react-cheminfo 0.11.0 → 0.12.0

package/lib/molecule3d/ui/measurements.js

@@ -0,0 +1,148 @@
+/**
+ * Distances, angles and dihedral angles over the displayed molecule.
+ *
+ * molstar ships the measuring itself — `managers.structure.measurement` draws
+ * the lines and labels — but its only way to pick the atoms is the panel of its
+ * own UI, which this component does not mount. That panel works from the
+ * selection history, and so does this module: while a tool is active the
+ * plugin is in selection mode, a click toggles one atom into the history
+ * 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 { 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';
+import { MEASUREMENT_ATOM_COUNTS } from "../core/measurement.js";
+import { moleculeStructure } from "./renderMolecule.js";
+// Lowercased: it is a factory, not a constructor.
+const elementLoci = StructureElement.Loci;
+/**
+ * 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.
+ * @returns Nothing; resolves once every label is on screen.
+ */
+export async function renderMeasurements(plugin, measurements) {
+    await clearMeasurements(plugin);
+    const structure = moleculeStructure(plugin);
+    if (structure === undefined)
+        return;
+    const manager = plugin.managers.structure.measurement;
+    for (const measurement of measurements) {
+        const [a, b, c, d] = atomLoci(structure, measurement.atoms);
+        /* eslint-disable no-await-in-loop -- each add commits to the state tree, and commits must not interleave */
+        if (measurement.kind === 'distance' && a && b) {
+            await manager.addDistance(a, b);
+        }
+        else if (measurement.kind === 'angle' && a && b && c) {
+            await manager.addAngle(a, b, c);
+        }
+        else if (measurement.kind === 'dihedral' && a && b && c && d) {
+            await manager.addDihedral(a, b, c, d);
+        }
+        /* eslint-enable no-await-in-loop */
+    }
+}
+/**
+ * Remove every measurement from the scene.
+ * @param plugin - The molstar context.
+ * @returns Nothing; resolves once the labels are gone.
+ */
+export async function clearMeasurements(plugin) {
+    const ref = StateSelection.findTagInSubtree(plugin.state.data.tree, StateTransform.RootRef, MeasurementGroupTag);
+    if (ref === undefined)
+        return;
+    await plugin.build().delete(ref).commit();
+}
+/** Turns the clicks on atoms into measurements, while a tool is active. */
+export class MeasurementPicker {
+    #plugin;
+    #onMeasure;
+    #unsubscribe;
+    #kind = null;
+    /**
+     * Start listening to the selection history of `plugin`.
+     * @param plugin - The molstar context.
+     * @param onMeasure - Called with each measurement once its atoms are picked.
+     */
+    constructor(plugin, onMeasure) {
+        this.#plugin = plugin;
+        this.#onMeasure = onMeasure;
+        // A molfile is one residue: at molstar's default granularity a click
+        // would pick the whole molecule.
+        plugin.managers.interactivity.setProps({ granularity: 'element' });
+        const subscription = plugin.managers.structure.selection.events.additionsHistoryUpdated.subscribe(() => {
+            this.#collect();
+        });
+        this.#unsubscribe = () => {
+            subscription.unsubscribe();
+        };
+    }
+    /**
+     * Choose what the next clicks measure. Atoms already picked are dropped.
+     * @param kind - The measurement to build, or `null` to give clicks back to
+     * the camera.
+     */
+    setKind(kind) {
+        if (kind === this.#kind)
+            return;
+        this.#kind = kind;
+        this.#plugin.selectionMode = kind !== null;
+        this.#plugin.managers.interactivity.lociSelects.deselectAll();
+    }
+    /** Stop listening to the plugin. */
+    dispose() {
+        this.#unsubscribe();
+    }
+    #collect() {
+        const kind = this.#kind;
+        const structure = moleculeStructure(this.#plugin);
+        if (kind === null || structure === undefined)
+            return;
+        const needed = MEASUREMENT_ATOM_COUNTS[kind];
+        // The history is newest first.
+        const history = this.#plugin.managers.structure.selection.additionsHistory;
+        const atoms = [];
+        for (let i = 0; i < history.length && atoms.length < needed; i++) {
+            const entry = history[i];
+            const atom = entry && atomReference(structure, entry.loci);
+            if (atom !== undefined)
+                atoms.push(atom);
+        }
+        if (atoms.length < needed)
+            return;
+        this.#plugin.managers.interactivity.lociSelects.deselectAll();
+        this.#onMeasure({ kind, atoms: atoms.toReversed() });
+    }
+}
+function atomReference(structure, loci) {
+    if (!StructureElement.Loci.is(loci))
+        return undefined;
+    if (StructureElement.Loci.size(loci) !== 1)
+        return undefined;
+    const entry = loci.elements[0];
+    if (entry === undefined)
+        return undefined;
+    const units = structure.units;
+    for (let unit = 0; unit < units.length; unit++) {
+        if (units[unit]?.id === entry.unit.id) {
+            return { unit, element: OrderedSet.getAt(entry.indices, 0) };
+        }
+    }
+    return undefined;
+}
+function atomLoci(structure, atoms) {
+    const loci = [];
+    for (const atom of atoms) {
+        const unit = structure.units[atom.unit];
+        if (unit === undefined || atom.element >= unit.elements.length)
+            return [];
+        loci.push(elementLoci(structure, [
+            { unit, indices: OrderedSet.ofSingleton(atom.element) },
+        ]));
+    }
+    return loci;
+}
+//# sourceMappingURL=measurements.js.map

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

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/molecule3dIcons.d.ts

@@ -0,0 +1,29 @@
+/**
+ * The glyphs of the molecule toolbar that Blueprint has no icon for, drawn in
+ * one language: atoms as dots, bonds as lines, 16 px, in `currentColor` so
+ * they follow the button's own state.
+ */
+import type { ReactElement } from 'react';
+import type { MeasurementKind } from '../core/measurement.ts';
+/**
+ * The glyph of one measuring tool.
+ * @param props - Which measurement.
+ * @param props.kind - The measurement the tool builds.
+ * @returns The 16 px glyph.
+ */
+export declare function MeasureIcon(props: {
+    kind: MeasurementKind;
+}): ReactElement;
+/**
+ * A measured distance crossed out: the button removes measurements, and only
+ * measurements, which a generic trash can would not say.
+ * @returns The 16 px glyph.
+ */
+export declare function ClearMeasurementsIcon(): ReactElement;
+/**
+ * A three-atom molecule wrapped in a translucent blob: the surface drawn over
+ * the model.
+ * @returns The 16 px glyph.
+ */
+export declare function SurfaceIcon(): ReactElement;
+//# sourceMappingURL=molecule3dIcons.d.ts.map

package/lib/molecule3d/ui/molecule3dIcons.d.ts.map

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/molecule3dIcons.js

@@ -0,0 +1,47 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+/** The atoms a measurement joins, drawn as dots and the bonds between them. */
+const ICON_POINTS = {
+    distance: [
+        [2.5, 8],
+        [13.5, 8],
+    ],
+    angle: [
+        [13, 3],
+        [3, 13],
+        [13.5, 13],
+    ],
+    dihedral: [
+        [2, 4],
+        [6, 12.5],
+        [10, 3.5],
+        [14, 12],
+    ],
+};
+/**
+ * The glyph of one measuring tool.
+ * @param props - Which measurement.
+ * @param props.kind - The measurement the tool builds.
+ * @returns The 16 px glyph.
+ */
+export function MeasureIcon(props) {
+    const { kind } = props;
+    const points = ICON_POINTS[kind];
+    return (_jsxs("svg", { width: 16, height: 16, viewBox: "0 0 16 16", "aria-hidden": true, children: [_jsx("polyline", { points: points.map((point) => point.join(',')).join(' '), fill: "none", stroke: "currentColor", strokeWidth: 1.3, strokeDasharray: kind === 'distance' ? '2 1.5' : undefined }), points.map(([x, y]) => (_jsx("circle", { cx: x, cy: y, r: 1.9, fill: "currentColor" }, `${x},${y}`)))] }));
+}
+/**
+ * A measured distance crossed out: the button removes measurements, and only
+ * measurements, which a generic trash can would not say.
+ * @returns The 16 px glyph.
+ */
+export function ClearMeasurementsIcon() {
+    return (_jsxs("svg", { width: 16, height: 16, viewBox: "0 0 16 16", "aria-hidden": true, children: [_jsx("polyline", { points: "2.2,5.5 11,5.5", fill: "none", stroke: "currentColor", strokeWidth: 1.3, strokeDasharray: "2 1.5" }), _jsx("circle", { cx: 2.2, cy: 5.5, r: 1.9, fill: "currentColor" }), _jsx("circle", { cx: 11, cy: 5.5, r: 1.9, fill: "currentColor" }), _jsx("path", { d: "M9.6 9.6l4.8 4.8M14.4 9.6l-4.8 4.8", stroke: "currentColor", strokeWidth: 1.8, strokeLinecap: "round" })] }));
+}
+/**
+ * A three-atom molecule wrapped in a translucent blob: the surface drawn over
+ * the model.
+ * @returns The 16 px glyph.
+ */
+export function SurfaceIcon() {
+    return (_jsxs("svg", { width: 16, height: 16, viewBox: "0 0 16 16", "aria-hidden": true, children: [_jsx("path", { d: "M8 1.2c2.9 0 5.9 1.7 6.3 4.6.3 1.9-.7 2.9-.4 4.4.4 2.2-1.9 4.6-5.1 4.6-3 0-6.3-1.6-6.8-4.4C1.6 8.8 2.6 7.8 2.4 6.2 2 3.4 5 1.2 8 1.2Z", fill: "currentColor", fillOpacity: 0.18, stroke: "currentColor", strokeWidth: 0.9 }), _jsx("polyline", { points: "5.1,10.2 8,5.8 10.9,10.2", fill: "none", stroke: "currentColor", strokeWidth: 1.1 }), _jsx("circle", { cx: 5.1, cy: 10.2, r: 1.4, fill: "currentColor" }), _jsx("circle", { cx: 8, cy: 5.8, r: 1.4, fill: "currentColor" }), _jsx("circle", { cx: 10.9, cy: 10.2, r: 1.4, fill: "currentColor" })] }));
+}
+//# sourceMappingURL=molecule3dIcons.js.map

package/lib/molecule3d/ui/molecule3dIcons.js.map

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/moleculeViewer3DProps.d.ts

@@ -0,0 +1,93 @@
+import type { ReactNode } from 'react';
+import type { ViewerCapability } from '../../orbital/ui/capability.ts';
+import type { Measurement } from '../core/measurement.ts';
+import type { Molecule3DFile, Molecule3DSettings, Molecule3DTools } from '../core/settings.ts';
+/**
+ * Props of `MoleculeViewer3D`.
+ *
+ * Settings, spin and measurements are each either owned by the site — pass
+ * the value and its `on…Change` — or left to the component, which then starts
+ * from the `default…` value.
+ */
+export interface MoleculeViewer3DProps {
+    /** The molecule to draw, with 3D coordinates, or `null` for none. */
+    molfile: Molecule3DFile | null;
+    /**
+     * Which buttons the toolbar over the canvas shows; tools not named stay on.
+     * @default every tool
+     */
+    tools?: Partial<Molecule3DTools>;
+    /**
+     * How the model is drawn, when the site owns it.
+     * @default undefined
+     */
+    settings?: Molecule3DSettings;
+    /**
+     * Starting settings when the component owns them.
+     * @default DEFAULT_MOLECULE_3D_SETTINGS
+     */
+    defaultSettings?: Partial<Molecule3DSettings>;
+    /**
+     * Called with the new settings after any change from the toolbar.
+     * @default undefined
+     */
+    onSettingsChange?: (settings: Molecule3DSettings) => void;
+    /**
+     * Whether the model turns on its own, when the site owns it.
+     * @default undefined
+     */
+    spinning?: boolean;
+    /**
+     * Starting spin when the component owns it.
+     * @default false
+     */
+    defaultSpinning?: boolean;
+    /**
+     * Called when the spin toggle is pressed.
+     * @default undefined
+     */
+    onSpinningChange?: (spinning: boolean) => void;
+    /**
+     * Turn rate, in molstar's own spin unit.
+     * @default 1 / 3
+     */
+    spinSpeed?: number;
+    /**
+     * The measurements drawn over the model, when the site owns them. They name
+     * atoms by position, so they carry over to another conformer of the same
+     * molecule; a site showing an unrelated molecule should clear them.
+     * @default undefined
+     */
+    measurements?: readonly Measurement[];
+    /**
+     * Called with the whole list after a measurement is added or cleared.
+     * @default undefined
+     */
+    onMeasurementsChange?: (measurements: readonly Measurement[]) => void;
+    /**
+     * Name of an exported image, without its extension.
+     * @default 'molecule'
+     */
+    fileName?: string;
+    /**
+     * Scene background, as `#rrggbb`.
+     * @default '#ffffff'
+     */
+    background?: string;
+    /**
+     * Smallest height of the canvas, pixels.
+     * @default 320
+     */
+    minHeight?: number;
+    /**
+     * What to show while molstar is downloading.
+     * @default 'Loading the 3D viewer…'
+     */
+    fallback?: ReactNode;
+    /**
+     * What to show when the machine cannot render at all.
+     * @default undefined — `capability.message` is written
+     */
+    renderUnsupported?: (capability: ViewerCapability) => ReactNode;
+}
+//# sourceMappingURL=moleculeViewer3DProps.d.ts.map

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

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/moleculeViewer3DProps.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=moleculeViewer3DProps.js.map

package/lib/molecule3d/ui/moleculeViewer3DProps.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"moleculeViewer3DProps.js","sourceRoot":"","sources":["../../../src/molecule3d/ui/moleculeViewer3DProps.ts"],"names":[],"mappings":""}

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

@@ -0,0 +1,20 @@
+/**
+ * A molstar colour theme showing the polar ends of a molecule: red over the
+ * positive end — cations, and the hydrogens bonded to nitrogen or oxygen —
+ * blue over the negative end — anions, nitrogen and oxygen — and grey over the
+ * rest.
+ */
+import type { ColorTheme } from 'molstar/lib/mol-theme/color.js';
+/** Registry name of the theme. */
+export declare const POLARITY_COLOR_THEME = "molecule3d-polarity";
+declare const POLARITY_PARAMS: {};
+type PolarityParams = typeof POLARITY_PARAMS;
+/** The theme provider, registered on a plugin by {@link registerPolarityTheme}. */
+export declare const polarityColorThemeProvider: ColorTheme.Provider<PolarityParams, typeof POLARITY_COLOR_THEME>;
+/**
+ * Make the theme available to a plugin. Idempotent.
+ * @param registry - The plugin's structure colour theme registry.
+ */
+export declare function registerPolarityTheme(registry: ColorTheme.Registry): void;
+export {};
+//# sourceMappingURL=polarityColorTheme.d.ts.map

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

@@ -0,0 +1 @@
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package/lib/molecule3d/ui/polarityColorTheme.js

@@ -0,0 +1,105 @@
+/**
+ * A molstar colour theme showing the polar ends of a molecule: red over the
+ * positive end — cations, and the hydrogens bonded to nitrogen or oxygen —
+ * blue over the negative end — anions, nitrogen and oxygen — and grey over the
+ * rest.
+ */
+import { StructureElement, Unit } from 'molstar/lib/mol-model/structure.js';
+import { ColorThemeCategory } from 'molstar/lib/mol-theme/color/categories.js';
+import { Color } from 'molstar/lib/mol-util/color/color.js';
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition.js';
+import { SURFACE_CHARGE_COLORS } from "../core/settings.js";
+/** Registry name of the theme. */
+export const POLARITY_COLOR_THEME = 'molecule3d-polarity';
+const POLARITY_PARAMS = {};
+const POSITIVE = Color.fromHexStyle(SURFACE_CHARGE_COLORS.positive);
+const NEGATIVE = Color.fromHexStyle(SURFACE_CHARGE_COLORS.negative);
+const NEUTRAL = Color.fromHexStyle(SURFACE_CHARGE_COLORS.neutral);
+/** The theme provider, registered on a plugin by {@link registerPolarityTheme}. */
+export const polarityColorThemeProvider = {
+    name: POLARITY_COLOR_THEME,
+    label: 'Polarity',
+    category: ColorThemeCategory.Atom,
+    factory: polarityColorTheme,
+    getParams: () => POLARITY_PARAMS,
+    defaultValues: PD.getDefaultValues(POLARITY_PARAMS),
+    isApplicable: (context) => context.structure !== undefined,
+};
+/**
+ * Make the theme available to a plugin. Idempotent.
+ * @param registry - The plugin's structure colour theme registry.
+ */
+export function registerPolarityTheme(registry) {
+    if (!registry.has(polarityColorThemeProvider)) {
+        registry.add(polarityColorThemeProvider);
+    }
+}
+function polarityColorTheme(context, props) {
+    const signs = context.structure === undefined
+        ? new Int8Array(0)
+        : atomSigns(context.structure);
+    function color(location) {
+        if (!StructureElement.Location.is(location))
+            return NEUTRAL;
+        const sign = signs[location.element];
+        if (sign === 1)
+            return POSITIVE;
+        if (sign === -1)
+            return NEGATIVE;
+        return NEUTRAL;
+    }
+    return {
+        factory: polarityColorTheme,
+        granularity: 'group',
+        preferSmoothing: true,
+        color,
+        props,
+        description: 'Positive end in red, negative end in blue, the rest in grey.',
+    };
+}
+/**
+ * The sign of every atom's partial charge, as far as the structure tells it.
+ * A formal charge decides first; otherwise nitrogen and oxygen are negative
+ * and a hydrogen bonded to either is positive.
+ * @param structure - The atoms, with their bonds and formal charges.
+ * @returns 1, -1 or 0 at the model index of every atom.
+ */
+function atomSigns(structure) {
+    let size = 0;
+    for (const unit of structure.units) {
+        size = Math.max(size, unit.model.atomicHierarchy.atoms._rowCount);
+    }
+    const signs = new Int8Array(size);
+    for (const unit of structure.units) {
+        if (!Unit.isAtomic(unit))
+            continue;
+        const { elements, model, bonds } = unit;
+        const { type_symbol: symbols, pdbx_formal_charge: charges } = model.atomicHierarchy.atoms;
+        const { offset, b } = bonds;
+        for (let index = 0; index < elements.length; index++) {
+            const element = elements[index];
+            const charge = charges.value(element);
+            if (charge !== 0) {
+                signs[element] = charge > 0 ? 1 : -1;
+                continue;
+            }
+            const symbol = symbols.value(element);
+            if (symbol === 'N' || symbol === 'O') {
+                signs[element] = -1;
+                continue;
+            }
+            if (symbol !== 'H')
+                continue;
+            const end = offset[index + 1] ?? 0;
+            for (let bond = offset[index] ?? end; bond < end; bond++) {
+                const neighbour = symbols.value(elements[b[bond] ?? 0]);
+                if (neighbour === 'N' || neighbour === 'O') {
+                    signs[element] = 1;
+                    break;
+                }
+            }
+        }
+    }
+    return signs;
+}
+//# sourceMappingURL=polarityColorTheme.js.map

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

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

@@ -0,0 +1,38 @@
+/**
+ * The 3D model of one molecule, built from an in-memory molfile.
+ *
+ * The whole molecule hangs off a single data node, and the drawn model hangs
+ * off the structure under it with a fixed ref of its own, so a surface can
+ * attach to the same atoms and loading another molecule deletes the subtree —
+ * surface included.
+ */
+import type { Structure } from 'molstar/lib/mol-model/structure.js';
+import type { PluginContext } from 'molstar/lib/mol-plugin/context.js';
+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";
+/**
+ * Replace the displayed molecule. Everything already on screen goes first.
+ * @param plugin - The molstar context.
+ * @param molfile - Molfile text plus the format id.
+ * @param style - See {@link MoleculeStyle}.
+ * @returns Nothing; resolves once the model is on screen.
+ * @throws {Error} When the file parses to zero atoms. molstar's `mol` parser returns
+ * exactly that on a V3000 file, with no error, so without this check the viewer
+ * would show an empty scene and report nothing.
+ */
+export declare function renderMolecule(plugin: PluginContext, molfile: Molecule3DFile, style?: MoleculeStyle): Promise<void>;
+/**
+ * Remove the molecule, and with it any surface drawn on the same atoms.
+ * @param plugin - The molstar context.
+ * @returns Nothing; resolves once the scene is empty.
+ */
+export declare function clearMolecule(plugin: PluginContext): Promise<void>;
+/**
+ * The atoms currently on screen, for anything that draws on top of them.
+ * @param plugin - The molstar context.
+ * @returns The loaded structure, or `undefined` when no molecule is displayed.
+ */
+export declare function moleculeStructure(plugin: PluginContext): Structure | undefined;
+//# sourceMappingURL=renderMolecule.d.ts.map

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

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