAE,aAAa,EACrB,OAAO,EAAE,cAAc,EACvB,KAAK,GAAE,aAAkB,GACxB,OAAO,CAAC,IAAI,CAAC,CA0Cf;AAED;;;;GAIG;AACH,wBAAsB,aAAa,CAAC,MAAM,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAGxE;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,aAAa,GACpB,SAAS,GAAG,SAAS,CAIvB"}

package/lib/molecule3d/ui/renderMolecule.js

@@ -15,7 +15,7 @@ export const MOLECULE_STRUCTURE_REF = 'molecule3d-structure';
 /** Root of the molecule subtree: deleting it removes model and surface. */
 const MOLECULE_DATA_REF = 'molecule3d-data';
 /** The drawn model, replaced in place whenever the style changes. */
-const MODEL_REPRESENTATION_REF = 'molecule3d-model';
+export const MODEL_REPRESENTATION_REF = 'molecule3d-model';
 /**
  * molstar's ball-and-stick radius factor that a size factor of 1 stands for:
  * thin sticks and readable balls.

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

@@ -1 +1 @@
-{"version":3,"file":"renderMolecule.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/renderMolecule.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAE,mCAAmC,EAAE,MAAM,yEAAyE,CAAC;AAC9H,OAAO,EAAE,iBAAiB,EAAE,MAAM,yCAAyC,CAAC;AAC5E,OAAO,EAAE,kBAAkB,EAAE,MAAM,kDAAkD,CAAC;AACtF,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AAOtG,sEAAsE;AACtE,MAAM,CAAC,MAAM,sBAAsB,GAAG,sBAAsB,CAAC;AAE7D,2EAA2E;AAC3E,MAAM,iBAAiB,GAAG,iBAAiB,CAAC;AAE5C,qEAAqE;AACrE,MAAM,wBAAwB,GAAG,kBAAkB,CAAC;AAEpD;;;GAGG;AACH,MAAM,mBAAmB,GAAG,IAAI,CAAC;AAEjC,2EAA2E;AAC3E,MAAM,2BAA2B,GAAG,CAAC,GAAG,CAAC,CAAC;AAE1C,8EAA8E;AAC9E,MAAM,eAAe,GAAG,CAAC,CAAC;AAE1B,yEAAyE;AACzE,MAAM,WAAW,GAAG,GAAG,CAAC;AAExB;;;;;;;;;GASG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,MAAqB,EACrB,OAAuB,EACvB,QAAuB,EAAE;IAEzB,MAAM,EAAE,cAAc,GAAG,gBAAgB,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,KAAK,CAAC;IACpE,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;IAC5B,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAC7C,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,EACtB,EAAE,GAAG,EAAE,iBAAiB,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,EAAE,CACrD,CAAC;IACF,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,IAAI,EACJ,OAAO,CAAC,MAAM,CACf,CAAC;IACF,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC;IACtE,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,EAAE,eAAe,CAAC,KAAK,CAAC,SAAS,IAAI,CAAC,CAAC;IACnE,IAAI,SAAS,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;QAC5B,MAAM,IAAI,KAAK,CACb,oCAAoC,OAAO,CAAC,MAAM,4EAA4E,CAC/H,CAAC;IACJ,CAAC;IACD,MAAM,MAAM;SACT,KAAK,EAAE;SACP,EAAE,CAAC,KAAK,CAAC;SACT,KAAK,CAAC,kBAAkB,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,sBAAsB,EAAE,CAAC;SACrE,MAAM,EAAE,CAAC;IACZ,MAAM,SAAS,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;QAC5B,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAC;IACnE,CAAC;IACD,MAAM,MAAM;SACT,KAAK,EAAE;SACP,EAAE,CAAC,sBAAsB,CAAC;SAC1B,aAAa,CACZ,wBAAwB,EACxB,yBAAyB,EACzB,WAAW,CACT,MAAM,EACN,SAAS,EACT,cAAc,EACd,UAAU,GAAG,mBAAmB,CACjC,CACF;SACA,MAAM,EAAE,CAAC;AACd,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,MAAqB;IACvD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,iBAAiB,CAAC;QAAE,OAAO;IAC5D,MAAM,MAAM,CAAC,KAAK,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,MAAM,EAAE,CAAC;AAC1D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,iBAAiB,CAC/B,MAAqB;IAErB,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,sBAAsB,CAAC,EAAE,GAAG,CAAC;IACxE,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC,MAAM,CAAC;QAAE,OAAO,SAAS,CAAC;IACvE,OAAO,MAAM,CAAC,IAAI,CAAC;AACrB,CAAC;AAED;;;;;;;;;GASG;AACH,SAAS,WAAW,CAClB,MAAqB,EACrB,SAAoB,EACpB,cAAgC,EAChC,UAAkB;IAElB,MAAM,KAAK,GAAG,gBAAyB,CAAC;IACxC,MAAM,WAAW,GAAG;QAClB,WAAW,EAAE,EAAE,IAAI,EAAE,gBAAgB,EAAE,MAAM,EAAE,EAAE,EAAE;KAC3C,CAAC;IACX,IAAI,cAAc,KAAK,WAAW,EAAE,CAAC;QACnC,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;YAC5D,IAAI,EAAE,WAAW;YACjB,UAAU,EAAE,EAAE,UAAU,EAAE,UAAU,GAAG,eAAe,EAAE;YACxD,KAAK;YACL,WAAW;SACZ,CAAC,CAAC;IACL,CAAC;IACD,IAAI,cAAc,KAAK,OAAO,EAAE,CAAC;QAC/B,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;YAC5D,IAAI,EAAE,gBAAgB;YACtB,UAAU,EAAE;gBACV,UAAU,EAAE,UAAU,GAAG,WAAW;gBACpC,eAAe,EAAE,CAAC;gBAClB,aAAa,EAAE,KAAK;aACrB;YACD,KAAK;YACL,WAAW;YACX,IAAI,EAAE,SAAS;YACf,UAAU,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE;SACzB,CAAC,CAAC;IACL,CAAC;IACD,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;QAC5D,IAAI,EAAE,gBAAgB;QACtB,UAAU,EAAE;YACV,UAAU;YACV,eAAe,EAAE,2BAA2B;YAC5C,aAAa,EAAE,KAAK;SACrB;QACD,KAAK;QACL,WAAW;KACZ,CAAC,CAAC;AACL,CAAC"}
+{"version":3,"file":"renderMolecule.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/renderMolecule.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAE,mCAAmC,EAAE,MAAM,yEAAyE,CAAC;AAC9H,OAAO,EAAE,iBAAiB,EAAE,MAAM,yCAAyC,CAAC;AAC5E,OAAO,EAAE,kBAAkB,EAAE,MAAM,kDAAkD,CAAC;AACtF,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AAOtG,sEAAsE;AACtE,MAAM,CAAC,MAAM,sBAAsB,GAAG,sBAAsB,CAAC;AAE7D,2EAA2E;AAC3E,MAAM,iBAAiB,GAAG,iBAAiB,CAAC;AAE5C,qEAAqE;AACrE,MAAM,CAAC,MAAM,wBAAwB,GAAG,kBAAkB,CAAC;AAE3D;;;GAGG;AACH,MAAM,mBAAmB,GAAG,IAAI,CAAC;AAEjC,2EAA2E;AAC3E,MAAM,2BAA2B,GAAG,CAAC,GAAG,CAAC,CAAC;AAE1C,8EAA8E;AAC9E,MAAM,eAAe,GAAG,CAAC,CAAC;AAE1B,yEAAyE;AACzE,MAAM,WAAW,GAAG,GAAG,CAAC;AAExB;;;;;;;;;GASG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,MAAqB,EACrB,OAAuB,EACvB,QAAuB,EAAE;IAEzB,MAAM,EAAE,cAAc,GAAG,gBAAgB,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,KAAK,CAAC;IACpE,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;IAC5B,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAC7C,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,EACtB,EAAE,GAAG,EAAE,iBAAiB,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,EAAE,CACrD,CAAC;IACF,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,IAAI,EACJ,OAAO,CAAC,MAAM,CACf,CAAC;IACF,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC;IACtE,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,EAAE,eAAe,CAAC,KAAK,CAAC,SAAS,IAAI,CAAC,CAAC;IACnE,IAAI,SAAS,KAAK,CAAC,EAAE,CAAC;QACpB,MAAM,aAAa,CAAC,MAAM,CAAC,CAAC;QAC5B,MAAM,IAAI,KAAK,CACb,oCAAoC,OAAO,CAAC,MAAM,4EAA4E,CAC/H,CAAC;IACJ,CAAC;IACD,MAAM,MAAM;SACT,KAAK,EAAE;SACP,EAAE,CAAC,KAAK,CAAC;SACT,KAAK,CAAC,kBAAkB,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,sBAAsB,EAAE,CAAC;SACrE,MAAM,EAAE,CAAC;IACZ,MAAM,SAAS,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;QAC5B,MAAM,IAAI,KAAK,CAAC,+CAA+C,CAAC,CAAC;IACnE,CAAC;IACD,MAAM,MAAM;SACT,KAAK,EAAE;SACP,EAAE,CAAC,sBAAsB,CAAC;SAC1B,aAAa,CACZ,wBAAwB,EACxB,yBAAyB,EACzB,WAAW,CACT,MAAM,EACN,SAAS,EACT,cAAc,EACd,UAAU,GAAG,mBAAmB,CACjC,CACF;SACA,MAAM,EAAE,CAAC;AACd,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,aAAa,CAAC,MAAqB;IACvD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,iBAAiB,CAAC;QAAE,OAAO;IAC5D,MAAM,MAAM,CAAC,KAAK,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,MAAM,EAAE,CAAC;AAC1D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,iBAAiB,CAC/B,MAAqB;IAErB,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,sBAAsB,CAAC,EAAE,GAAG,CAAC;IACxE,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC,MAAM,CAAC;QAAE,OAAO,SAAS,CAAC;IACvE,OAAO,MAAM,CAAC,IAAI,CAAC;AACrB,CAAC;AAED;;;;;;;;;GASG;AACH,SAAS,WAAW,CAClB,MAAqB,EACrB,SAAoB,EACpB,cAAgC,EAChC,UAAkB;IAElB,MAAM,KAAK,GAAG,gBAAyB,CAAC;IACxC,MAAM,WAAW,GAAG;QAClB,WAAW,EAAE,EAAE,IAAI,EAAE,gBAAgB,EAAE,MAAM,EAAE,EAAE,EAAE;KAC3C,CAAC;IACX,IAAI,cAAc,KAAK,WAAW,EAAE,CAAC;QACnC,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;YAC5D,IAAI,EAAE,WAAW;YACjB,UAAU,EAAE,EAAE,UAAU,EAAE,UAAU,GAAG,eAAe,EAAE;YACxD,KAAK;YACL,WAAW;SACZ,CAAC,CAAC;IACL,CAAC;IACD,IAAI,cAAc,KAAK,OAAO,EAAE,CAAC;QAC/B,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;YAC5D,IAAI,EAAE,gBAAgB;YACtB,UAAU,EAAE;gBACV,UAAU,EAAE,UAAU,GAAG,WAAW;gBACpC,eAAe,EAAE,CAAC;gBAClB,aAAa,EAAE,KAAK;aACrB;YACD,KAAK;YACL,WAAW;YACX,IAAI,EAAE,SAAS;YACf,UAAU,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE;SACzB,CAAC,CAAC;IACL,CAAC;IACD,OAAO,mCAAmC,CAAC,MAAM,EAAE,SAAS,EAAE;QAC5D,IAAI,EAAE,gBAAgB;QACtB,UAAU,EAAE;YACV,UAAU;YACV,eAAe,EAAE,2BAA2B;YAC5C,aAAa,EAAE,KAAK;SACrB;QACD,KAAK;QACL,WAAW;KACZ,CAAC,CAAC;AACL,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 @@
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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 @@
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