react-cheminfo 0.75.0 → 0.77.0

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

@@ -0,0 +1,20 @@
+/**
+ * One prediction, wherever it runs.
+ *
+ * The worker serves this, and a page with no `Worker` at all — a unit test,
+ * Node — runs the same function on its own thread. One code path, so what the
+ * tests prove is what the page does.
+ */
+import type { PredictRequest, PredictResponse } from './predictProtocol.ts';
+/**
+ * Answer one job.
+ *
+ * A structure that cannot be read, or that holds no atoms, throws: that is one
+ * bad row, and the run carries on without it. Resources that did not load
+ * return `unavailable` instead, because that is every row and the run must stop.
+ * @param request - The job.
+ * @returns The answer.
+ * @throws {Error} When the molecule itself could not be read or predicted.
+ */
+export declare function runPredictionJob(request: PredictRequest): Promise<PredictResponse>;
+//# sourceMappingURL=runPredictionJob.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"runPredictionJob.d.ts","sourceRoot":"","sources":["../../../src/osiris/core/runPredictionJob.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,KAAK,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AAG5E;;;;;;;;;GASG;AACH,wBAAsB,gBAAgB,CACpC,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,eAAe,CAAC,CAsB1B"}

package/lib/osiris/core/runPredictionJob.js

@@ -0,0 +1,43 @@
+/**
+ * One prediction, wherever it runs.
+ *
+ * The worker serves this, and a page with no `Worker` at all — a unit test,
+ * Node — runs the same function on its own thread. One code path, so what the
+ * tests prove is what the page does.
+ */
+import { errorMessage } from "../../error/core/toError.js";
+import { predictIdCode, riskDetailOfIdCode } from "./predictIdCode.js";
+import { loadPredictors } from "./predictors.js";
+/**
+ * Answer one job.
+ *
+ * A structure that cannot be read, or that holds no atoms, throws: that is one
+ * bad row, and the run carries on without it. Resources that did not load
+ * return `unavailable` instead, because that is every row and the run must stop.
+ * @param request - The job.
+ * @returns The answer.
+ * @throws {Error} When the molecule itself could not be read or predicted.
+ */
+export async function runPredictionJob(request) {
+    let predictors;
+    try {
+        predictors = await loadPredictors(request.resources);
+    }
+    catch (error) {
+        return { kind: 'unavailable', message: errorMessage(error) };
+    }
+    if (request.kind === 'riskDetail') {
+        return {
+            kind: 'riskDetail',
+            detail: riskDetailOfIdCode(request.idCode, request.risk, predictors),
+        };
+    }
+    return {
+        kind: 'properties',
+        key: request.key,
+        properties: predictIdCode(request.idCode, predictors, {
+            ...(request.label === undefined ? {} : { label: request.label }),
+        }),
+    };
+}
+//# sourceMappingURL=runPredictionJob.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"runPredictionJob.js","sourceRoot":"","sources":["../../../src/osiris/core/runPredictionJob.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,YAAY,EAAE,MAAM,6BAA6B,CAAC;AAE3D,OAAO,EAAE,aAAa,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAEvE,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAEjD;;;;;;;;;GASG;AACH,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,OAAuB;IAEvB,IAAI,UAAU,CAAC;IACf,IAAI,CAAC;QACH,UAAU,GAAG,MAAM,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IACvD,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,EAAE,IAAI,EAAE,aAAa,EAAE,OAAO,EAAE,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC;IAC/D,CAAC;IAED,IAAI,OAAO,CAAC,IAAI,KAAK,YAAY,EAAE,CAAC;QAClC,OAAO;YACL,IAAI,EAAE,YAAY;YAClB,MAAM,EAAE,kBAAkB,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,IAAI,EAAE,UAAU,CAAC;SACrE,CAAC;IACJ,CAAC;IAED,OAAO;QACL,IAAI,EAAE,YAAY;QAClB,GAAG,EAAE,OAAO,CAAC,GAAG;QAChB,UAAU,EAAE,aAAa,CAAC,OAAO,CAAC,MAAM,EAAE,UAAU,EAAE;YACpD,GAAG,CAAC,OAAO,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,KAAK,EAAE,CAAC;SACjE,CAAC;KACH,CAAC;AACJ,CAAC"}

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

@@ -0,0 +1,70 @@
+/**
+ * The scale every displayed property is read on: how wide the bar is, where
+ * the good band sits, and which published number the labelled mark names.
+ *
+ * Eight of the ten come verbatim from DataWarrior's own `MolecularPropertyHelper.SPEC`
+ * table — the same ranges its own property views draw — so nothing here is a
+ * cut-off picked to look right. The two it has no entry for, drug-likeness and
+ * the drug score, keep the legacy explorer's ranges, and take their fitness
+ * from `DrugScoreCalculator`'s own terms rather than from a new guess.
+ *
+ * The preferred band and the published threshold are different numbers on
+ * purpose: cLogP's band closes at 4, where DataWarrior puts it, while the
+ * published rule of thumb the mark names is 5. The band draws the colour, the
+ * threshold draws the line.
+ */
+import type { PropertyKey } from './propertyKeys.ts';
+/** A published rule of thumb, drawn on the bar as a labelled mark. */
+export interface PropertyThreshold {
+    /** Where on the bar the mark goes. */
+    value: number;
+    /** How it reads, e.g. `≤ 5`. */
+    label: string;
+}
+/** Where a shared scale's numbers come from. */
+export type ScaleSource = 'datawarrior' | 'legacy';
+/** How one property is drawn, ranged and judged. */
+export interface PropertyScale {
+    /** The field of `OsirisProperties` this describes. */
+    key: PropertyKey;
+    /** What the panel and the table column call it. */
+    label: string;
+    /** The unit, empty where the quantity is dimensionless. */
+    unit: string;
+    /** Decimals the value is shown to; `0` for a count. */
+    decimals: number;
+    /** The left end of the bar, and of the plot axis. */
+    rangeMin: number;
+    /** The right end of the bar, and of the plot axis. */
+    rangeMax: number;
+    /** The bottom of the preferred band, or `null` when it has no lower bound. */
+    preferredMin: number | null;
+    /** The top of the preferred band, or `null` when it has no upper bound. */
+    preferredMax: number | null;
+    /**
+     * How far outside the band the fitness takes to fall away. `null` for a
+     * quantity that is already a 0-to-1 fitness.
+     */
+    halfWidth: number | null;
+    /**
+     * Whether a larger number is the better one. `null` where the property has a
+     * band rather than a direction — a molecule wants some stereocentres, not as
+     * many or as few as possible.
+     */
+    higherIsBetter: boolean | null;
+    /** The published rule of thumb to mark, or `null` where there is none. */
+    threshold: PropertyThreshold | null;
+    /** Whether the bar grows from the middle rather than from the left. */
+    diverging: boolean;
+    /** Where the range and the band came from. */
+    source: ScaleSource;
+}
+/** How each displayed property is drawn, ranged and judged. */
+export declare const PROPERTY_SCALES: Record<PropertyKey, PropertyScale>;
+/**
+ * How one property is drawn, ranged and judged.
+ * @param key - Which of the ten.
+ * @returns Its scale.
+ */
+export declare function propertyScale(key: PropertyKey): PropertyScale;
+//# sourceMappingURL=scales.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"scales.d.ts","sourceRoot":"","sources":["../../../src/osiris/core/scales.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAErD,sEAAsE;AACtE,MAAM,WAAW,iBAAiB;IAChC,sCAAsC;IACtC,KAAK,EAAE,MAAM,CAAC;IACd,gCAAgC;IAChC,KAAK,EAAE,MAAM,CAAC;CACf;AAED,gDAAgD;AAChD,MAAM,MAAM,WAAW,GAAG,aAAa,GAAG,QAAQ,CAAC;AAEnD,oDAAoD;AACpD,MAAM,WAAW,aAAa;IAC5B,sDAAsD;IACtD,GAAG,EAAE,WAAW,CAAC;IACjB,mDAAmD;IACnD,KAAK,EAAE,MAAM,CAAC;IACd,2DAA2D;IAC3D,IAAI,EAAE,MAAM,CAAC;IACb,uDAAuD;IACvD,QAAQ,EAAE,MAAM,CAAC;IACjB,qDAAqD;IACrD,QAAQ,EAAE,MAAM,CAAC;IACjB,sDAAsD;IACtD,QAAQ,EAAE,MAAM,CAAC;IACjB,8EAA8E;IAC9E,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,2EAA2E;IAC3E,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B;;;OAGG;IACH,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB;;;;OAIG;IACH,cAAc,EAAE,OAAO,GAAG,IAAI,CAAC;IAC/B,0EAA0E;IAC1E,SAAS,EAAE,iBAAiB,GAAG,IAAI,CAAC;IACpC,uEAAuE;IACvE,SAAS,EAAE,OAAO,CAAC;IACnB,8CAA8C;IAC9C,MAAM,EAAE,WAAW,CAAC;CACrB;AAED,+DAA+D;AAC/D,eAAO,MAAM,eAAe,EAAE,MAAM,CAAC,WAAW,EAAE,aAAa,CA+J9D,CAAC;AAEF;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,WAAW,GAAG,aAAa,CAE7D"}

package/lib/osiris/core/scales.js

@@ -0,0 +1,185 @@
+/**
+ * The scale every displayed property is read on: how wide the bar is, where
+ * the good band sits, and which published number the labelled mark names.
+ *
+ * Eight of the ten come verbatim from DataWarrior's own `MolecularPropertyHelper.SPEC`
+ * table — the same ranges its own property views draw — so nothing here is a
+ * cut-off picked to look right. The two it has no entry for, drug-likeness and
+ * the drug score, keep the legacy explorer's ranges, and take their fitness
+ * from `DrugScoreCalculator`'s own terms rather than from a new guess.
+ *
+ * The preferred band and the published threshold are different numbers on
+ * purpose: cLogP's band closes at 4, where DataWarrior puts it, while the
+ * published rule of thumb the mark names is 5. The band draws the colour, the
+ * threshold draws the line.
+ */
+/** How each displayed property is drawn, ranged and judged. */
+export const PROPERTY_SCALES = {
+    logP: {
+        key: 'logP',
+        label: 'cLogP',
+        unit: '',
+        decimals: 2,
+        rangeMin: 0,
+        rangeMax: 8,
+        preferredMin: null,
+        preferredMax: 4,
+        halfWidth: 0.5,
+        higherIsBetter: false,
+        threshold: { value: 5, label: '≤ 5' },
+        diverging: false,
+        source: 'datawarrior',
+    },
+    logS: {
+        key: 'logS',
+        label: 'Solubility',
+        unit: 'log(mol/L)',
+        decimals: 2,
+        rangeMin: -8,
+        rangeMax: 2,
+        preferredMin: -4,
+        preferredMax: null,
+        halfWidth: 0.5,
+        higherIsBetter: true,
+        threshold: { value: -4, label: '> −4' },
+        diverging: false,
+        source: 'datawarrior',
+    },
+    molecularWeight: {
+        key: 'molecularWeight',
+        label: 'Molweight',
+        unit: 'g/mol',
+        decimals: 2,
+        rangeMin: 0,
+        rangeMax: 800,
+        preferredMin: null,
+        preferredMax: 400,
+        halfWidth: 50,
+        higherIsBetter: false,
+        threshold: { value: 450, label: '< 450' },
+        diverging: false,
+        source: 'datawarrior',
+    },
+    polarSurfaceArea: {
+        key: 'polarSurfaceArea',
+        label: 'TPSA',
+        unit: 'Ų',
+        decimals: 2,
+        rangeMin: 0,
+        rangeMax: 250,
+        preferredMin: null,
+        preferredMax: 120,
+        halfWidth: 20,
+        higherIsBetter: false,
+        threshold: null,
+        diverging: false,
+        source: 'datawarrior',
+    },
+    druglikeness: {
+        key: 'druglikeness',
+        label: 'Druglikeness',
+        unit: '',
+        decimals: 2,
+        rangeMin: -10,
+        rangeMax: 10,
+        preferredMin: 0,
+        preferredMax: null,
+        // `DrugScoreCalculator` scores drug-likeness as 1/(1+e^-d), which is this
+        // same valuation with a lower bound of 0 and a half-width of 1. So the
+        // ramp behind the bar is the library's own term, not a second opinion.
+        halfWidth: 1,
+        higherIsBetter: true,
+        threshold: { value: 0, label: '> 0' },
+        diverging: true,
+        source: 'legacy',
+    },
+    acceptorCount: {
+        key: 'acceptorCount',
+        label: 'H-bond acceptors',
+        unit: '',
+        decimals: 0,
+        rangeMin: 0,
+        rangeMax: 16,
+        preferredMin: null,
+        preferredMax: 10,
+        halfWidth: 1,
+        higherIsBetter: false,
+        threshold: null,
+        diverging: false,
+        source: 'datawarrior',
+    },
+    donorCount: {
+        key: 'donorCount',
+        label: 'H-bond donors',
+        unit: '',
+        decimals: 0,
+        rangeMin: 0,
+        rangeMax: 8,
+        preferredMin: null,
+        preferredMax: 5,
+        halfWidth: 0.5,
+        higherIsBetter: false,
+        threshold: null,
+        diverging: false,
+        source: 'datawarrior',
+    },
+    stereoCenterCount: {
+        key: 'stereoCenterCount',
+        label: 'Stereocentres',
+        unit: '',
+        decimals: 0,
+        rangeMin: 0,
+        rangeMax: 8,
+        preferredMin: 1,
+        preferredMax: 3,
+        halfWidth: 2,
+        higherIsBetter: null,
+        threshold: null,
+        diverging: false,
+        source: 'datawarrior',
+    },
+    rotatableBondCount: {
+        key: 'rotatableBondCount',
+        label: 'Rotatable bonds',
+        unit: '',
+        decimals: 0,
+        rangeMin: 0,
+        rangeMax: 20,
+        preferredMin: null,
+        preferredMax: 4,
+        halfWidth: 5,
+        higherIsBetter: false,
+        threshold: null,
+        diverging: false,
+        source: 'datawarrior',
+    },
+    drugScore: {
+        key: 'drugScore',
+        label: 'Drug score',
+        unit: '',
+        decimals: 2,
+        // The legacy bar, kept: it grows from the middle and runs -1 to 1, so a
+        // score always sits in its right half. The quantity itself is a product of
+        // terms in (0.5, 1) and four risk factors, so it cannot leave (0, 1).
+        rangeMin: -1,
+        rangeMax: 1,
+        preferredMin: null,
+        preferredMax: null,
+        // Already a 0-to-1 fitness: it is the product of the four valuations
+        // `DrugScoreCalculator` computes, so valuing it again would square it.
+        halfWidth: null,
+        higherIsBetter: true,
+        threshold: null,
+        diverging: true,
+        source: 'legacy',
+    },
+};
+/**
+ * How one property is drawn, ranged and judged.
+ * @param key - Which of the ten.
+ * @returns Its scale.
+ */
+export function propertyScale(key) {
+    return PROPERTY_SCALES[key];
+}
+//# sourceMappingURL=scales.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"scales.js","sourceRoot":"","sources":["../../../src/osiris/core/scales.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAoDH,+DAA+D;AAC/D,MAAM,CAAC,MAAM,eAAe,GAAuC;IACjE,IAAI,EAAE;QACJ,GAAG,EAAE,MAAM;QACX,KAAK,EAAE,OAAO;QACd,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,CAAC;QACf,SAAS,EAAE,GAAG;QACd,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE;QACrC,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,IAAI,EAAE;QACJ,GAAG,EAAE,MAAM;QACX,KAAK,EAAE,YAAY;QACnB,IAAI,EAAE,YAAY;QAClB,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC,CAAC;QACZ,QAAQ,EAAE,CAAC;QACX,YAAY,EAAE,CAAC,CAAC;QAChB,YAAY,EAAE,IAAI;QAClB,SAAS,EAAE,GAAG;QACd,cAAc,EAAE,IAAI;QACpB,SAAS,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE;QACvC,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,eAAe,EAAE;QACf,GAAG,EAAE,iBAAiB;QACtB,KAAK,EAAE,WAAW;QAClB,IAAI,EAAE,OAAO;QACb,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,GAAG;QACb,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,GAAG;QACjB,SAAS,EAAE,EAAE;QACb,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,OAAO,EAAE;QACzC,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,gBAAgB,EAAE;QAChB,GAAG,EAAE,kBAAkB;QACvB,KAAK,EAAE,MAAM;QACb,IAAI,EAAE,IAAI;QACV,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,GAAG;QACb,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,GAAG;QACjB,SAAS,EAAE,EAAE;QACb,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,YAAY,EAAE;QACZ,GAAG,EAAE,cAAc;QACnB,KAAK,EAAE,cAAc;QACrB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC,EAAE;QACb,QAAQ,EAAE,EAAE;QACZ,YAAY,EAAE,CAAC;QACf,YAAY,EAAE,IAAI;QAClB,0EAA0E;QAC1E,uEAAuE;QACvE,uEAAuE;QACvE,SAAS,EAAE,CAAC;QACZ,cAAc,EAAE,IAAI;QACpB,SAAS,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE;QACrC,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,QAAQ;KACjB;IACD,aAAa,EAAE;QACb,GAAG,EAAE,eAAe;QACpB,KAAK,EAAE,kBAAkB;QACzB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,EAAE;QACZ,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,EAAE;QAChB,SAAS,EAAE,CAAC;QACZ,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,UAAU,EAAE;QACV,GAAG,EAAE,YAAY;QACjB,KAAK,EAAE,eAAe;QACtB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,CAAC;QACf,SAAS,EAAE,GAAG;QACd,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,iBAAiB,EAAE;QACjB,GAAG,EAAE,mBAAmB;QACxB,KAAK,EAAE,eAAe;QACtB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,YAAY,EAAE,CAAC;QACf,YAAY,EAAE,CAAC;QACf,SAAS,EAAE,CAAC;QACZ,cAAc,EAAE,IAAI;QACpB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,kBAAkB,EAAE;QAClB,GAAG,EAAE,oBAAoB;QACzB,KAAK,EAAE,iBAAiB;QACxB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,CAAC;QACX,QAAQ,EAAE,EAAE;QACZ,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,CAAC;QACf,SAAS,EAAE,CAAC;QACZ,cAAc,EAAE,KAAK;QACrB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,aAAa;KACtB;IACD,SAAS,EAAE;QACT,GAAG,EAAE,WAAW;QAChB,KAAK,EAAE,YAAY;QACnB,IAAI,EAAE,EAAE;QACR,QAAQ,EAAE,CAAC;QACX,wEAAwE;QACxE,2EAA2E;QAC3E,sEAAsE;QACtE,QAAQ,EAAE,CAAC,CAAC;QACZ,QAAQ,EAAE,CAAC;QACX,YAAY,EAAE,IAAI;QAClB,YAAY,EAAE,IAAI;QAClB,qEAAqE;QACrE,uEAAuE;QACvE,SAAS,EAAE,IAAI;QACf,cAAc,EAAE,IAAI;QACpB,SAAS,EAAE,IAAI;QACf,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,QAAQ;KACjB;CACF,CAAC;AAEF;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAAC,GAAgB;IAC5C,OAAO,eAAe,CAAC,GAAG,CAAC,CAAC;AAC9B,CAAC"}

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

@@ -0,0 +1,91 @@
+/**
+ * What the tool predicts about one molecule, and how a risk is explained.
+ *
+ * Every quantity OpenChemLib can fail to compute is `number | null` here, never
+ * the library's own sentinel: cLogP and solubility answer `-999`, the polar
+ * surface area `-1`, drug-likeness `-999` when the tables did not load and `-1`
+ * when no fragment matched, and a risk `0`. None of them is `NaN`, and
+ * `DrugScoreCalculator` consumes every one of them and returns a plausible
+ * number, so a sentinel that leaves this module is a wrong value on screen with
+ * nothing to say it is wrong.
+ */
+/** The four risks OSIRIS assesses, in the order the library numbers them. */
+export declare const RISK_TYPES: readonly ["mutagenic", "tumorigenic", "irritant", "reproductive"];
+/** One of the four risks. */
+export type RiskType = (typeof RISK_TYPES)[number];
+/**
+ * How risky one type came back.
+ *
+ * `unknown` is the library's `RISK_UNKNOWN`, which it returns when its fragment
+ * tables did not load — never "nothing was found", which is `none`.
+ */
+export type RiskLevel = 'unknown' | 'none' | 'low' | 'high';
+/** Everything the tool shows for one molecule. */
+export interface OsirisProperties {
+    /** The canonical idCode, read before anything touched the molecule. */
+    idCode: string;
+    /** The canonical SMILES, for a link and for a download. */
+    smiles: string;
+    /** A name from the source, or the SMILES when it carried none. */
+    label: string;
+    /** e.g. `C6H6`. */
+    molecularFormula: string;
+    /** The relative molecular weight in g/mol — 78.11 for benzene, never the monoisotopic mass. */
+    molecularWeight: number;
+    /** cLogP, the octanol/water partition coefficient. */
+    logP: number | null;
+    /** Aqueous solubility, log10 of mol/L at 25 °C and pH 7.5. */
+    logS: number | null;
+    /** Topological polar surface area, in Ų. */
+    polarSurfaceArea: number | null;
+    /** Drug-likeness: positive is drug-like, negative is not. */
+    druglikeness: number | null;
+    /** The drug score, 0 to 1. `null` whenever any of its inputs was unknown. */
+    drugScore: number | null;
+    /** Every nitrogen and oxygen — the OSIRIS definition, not Lipinski's. */
+    acceptorCount: number;
+    /** Every nitrogen and oxygen carrying at least one hydrogen. */
+    donorCount: number;
+    /** Atoms with a real, non-pseudo parity. */
+    stereoCenterCount: number;
+    /** Single, non-ring, non-terminal, non-amide bonds. */
+    rotatableBondCount: number;
+    /** How the four risks came back. */
+    risks: Record<RiskType, RiskLevel>;
+}
+/** Which branch of the predictor produced one line of a risk explanation. */
+export type RiskFindingKind = 'known' | 'fragment' | 'none' | 'note';
+/** One line of why a risk came back as it did. */
+export interface RiskFinding {
+    /**
+     * `known` — the molecule's own idCode is in the RTECS-derived list, so there
+     * is nothing to highlight. `fragment` — an alerting substructure matched.
+     * `none` — nothing was found. `note` — anything else the predictor printed.
+     */
+    kind: RiskFindingKind;
+    /** The sentence the predictor printed, verbatim. */
+    description: string;
+    /** How alerting the matched fragment is, or `null` when this is not a fragment. */
+    severity: 'high' | 'medium' | null;
+    /** The fragment's idCode, or `null` — a known molecule carries no fragment. */
+    idCode: string | null;
+    /** The molecule's atoms the fragment matched, so the page can highlight them. */
+    atoms: readonly number[];
+    /** The molecule's bonds the fragment matched. */
+    bonds: readonly number[];
+}
+/** Why one risk came back as it did. */
+export interface RiskDetail {
+    /** Which of the four risks this explains. */
+    risk: RiskType;
+    /** What the predictor printed, one entry per sentence or matched fragment. */
+    findings: readonly RiskFinding[];
+}
+/** One entry of a `ParameterizedString[]`, as OpenChemLib hands it over. */
+export interface DetailEntry {
+    /** 1 is an idCode, 2 is text, 3 is a number written out. */
+    type: number;
+    /** The entry itself. */
+    value: string;
+}
+//# sourceMappingURL=types.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/osiris/core/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,6EAA6E;AAC7E,eAAO,MAAM,UAAU,mEAKb,CAAC;AAEX,6BAA6B;AAC7B,MAAM,MAAM,QAAQ,GAAG,CAAC,OAAO,UAAU,CAAC,CAAC,MAAM,CAAC,CAAC;AAEnD;;;;;GAKG;AACH,MAAM,MAAM,SAAS,GAAG,SAAS,GAAG,MAAM,GAAG,KAAK,GAAG,MAAM,CAAC;AAE5D,kDAAkD;AAClD,MAAM,WAAW,gBAAgB;IAC/B,uEAAuE;IACvE,MAAM,EAAE,MAAM,CAAC;IACf,2DAA2D;IAC3D,MAAM,EAAE,MAAM,CAAC;IACf,kEAAkE;IAClE,KAAK,EAAE,MAAM,CAAC;IACd,mBAAmB;IACnB,gBAAgB,EAAE,MAAM,CAAC;IACzB,+FAA+F;IAC/F,eAAe,EAAE,MAAM,CAAC;IACxB,sDAAsD;IACtD,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,8DAA8D;IAC9D,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,6CAA6C;IAC7C,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,6DAA6D;IAC7D,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,6EAA6E;IAC7E,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,yEAAyE;IACzE,aAAa,EAAE,MAAM,CAAC;IACtB,gEAAgE;IAChE,UAAU,EAAE,MAAM,CAAC;IACnB,4CAA4C;IAC5C,iBAAiB,EAAE,MAAM,CAAC;IAC1B,uDAAuD;IACvD,kBAAkB,EAAE,MAAM,CAAC;IAC3B,oCAAoC;IACpC,KAAK,EAAE,MAAM,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;CACpC;AAED,6EAA6E;AAC7E,MAAM,MAAM,eAAe,GAAG,OAAO,GAAG,UAAU,GAAG,MAAM,GAAG,MAAM,CAAC;AAErE,kDAAkD;AAClD,MAAM,WAAW,WAAW;IAC1B;;;;OAIG;IACH,IAAI,EAAE,eAAe,CAAC;IACtB,oDAAoD;IACpD,WAAW,EAAE,MAAM,CAAC;IACpB,mFAAmF;IACnF,QAAQ,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IACnC,+EAA+E;IAC/E,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,iFAAiF;IACjF,KAAK,EAAE,SAAS,MAAM,EAAE,CAAC;IACzB,iDAAiD;IACjD,KAAK,EAAE,SAAS,MAAM,EAAE,CAAC;CAC1B;AAED,wCAAwC;AACxC,MAAM,WAAW,UAAU;IACzB,6CAA6C;IAC7C,IAAI,EAAE,QAAQ,CAAC;IACf,8EAA8E;IAC9E,QAAQ,EAAE,SAAS,WAAW,EAAE,CAAC;CAClC;AAED,4EAA4E;AAC5E,MAAM,WAAW,WAAW;IAC1B,4DAA4D;IAC5D,IAAI,EAAE,MAAM,CAAC;IACb,wBAAwB;IACxB,KAAK,EAAE,MAAM,CAAC;CACf"}

package/lib/osiris/core/types.js

@@ -0,0 +1,19 @@
+/**
+ * What the tool predicts about one molecule, and how a risk is explained.
+ *
+ * Every quantity OpenChemLib can fail to compute is `number | null` here, never
+ * the library's own sentinel: cLogP and solubility answer `-999`, the polar
+ * surface area `-1`, drug-likeness `-999` when the tables did not load and `-1`
+ * when no fragment matched, and a risk `0`. None of them is `NaN`, and
+ * `DrugScoreCalculator` consumes every one of them and returns a plausible
+ * number, so a sentinel that leaves this module is a wrong value on screen with
+ * nothing to say it is wrong.
+ */
+/** The four risks OSIRIS assesses, in the order the library numbers them. */
+export const RISK_TYPES = [
+    'mutagenic',
+    'tumorigenic',
+    'irritant',
+    'reproductive',
+];
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/osiris/core/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,6EAA6E;AAC7E,MAAM,CAAC,MAAM,UAAU,GAAG;IACxB,WAAW;IACX,aAAa;IACb,UAAU;IACV,cAAc;CACN,CAAC"}

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

@@ -0,0 +1,28 @@
+/**
+ * DataWarrior's own fuzzy fitness, ported from
+ * `com.actelion.research.chem.prediction.MolecularPropertyHelper`.
+ *
+ * It is what turns a predicted number into the green-to-red ramp behind it,
+ * and it is the library's arithmetic rather than a cut-off invented here: a
+ * property inside its preferred band scores 1, and the score falls away
+ * smoothly outside it over `halfWidth`. There is no cliff anywhere, so a cLogP
+ * of 4.01 does not look categorically worse than one of 3.99.
+ */
+/**
+ * How well one value sits in a preferred band, from 0 to 1.
+ *
+ * A bound given as `null` is simply not applied, which is how a property
+ * bounded on one side only — a solubility that must be high enough, a weight
+ * that must be low enough — scores against the one bound it has. The original
+ * passes `Double.NaN` for an absent bound and `NaN` is accepted here too.
+ *
+ * The Java comment claims the fitness at `max + halfWidth` is `1/e`; the
+ * arithmetic gives `1/(1+e)`, and the arithmetic is what was ported.
+ * @param value - The predicted number.
+ * @param min - The bottom of the preferred band, or `null` when there is none.
+ * @param max - The top of the preferred band, or `null` when there is none.
+ * @param halfWidth - How far outside the band the score takes to fall away.
+ * @returns The fitness, or `NaN` when the value is `NaN`.
+ */
+export declare function getValuation(value: number, min: number | null, max: number | null, halfWidth: number): number;
+//# sourceMappingURL=valuation.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"valuation.d.ts","sourceRoot":"","sources":["../../../src/osiris/core/valuation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,MAAM,GAAG,IAAI,EAClB,GAAG,EAAE,MAAM,GAAG,IAAI,EAClB,SAAS,EAAE,MAAM,GAChB,MAAM,CAWR"}

package/lib/osiris/core/valuation.js

@@ -0,0 +1,39 @@
+/**
+ * DataWarrior's own fuzzy fitness, ported from
+ * `com.actelion.research.chem.prediction.MolecularPropertyHelper`.
+ *
+ * It is what turns a predicted number into the green-to-red ramp behind it,
+ * and it is the library's arithmetic rather than a cut-off invented here: a
+ * property inside its preferred band scores 1, and the score falls away
+ * smoothly outside it over `halfWidth`. There is no cliff anywhere, so a cLogP
+ * of 4.01 does not look categorically worse than one of 3.99.
+ */
+/**
+ * How well one value sits in a preferred band, from 0 to 1.
+ *
+ * A bound given as `null` is simply not applied, which is how a property
+ * bounded on one side only — a solubility that must be high enough, a weight
+ * that must be low enough — scores against the one bound it has. The original
+ * passes `Double.NaN` for an absent bound and `NaN` is accepted here too.
+ *
+ * The Java comment claims the fitness at `max + halfWidth` is `1/e`; the
+ * arithmetic gives `1/(1+e)`, and the arithmetic is what was ported.
+ * @param value - The predicted number.
+ * @param min - The bottom of the preferred band, or `null` when there is none.
+ * @param max - The top of the preferred band, or `null` when there is none.
+ * @param halfWidth - How far outside the band the score takes to fall away.
+ * @returns The fitness, or `NaN` when the value is `NaN`.
+ */
+export function getValuation(value, min, max, halfWidth) {
+    if (Number.isNaN(value))
+        return Number.NaN;
+    let v = 1;
+    if (min !== null && !Number.isNaN(min)) {
+        v *= 1 / (1 + Math.exp((min - value) / halfWidth));
+    }
+    if (max !== null && !Number.isNaN(max)) {
+        v *= 1 / (1 + Math.exp((value - max) / halfWidth));
+    }
+    return v;
+}
+//# sourceMappingURL=valuation.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"valuation.js","sourceRoot":"","sources":["../../../src/osiris/core/valuation.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,MAAM,UAAU,YAAY,CAC1B,KAAa,EACb,GAAkB,EAClB,GAAkB,EAClB,SAAiB;IAEjB,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC;QAAE,OAAO,MAAM,CAAC,GAAG,CAAC;IAE3C,IAAI,CAAC,GAAG,CAAC,CAAC;IACV,IAAI,GAAG,KAAK,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QACvC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,IAAI,GAAG,KAAK,IAAI,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QACvC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,OAAO,CAAC,CAAC;AACX,CAAC"}

package/lib/osiris/ui/PropertyBar.d.ts

@@ -0,0 +1,27 @@
+/**
+ * One property's bar: a track, a fill whose colour is how good the value is,
+ * and the published rule of thumb marked on it.
+ *
+ * The colour is handed to the stylesheet as a number rather than mixed here.
+ * A ramp computed in JavaScript would be a hex code in a component, which is
+ * the one thing a site of this family may not write: the green, the amber and
+ * the red are the shared status tokens, and `properties.css` mixes them.
+ *
+ * The bar carries no accessible text of its own. It draws the same number the
+ * row already prints beside it, so announcing it twice would only make the
+ * panel longer to listen to.
+ */
+import type { ReactElement } from 'react';
+import type { BarGeometry } from '../core/barGeometry.ts';
+/** What {@link PropertyBar} needs. */
+export interface PropertyBarProps {
+    /** Where the fill and the mark go, from `barGeometry`. */
+    geometry: BarGeometry;
+}
+/**
+ * Draw one property's bar.
+ * @param props - See {@link PropertyBarProps}.
+ * @returns The track, its fill and its labelled mark.
+ */
+export declare function PropertyBar(props: PropertyBarProps): ReactElement;
+//# sourceMappingURL=PropertyBar.d.ts.map

package/lib/osiris/ui/PropertyBar.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"PropertyBar.d.ts","sourceRoot":"","sources":["../../../src/osiris/ui/PropertyBar.tsx"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,KAAK,EAAiB,YAAY,EAAE,MAAM,OAAO,CAAC;AAEzD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAE1D,sCAAsC;AACtC,MAAM,WAAW,gBAAgB;IAC/B,0DAA0D;IAC1D,QAAQ,EAAE,WAAW,CAAC;CACvB;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,gBAAgB,GAAG,YAAY,CAsCjE"}

package/lib/osiris/ui/PropertyBar.js

@@ -0,0 +1,27 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+/**
+ * Draw one property's bar.
+ * @param props - See {@link PropertyBarProps}.
+ * @returns The track, its fill and its labelled mark.
+ */
+export function PropertyBar(props) {
+    const { geometry } = props;
+    // `--fitness` is a custom property, which React sets verbatim and
+    // `CSSProperties` has no name for; the stylesheet reads it in the `calc()`
+    // that mixes the ramp.
+    const fill = {
+        left: percent(geometry.start),
+        width: percent(geometry.length),
+        '--fitness': geometry.fitness.toFixed(4),
+    };
+    return (_jsxs("div", { className: "property-bar", "aria-hidden": "true", children: [_jsxs("div", { className: "property-bar__track", children: [geometry.origin === 0 ? null : (_jsx("div", { className: "property-bar__origin", style: { left: percent(geometry.origin) } })), _jsx("div", { className: "property-bar__fill", style: fill }), geometry.mark === null ? null : (_jsx("div", { className: "property-bar__mark", style: { left: percent(geometry.mark) } }))] }), geometry.mark === null || geometry.markLabel === null ? null : (_jsx("span", { className: "property-bar__threshold", style: { left: percent(geometry.mark) }, children: geometry.markLabel }))] }));
+}
+/**
+ * A fraction of the track, as a CSS length.
+ * @param fraction - 0 at the left end, 1 at the right.
+ * @returns The percentage, to two decimals.
+ */
+function percent(fraction) {
+    return `${(fraction * 100).toFixed(2)}%`;
+}
+//# sourceMappingURL=PropertyBar.js.map

package/lib/osiris/ui/PropertyBar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"PropertyBar.js","sourceRoot":"","sources":["../../../src/osiris/ui/PropertyBar.tsx"],"names":[],"mappings":";AAwBA;;;;GAIG;AACH,MAAM,UAAU,WAAW,CAAC,KAAuB;IACjD,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAC;IAC3B,kEAAkE;IAClE,2EAA2E;IAC3E,uBAAuB;IACvB,MAAM,IAAI,GAAG;QACX,IAAI,EAAE,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC;QAC7B,KAAK,EAAE,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAC;QAC/B,WAAW,EAAE,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;KACxB,CAAC;IAEnB,OAAO,CACL,eAAK,SAAS,EAAC,cAAc,iBAAa,MAAM,aAC9C,eAAK,SAAS,EAAC,qBAAqB,aACjC,QAAQ,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC9B,cACE,SAAS,EAAC,sBAAsB,EAChC,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,GACzC,CACH,EACD,cAAK,SAAS,EAAC,oBAAoB,EAAC,KAAK,EAAE,IAAI,GAAI,EAClD,QAAQ,CAAC,IAAI,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC/B,cACE,SAAS,EAAC,oBAAoB,EAC9B,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,GACvC,CACH,IACG,EACL,QAAQ,CAAC,IAAI,KAAK,IAAI,IAAI,QAAQ,CAAC,SAAS,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC9D,eACE,SAAS,EAAC,yBAAyB,EACnC,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,YAEtC,QAAQ,CAAC,SAAS,GACd,CACR,IACG,CACP,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAS,OAAO,CAAC,QAAgB;IAC/B,OAAO,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC;AAC3C,CAAC"}