react-cheminfo 0.76.0 → 0.77.0

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

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

@@ -0,0 +1,100 @@
+/**
+ * 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 { NO_FRAGMENT_MATCHED, RISK_TYPE_CODES, UNKNOWN_NUMBER, } from "./constants.js";
+/** The tables did not load, so nothing may be predicted. */
+export class PredictorsUnavailableError extends Error {
+    name = 'PredictorsUnavailableError';
+}
+/**
+ * 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 function loadPredictors(source) {
+    if (loaded === null)
+        loaded = start(source);
+    return loaded;
+}
+/** Forget the loaded predictors, so the next call registers again. */
+export function resetPredictors() {
+    loaded = null;
+}
+let loaded = null;
+/**
+ * A failed load is not kept: a fetch that failed once may well answer on the
+ * next try, and a cached rejection would turn one lost packet into a page that
+ * stays broken until it is reloaded.
+ * @param source - The resources URL, or the parsed resources themselves.
+ * @returns The predictors, proved to answer.
+ */
+function start(source) {
+    const pending = build(source);
+    void pending.catch(() => {
+        if (loaded === pending)
+            loaded = null;
+    });
+    return pending;
+}
+/** Benzidine — its mutagenicity comes from a fragment match, not from a list. */
+const PROBE_ID_CODE = 'dg}@@@mIe]e^ftx@H@H@@';
+const UNAVAILABLE = 'The prediction tables did not load, so no risk or drug-likeness can be computed. Reload the page.';
+async function build(source) {
+    const ocl = await import('openchemlib');
+    try {
+        if (typeof source === 'string')
+            await ocl.Resources.registerFromUrl(source);
+        else
+            ocl.Resources.register({ ...source });
+    }
+    catch {
+        throw new PredictorsUnavailableError(UNAVAILABLE);
+    }
+    let toxicity;
+    let druglikeness;
+    try {
+        toxicity = new ocl.ToxicityPredictor();
+        druglikeness = new ocl.DruglikenessPredictor();
+    }
+    catch {
+        throw new PredictorsUnavailableError(UNAVAILABLE);
+    }
+    const probe = ocl.Molecule.fromIDCode(PROBE_ID_CODE);
+    const risk = toxicity.assessRisk(probe, RISK_TYPE_CODES.mutagenic);
+    const likeness = druglikeness.assessDruglikeness(probe);
+    if (risk !== 3 ||
+        likeness === UNKNOWN_NUMBER ||
+        likeness === NO_FRAGMENT_MATCHED) {
+        throw new PredictorsUnavailableError(UNAVAILABLE);
+    }
+    return {
+        Molecule: ocl.Molecule,
+        MoleculeProperties: ocl.MoleculeProperties,
+        SSSearcher: ocl.SSSearcher,
+        DrugScoreCalculator: ocl.DrugScoreCalculator,
+        toxicity,
+        druglikeness,
+    };
+}
+//# sourceMappingURL=predictors.js.map

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

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

@@ -0,0 +1,32 @@
+/**
+ * Which of a molecule's predicted numbers the tool shows, and in which order.
+ *
+ * The order is the legacy panel's, top to bottom, and it is the same order the
+ * comparison table's columns and the plot's default axes take: a reader who
+ * learned the panel reads the table without relearning it. The keys are the
+ * field names of {@link OsirisProperties}, so an address carrying
+ * `axes=logP,logS` names the same things the panel does.
+ */
+import type { OsirisProperties } from './types.ts';
+/** The ten numbers the tool shows, in the order it shows them. */
+export declare const PROPERTY_KEYS: readonly ["logP", "logS", "molecularWeight", "polarSurfaceArea", "druglikeness", "acceptorCount", "donorCount", "stereoCenterCount", "rotatableBondCount", "drugScore"];
+/** One of the ten displayed properties. */
+export type PropertyKey = (typeof PROPERTY_KEYS)[number];
+/**
+ * Whether a string names a displayed property, so an address that carries
+ * something else is ignored rather than plotted as a blank axis.
+ * @param value - Whatever the address or the reader supplied.
+ * @returns True when it is one of the ten.
+ */
+export declare function isPropertyKey(value: string): value is PropertyKey;
+/**
+ * One property of one molecule.
+ *
+ * `null` means the predictor could not answer — never zero, and never the
+ * library's own sentinel, both of which plot and sort as real values.
+ * @param properties - What was predicted for the molecule.
+ * @param key - Which of the ten to read.
+ * @returns The number, or `null` when it is unknown.
+ */
+export declare function propertyValue(properties: OsirisProperties, key: PropertyKey): number | null;
+//# sourceMappingURL=propertyKeys.d.ts.map

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

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package/lib/osiris/core/propertyKeys.js

@@ -0,0 +1,44 @@
+/**
+ * Which of a molecule's predicted numbers the tool shows, and in which order.
+ *
+ * The order is the legacy panel's, top to bottom, and it is the same order the
+ * comparison table's columns and the plot's default axes take: a reader who
+ * learned the panel reads the table without relearning it. The keys are the
+ * field names of {@link OsirisProperties}, so an address carrying
+ * `axes=logP,logS` names the same things the panel does.
+ */
+/** The ten numbers the tool shows, in the order it shows them. */
+export const PROPERTY_KEYS = [
+    'logP',
+    'logS',
+    'molecularWeight',
+    'polarSurfaceArea',
+    'druglikeness',
+    'acceptorCount',
+    'donorCount',
+    'stereoCenterCount',
+    'rotatableBondCount',
+    'drugScore',
+];
+/**
+ * Whether a string names a displayed property, so an address that carries
+ * something else is ignored rather than plotted as a blank axis.
+ * @param value - Whatever the address or the reader supplied.
+ * @returns True when it is one of the ten.
+ */
+export function isPropertyKey(value) {
+    return PROPERTY_KEYS.includes(value);
+}
+/**
+ * One property of one molecule.
+ *
+ * `null` means the predictor could not answer — never zero, and never the
+ * library's own sentinel, both of which plot and sort as real values.
+ * @param properties - What was predicted for the molecule.
+ * @param key - Which of the ten to read.
+ * @returns The number, or `null` when it is unknown.
+ */
+export function propertyValue(properties, key) {
+    return properties[key];
+}
+//# sourceMappingURL=propertyKeys.js.map

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

@@ -0,0 +1,60 @@
+/**
+ * How one risk reads on screen: the word for it, and the tone its square takes.
+ *
+ * Three levels, and they are exactly the three `DrugScoreCalculator` multiplies
+ * by — no risk ×1, medium ×0.8, high ×0.6 — so the colours say what the score
+ * already counted. A fourth tone exists for the state the library calls
+ * `RISK_UNKNOWN`, which means its tables did not load: it is grey, never green,
+ * because "nothing was assessed" and "nothing was found" are different answers
+ * and showing them alike is the one mistake that makes the panel dishonest.
+ *
+ * A fifth, `pending`, is ours: the prediction costs a fifth of a second and the
+ * square is on screen before it comes back.
+ */
+import type { RiskLevel } from './types.ts';
+/** What a square is painted with, before the stylesheet turns it into a colour. */
+export type RiskTone = 'pending' | 'unknown' | 'none' | 'low' | 'high';
+/** How one risk is shown. */
+export interface RiskAppearance {
+    /** The stylesheet's `data-level`, which picks the square's colour. */
+    tone: RiskTone;
+    /** What the square says next to the risk's name, e.g. `High risk`. */
+    label: string;
+    /**
+     * Whether the level is worth opening: an explanation exists for an assessed
+     * risk and for nothing else.
+     */
+    explainable: boolean;
+}
+/** What a square says while its molecule is still being predicted. */
+export declare const PENDING_RISK_LABEL = "Predicting\u2026";
+/**
+ * What a square says when there is no molecule to predict.
+ *
+ * The comparison page draws the panel before a row is picked, and a square that
+ * said `Predicting…` there would claim work nobody asked for — under a heading
+ * inviting the reader to pick a row, which is a plain contradiction.
+ */
+export declare const IDLE_RISK_LABEL = "Not predicted yet";
+/**
+ * What the predictor's own page says about its alerts, word for word.
+ *
+ * Quoted rather than paraphrased: it is the sentence that stops a red square
+ * being read as a verdict, and rewriting it would put our words over his.
+ */
+export declare const RISK_CAVEAT = "Toxicity risk alerts are by no means meant to be a fully reliable toxicity prediction. Nor should be concluded from the absence of risk alerts that a particular substance is completely free of any toxic effect.";
+/**
+ * What is said in place of a highlight when the compound's own idCode is on one
+ * of the RTECS-derived lists. There is no fragment to point at, and painting the
+ * whole molecule would call the compound its own toxicophore.
+ */
+export declare const KNOWN_MOLECULE_NOTE = "This exact compound is on the list, so there is no fragment to point at.";
+/**
+ * The tone and the word for one risk.
+ * @param level - How the risk came back, or `undefined` when there is none yet.
+ * @param pending - Whether a prediction is actually running for this molecule.
+ * @default false
+ * @returns See {@link RiskAppearance}.
+ */
+export declare function riskAppearance(level: RiskLevel | undefined, pending?: boolean): RiskAppearance;
+//# sourceMappingURL=riskAppearance.d.ts.map

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

@@ -0,0 +1 @@
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