react-cheminfo 0.22.0 → 0.24.0

package/lib/structure/core/conformerRefineRank.js

@@ -0,0 +1,69 @@
+import { isSameShape } from "./conformerMinimum.js";
+/**
+ * Order refined conformers from the most stable down, number them from one in
+ * that order, and measure every refined energy from the lowest.
+ *
+ * `reordered` counts the conformers whose position changed, which is the number
+ * worth showing: it says how much the better method disagreed with the force
+ * field.
+ * @param conformers - The refined conformers, in the force field's own order.
+ * @returns The ranked conformers and the disagreement count.
+ */
+export function rankByRefinedEnergy(conformers) {
+    let lowest = Number.POSITIVE_INFINITY;
+    for (const conformer of conformers) {
+        const energy = conformer.refinement?.energy;
+        if (energy !== undefined && energy < lowest)
+            lowest = energy;
+    }
+    const ranked = conformers.toSorted(compareRefined);
+    const result = [];
+    let reordered = 0;
+    for (const [index, conformer] of ranked.entries()) {
+        if (conformer.id !== index + 1)
+            reordered++;
+        const refinement = conformer.refinement;
+        result.push({
+            ...conformer,
+            id: index + 1,
+            refinement: refinement === null
+                ? null
+                : { ...refinement, relativeEnergy: refinement.energy - lowest },
+        });
+    }
+    return { conformers: result, reordered };
+}
+/**
+ * Whether a refined conformer landed in a minimum one of `kept` already holds:
+ * the same energy within `tolerance`, and the same shape.
+ * @param candidate - The refined conformer's energy and shape.
+ * @param kept - The minima kept so far.
+ * @param tolerance - Energy gap in kcal/mol under which two energies are one.
+ * @returns `true` when one of them is the same minimum.
+ */
+export function isRefinedDuplicate(candidate, kept, tolerance) {
+    for (const entry of kept) {
+        if (Math.abs(candidate.energy - entry.energy) > tolerance)
+            continue;
+        if (isSameShape(candidate.shape, entry.shape))
+            return true;
+    }
+    return false;
+}
+/**
+ * Order two conformers by refined energy; one without a refinement ranks after
+ * every one that has one.
+ * @param a - One conformer.
+ * @param b - The other.
+ * @returns Negative when `a` is the more stable, positive when `b` is.
+ */
+function compareRefined(a, b) {
+    const energyA = a.refinement?.energy;
+    const energyB = b.refinement?.energy;
+    if (energyA === undefined)
+        return energyB === undefined ? 0 : 1;
+    if (energyB === undefined)
+        return -1;
+    return energyA - energyB;
+}
+//# sourceMappingURL=conformerRefineRank.js.map

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

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

@@ -0,0 +1,50 @@
+import type { Molecule } from 'openchemlib';
+import { ConformerGenerator } from 'openchemlib';
+import type { ConformerOptions, ConformerStrategy } from './conformerOptions.ts';
+/** A generator, positioned after the conformers it has already handed back. */
+export interface ConformerSession {
+    generator: ConformerGenerator;
+    /** Conformers handed back so far, kept or dropped. */
+    produced: number;
+    /**
+     * A conformer drawn from the generator but not yet processed, because the
+     * deadline passed while it was drawn. Not counted in `produced`.
+     */
+    pending: Molecule | null;
+}
+/**
+ * A generator for a prepared structure, positioned after `produced` conformers.
+ *
+ * The generator is seeded, so the same structure and options always hand back
+ * the same sequence. The last session is kept, and resumed when it is exactly
+ * where the caller left it; otherwise a fresh generator is initialised and the
+ * first `produced` conformers are drawn and discarded, which yields the same
+ * position without their minimisation.
+ * @param prepared - The hydrogen-saturated copy the run embeds.
+ * @param options - The options that fixed the sequence: strategy, seed, torsion sets.
+ * @param produced - How far into the sequence the caller already is.
+ * @returns The session, to be handed back through {@link keepConformerSession}.
+ * @throws {Error} When OpenChemLib refuses to initialise the structure.
+ */
+export declare function openConformerSession(prepared: Molecule, options: ConformerOptions, produced: number): ConformerSession;
+/**
+ * Keep a session so the next continuation of the same run resumes it.
+ * @param prepared - The structure the session was opened on.
+ * @param options - The options it was opened with.
+ * @param session - The session, positioned where the run stopped.
+ */
+export declare function keepConformerSession(prepared: Molecule, options: ConformerOptions, session: ConformerSession): void;
+/**
+ * OpenChemLib's estimate of the conformers a session can reach.
+ * @param session - A freshly opened session.
+ * @returns The estimate, or `-1` when the generator declines to make one.
+ */
+export declare function readPotentialCount(session: ConformerSession): number;
+/**
+ * Map one of our strategy ids onto the `ConformerGenerator` constant it stands
+ * for.
+ * @param strategy - The id stored in the preferences.
+ * @returns The numeric constant OpenChemLib expects.
+ */
+export declare function strategyConstant(strategy: ConformerStrategy): number;
+//# sourceMappingURL=conformerSession.d.ts.map

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

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package/lib/structure/core/conformerSession.js

@@ -0,0 +1,88 @@
+import { ConformerGenerator } from 'openchemlib';
+/**
+ * A generator for a prepared structure, positioned after `produced` conformers.
+ *
+ * The generator is seeded, so the same structure and options always hand back
+ * the same sequence. The last session is kept, and resumed when it is exactly
+ * where the caller left it; otherwise a fresh generator is initialised and the
+ * first `produced` conformers are drawn and discarded, which yields the same
+ * position without their minimisation.
+ * @param prepared - The hydrogen-saturated copy the run embeds.
+ * @param options - The options that fixed the sequence: strategy, seed, torsion sets.
+ * @param produced - How far into the sequence the caller already is.
+ * @returns The session, to be handed back through {@link keepConformerSession}.
+ * @throws {Error} When OpenChemLib refuses to initialise the structure.
+ */
+export function openConformerSession(prepared, options, produced) {
+    const key = sessionKey(prepared, options);
+    if (produced > 0 && last?.key === key && last.session.produced === produced) {
+        const session = last.session;
+        last = null;
+        return session;
+    }
+    last = null;
+    const generator = new ConformerGenerator(options.seed);
+    const initialised = generator.initializeConformers(prepared, {
+        strategy: strategyConstant(options.strategy),
+        maxTorsionSets: options.maxTorsionSets,
+        use60degreeSteps: options.use60DegreeSteps,
+    });
+    if (!initialised) {
+        throw new Error(`OpenChemLib could not set up conformer generation for ${prepared.getMolecularFormula().formula}. The structure has a problem the generator cannot resolve, such as an impossible valence or an over-constrained ring.`);
+    }
+    let skipped = 0;
+    while (skipped < produced &&
+        generator.getNextConformerAsMolecule() !== null) {
+        skipped++;
+    }
+    return { generator, produced: skipped, pending: null };
+}
+/**
+ * Keep a session so the next continuation of the same run resumes it.
+ * @param prepared - The structure the session was opened on.
+ * @param options - The options it was opened with.
+ * @param session - The session, positioned where the run stopped.
+ */
+export function keepConformerSession(prepared, options, session) {
+    last = { key: sessionKey(prepared, options), session };
+}
+/**
+ * OpenChemLib's estimate of the conformers a session can reach.
+ * @param session - A freshly opened session.
+ * @returns The estimate, or `-1` when the generator declines to make one.
+ */
+export function readPotentialCount(session) {
+    try {
+        return session.generator.getPotentialConformerCount();
+    }
+    catch {
+        return -1;
+    }
+}
+/**
+ * Map one of our strategy ids onto the `ConformerGenerator` constant it stands
+ * for.
+ * @param strategy - The id stored in the preferences.
+ * @returns The numeric constant OpenChemLib expects.
+ */
+export function strategyConstant(strategy) {
+    return STRATEGY_CONSTANTS[strategy];
+}
+const STRATEGY_CONSTANTS = {
+    'adaptive-random': ConformerGenerator.STRATEGY_ADAPTIVE_RANDOM,
+    'likely-random': ConformerGenerator.STRATEGY_LIKELY_RANDOM,
+    'pure-random': ConformerGenerator.STRATEGY_PURE_RANDOM,
+    'likely-systematic': ConformerGenerator.STRATEGY_LIKELY_SYSTEMATIC,
+};
+let last = null;
+// The atom order matters as much as the structure, so the molfile is the key.
+function sessionKey(prepared, options) {
+    return [
+        options.strategy,
+        options.seed,
+        options.maxTorsionSets,
+        options.use60DegreeSteps,
+        prepared.toMolfileV3(),
+    ].join('\n');
+}
+//# sourceMappingURL=conformerSession.js.map

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

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

@@ -0,0 +1,36 @@
+import type { Molecule } from 'openchemlib';
+/** Principal second moments of a conformer's atoms, in increasing order. */
+export type PrincipalMoments = readonly [number, number, number];
+/** What tells two minimised conformers of one energy apart. */
+export interface ConformerShape {
+    /** Principal second moments, smallest first. */
+    moments: PrincipalMoments;
+    /** Handedness in [-1, 1]: opposite for mirror images, 0 for a shape that is its own mirror image. */
+    chirality: number;
+}
+/**
+ * Shape of a conformer: the principal second moments of its atoms, weighted by
+ * atomic number, about their weighted centre, and the handedness of the atoms
+ * in that principal frame.
+ *
+ * Neither changes when the conformer is turned or has its symmetry-equivalent
+ * atoms numbered differently, which is how the generator hands back the same
+ * minimum twice, as with a cyclohexane chair and its flipped copy. A mirror
+ * image keeps the moments and flips the sign of the chirality, so gauche butane
+ * and its mirror image share the one and not the other.
+ *
+ * The chirality is Σ w·u₁u₂u₃ over Σ w·|u₁u₂u₃|, u being the coordinates along
+ * right-handed principal axes. A mirror plane or an inversion centre makes it
+ * vanish. It is 0 as well for a flat conformer, and when the principal axes
+ * cannot be drawn.
+ * @param molecule - A conformer with 3D coordinates.
+ * @returns Its moments, smallest first, and its chirality.
+ */
+export declare function conformerShape(molecule: Molecule): ConformerShape;
+/**
+ * Whether every atom of a conformer sits at finite coordinates.
+ * @param conformer - A conformer with 3D coordinates.
+ * @returns `false` as soon as one coordinate is `NaN` or infinite.
+ */
+export declare function hasFiniteCoordinates(conformer: Molecule): boolean;
+//# sourceMappingURL=conformerShape.d.ts.map

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

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package/lib/structure/core/conformerShape.js

@@ -0,0 +1,150 @@
+/**
+ * Shape of a conformer: the principal second moments of its atoms, weighted by
+ * atomic number, about their weighted centre, and the handedness of the atoms
+ * in that principal frame.
+ *
+ * Neither changes when the conformer is turned or has its symmetry-equivalent
+ * atoms numbered differently, which is how the generator hands back the same
+ * minimum twice, as with a cyclohexane chair and its flipped copy. A mirror
+ * image keeps the moments and flips the sign of the chirality, so gauche butane
+ * and its mirror image share the one and not the other.
+ *
+ * The chirality is Σ w·u₁u₂u₃ over Σ w·|u₁u₂u₃|, u being the coordinates along
+ * right-handed principal axes. A mirror plane or an inversion centre makes it
+ * vanish. It is 0 as well for a flat conformer, and when the principal axes
+ * cannot be drawn.
+ * @param molecule - A conformer with 3D coordinates.
+ * @returns Its moments, smallest first, and its chirality.
+ */
+export function conformerShape(molecule) {
+    const atomCount = molecule.getAllAtoms();
+    let total = 0;
+    let centreX = 0;
+    let centreY = 0;
+    let centreZ = 0;
+    for (let atom = 0; atom < atomCount; atom++) {
+        const weight = molecule.getAtomicNo(atom);
+        total += weight;
+        centreX += weight * molecule.getAtomX(atom);
+        centreY += weight * molecule.getAtomY(atom);
+        centreZ += weight * molecule.getAtomZ(atom);
+    }
+    if (total === 0)
+        return { moments: [0, 0, 0], chirality: 0 };
+    centreX /= total;
+    centreY /= total;
+    centreZ /= total;
+    const tensor = { xx: 0, yy: 0, zz: 0, xy: 0, xz: 0, yz: 0 };
+    for (let atom = 0; atom < atomCount; atom++) {
+        const weight = molecule.getAtomicNo(atom);
+        const x = molecule.getAtomX(atom) - centreX;
+        const y = molecule.getAtomY(atom) - centreY;
+        const z = molecule.getAtomZ(atom) - centreZ;
+        tensor.xx += weight * x * x;
+        tensor.yy += weight * y * y;
+        tensor.zz += weight * z * z;
+        tensor.xy += weight * x * y;
+        tensor.xz += weight * x * z;
+        tensor.yz += weight * y * z;
+    }
+    const moments = symmetricEigenvalues(tensor);
+    const first = principalAxis(tensor, moments[0]);
+    const third = principalAxis(tensor, moments[2]);
+    if (first === null || third === null)
+        return { moments, chirality: 0 };
+    const second = cross(third, first);
+    let signed = 0;
+    let absolute = 0;
+    for (let atom = 0; atom < atomCount; atom++) {
+        const weight = molecule.getAtomicNo(atom);
+        const x = molecule.getAtomX(atom) - centreX;
+        const y = molecule.getAtomY(atom) - centreY;
+        const z = molecule.getAtomZ(atom) - centreZ;
+        const product = (x * first[0] + y * first[1] + z * first[2]) *
+            (x * second[0] + y * second[1] + z * second[2]) *
+            (x * third[0] + y * third[1] + z * third[2]);
+        signed += weight * product;
+        absolute += weight * Math.abs(product);
+    }
+    const radius = Math.sqrt((moments[0] + moments[1] + moments[2]) / total);
+    if (absolute <= FLAT_TOLERANCE * total * radius * radius * radius) {
+        return { moments, chirality: 0 };
+    }
+    return { moments, chirality: signed / absolute };
+}
+/**
+ * Whether every atom of a conformer sits at finite coordinates.
+ * @param conformer - A conformer with 3D coordinates.
+ * @returns `false` as soon as one coordinate is `NaN` or infinite.
+ */
+export function hasFiniteCoordinates(conformer) {
+    const atomCount = conformer.getAllAtoms();
+    for (let atom = 0; atom < atomCount; atom++) {
+        if (!Number.isFinite(conformer.getAtomX(atom)) ||
+            !Number.isFinite(conformer.getAtomY(atom)) ||
+            !Number.isFinite(conformer.getAtomZ(atom))) {
+            return false;
+        }
+    }
+    return true;
+}
+/**
+ * Σ w·|u₁u₂u₃|, relative to the total weight times the cubed radius of
+ * gyration, under which a conformer is flat: its handedness is rounding noise.
+ */
+const FLAT_TOLERANCE = 1e-4;
+// Unit eigenvector of `moment`: the longest cross product of two rows of the tensor minus `moment`.
+function principalAxis(tensor, moment) {
+    const rows = [
+        [tensor.xx - moment, tensor.xy, tensor.xz],
+        [tensor.xy, tensor.yy - moment, tensor.yz],
+        [tensor.xz, tensor.yz, tensor.zz - moment],
+    ];
+    let best = [0, 0, 0];
+    let bestLength = 0;
+    for (let a = 0; a < 3; a++) {
+        for (let b = a + 1; b < 3; b++) {
+            const candidate = cross(rows[a], rows[b]);
+            const length = Math.hypot(candidate[0], candidate[1], candidate[2]);
+            if (length > bestLength) {
+                best = candidate;
+                bestLength = length;
+            }
+        }
+    }
+    if (bestLength === 0)
+        return null;
+    return [best[0] / bestLength, best[1] / bestLength, best[2] / bestLength];
+}
+function cross(a, b) {
+    return [
+        a[1] * b[2] - a[2] * b[1],
+        a[2] * b[0] - a[0] * b[2],
+        a[0] * b[1] - a[1] * b[0],
+    ];
+}
+// Closed-form eigenvalues of a symmetric 3×3 matrix (Smith, 1961).
+function symmetricEigenvalues(tensor) {
+    const { xx, yy, zz, xy, xz, yz } = tensor;
+    const mean = (xx + yy + zz) / 3;
+    const offDiagonal = xy * xy + xz * xz + yz * yz;
+    const spread = (xx - mean) * (xx - mean) +
+        (yy - mean) * (yy - mean) +
+        (zz - mean) * (zz - mean) +
+        2 * offDiagonal;
+    if (spread === 0)
+        return [mean, mean, mean];
+    const p = Math.sqrt(spread / 6);
+    const a = (xx - mean) / p;
+    const b = (yy - mean) / p;
+    const c = (zz - mean) / p;
+    const d = xy / p;
+    const e = xz / p;
+    const f = yz / p;
+    const halfDeterminant = (a * (b * c - f * f) - d * (d * c - f * e) + e * (d * f - b * e)) / 2;
+    const angle = Math.acos(Math.min(1, Math.max(-1, halfDeterminant))) / 3;
+    const largest = mean + 2 * p * Math.cos(angle);
+    const smallest = mean + 2 * p * Math.cos(angle + (2 * Math.PI) / 3);
+    return [smallest, 3 * mean - largest - smallest, largest];
+}
+//# sourceMappingURL=conformerShape.js.map

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

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

@@ -0,0 +1,107 @@
+import type { Molecule } from 'openchemlib';
+import type { ConformerOptions, MinimisationAlgorithm } from './conformerOptions.ts';
+import type { ConformerRefinement, ConformerSetRefinement } from './conformerRefine.ts';
+import type { MolfileExport } from './molfileExport.ts';
+export { strategyConstant } from './conformerSession.ts';
+/** One conformer of the input structure, ready to display and to export. */
+export interface Conformer {
+    /** 1-based position in {@link ConformerSet.conformers}. */
+    id: number;
+    /** The 3D structure, as a molfile the viewer can parse. */
+    molfile: MolfileExport;
+    /** Total force-field energy in kcal/mol, `null` when it was not computed. */
+    energy: number | null;
+    /** Energy above the lowest conformer of the set, `null` without an energy. */
+    relativeEnergy: number | null;
+    /**
+     * What a better method said about this conformer, once `refineConformers` has
+     * relaxed it. `null` until then, which is what a plain force-field run leaves.
+     * @default null
+     */
+    refinement: ConformerRefinement | null;
+}
+/**
+ * Which energies a set is ordered by: the force field's own, or the ones a
+ * refinement pass produced.
+ */
+export type ConformerRanking = 'force-field' | 'refined';
+/** Why {@link generateConformers} stopped asking for more conformers. */
+export type StopReason = 'exhausted' | 'count' | 'timeout';
+/** The complete outcome of one conformer run. */
+export interface ConformerSet {
+    /** The conformers kept, most stable first; one without an energy follows every one that has one. */
+    conformers: Conformer[];
+    /** OpenChemLib's estimate of the reachable conformers, `-1` when unavailable. */
+    potentialConformerCount: number;
+    /** Which of the three limits ended the run. */
+    stoppedBy: StopReason;
+    /** Wall-clock duration of the run, initialisation and continuations included. */
+    elapsedMilliseconds: number;
+    /** Plain sentences about conformers that were dropped or left unminimised. */
+    warnings: string[];
+    /** The force field that was asked for, echoed so a reader knows what the energies mean. */
+    minimisation: MinimisationAlgorithm;
+    /** Conformers the generator handed back, dropped ones included: where a continuation resumes. */
+    produced: number;
+    /** The options of the run, so a continuation draws from the same sequence. */
+    options: ConformerOptions;
+    /** Which of the two energies {@link ConformerSet.conformers} is ordered by. */
+    rankedBy: ConformerRanking;
+    /**
+     * What the refinement pass did, `null` for a set no better method has seen.
+     * @default null
+     */
+    refinement: ConformerSetRefinement | null;
+}
+/** The two options a continuation takes from the caller rather than from the run. */
+export type ConformerLimits = Pick<ConformerOptions, 'maxConformers' | 'timeoutSeconds'>;
+/**
+ * Generate conformers of a structure, optionally relaxing each one with MMFF94.
+ *
+ * The caller's molecule is never touched: the run works on a compact copy that
+ * receives the explicit hydrogens the generator needs.
+ *
+ * The run ends on the first of three limits — the generator runs out of new
+ * torsion sets, `maxConformers` conformers are in hand, or the time budget is
+ * spent. **A timeout is not an error**: whatever was produced is returned, with
+ * `stoppedBy` saying why there is not more.
+ *
+ * The budget covers the whole call, initialisation included, and is read again
+ * once a conformer is in hand, so no further minimisation starts past the
+ * deadline. The one step already running cannot be cut short, so a caller
+ * waiting from another thread must allow one step on top of `timeoutSeconds`.
+ *
+ * Minimisation is best-effort: a conformer MMFF94 refuses is kept with a `null`
+ * energy and a warning rather than lost. A minimised conformer that lands in a
+ * minimum already kept, such as the flipped copy of a cyclohexane chair, is
+ * not kept a second time; the mirror image of a chiral minimum, such as the
+ * second gauche butane, is a minimum of its own.
+ * @param molecule - Structure to embed. Not mutated.
+ * @param options - Strategy, limits, seed and force field.
+ * @param now - Clock used for the time budget, injectable for tests.
+ * @returns Every conformer kept, most stable first, with relative energies and any warnings.
+ * @throws {Error} When the structure is empty or OpenChemLib refuses to initialise it.
+ */
+export declare function generateConformers(molecule: Molecule, options: ConformerOptions, now?: () => number): ConformerSet;
+/**
+ * Ask the run that produced `previous` for more conformers.
+ *
+ * The continuation draws from the same seeded sequence with the same force
+ * field, so the result is the set a single larger run would have produced:
+ * the new conformers are ranked among the previous ones, the ids follow that
+ * order, and every relative energy is measured again from the lowest of all.
+ * A refined set cannot be extended: its molfiles hold the relaxed geometries
+ * while its `energy` fields still hold the force field's numbers, so the two
+ * would no longer describe one conformer and the duplicate check would compare
+ * shapes against energies that do not belong to them. Generate a larger set and
+ * refine that instead.
+ * @param molecule - The structure `previous` was generated from. Not mutated.
+ * @param previous - The set to extend. Not mutated.
+ * @param limits - How many more conformers to find, and the time budget of this call.
+ * @param now - Clock used for the time budget, injectable for tests.
+ * @returns The extended set, its duration the sum of both runs.
+ * @throws {Error} When the structure is empty, when `previous` has been refined,
+ * or when OpenChemLib refuses to initialise it.
+ */
+export declare function continueConformers(molecule: Molecule, previous: ConformerSet, limits: ConformerLimits, now?: () => number): ConformerSet;
+//# sourceMappingURL=conformers.d.ts.map

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

@@ -0,0 +1 @@
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