react-cheminfo 0.23.0 → 0.25.0

package/lib/structure/core/geometryRelaxer.d.ts

@@ -0,0 +1,66 @@
+/**
+ * A geometry a relaxer is handed: element symbols plus flat Cartesian
+ * coordinates in ångström, `x,y,z` per atom.
+ */
+export interface RelaxableGeometry {
+    /** Element symbol per atom, explicit hydrogens included. */
+    elements: string[];
+    /** Flat `x,y,z` per atom in ångström, length `3 · elements.length`. */
+    coordinates: Float64Array;
+}
+/** What a relaxer reports for one structure. */
+export interface RelaxedGeometry {
+    /**
+     * The relaxed coordinates, in the input's atom order. Translated freely;
+     * never rotated, which is what lets {@link RelaxedGeometry} be compared with
+     * the geometry it came from by removing both centroids.
+     */
+    coordinates: Float64Array;
+    /**
+     * Total energy at `coordinates`, **in kcal/mol**, so it can be read against a
+     * force-field energy without a second unit in the UI.
+     */
+    energy: number;
+    /**
+     * The dispersion term of `energy`, kcal/mol, or `null` from a method that has
+     * none. It is the part a force field of the MMFF94 era does not model at all,
+     * and a large part of why conformers re-rank.
+     * @default null
+     */
+    dispersionEnergy: number | null;
+    /** Optimizer cycles spent. `0` when there was nothing to relax. */
+    cycles: number;
+    /** Whether the optimizer met its convergence criteria. */
+    converged: boolean;
+    /** Plain sentences about anything the caller should know. */
+    warnings: string[];
+}
+/** How a relaxation run is watched and cancelled. */
+export interface RelaxerOptions {
+    /**
+     * Called as each structure finishes, so a caller can show progress over a
+     * batch that runs for seconds.
+     * @default undefined
+     */
+    onSettled?: (done: number, total: number) => void;
+    /**
+     * Gives the run up. A relaxer is not obliged to be able to interrupt a
+     * structure already in flight.
+     * @default undefined
+     */
+    signal?: AbortSignal;
+}
+/**
+ * Something that relaxes geometries with a real electronic structure behind it,
+ * and reports the energy **at the geometry it returns**.
+ *
+ * This is the seam between a site and the semi-empirical engine: nothing in
+ * `react-cheminfo/core` imports one, so a site that never refines a geometry
+ * downloads no WebAssembly. `xtbRelaxer` from `react-cheminfo/xtb` is the
+ * implementation, GFN2-xTB through `xtb-wasm`.
+ *
+ * An implementation must return one result per request, in request order, and
+ * must keep each structure's atom order.
+ */
+export type GeometryRelaxer = (geometries: readonly RelaxableGeometry[], options?: RelaxerOptions) => Promise<RelaxedGeometry[]>;
+//# sourceMappingURL=geometryRelaxer.d.ts.map

package/lib/structure/core/geometryRelaxer.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/geometryRelaxer.js

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

package/lib/structure/core/geometryRelaxer.js.map

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

package/lib/structure/core/index.d.ts

@@ -11,8 +11,12 @@ export type { IdCodeValue } from './editorValue.ts';
 export { isEmptyIdCode, splitEditorValue, splitIdCode } from './editorValue.ts';
 export type { FragmentQuery } from './fragmentQuery.ts';
 export { fragmentQuery, sameFragmentQuery } from './fragmentQuery.ts';
+export type { GeometryRelaxer, RelaxableGeometry, RelaxedGeometry, RelaxerOptions, } from './geometryRelaxer.ts';
+export { centredRmsd, readRelaxableGeometry, writeRelaxedCoordinates, } from './moleculeCoordinates.ts';
 export type { MolfileClassification, MolfileVersion } from './molfile.ts';
 export { classifyMolfile, looksLikeMolfile, molfileAtomCount, } from './molfile.ts';
+export type { MolfileExport } from './molfileExport.ts';
+export { readMolfileExport, toMolfileExport } from './molfileExport.ts';
 export type { ReadStructureResult, StructureKind } from './readStructure.ts';
 export { looksLikeSmarts, readStructure } from './readStructure.ts';
 export type { StructureError } from './structureError.ts';

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

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

@@ -4,7 +4,9 @@ export { EDITOR_TOOLBAR_BUTTONS, isEditorToolbarButtonAvailable, } from "./edito
 export { EDITOR_TOOLBAR_COLUMNS, EDITOR_TOOLBAR_ROWS, editorToolbarButtonAt, editorToolbarButtonBox, } from "./editorToolbarGeometry.js";
 export { isEmptyIdCode, splitEditorValue, splitIdCode } from "./editorValue.js";
 export { fragmentQuery, sameFragmentQuery } from "./fragmentQuery.js";
+export { centredRmsd, readRelaxableGeometry, writeRelaxedCoordinates, } from "./moleculeCoordinates.js";
 export { classifyMolfile, looksLikeMolfile, molfileAtomCount, } from "./molfile.js";
+export { readMolfileExport, toMolfileExport } from "./molfileExport.js";
 export { looksLikeSmarts, readStructure } from "./readStructure.js";
 export { structureError } from "./structureError.js";
 export { structureSource } from "./structureSource.js";

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

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package/lib/structure/core/moleculeCoordinates.d.ts

@@ -0,0 +1,31 @@
+import type { Molecule } from 'openchemlib';
+import type { RelaxableGeometry } from './geometryRelaxer.ts';
+/**
+ * Read the elements and 3D coordinates of a molecule into the flat form an
+ * engine takes.
+ * @param molecule - A molecule carrying 3D coordinates. Not modified.
+ * @returns Its geometry in ångström, one entry per atom of `getAllAtoms()`.
+ */
+export declare function readRelaxableGeometry(molecule: Molecule): RelaxableGeometry;
+/**
+ * Write flat coordinates back onto a molecule, atom for atom.
+ * @param molecule - The molecule to move. Mutated.
+ * @param coordinates - Flat `x,y,z` per atom in ångström.
+ * @throws {Error} When there is not one position per atom.
+ */
+export declare function writeRelaxedCoordinates(molecule: Molecule, coordinates: Float64Array): void;
+/**
+ * Root-mean-square displacement between two geometries of the same atoms, each
+ * taken about its own centroid, in ångström.
+ *
+ * Removing the centroids is what makes the number mean "how far the atoms
+ * moved" rather than "how far the molecule was translated": a relaxer is free
+ * to recentre a molecule, and the `GeometryRelaxer` contract forbids it to
+ * rotate one.
+ * @param before - Flat coordinates before.
+ * @param after - Flat coordinates after.
+ * @returns The RMSD in ångström, `0` for an empty geometry.
+ * @throws {Error} When the two do not hold the same number of atoms.
+ */
+export declare function centredRmsd(before: Float64Array, after: Float64Array): number;
+//# sourceMappingURL=moleculeCoordinates.d.ts.map

package/lib/structure/core/moleculeCoordinates.d.ts.map

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package/lib/structure/core/moleculeCoordinates.js

@@ -0,0 +1,80 @@
+/**
+ * Read the elements and 3D coordinates of a molecule into the flat form an
+ * engine takes.
+ * @param molecule - A molecule carrying 3D coordinates. Not modified.
+ * @returns Its geometry in ångström, one entry per atom of `getAllAtoms()`.
+ */
+export function readRelaxableGeometry(molecule) {
+    const atoms = molecule.getAllAtoms();
+    const elements = new Array(atoms);
+    const coordinates = new Float64Array(atoms * 3);
+    for (let atom = 0; atom < atoms; atom++) {
+        elements[atom] = molecule.getAtomLabel(atom);
+        coordinates[atom * 3] = molecule.getAtomX(atom);
+        coordinates[atom * 3 + 1] = molecule.getAtomY(atom);
+        coordinates[atom * 3 + 2] = molecule.getAtomZ(atom);
+    }
+    return { elements, coordinates };
+}
+/**
+ * Write flat coordinates back onto a molecule, atom for atom.
+ * @param molecule - The molecule to move. Mutated.
+ * @param coordinates - Flat `x,y,z` per atom in ångström.
+ * @throws {Error} When there is not one position per atom.
+ */
+export function writeRelaxedCoordinates(molecule, coordinates) {
+    const atoms = molecule.getAllAtoms();
+    if (coordinates.length !== atoms * 3) {
+        throw new Error(`The relaxed geometry has ${coordinates.length / 3} positions for ${atoms} atoms.`);
+    }
+    for (let atom = 0; atom < atoms; atom++) {
+        molecule.setAtomX(atom, coordinates[atom * 3]);
+        molecule.setAtomY(atom, coordinates[atom * 3 + 1]);
+        molecule.setAtomZ(atom, coordinates[atom * 3 + 2]);
+    }
+}
+/**
+ * Root-mean-square displacement between two geometries of the same atoms, each
+ * taken about its own centroid, in ångström.
+ *
+ * Removing the centroids is what makes the number mean "how far the atoms
+ * moved" rather than "how far the molecule was translated": a relaxer is free
+ * to recentre a molecule, and the `GeometryRelaxer` contract forbids it to
+ * rotate one.
+ * @param before - Flat coordinates before.
+ * @param after - Flat coordinates after.
+ * @returns The RMSD in ångström, `0` for an empty geometry.
+ * @throws {Error} When the two do not hold the same number of atoms.
+ */
+export function centredRmsd(before, after) {
+    if (before.length !== after.length) {
+        throw new Error(`Cannot compare ${before.length / 3} positions with ${after.length / 3}.`);
+    }
+    const atoms = before.length / 3;
+    if (atoms === 0)
+        return 0;
+    const centreBefore = centroid(before, atoms);
+    const centreAfter = centroid(after, atoms);
+    let total = 0;
+    for (let atom = 0; atom < atoms; atom++) {
+        for (let axis = 0; axis < 3; axis++) {
+            const gap = before[atom * 3 + axis] -
+                centreBefore[axis] -
+                (after[atom * 3 + axis] - centreAfter[axis]);
+            total += gap * gap;
+        }
+    }
+    return Math.sqrt(total / atoms);
+}
+function centroid(coordinates, atoms) {
+    let x = 0;
+    let y = 0;
+    let z = 0;
+    for (let atom = 0; atom < atoms; atom++) {
+        x += coordinates[atom * 3];
+        y += coordinates[atom * 3 + 1];
+        z += coordinates[atom * 3 + 2];
+    }
+    return new Float64Array([x / atoms, y / atoms, z / atoms]);
+}
+//# sourceMappingURL=moleculeCoordinates.js.map

package/lib/structure/core/moleculeCoordinates.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/molfileExport.d.ts

@@ -0,0 +1,42 @@
+import type { Molecule } from 'openchemlib';
+/** A molfile plus the molstar format id that can actually parse it. */
+export interface MolfileExport {
+    /** molstar's format id: `mol` reads V2000, `sdf` reads V2000 and V3000. */
+    format: 'mol' | 'sdf';
+    /** The molfile text, exactly as OpenChemLib wrote it. */
+    data: string;
+}
+/**
+ * Serialise a molecule for the 3D viewer and for export.
+ *
+ * V2000 is written whenever it can be: its counts line holds three digits per
+ * field, so above 999 atoms OpenChemLib writes `?` where the count belongs and
+ * the file becomes unreadable. V3000 is used from that size on.
+ *
+ * Coordinates are emitted exactly as OpenChemLib writes them — the whole
+ * molecule is negated in y and z relative to `getAtomY/Z`, which is a rigid
+ * rotation and therefore invisible to the viewer, to the energies and to any
+ * other file consumer.
+ *
+ * Hydrogens are in the file only if they are explicit atoms, so call this on a
+ * conformer, which always carries them.
+ * @param molecule - Structure with 3D coordinates already set. Not mutated.
+ * @returns The molfile and the format id to hand molstar.
+ * @throws {Error} When the molfile carries no atoms.
+ */
+export declare function toMolfileExport(molecule: Molecule): MolfileExport;
+/**
+ * Pick the molstar format id for a molfile of unknown version, and refuse the
+ * ones that would render nothing.
+ *
+ * molstar's `mol` parser does not understand a V3000 CTAB: it returns zero atoms
+ * with `isError: false`, so the viewer shows an empty scene and reports no
+ * error. The version is read from the text rather than assumed from whichever
+ * writer produced it, because the text is the only thing molstar itself looks
+ * at.
+ * @param data - A molfile, V2000 or V3000.
+ * @returns The format id paired with the unchanged text.
+ * @throws {Error} When the molfile carries no atoms — the silent failure this guards.
+ */
+export declare function readMolfileExport(data: string): MolfileExport;
+//# sourceMappingURL=molfileExport.d.ts.map

package/lib/structure/core/molfileExport.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/molfileExport.js

@@ -0,0 +1,47 @@
+import { classifyMolfile } from "./molfile.js";
+/**
+ * Serialise a molecule for the 3D viewer and for export.
+ *
+ * V2000 is written whenever it can be: its counts line holds three digits per
+ * field, so above 999 atoms OpenChemLib writes `?` where the count belongs and
+ * the file becomes unreadable. V3000 is used from that size on.
+ *
+ * Coordinates are emitted exactly as OpenChemLib writes them — the whole
+ * molecule is negated in y and z relative to `getAtomY/Z`, which is a rigid
+ * rotation and therefore invisible to the viewer, to the energies and to any
+ * other file consumer.
+ *
+ * Hydrogens are in the file only if they are explicit atoms, so call this on a
+ * conformer, which always carries them.
+ * @param molecule - Structure with 3D coordinates already set. Not mutated.
+ * @returns The molfile and the format id to hand molstar.
+ * @throws {Error} When the molfile carries no atoms.
+ */
+export function toMolfileExport(molecule) {
+    const data = molecule.getAllAtoms() > V2000_MAX_ATOMS
+        ? molecule.toMolfileV3()
+        : molecule.toMolfile();
+    return readMolfileExport(data);
+}
+/**
+ * Pick the molstar format id for a molfile of unknown version, and refuse the
+ * ones that would render nothing.
+ *
+ * molstar's `mol` parser does not understand a V3000 CTAB: it returns zero atoms
+ * with `isError: false`, so the viewer shows an empty scene and reports no
+ * error. The version is read from the text rather than assumed from whichever
+ * writer produced it, because the text is the only thing molstar itself looks
+ * at.
+ * @param data - A molfile, V2000 or V3000.
+ * @returns The format id paired with the unchanged text.
+ * @throws {Error} When the molfile carries no atoms — the silent failure this guards.
+ */
+export function readMolfileExport(data) {
+    const { version, atomCount } = classifyMolfile(data);
+    if (atomCount === 0) {
+        throw new Error('Molfile has an empty atom block: molstar would render an empty scene without reporting an error.');
+    }
+    return { format: version === 'v3000' ? 'sdf' : 'mol', data };
+}
+const V2000_MAX_ATOMS = 999;
+//# sourceMappingURL=molfileExport.js.map

package/lib/structure/core/molfileExport.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/oclResources.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Register OpenChemLib's static resources once, without which
+ * `ConformerGenerator` and `ForceFieldMMFF94` throw on construction.
+ *
+ * Repeated calls share the first call's promise; a failed registration is
+ * forgotten so a later call can retry.
+ * @param url - Where to fetch `resources.json`. Omit under Node.js to read it
+ * from the installed package; in a browser or a worker it is required.
+ * @returns A promise that settles once the resources are usable.
+ */
+export declare function registerResources(url?: string): Promise<void>;
+//# sourceMappingURL=oclResources.d.ts.map

package/lib/structure/core/oclResources.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"oclResources.d.ts","sourceRoot":"","sources":["../../../src/structure/core/oclResources.ts"],"names":[],"mappings":"AAEA;;;;;;;;;GASG;AACH,wBAAgB,iBAAiB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAM7D"}

package/lib/structure/core/oclResources.js

@@ -0,0 +1,35 @@
+import { Resources } from 'openchemlib';
+/**
+ * Register OpenChemLib's static resources once, without which
+ * `ConformerGenerator` and `ForceFieldMMFF94` throw on construction.
+ *
+ * Repeated calls share the first call's promise; a failed registration is
+ * forgotten so a later call can retry.
+ * @param url - Where to fetch `resources.json`. Omit under Node.js to read it
+ * from the installed package; in a browser or a worker it is required.
+ * @returns A promise that settles once the resources are usable.
+ */
+export function registerResources(url) {
+    registration ??= register(url).catch((error) => {
+        registration = null;
+        throw error;
+    });
+    return registration;
+}
+let registration = null;
+async function register(url) {
+    if (url !== undefined) {
+        await Resources.registerFromUrl(url);
+        return;
+    }
+    const runtime = globalThis;
+    if (runtime.process?.versions?.node === undefined) {
+        throw new Error('registerResources needs a url outside Node.js: a browser page or worker cannot read resources.json from node_modules');
+    }
+    const { createRequire } = await import('node:module');
+    const require = createRequire(import.meta.url);
+    Resources.registerFromNodejs(require
+        .resolve('openchemlib')
+        .replace(/openchemlib\.js$/, 'resources.json'));
+}
+//# sourceMappingURL=oclResources.js.map

package/lib/structure/core/oclResources.js.map

@@ -0,0 +1 @@
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package/lib/translate/core/catalog.d.ts

@@ -0,0 +1,61 @@
+/**
+ * The shape of the messages a site or a library owns, and where they are kept.
+ *
+ * A catalog is one directory of a repository holding `en.json`, the source of
+ * truth, and one flat file per locale beside it. The site registers each of
+ * its catalogs with the repository and the directory, so a translation made
+ * anywhere on the page can be sent back to the file it belongs to.
+ */
+/** Messages by key; every value is an ICU MessageFormat string. */
+export type Messages = Record<string, string>;
+/** The locale every catalog is written in first. */
+export declare const SOURCE_LOCALE = "en";
+/** One catalog a page renders messages from. */
+export interface CatalogSource {
+    /**
+     * The name the page knows the catalog by, unique on the page, e.g.
+     * `translate.cheminfo.org` or `react-cheminfo/share`.
+     */
+    id: string;
+    /** The GitHub repository the files live in, written `owner/repo`. */
+    repository: string;
+    /**
+     * The directory holding `en.json` and the locale files, relative to the
+     * repository root, e.g. `frontend/src/locales`.
+     */
+    directory: string;
+    /** The English messages. */
+    messages: Messages;
+}
+/** Which message of which catalog. */
+export interface MessageRef {
+    /** The catalog, by the id the page registered it under. */
+    catalogId: string;
+    /** The key of the message in that catalog. */
+    key: string;
+}
+/**
+ * The message a catalog holds under a key, never one inherited from
+ * `Object.prototype`: a key like `constructor` is only a message when the
+ * catalog defines it.
+ * @param messages - The catalog's messages.
+ * @param key - The key asked for.
+ * @returns The message, or `undefined` when the catalog has none.
+ */
+export declare function ownMessage(messages: Messages, key: string): string | undefined;
+/**
+ * Whether a path can name a catalog directory: relative, without `.` or `..`
+ * segments, and ending in a directory called `locales`. The server only ever
+ * writes inside such a directory.
+ * @param value - The candidate path, e.g. `frontend/src/locales`.
+ * @returns True when the path is acceptable.
+ */
+export declare function isCatalogDirectory(value: string): boolean;
+/**
+ * The file a catalog keeps one locale's messages in.
+ * @param directory - The catalog directory.
+ * @param locale - The locale.
+ * @returns The path, relative to the repository root.
+ */
+export declare function catalogFile(directory: string, locale: string): string;
+//# sourceMappingURL=catalog.d.ts.map

package/lib/translate/core/catalog.d.ts.map

@@ -0,0 +1 @@
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package/lib/translate/core/catalog.js

@@ -0,0 +1,49 @@
+/**
+ * The shape of the messages a site or a library owns, and where they are kept.
+ *
+ * A catalog is one directory of a repository holding `en.json`, the source of
+ * truth, and one flat file per locale beside it. The site registers each of
+ * its catalogs with the repository and the directory, so a translation made
+ * anywhere on the page can be sent back to the file it belongs to.
+ */
+/** The locale every catalog is written in first. */
+export const SOURCE_LOCALE = 'en';
+const DIRECTORY_SEGMENT = /^[\w-][\w.-]*$/;
+/**
+ * The message a catalog holds under a key, never one inherited from
+ * `Object.prototype`: a key like `constructor` is only a message when the
+ * catalog defines it.
+ * @param messages - The catalog's messages.
+ * @param key - The key asked for.
+ * @returns The message, or `undefined` when the catalog has none.
+ */
+export function ownMessage(messages, key) {
+    return Object.hasOwn(messages, key) ? messages[key] : undefined;
+}
+/**
+ * Whether a path can name a catalog directory: relative, without `.` or `..`
+ * segments, and ending in a directory called `locales`. The server only ever
+ * writes inside such a directory.
+ * @param value - The candidate path, e.g. `frontend/src/locales`.
+ * @returns True when the path is acceptable.
+ */
+export function isCatalogDirectory(value) {
+    const segments = value.split('/');
+    if (segments.at(-1) !== 'locales')
+        return false;
+    for (const segment of segments) {
+        if (!DIRECTORY_SEGMENT.test(segment))
+            return false;
+    }
+    return true;
+}
+/**
+ * The file a catalog keeps one locale's messages in.
+ * @param directory - The catalog directory.
+ * @param locale - The locale.
+ * @returns The path, relative to the repository root.
+ */
+export function catalogFile(directory, locale) {
+    return `${directory}/${locale}.json`;
+}
+//# sourceMappingURL=catalog.js.map

package/lib/translate/core/catalog.js.map

@@ -0,0 +1 @@
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package/lib/translate/core/checkTranslation.d.ts

@@ -0,0 +1,32 @@
+/** What can be wrong with one translated message. */
+export type MessageProblemKind = 'empty' | 'syntax' | 'source-syntax' | 'missing-argument' | 'unknown-argument';
+/** One thing wrong with a translated message, worded for the translator. */
+export interface MessageProblem {
+    /** What kind of problem it is. */
+    kind: MessageProblemKind;
+    /** The sentence the translator reads. */
+    message: string;
+    /**
+     * The placeholder or tag the problem is about, written as it appears in a
+     * message: `{count}` or `<link>`.
+     * @default undefined
+     */
+    argument?: string;
+}
+/**
+ * Check a translation against the English message it translates: it must be
+ * a valid ICU message and use exactly the placeholders and tags of the source.
+ * @param source - The English message.
+ * @param translation - The translated message.
+ * @returns Every problem found; empty when the translation can be used.
+ */
+export declare function checkTranslation(source: string, translation: string): MessageProblem[];
+/**
+ * The placeholders and tags a message uses, each written as it appears in the
+ * message: `{count}` for an argument, `<link>` for a tag.
+ * @param message - An ICU message.
+ * @returns The set of placeholders and tags.
+ * @throws {SyntaxError} When the message does not parse.
+ */
+export declare function messageArguments(message: string): Set<string>;
+//# sourceMappingURL=checkTranslation.d.ts.map

package/lib/translate/core/checkTranslation.d.ts.map

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