react-cheminfo 0.39.0 → 0.40.0

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

@@ -1,6 +1,10 @@
 import type { FigureFormat } from '../../download/core/downloadFigure.ts';
 import type { ImageSize } from '../core/exportImage.ts';
-import type { Molecule3DViewer } from './viewer.ts';
+/** The one thing an export asks of a viewer: a picture of its scene. */
+export interface SceneCapture {
+    /** Render the scene at that pixel size, as a `data:` URI. */
+    captureImage: (size: ImageSize) => Promise<string | undefined>;
+}
 /** What {@link exportMoleculeImage} writes. */
 export interface MoleculeImageRequest {
     format: FigureFormat;
@@ -17,5 +21,5 @@ export interface MoleculeImageRequest {
  * @param request - See {@link MoleculeImageRequest}.
  * @returns Nothing; resolves once the download has been started.
  */
-export declare function exportMoleculeImage(viewer: Molecule3DViewer, request: MoleculeImageRequest): Promise<void>;
+export declare function exportMoleculeImage(viewer: SceneCapture, request: MoleculeImageRequest): Promise<void>;
 //# sourceMappingURL=exportMoleculeImage.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"exportMoleculeImage.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/exportMoleculeImage.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,uCAAuC,CAAC;AAK1E,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAGxD,wEAAwE;AACxE,MAAM,WAAW,YAAY;IAC3B,6DAA6D;IAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,SAAS,KAAK,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC;CAChE;AAED,+CAA+C;AAC/C,MAAM,WAAW,oBAAoB;IACnC,MAAM,EAAE,YAAY,CAAC;IACrB,mEAAmE;IACnE,KAAK,EAAE,MAAM,CAAC;IACd,gDAAgD;IAChD,IAAI,EAAE,SAAS,CAAC;IAChB,uCAAuC;IACvC,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED;;;;;GAKG;AACH,wBAAsB,mBAAmB,CACvC,MAAM,EAAE,YAAY,EACpB,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,IAAI,CAAC,CAiBf"}

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

@@ -1 +1 @@
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+{"version":3,"file":"exportMoleculeImage.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/exportMoleculeImage.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,qCAAqC,CAAC;AAEnE,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,oCAAoC,CAAC;AAClE,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AACnE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yCAAyC,CAAC;AAE3E,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAC;AAmBvE;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,MAAoB,EACpB,OAA6B;IAE7B,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAC;IAClD,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;IACzC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;IAClD,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO;IAClC,MAAM,IAAI,GAAG,gBAAgB,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;IACpD,IAAI,MAAM,KAAK,KAAK,EAAE,CAAC;QACrB,YAAY,CACV,IAAI,IAAI,CAAC,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,EAC5D,GAAG,IAAI,MAAM,CACd,CAAC;QACF,OAAO;IACT,CAAC;IACD,YAAY,CACV,IAAI,IAAI,CAAC,CAAC,eAAe,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC,EAAE,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,EACvE,GAAG,IAAI,MAAM,CACd,CAAC;AACJ,CAAC"}

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

@@ -6,6 +6,15 @@
  * `React.lazy` boundary inside `MoleculeViewer3D`. Type-only re-exports are
  * erased and so are safe.
  */
+export { Molecule3DExport } from './Molecule3DExport.tsx';
+export type { Molecule3DExportProps } from './Molecule3DExport.tsx';
+export { Molecule3DHelp } from './Molecule3DHelp.tsx';
+export { Molecule3DToolbar } from './Molecule3DToolbar.tsx';
+export type { Molecule3DToolbarProps } from './Molecule3DToolbar.tsx';
+export type { MoleculeImageRequest, SceneCapture, } from './exportMoleculeImage.ts';
+export { exportMoleculeImage } from './exportMoleculeImage.ts';
+export type { ImageExport } from './useImageExport.ts';
+export { useImageExport } from './useImageExport.ts';
 export { MoleculeViewer3D } from './MoleculeViewer3D.tsx';
 export type { MoleculeViewer3DProps } from './moleculeViewer3DProps.ts';
 //# sourceMappingURL=index.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,YAAY,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,YAAY,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAC5D,YAAY,EAAE,sBAAsB,EAAE,MAAM,yBAAyB,CAAC;AACtE,YAAY,EACV,oBAAoB,EACpB,YAAY,GACb,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAC/D,YAAY,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AACvD,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,YAAY,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC"}

package/lib/molecule3d/ui/index.js

@@ -6,5 +6,10 @@
  * `React.lazy` boundary inside `MoleculeViewer3D`. Type-only re-exports are
  * erased and so are safe.
  */
+export { Molecule3DExport } from "./Molecule3DExport.js";
+export { Molecule3DHelp } from "./Molecule3DHelp.js";
+export { Molecule3DToolbar } from "./Molecule3DToolbar.js";
+export { exportMoleculeImage } from "./exportMoleculeImage.js";
+export { useImageExport } from "./useImageExport.js";
 export { MoleculeViewer3D } from "./MoleculeViewer3D.js";
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAwB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAwB,CAAC;AAE1D,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAsB,CAAC;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAyB,CAAC;AAM5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAE/D,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAwB,CAAC"}

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

@@ -9,16 +9,26 @@
  * instead of moving the camera, and once enough atoms are in it they become a
  * measurement.
  */
+import type { ElementIndex, Structure } from 'molstar/lib/mol-model/structure.js';
 import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
-import type { Measurement, MeasurementKind } from '../core/measurement.ts';
+import type { AtomReference, Measurement, MeasurementKind } from '../core/measurement.ts';
+/**
+ * Where the atoms a measurement addresses are found in the plugin's state.
+ *
+ * A site that mounts a molstar plugin of its own builds its scene under refs of
+ * its own, so it says here which structure the clicks are read against; the
+ * default is the one `<MoleculeViewer3D>` draws.
+ */
+export type MoleculeStructureSource = (plugin: PluginContext) => Structure | undefined;
 /**
  * Draw exactly `measurements` over the current molecule. An atom the structure
  * does not have skips its measurement rather than failing the scene.
  * @param plugin - The molstar context.
  * @param measurements - Everything to show, replacing what is shown.
+ * @param structureOf - See {@link MoleculeStructureSource}.
  * @returns Nothing; resolves once every label is on screen.
  */
-export declare function renderMeasurements(plugin: PluginContext, measurements: readonly Measurement[]): Promise<void>;
+export declare function renderMeasurements(plugin: PluginContext, measurements: readonly Measurement[], structureOf?: MoleculeStructureSource): Promise<void>;
 /**
  * Remove every measurement from the scene.
  * @param plugin - The molstar context.
@@ -43,4 +53,14 @@ export declare class MeasurementPicker {
     /** Stop listening to the plugin. */
     dispose(): void;
 }
+/**
+ * Address one atom of a structure the way a {@link Measurement} does.
+ *
+ * A site that builds its own scene numbers atoms by their position in the file
+ * it drew; this is how that number becomes a reference a measurement keeps.
+ * @param structure - The structure on screen.
+ * @param element - The atom's index in the model, i.e. its position in the file.
+ * @returns The reference, or `undefined` when the structure has no such atom.
+ */
+export declare function atomReferenceOf(structure: Structure, element: ElementIndex): AtomReference | undefined;
 //# sourceMappingURL=measurements.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"measurements.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/measurements.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAKH,OAAO,KAAK,EACV,YAAY,EACZ,SAAS,EACV,MAAM,oCAAoC,CAAC;AAE5C,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,mCAAmC,CAAC;AAIvE,OAAO,KAAK,EACV,aAAa,EACb,WAAW,EACX,eAAe,EAChB,MAAM,wBAAwB,CAAC;AAQhC;;;;;;GAMG;AACH,MAAM,MAAM,uBAAuB,GAAG,CACpC,MAAM,EAAE,aAAa,KAClB,SAAS,GAAG,SAAS,CAAC;AAE3B;;;;;;;GAOG;AACH,wBAAsB,kBAAkB,CACtC,MAAM,EAAE,aAAa,EACrB,YAAY,EAAE,SAAS,WAAW,EAAE,EACpC,WAAW,GAAE,uBAA2C,GACvD,OAAO,CAAC,IAAI,CAAC,CAiBf;AAED;;;;GAIG;AACH,wBAAsB,iBAAiB,CAAC,MAAM,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC,CAQ5E;AAED,2EAA2E;AAC3E,qBAAa,iBAAiB;;IAM5B;;;;OAIG;gBAED,MAAM,EAAE,aAAa,EACrB,SAAS,EAAE,CAAC,WAAW,EAAE,WAAW,KAAK,IAAI;IAkB/C;;;;OAIG;IACH,OAAO,CAAC,IAAI,EAAE,eAAe,GAAG,IAAI,GAAG,IAAI;IAO3C,oCAAoC;IACpC,OAAO,IAAI,IAAI;CAqBhB;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAC7B,SAAS,EAAE,SAAS,EACpB,OAAO,EAAE,YAAY,GACpB,aAAa,GAAG,SAAS,CAS3B"}

package/lib/molecule3d/ui/measurements.js

@@ -9,7 +9,7 @@
  * instead of moving the camera, and once enough atoms are in it they become a
  * measurement.
  */
-import { OrderedSet } from 'molstar/lib/mol-data/int.js';
+import { OrderedSet, SortedArray } from 'molstar/lib/mol-data/int.js';
 import { StructureElement } from 'molstar/lib/mol-model/structure.js';
 import { MeasurementGroupTag } from 'molstar/lib/mol-plugin-state/manager/structure/measurement.js';
 import { StateSelection, StateTransform } from 'molstar/lib/mol-state/index.js';
@@ -22,11 +22,12 @@ const elementLoci = StructureElement.Loci;
  * does not have skips its measurement rather than failing the scene.
  * @param plugin - The molstar context.
  * @param measurements - Everything to show, replacing what is shown.
+ * @param structureOf - See {@link MoleculeStructureSource}.
  * @returns Nothing; resolves once every label is on screen.
  */
-export async function renderMeasurements(plugin, measurements) {
+export async function renderMeasurements(plugin, measurements, structureOf = moleculeStructure) {
     await clearMeasurements(plugin);
-    const structure = moleculeStructure(plugin);
+    const structure = structureOf(plugin);
     if (structure === undefined)
         return;
     const manager = plugin.managers.structure.measurement;
@@ -117,6 +118,27 @@ export class MeasurementPicker {
         this.#onMeasure({ kind, atoms: atoms.toReversed() });
     }
 }
+/**
+ * Address one atom of a structure the way a {@link Measurement} does.
+ *
+ * A site that builds its own scene numbers atoms by their position in the file
+ * it drew; this is how that number becomes a reference a measurement keeps.
+ * @param structure - The structure on screen.
+ * @param element - The atom's index in the model, i.e. its position in the file.
+ * @returns The reference, or `undefined` when the structure has no such atom.
+ */
+export function atomReferenceOf(structure, element) {
+    const units = structure.units;
+    for (let unit = 0; unit < units.length; unit++) {
+        const elements = units[unit]?.elements;
+        if (elements === undefined)
+            continue;
+        const index = SortedArray.indexOf(elements, element);
+        if (index !== -1)
+            return { unit, element: index };
+    }
+    return undefined;
+}
 function atomReference(structure, loci) {
     if (!StructureElement.Loci.is(loci))
         return undefined;

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

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

@@ -1,7 +1,7 @@
 import type { RefObject } from 'react';
 import type { FigureFormat } from '../../download/core/downloadFigure.ts';
 import type { FigurePixels } from '../../download/core/figureScale.ts';
-import type { Molecule3DViewer } from './viewer.ts';
+import type { SceneCapture } from './exportMoleculeImage.ts';
 /** What {@link useImageExport} hands the export panel. */
 export interface ImageExport {
     /** Size of the canvas on screen, or `null` before it is laid out. */
@@ -16,5 +16,5 @@ export interface ImageExport {
  * @param fileName - File name without its extension.
  * @returns See {@link ImageExport}.
  */
-export declare function useImageExport(container: HTMLDivElement | null, viewerRef: RefObject<Molecule3DViewer | null>, fileName: string): ImageExport;
+export declare function useImageExport(container: HTMLDivElement | null, viewerRef: RefObject<SceneCapture | null>, fileName: string): ImageExport;
 //# sourceMappingURL=useImageExport.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"useImageExport.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/useImageExport.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC;AAGvC,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,uCAAuC,CAAC;AAC1E,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,oCAAoC,CAAC;AAEvE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AAG7D,0DAA0D;AAC1D,MAAM,WAAW,WAAW;IAC1B,qEAAqE;IACrE,UAAU,EAAE,MAAM,YAAY,GAAG,IAAI,CAAC;IACtC,+DAA+D;IAC/D,WAAW,EAAE,CAAC,MAAM,EAAE,YAAY,EAAE,KAAK,EAAE,MAAM,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;CACrE;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAC5B,SAAS,EAAE,cAAc,GAAG,IAAI,EAChC,SAAS,EAAE,SAAS,CAAC,YAAY,GAAG,IAAI,CAAC,EACzC,QAAQ,EAAE,MAAM,GACf,WAAW,CAqBb"}

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

@@ -1 +1 @@
-{"version":3,"file":"useImageExport.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/useImageExport.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,OAAO,CAAC;AAKpC,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAW/D;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAC5B,SAAgC,EAChC,SAA6C,EAC7C,QAAgB;IAEhB,MAAM,UAAU,GAAG,WAAW,CAAC,GAAwB,EAAE;QACvD,IAAI,SAAS,KAAK,IAAI;YAAE,OAAO,IAAI,CAAC;QACpC,MAAM,GAAG,GAAG,SAAS,CAAC,qBAAqB,EAAE,CAAC;QAC9C,IAAI,GAAG,CAAC,KAAK,IAAI,CAAC,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC;QACnD,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;IAC1E,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;IAEhB,MAAM,WAAW,GAAG,WAAW,CAC7B,KAAK,EAAE,MAAoB,EAAE,KAAa,EAAE,EAAE;QAC5C,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC;QACjC,MAAM,IAAI,GAAG,UAAU,EAAE,CAAC;QAC1B,IAAI,MAAM,KAAK,IAAI,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;QACxD,CAAC;QACD,MAAM,mBAAmB,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC,CAAC;IACvE,CAAC,EACD,CAAC,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,CAClC,CAAC;IAEF,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,CAAC;AACrC,CAAC"}
+{"version":3,"file":"useImageExport.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/useImageExport.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,OAAO,CAAC;AAMpC,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAC;AAU/D;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAC5B,SAAgC,EAChC,SAAyC,EACzC,QAAgB;IAEhB,MAAM,UAAU,GAAG,WAAW,CAAC,GAAwB,EAAE;QACvD,IAAI,SAAS,KAAK,IAAI;YAAE,OAAO,IAAI,CAAC;QACpC,MAAM,GAAG,GAAG,SAAS,CAAC,qBAAqB,EAAE,CAAC;QAC9C,IAAI,GAAG,CAAC,KAAK,IAAI,CAAC,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC;YAAE,OAAO,IAAI,CAAC;QACnD,OAAO,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;IAC1E,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;IAEhB,MAAM,WAAW,GAAG,WAAW,CAC7B,KAAK,EAAE,MAAoB,EAAE,KAAa,EAAE,EAAE;QAC5C,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC;QACjC,MAAM,IAAI,GAAG,UAAU,EAAE,CAAC;QAC1B,IAAI,MAAM,KAAK,IAAI,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;QACxD,CAAC;QACD,MAAM,mBAAmB,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC,CAAC;IACvE,CAAC,EACD,CAAC,UAAU,EAAE,SAAS,EAAE,QAAQ,CAAC,CAClC,CAAC;IAEF,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,CAAC;AACrC,CAAC"}

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;AAKH,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;AAmB1D,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;IAczE;;;;;;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;IAIrE;;;;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;IAa5E;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,KAAK,SAAqB,GAAG,OAAO,CAAC,IAAI,CAAC;IAMrE,kEAAkE;IAClE,YAAY,IAAI,IAAI;IAKpB,sEAAsE;IACtE,OAAO,IAAI,IAAI;CAwBhB"}
+{"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["../../../src/molecule3d/ui/viewer.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAUH,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;AAW1D,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;IAYzE;;;;;;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;IAIrE;;;;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"}

package/lib/molecule3d/ui/viewer.js

@@ -7,20 +7,19 @@
  * 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, applyCamera, resetCamera, setSpin, watchCamera, } from "./camera.js";
+import { DEFAULT_CAMERA_DURATION, DEFAULT_SPIN_SPEED, MolstarPlugin, setSpin, } from "../../molstar/core/index.js";
+import { applyCamera, resetCamera, watchCamera } from "./camera.js";
 import { captureScene } from "./captureScene.js";
 import { MeasurementPicker, clearMeasurements, renderMeasurements, } from "./measurements.js";
 import { clearMolecule, renderMolecule } from "./renderMolecule.js";
 import { clearSurface, renderSurface } from "./renderSurface.js";
-import { mountMolecule3DPlugin } from "./viewerSpec.js";
 /**
  * One molstar canvas, and every operation the component performs on it. Every
  * method resolves to nothing once `dispose` has been called.
  */
 export class Molecule3DViewer {
-    #model;
+    #plugin;
     #picker;
-    #disposed = false;
     /** Resolves once the canvas exists; every method awaits it internally. */
     ready;
     /**
@@ -29,16 +28,15 @@ export class Molecule3DViewer {
      * @param options - See {@link Molecule3DViewerOptions}.
      */
     constructor(container, options = {}) {
-        const { background = '#ffffff', // tokens-ok: a WebGL clear colour
-        onMeasure = ignore, } = options;
-        this.#model = mountMolecule3DPlugin(container, background);
-        this.ready = this.#model.initialized;
+        const { background, onMeasure = ignore } = options;
+        this.#plugin = new MolstarPlugin(container, { background });
+        this.ready = this.#plugin.ready;
         // Registered before any `#run`, so the picker exists by the time one runs.
-        this.ready.then(() => {
-            if (this.#disposed)
-                return;
-            this.#picker = new MeasurementPicker(this.#model.plugin, onMeasure);
-        }, ignore);
+        void this.#plugin
+            .run((plugin) => {
+            this.#picker = new MeasurementPicker(plugin, onMeasure);
+        })
+            .catch(ignore);
     }
     /**
      * Replace the displayed molecule, clearing any surface and measurement.
@@ -135,17 +133,7 @@ export class Molecule3DViewer {
      * the canvas exists.
      */
     watchCamera(listener) {
-        let stop = null;
-        let cancelled = false;
-        void this.#run((plugin) => {
-            if (!cancelled)
-                stop = watchCamera(plugin, listener);
-        });
-        return () => {
-            cancelled = true;
-            stop?.();
-            stop = null;
-        };
+        return this.#plugin.subscribe((plugin) => watchCamera(plugin, listener));
     }
     /**
      * Turn the automatic spin on or off.
@@ -160,36 +148,15 @@ export class Molecule3DViewer {
     }
     /** Re-read the container's size. Call from a `ResizeObserver`. */
     handleResize() {
-        if (this.#disposed)
-            return;
-        this.#model.plugin.handleResize();
+        this.#plugin.handleResize();
     }
     /** Tear the viewer down and release its WebGL context. Idempotent. */
     dispose() {
-        if (this.#disposed)
-            return;
-        this.#disposed = true;
         this.#picker?.dispose();
-        void this.ready
-            .catch(() => undefined)
-            .then(() => {
-            this.#model.plugin.dispose();
-        });
+        this.#plugin.dispose();
     }
-    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;
-        }
+    #run(action) {
+        return this.#plugin.run(action);
     }
 }
 function ignore() {

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

@@ -1 +1 @@
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package/lib/molstar/core/camera.d.ts

@@ -0,0 +1,37 @@
+/**
+ * The camera moves every molstar scene of ours needs, and the one measurement
+ * they all take: how big a sphere has to be framed for a handful of atoms to
+ * be legible.
+ */
+import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
+/** Transition length used when the caller does not pick one, milliseconds. */
+export declare const DEFAULT_CAMERA_DURATION = 250;
+/** Turn rate used when the caller does not pick one, in molstar's spin unit. */
+export declare const DEFAULT_SPIN_SPEED: number;
+/**
+ * Fraction of the bounding sphere kept as breathing room around the scene.
+ *
+ * `camera.reset()` frames with molstar's own margin, which suits a protein
+ * filling a wide viewport and leaves a small molecule a speck in the middle:
+ * measured coverage was 20% of the pixels. Framing the visible bounding sphere
+ * directly, with a small margin, is what makes a single water molecule legible.
+ */
+export declare const FRAMING_MARGIN = 0.08;
+/** Smallest radius framed, ångström, so one atom is not a close-up. */
+export declare const MINIMUM_FRAMING_RADIUS = 0.5;
+/**
+ * The radius a reset frames, which is the length every stored camera is
+ * measured against — so reading a camera and applying it are the same move in
+ * opposite directions.
+ * @param radius - Radius of the scene's visible bounding sphere.
+ * @returns The framed radius.
+ */
+export declare function framedRadius(radius: number): number;
+/**
+ * Turn the automatic spin on or off. It moves the camera, never the object.
+ * @param plugin - The molstar context.
+ * @param spinning - Whether the scene should keep turning.
+ * @param speed - Turn rate, in molstar's own spin unit.
+ */
+export declare function setSpin(plugin: PluginContext, spinning: boolean, speed?: number): void;
+//# sourceMappingURL=camera.d.ts.map

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

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

@@ -0,0 +1,49 @@
+/**
+ * The camera moves every molstar scene of ours needs, and the one measurement
+ * they all take: how big a sphere has to be framed for a handful of atoms to
+ * be legible.
+ */
+import { Vec3 } from 'molstar/lib/mol-math/linear-algebra.js';
+/** Transition length used when the caller does not pick one, milliseconds. */
+export const DEFAULT_CAMERA_DURATION = 250;
+/** Turn rate used when the caller does not pick one, in molstar's spin unit. */
+export const DEFAULT_SPIN_SPEED = 1 / 3;
+/**
+ * Fraction of the bounding sphere kept as breathing room around the scene.
+ *
+ * `camera.reset()` frames with molstar's own margin, which suits a protein
+ * filling a wide viewport and leaves a small molecule a speck in the middle:
+ * measured coverage was 20% of the pixels. Framing the visible bounding sphere
+ * directly, with a small margin, is what makes a single water molecule legible.
+ */
+export const FRAMING_MARGIN = 0.08;
+/** Smallest radius framed, ångström, so one atom is not a close-up. */
+export const MINIMUM_FRAMING_RADIUS = 0.5;
+/** Axis the automatic spin turns about: screen up. */
+const SPIN_AXIS = Vec3.create(0, 1, 0);
+/**
+ * The radius a reset frames, which is the length every stored camera is
+ * measured against — so reading a camera and applying it are the same move in
+ * opposite directions.
+ * @param radius - Radius of the scene's visible bounding sphere.
+ * @returns The framed radius.
+ */
+export function framedRadius(radius) {
+    return Math.max(radius * (1 + FRAMING_MARGIN), MINIMUM_FRAMING_RADIUS);
+}
+/**
+ * Turn the automatic spin on or off. It moves the camera, never the object.
+ * @param plugin - The molstar context.
+ * @param spinning - Whether the scene should keep turning.
+ * @param speed - Turn rate, in molstar's own spin unit.
+ */
+export function setSpin(plugin, spinning, speed = DEFAULT_SPIN_SPEED) {
+    plugin.canvas3d?.setProps({
+        trackball: {
+            animate: spinning
+                ? { name: 'spin', params: { speed, axis: SPIN_AXIS } }
+                : { name: 'off', params: {} },
+        },
+    });
+}
+//# sourceMappingURL=camera.js.map

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

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

@@ -0,0 +1,54 @@
+/**
+ * The two directions between molstar's camera and the camera a shared link
+ * carries.
+ *
+ * A link stores the camera against what is drawn rather than against ångström —
+ * a rotation from the front view, a zoom against the distance that frames the
+ * scene, and a target offset in its own radii — so a view opens the same on any
+ * screen. Which sphere is the yardstick is the caller's to decide: a site whose
+ * scene grows after the model arrives measures against the model alone, or one
+ * view would read as two zooms.
+ */
+import { Vec3 } from 'molstar/lib/mol-math/linear-algebra.js';
+import type { Molecule3DCamera } from '../../molecule3d/core/camera.ts';
+/** Where the camera is and where it looks, in world coordinates. */
+export interface CameraPose {
+    position: Vec3;
+    target: Vec3;
+    up: Vec3;
+}
+/** The sphere a stored camera is measured against. */
+export interface CameraReference {
+    center: Vec3;
+    /** Radius, ångström, framing margin included. */
+    radius: number;
+}
+/** How small an offset, in radii, is written as none at all. */
+export interface PoseOptions {
+    /**
+     * Target offsets below this, in radii, are read as zero. The framing centres
+     * on the scene a hair off the atoms' own centre, and that hair would
+     * otherwise be written into every link as `,0,0,0`.
+     * @default 0
+     */
+    snapOffset?: number;
+}
+/**
+ * Measure a pose against what is drawn.
+ * @param pose - Where the camera is.
+ * @param reference - The sphere to measure against.
+ * @param framingDistance - How far from the target the camera stands to frame
+ * the reference sphere; the length `zoom: 1` means.
+ * @param options - See {@link PoseOptions}.
+ * @returns The camera, or `null` for a degenerate pose.
+ */
+export declare function poseToCamera(pose: CameraPose, reference: CameraReference, framingDistance: number, options?: PoseOptions): Molecule3DCamera | null;
+/**
+ * The pose a stored camera stands at: {@link poseToCamera} the other way round.
+ * @param camera - The stored camera.
+ * @param reference - The sphere it was measured against.
+ * @param framingDistance - See {@link poseToCamera}.
+ * @returns The pose.
+ */
+export declare function cameraToPose(camera: Molecule3DCamera, reference: CameraReference, framingDistance: number): CameraPose;
+//# sourceMappingURL=cameraPose.d.ts.map

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

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

@@ -0,0 +1,78 @@
+/**
+ * The two directions between molstar's camera and the camera a shared link
+ * carries.
+ *
+ * A link stores the camera against what is drawn rather than against ångström —
+ * a rotation from the front view, a zoom against the distance that frames the
+ * scene, and a target offset in its own radii — so a view opens the same on any
+ * screen. Which sphere is the yardstick is the caller's to decide: a site whose
+ * scene grows after the model arrives measures against the model alone, or one
+ * view would read as two zooms.
+ */
+import { Quat, Vec3 } from 'molstar/lib/mol-math/linear-algebra.js';
+import { normalizeMolecule3DCamera } from "../../molecule3d/core/camera.js";
+/** The camera's own axes, which a stored rotation turns into world ones. */
+const CAMERA_UP = Vec3.create(0, 1, 0);
+const CAMERA_BACK = Vec3.create(0, 0, 1);
+/**
+ * Measure a pose against what is drawn.
+ * @param pose - Where the camera is.
+ * @param reference - The sphere to measure against.
+ * @param framingDistance - How far from the target the camera stands to frame
+ * the reference sphere; the length `zoom: 1` means.
+ * @param options - See {@link PoseOptions}.
+ * @returns The camera, or `null` for a degenerate pose.
+ */
+export function poseToCamera(pose, reference, framingDistance, options = {}) {
+    const { snapOffset = 0 } = options;
+    const { position, target, up } = pose;
+    const back = Vec3.sub(Vec3.zero(), position, target);
+    const distance = Vec3.magnitude(back);
+    if (distance <= 0)
+        return null;
+    Vec3.scale(back, back, 1 / distance);
+    // The trackball keeps up and back close to square, never exactly so.
+    const trueUp = Vec3.scaleAndAdd(Vec3.zero(), up, back, -Vec3.dot(up, back));
+    if (Vec3.magnitude(trueUp) <= 0)
+        return null;
+    Vec3.normalize(trueUp, trueUp);
+    const right = Vec3.cross(Vec3.zero(), trueUp, back);
+    const rotation = Quat.fromBasis(Quat.identity(), right, trueUp, back);
+    const offset = Vec3.sub(Vec3.zero(), target, reference.center);
+    Vec3.scale(offset, offset, 1 / reference.radius);
+    return normalizeMolecule3DCamera({
+        rotation: [
+            rotation[0] ?? 0,
+            rotation[1] ?? 0,
+            rotation[2] ?? 0,
+            rotation[3] ?? 1,
+        ],
+        zoom: framingDistance / distance,
+        offset: [
+            snap(offset[0], snapOffset),
+            snap(offset[1], snapOffset),
+            snap(offset[2], snapOffset),
+        ],
+    });
+}
+/**
+ * The pose a stored camera stands at: {@link poseToCamera} the other way round.
+ * @param camera - The stored camera.
+ * @param reference - The sphere it was measured against.
+ * @param framingDistance - See {@link poseToCamera}.
+ * @returns The pose.
+ */
+export function cameraToPose(camera, reference, framingDistance) {
+    const { rotation, zoom, offset } = normalizeMolecule3DCamera(camera);
+    const turn = Quat.create(rotation[0], rotation[1], rotation[2], rotation[3]);
+    const up = Vec3.transformQuat(Vec3.zero(), CAMERA_UP, turn);
+    const back = Vec3.transformQuat(Vec3.zero(), CAMERA_BACK, turn);
+    const shift = Vec3.create(offset[0], offset[1], offset[2]);
+    const target = Vec3.scaleAndAdd(Vec3.zero(), reference.center, shift, reference.radius);
+    const position = Vec3.scaleAndAdd(Vec3.zero(), target, back, framingDistance / zoom);
+    return { position, target, up };
+}
+function snap(value, threshold) {
+    return value === undefined || Math.abs(value) < threshold ? 0 : value;
+}
+//# sourceMappingURL=cameraPose.js.map

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