react-cheminfo 0.75.0 → 0.77.0

package/lib/osiris/core/poolTypes.js

@@ -0,0 +1,12 @@
+/**
+ * What a page asks the prediction pool, and what it hears back.
+ *
+ * A prediction costs 210 to 380 ms of one thread, so a set of any size is
+ * answered a molecule at a time rather than all at once: a row appears as soon
+ * as it is read and fills in when its worker returns. Everything here is shaped
+ * around that — a per-result callback rather than a promise over the set, a
+ * progress figure, a cancel that works, and a way to say which rows the reader
+ * can actually see so those are computed first.
+ */
+export {};
+//# sourceMappingURL=poolTypes.js.map

package/lib/osiris/core/poolTypes.js.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictIdCode.d.ts

@@ -0,0 +1,39 @@
+/**
+ * Prediction from the only thing worth keeping per row.
+ *
+ * A row never holds an `OCL.Molecule` — ten thousand of them cost 198 MB — so
+ * what travels to a worker is the idCode, and the molecule is rebuilt there in
+ * a quarter of a millisecond against the 380 ms the prediction itself costs.
+ */
+import type { ComputePropertiesOptions } from './computeProperties.ts';
+import type { OsirisPredictors } from './predictors.ts';
+import type { OsirisProperties, RiskDetail, RiskType } from './types.ts';
+/**
+ * What is said when an idCode cannot be read.
+ *
+ * An idCode is written by a program, not typed by a chemist, so there is no
+ * position to point at and no parser reason worth repeating: OpenChemLib
+ * answers a malformed one with `Cannot set properties of undefined`, which
+ * names nothing anyone can act on. Worse, it does not always throw — `zzzz`
+ * reads as a 117-atom molecule — so this is the floor, not the whole guard.
+ */
+export declare const UNREADABLE_ID_CODE_MESSAGE = "This structure could not be read.";
+/**
+ * Predict everything the tool shows, from an idCode.
+ * @param value - The idCode, with the editor's atom coordinates after a space or without them.
+ * @param predictors - OpenChemLib with its resources registered and checked.
+ * @param options - See {@link ComputePropertiesOptions}.
+ * @returns The ten numbers, the four risks, and what to call the molecule.
+ * @throws {Error} When the idCode cannot be read, or describes no atoms.
+ */
+export declare function predictIdCode(value: string, predictors: OsirisPredictors, options?: ComputePropertiesOptions): OsirisProperties;
+/**
+ * Why one risk came back as it did, from an idCode.
+ * @param value - The idCode, coordinates included or not.
+ * @param risk - Which of the four risks to explain.
+ * @param predictors - OpenChemLib with its resources registered and checked.
+ * @returns The findings, with the matched atoms and bonds of every fragment.
+ * @throws {Error} When the idCode cannot be read.
+ */
+export declare function riskDetailOfIdCode(value: string, risk: RiskType, predictors: OsirisPredictors): RiskDetail;
+//# sourceMappingURL=predictIdCode.d.ts.map

package/lib/osiris/core/predictIdCode.d.ts.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictIdCode.js

@@ -0,0 +1,54 @@
+/**
+ * Prediction from the only thing worth keeping per row.
+ *
+ * A row never holds an `OCL.Molecule` — ten thousand of them cost 198 MB — so
+ * what travels to a worker is the idCode, and the molecule is rebuilt there in
+ * a quarter of a millisecond against the 380 ms the prediction itself costs.
+ */
+import { splitIdCode } from "../../structure/core/editorValue.js";
+import { computeProperties } from "./computeProperties.js";
+import { riskDetail } from "./riskDetail.js";
+/**
+ * What is said when an idCode cannot be read.
+ *
+ * An idCode is written by a program, not typed by a chemist, so there is no
+ * position to point at and no parser reason worth repeating: OpenChemLib
+ * answers a malformed one with `Cannot set properties of undefined`, which
+ * names nothing anyone can act on. Worse, it does not always throw — `zzzz`
+ * reads as a 117-atom molecule — so this is the floor, not the whole guard.
+ */
+export const UNREADABLE_ID_CODE_MESSAGE = 'This structure could not be read.';
+/**
+ * Predict everything the tool shows, from an idCode.
+ * @param value - The idCode, with the editor's atom coordinates after a space or without them.
+ * @param predictors - OpenChemLib with its resources registered and checked.
+ * @param options - See {@link ComputePropertiesOptions}.
+ * @returns The ten numbers, the four risks, and what to call the molecule.
+ * @throws {Error} When the idCode cannot be read, or describes no atoms.
+ */
+export function predictIdCode(value, predictors, options = {}) {
+    return computeProperties(read(value, predictors), predictors, options);
+}
+/**
+ * Why one risk came back as it did, from an idCode.
+ * @param value - The idCode, coordinates included or not.
+ * @param risk - Which of the four risks to explain.
+ * @param predictors - OpenChemLib with its resources registered and checked.
+ * @returns The findings, with the matched atoms and bonds of every fragment.
+ * @throws {Error} When the idCode cannot be read.
+ */
+export function riskDetailOfIdCode(value, risk, predictors) {
+    return riskDetail(read(value, predictors), risk, predictors);
+}
+function read(value, predictors) {
+    const { idCode, coordinates } = splitIdCode(value);
+    try {
+        return coordinates === undefined
+            ? predictors.Molecule.fromIDCode(idCode)
+            : predictors.Molecule.fromIDCode(idCode, coordinates);
+    }
+    catch (error) {
+        throw new Error(UNREADABLE_ID_CODE_MESSAGE, { cause: error });
+    }
+}
+//# sourceMappingURL=predictIdCode.js.map

package/lib/osiris/core/predictIdCode.js.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictProtocol.d.ts

@@ -0,0 +1,67 @@
+/**
+ * What the page asks a prediction worker, and what it answers.
+ *
+ * One molecule per request. Two of the three answers are ordinary results; the
+ * third, `unavailable`, is how a worker says its resource tables did not load.
+ * That one travels as a *successful* answer on purpose: a rejection would be
+ * indistinguishable from the ordinary failure of one unreadable structure,
+ * whereas this one means every answer from every worker is worthless and the
+ * run must stop and say so.
+ */
+import type { ResourceSource } from './predictors.ts';
+import type { OsirisProperties, RiskDetail, RiskType } from './types.ts';
+/** What every request carries, whichever job it asks for. */
+interface BaseRequest {
+    /**
+     * Where the worker registers OpenChemLib's resources from. In a browser this
+     * is always the absolute URL of the site's own `openchemlib-resources.json`,
+     * resolved on the main thread: a worker has no `document`, so it cannot read
+     * the deployment's mount path itself. The parsed tables are accepted as well,
+     * for the in-process fallback where there is no worker to post them to.
+     */
+    resources: ResourceSource;
+}
+/** Predict everything the tool shows for one molecule. */
+export interface PropertiesRequest extends BaseRequest {
+    kind: 'properties';
+    /** The caller's key for the row, echoed back so answers can arrive in any order. */
+    key: string;
+    /** The idCode, with the editor's atom coordinates after a space or without. */
+    idCode: string;
+    /**
+     * The name the source carried.
+     * @default the canonical SMILES
+     */
+    label?: string;
+}
+/** Explain why one risk came back as it did. */
+export interface RiskDetailRequest extends BaseRequest {
+    kind: 'riskDetail';
+    /** The idCode, coordinates included or not. */
+    idCode: string;
+    /** Which of the four risks to explain. */
+    risk: RiskType;
+}
+/** One job for a prediction worker. */
+export type PredictRequest = PropertiesRequest | RiskDetailRequest;
+/** What a prediction worker answers. */
+export type PredictResponse = {
+    kind: 'properties';
+    key: string;
+    properties: OsirisProperties;
+} | {
+    kind: 'riskDetail';
+    detail: RiskDetail;
+} | {
+    kind: 'unavailable';
+    message: string;
+};
+/**
+ * Whether a message is a job this worker handles, so anything else is refused
+ * rather than read as one.
+ * @param value - Whatever was posted.
+ * @returns True when it is a well-formed request.
+ */
+export declare function isPredictRequest(value: unknown): value is PredictRequest;
+export {};
+//# sourceMappingURL=predictProtocol.d.ts.map

package/lib/osiris/core/predictProtocol.d.ts.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictProtocol.js

@@ -0,0 +1,29 @@
+/**
+ * What the page asks a prediction worker, and what it answers.
+ *
+ * One molecule per request. Two of the three answers are ordinary results; the
+ * third, `unavailable`, is how a worker says its resource tables did not load.
+ * That one travels as a *successful* answer on purpose: a rejection would be
+ * indistinguishable from the ordinary failure of one unreadable structure,
+ * whereas this one means every answer from every worker is worthless and the
+ * run must stop and say so.
+ */
+/**
+ * Whether a message is a job this worker handles, so anything else is refused
+ * rather than read as one.
+ * @param value - Whatever was posted.
+ * @returns True when it is a well-formed request.
+ */
+export function isPredictRequest(value) {
+    if (typeof value !== 'object' || value === null)
+        return false;
+    const request = value;
+    if (typeof request.idCode !== 'string')
+        return false;
+    if (request.resources === undefined)
+        return false;
+    if (request.kind === 'properties')
+        return typeof request.key === 'string';
+    return request.kind === 'riskDetail' && typeof request.risk === 'string';
+}
+//# sourceMappingURL=predictProtocol.js.map

package/lib/osiris/core/predictProtocol.js.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictionPool.d.ts

@@ -0,0 +1,23 @@
+/**
+ * A pool of prediction workers, answering one molecule at a time each.
+ *
+ * `createWorkerChannel` from `react-cheminfo/core` does the per-worker half —
+ * request identifiers so answers match callers whatever order they arrive in,
+ * timeouts, cancellation, and the in-process fallback where a page has no
+ * `Worker` at all. What it does not do is spread work over several workers, so
+ * that is what this adds: one channel per worker, a queue the pool owns, and at
+ * most one outstanding job per channel, which is what makes reordering possible
+ * at all. A channel asked for everything at once would post everything at once,
+ * and the row the reader is looking at would be answered forty-eighth.
+ */
+import type { PredictionPool, PredictionPoolOptions } from './poolTypes.ts';
+/**
+ * Start a pool of prediction workers.
+ *
+ * Workers are created lazily by the channels, on their first job, so a page
+ * that never predicts anything never loads OpenChemLib.
+ * @param options - See {@link PredictionPoolOptions}.
+ * @returns The pool.
+ */
+export declare function createPredictionPool(options: PredictionPoolOptions): PredictionPool;
+//# sourceMappingURL=predictionPool.d.ts.map

package/lib/osiris/core/predictionPool.d.ts.map

@@ -0,0 +1 @@
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package/lib/osiris/core/predictionPool.js

@@ -0,0 +1,186 @@
+/**
+ * A pool of prediction workers, answering one molecule at a time each.
+ *
+ * `createWorkerChannel` from `react-cheminfo/core` does the per-worker half —
+ * request identifiers so answers match callers whatever order they arrive in,
+ * timeouts, cancellation, and the in-process fallback where a page has no
+ * `Worker` at all. What it does not do is spread work over several workers, so
+ * that is what this adds: one channel per worker, a queue the pool owns, and at
+ * most one outstanding job per channel, which is what makes reordering possible
+ * at all. A channel asked for everything at once would post everything at once,
+ * and the row the reader is looking at would be answered forty-eighth.
+ */
+import { errorMessage } from "../../error/core/toError.js";
+import { CancelledRequestError } from "../../worker/core/errors.js";
+import { createWorkerChannel } from "../../worker/core/workerChannel.js";
+import { predictionPoolSize } from "./poolSize.js";
+import { createPredictionQueue } from "./predictionQueue.js";
+import { PredictorsUnavailableError } from "./predictors.js";
+import { requestRiskDetail } from "./riskDetailRequest.js";
+import { runPredictionJob } from "./runPredictionJob.js";
+/**
+ * Start a pool of prediction workers.
+ *
+ * Workers are created lazily by the channels, on their first job, so a page
+ * that never predicts anything never loads OpenChemLib.
+ * @param options - See {@link PredictionPoolOptions}.
+ * @returns The pool.
+ */
+export function createPredictionPool(options) {
+    const { resources, onResult, onProgress, onUnavailable, createWorker, runInProcess, timeoutMs = 60_000, } = options;
+    const size = predictionPoolSize(options.size);
+    const run = runInProcess ?? runPredictionJob;
+    const slots = [];
+    for (let index = 0; index < size; index++) {
+        slots.push({
+            channel: createWorkerChannel(createWorker, {
+                name: `osiris-prediction-${index}`,
+                defaultTimeoutMs: timeoutMs,
+                runInProcess: run,
+            }),
+            busy: false,
+        });
+    }
+    const queue = createPredictionQueue();
+    const inFlight = new Set();
+    let generation = 0;
+    let done = 0;
+    let total = 0;
+    let running = false;
+    let terminated = false;
+    let unavailable = null;
+    function progress() {
+        return { done, total, pending: queue.size + inFlight.size, running };
+    }
+    function report() {
+        onProgress?.(progress());
+    }
+    function pump() {
+        if (unavailable !== null)
+            return;
+        for (const slot of slots) {
+            if (slot.busy)
+                continue;
+            const next = queue.take();
+            if (next === undefined)
+                break;
+            dispatch(slot, next);
+        }
+    }
+    function dispatch(slot, input) {
+        const era = generation;
+        slot.busy = true;
+        inFlight.add(input.key);
+        const request = {
+            kind: 'properties',
+            resources,
+            key: input.key,
+            idCode: input.idCode,
+            ...(input.label === undefined ? {} : { label: input.label }),
+        };
+        slot.channel.request(request).then((response) => {
+            settle(slot, input, era, response, null);
+        }, (error) => {
+            settle(slot, input, era, null, error);
+        });
+    }
+    function settle(slot, input, era, response, error) {
+        slot.busy = false;
+        inFlight.delete(input.key);
+        // An answer from a cancelled run is not counted and not reported, but the
+        // slot it just freed is still dispatched from: a submit made in the same
+        // turn as the cancel found every slot busy and queued its molecules here.
+        if (era === generation) {
+            if (response?.kind === 'unavailable') {
+                stop(response.message);
+                return;
+            }
+            if (response?.kind === 'properties') {
+                done += 1;
+                onResult?.({
+                    key: input.key,
+                    ok: true,
+                    properties: response.properties,
+                });
+            }
+            else if (error !== null && !(error instanceof CancelledRequestError)) {
+                done += 1;
+                onResult?.({ key: input.key, ok: false, message: errorMessage(error) });
+            }
+        }
+        pump();
+        if (queue.size === 0 && inFlight.size === 0)
+            running = false;
+        report();
+    }
+    function clear() {
+        generation += 1;
+        queue.clear();
+        inFlight.clear();
+        running = false;
+        for (const slot of slots)
+            slot.channel.cancel();
+    }
+    function stop(message) {
+        clear();
+        unavailable = message;
+        report();
+        onUnavailable?.(message);
+    }
+    function leastBusy() {
+        let best = slots[0];
+        for (const slot of slots) {
+            if (slot.channel.pendingCount < best.channel.pendingCount)
+                best = slot;
+        }
+        return best;
+    }
+    return {
+        size,
+        get progress() {
+            return progress();
+        },
+        submit(molecules) {
+            if (unavailable !== null)
+                return;
+            if (!running && queue.size === 0 && inFlight.size === 0) {
+                done = 0;
+                total = 0;
+            }
+            for (const input of molecules) {
+                if (inFlight.has(input.key))
+                    continue;
+                if (queue.add(input))
+                    total += 1;
+            }
+            running = queue.size > 0 || inFlight.size > 0;
+            pump();
+            report();
+        },
+        prioritize(keys) {
+            queue.prioritize(keys);
+        },
+        async riskDetail(idCode, risk) {
+            const response = await requestRiskDetail(() => leastBusy().channel, { kind: 'riskDetail', resources, idCode, risk }, () => !terminated && unavailable === null);
+            if (response.kind === 'unavailable') {
+                stop(response.message);
+                throw new PredictorsUnavailableError(response.message);
+            }
+            if (response.kind !== 'riskDetail') {
+                throw new Error('The worker answered something other than a detail.');
+            }
+            return response.detail;
+        },
+        cancel() {
+            clear();
+            report();
+        },
+        terminate() {
+            terminated = true;
+            clear();
+            for (const slot of slots)
+                slot.channel.terminate();
+        },
+    };
+}
+//# sourceMappingURL=predictionPool.js.map

package/lib/osiris/core/predictionPool.js.map

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package/lib/osiris/core/predictionQueue.d.ts

@@ -0,0 +1,46 @@
+/**
+ * What is still to be predicted, in the order it will be.
+ *
+ * Arrival order by default, because that is the order the reader read the file
+ * in. On top of it sits a short list of keys to answer first — the rows
+ * actually on screen — which is re-laid every time the reader scrolls or
+ * focuses a row. A key named as wanted that has since been answered or removed
+ * is skipped rather than looked up again.
+ */
+import type { PredictionInput } from './poolTypes.ts';
+/** The molecules waiting, and which of them to take next. */
+export interface PredictionQueue {
+    /** How many are waiting. */
+    readonly size: number;
+    /**
+     * Whether one is waiting.
+     * @param key - The row's key.
+     * @returns True when it is still queued.
+     */
+    has: (key: string) => boolean;
+    /**
+     * Queue one molecule, unless its key is already waiting.
+     * @param input - The molecule.
+     * @returns True when it was added.
+     */
+    add: (input: PredictionInput) => boolean;
+    /**
+     * Take the next molecule to predict: the first still-queued key of the wanted
+     * list, else the one that has waited longest.
+     * @returns The molecule, or `undefined` when nothing is waiting.
+     */
+    take: () => PredictionInput | undefined;
+    /**
+     * Replace the list of keys to answer first.
+     * @param keys - The keys, most wanted first.
+     */
+    prioritize: (keys: readonly string[]) => void;
+    /** Forget everything waiting. */
+    clear: () => void;
+}
+/**
+ * A queue of molecules to predict.
+ * @returns The queue, empty.
+ */
+export declare function createPredictionQueue(): PredictionQueue;
+//# sourceMappingURL=predictionQueue.d.ts.map

package/lib/osiris/core/predictionQueue.d.ts.map

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package/lib/osiris/core/predictionQueue.js

@@ -0,0 +1,57 @@
+/**
+ * What is still to be predicted, in the order it will be.
+ *
+ * Arrival order by default, because that is the order the reader read the file
+ * in. On top of it sits a short list of keys to answer first — the rows
+ * actually on screen — which is re-laid every time the reader scrolls or
+ * focuses a row. A key named as wanted that has since been answered or removed
+ * is skipped rather than looked up again.
+ */
+/**
+ * A queue of molecules to predict.
+ * @returns The queue, empty.
+ */
+export function createPredictionQueue() {
+    const waiting = new Map();
+    let wanted = [];
+    let cursor = 0;
+    return {
+        get size() {
+            return waiting.size;
+        },
+        has: (key) => waiting.has(key),
+        add(input) {
+            if (waiting.has(input.key))
+                return false;
+            waiting.set(input.key, input);
+            return true;
+        },
+        take() {
+            while (cursor < wanted.length) {
+                const key = wanted[cursor];
+                cursor += 1;
+                const next = waiting.get(key);
+                if (next !== undefined) {
+                    waiting.delete(key);
+                    return next;
+                }
+            }
+            const first = waiting.keys().next();
+            if (first.done === true)
+                return undefined;
+            const next = waiting.get(first.value);
+            waiting.delete(first.value);
+            return next;
+        },
+        prioritize(keys) {
+            wanted = [...keys];
+            cursor = 0;
+        },
+        clear() {
+            waiting.clear();
+            wanted = [];
+            cursor = 0;
+        },
+    };
+}
+//# sourceMappingURL=predictionQueue.js.map

package/lib/osiris/core/predictionQueue.js.map

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package/lib/osiris/core/predictors.d.ts

@@ -0,0 +1,62 @@
+/**
+ * OpenChemLib, loaded once and proved to be working before anything is
+ * predicted with it.
+ *
+ * Both predictors throw `static resources must be registered first` until
+ * `Resources.register*` has run — but only when *nothing* was registered. If
+ * something else was, `new ToxicityPredictor()` constructs happily, prints to
+ * the console, and answers every `assessRisk` with `RISK_UNKNOWN`, on which
+ * `DrugScoreCalculator` applies no penalty at all. The failure therefore reads
+ * on screen as four clean molecules and a healthy score. So the tables are
+ * proved here, at start-up, against a molecule whose answer is known: a
+ * fragment match that must come back high, and a drug-likeness that must be a
+ * real number. Between them the two families of resource file are both covered.
+ *
+ * The check costs about 160 ms once per worker, most of which is warm-up the
+ * first real molecule would have paid anyway — measured, a first prediction is
+ * 320 ms cold against 191 ms warm.
+ */
+import type * as OCL from 'openchemlib';
+/**
+ * Where the resource tables come from: the URL of the site's own
+ * `openchemlib-resources.json`, or the parsed file itself.
+ *
+ * A URL must be absolute. `registerFromUrl` resolves a relative one against
+ * `import.meta.url`, which after a build is a hashed chunk under `assets/`, so
+ * it answers 404 and every prediction quietly becomes unknown.
+ */
+export type ResourceSource = string | Readonly<Record<string, string>>;
+/** OpenChemLib, registered, checked and ready to predict with. */
+export interface OsirisPredictors {
+    /** Reads an idCode or a SMILES into a molecule. */
+    Molecule: typeof OCL.Molecule;
+    /** cLogP, solubility, TPSA and the four counts. */
+    MoleculeProperties: typeof OCL.MoleculeProperties;
+    /** Finds a toxicophore on a molecule, in the predictor's own match mode. */
+    SSSearcher: typeof OCL.SSSearcher;
+    /** The four spline terms and the four risk factors. */
+    DrugScoreCalculator: typeof OCL.DrugScoreCalculator;
+    /** The four risk assessments and their explanations. */
+    toxicity: OCL.ToxicityPredictor;
+    /** The 5294-fragment drug-likeness table. */
+    druglikeness: OCL.DruglikenessPredictor;
+}
+/** The tables did not load, so nothing may be predicted. */
+export declare class PredictorsUnavailableError extends Error {
+    name: string;
+}
+/**
+ * OpenChemLib with its resources registered and checked.
+ *
+ * Loaded lazily — the library is 340 kB gzipped and does not tree-shake — and
+ * kept, because `Resources.register` replaces the whole map rather than merging
+ * into it, so registering twice with different keys silently unregisters the
+ * first set.
+ * @param source - The resources URL, or the parsed resources themselves.
+ * @returns The predictors, proved to answer.
+ * @throws {PredictorsUnavailableError} When the resources did not load, or loaded and answer nothing.
+ */
+export declare function loadPredictors(source: ResourceSource): Promise<OsirisPredictors>;
+/** Forget the loaded predictors, so the next call registers again. */
+export declare function resetPredictors(): void;
+//# sourceMappingURL=predictors.d.ts.map

package/lib/osiris/core/predictors.d.ts.map

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