react-cheminfo 0.28.0 → 0.30.0

package/lib/panel/ui/useVirtualRows.js

@@ -0,0 +1,56 @@
+import { useVirtualizer } from '@tanstack/react-virtual';
+import { rowSpacers } from "../core/rowSpacers.js";
+/**
+ * Draw only the rows the scroll region is showing, however long the list is.
+ *
+ * A peak table is a few hundred rows at rest and several thousand once the
+ * window is opened onto the whole spectrum, and every one of those rows is four
+ * cells the browser lays out, styles and keeps — a cost paid on the sort, on the
+ * filter, and on every zoom, for rows nobody is looking at. Drawing the twenty
+ * or so in view and standing two empty rows in for the rest makes that cost the
+ * size of the panel rather than the size of the spectrum.
+ *
+ * The rows are measured rather than assumed: a row is a line of text, so its
+ * height follows the font the page is rendered at and a hard-coded one would
+ * put the end of a five thousand row list several screens away from the bottom
+ * of the scrollbar. `estimatedRowHeight` is only what the list is worth before
+ * a single row has been drawn.
+ *
+ * The table header scrolls inside the same region and is not part of the list,
+ * so the rows really sit one header lower than this reckons. It is left that
+ * way deliberately: the overscan already draws more rows than are in view, on
+ * both sides, and it absorbs a header's worth of offset without the extra
+ * measurement — and without the render that measuring it would cost on the way
+ * to the same picture.
+ * @param scrollRef - The region the rows scroll in.
+ * @param count - How many rows the list holds.
+ * @param estimatedRowHeight - What one row is worth until one has been drawn.
+ * @returns The rows to draw and the spacers standing in for the others.
+ */
+export function useVirtualRows(scrollRef, count, estimatedRowHeight) {
+    const virtualizer = useVirtualizer({
+        count,
+        getScrollElement: () => scrollRef.current,
+        estimateSize: () => estimatedRowHeight,
+        overscan: OVERSCAN,
+    });
+    const drawn = virtualizer.getVirtualItems();
+    const indices = new Array(drawn.length);
+    for (let position = 0; position < drawn.length; position++) {
+        indices[position] = drawn[position].index;
+    }
+    return {
+        indices,
+        ...rowSpacers(drawn, virtualizer.getTotalSize()),
+        measure: virtualizer.measureElement,
+    };
+}
+/**
+ * How many rows are drawn beyond each end of the region.
+ *
+ * Enough that a wheel gesture or a drag of the scrollbar never reaches the edge
+ * of what was drawn before the next render has run, and enough to cover the
+ * header the list is offset by.
+ */
+const OVERSCAN = 12;
+//# sourceMappingURL=useVirtualRows.js.map

package/lib/panel/ui/useVirtualRows.js.map

@@ -0,0 +1 @@
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package/lib/panel/ui/useVirtualWindowRows.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Drawing only the rows the page is showing, for a list that scrolls with it.
+ *
+ * `useVirtualRows` measures a scroll region of its own, which is what a panel
+ * beside a chart has. A table filling a tab has none: it flows down the document
+ * and the browser window is what scrolls it, so giving the list its own
+ * `overflow` would grow a second scrollbar inside the first and cap the table at
+ * whatever height it was handed — a layout change made to serve the virtualiser
+ * rather than the reader.
+ */
+import type { VirtualRows } from './useVirtualRows.ts';
+/** The rows to draw, and what the list reports its own position through. */
+export interface VirtualWindowRows extends VirtualRows {
+    /**
+     * What the element holding the rows reports its position through, as its
+     * `ref`. Without it every offset is reckoned from the top of the document and
+     * the wrong rows are drawn, by however tall whatever sits above the list is.
+     */
+    measureList: (node: HTMLElement | null) => void;
+}
+/**
+ * Draw only the rows the page is showing, however long the list is.
+ *
+ * The rows are measured against the window, so the list only has to say how far
+ * down the page it begins — which is what the virtualiser calls its scroll
+ * margin, and what `measureList` reports.
+ *
+ * That position is read in a ref callback rather than in an effect, which is
+ * how `useChartSize` reads a box for the same reason: the node is the only
+ * thing the measurement needs, so it is taken the moment React has one and
+ * taken again whenever it hands over another. A filter that cuts a thousand
+ * rows to fifty changes how tall the list is and not where it starts, so there
+ * is nothing to remeasure when the count moves.
+ * @param count - How many rows the list holds.
+ * @param estimatedRowHeight - What one row is worth until one has been drawn.
+ * @returns The rows to draw, the spacers standing in for the others, and the
+ * ref the list reports its position through.
+ */
+export declare function useVirtualWindowRows(count: number, estimatedRowHeight: number): VirtualWindowRows;
+//# sourceMappingURL=useVirtualWindowRows.d.ts.map

package/lib/panel/ui/useVirtualWindowRows.d.ts.map

@@ -0,0 +1 @@
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package/lib/panel/ui/useVirtualWindowRows.js

@@ -0,0 +1,65 @@
+/**
+ * Drawing only the rows the page is showing, for a list that scrolls with it.
+ *
+ * `useVirtualRows` measures a scroll region of its own, which is what a panel
+ * beside a chart has. A table filling a tab has none: it flows down the document
+ * and the browser window is what scrolls it, so giving the list its own
+ * `overflow` would grow a second scrollbar inside the first and cap the table at
+ * whatever height it was handed — a layout change made to serve the virtualiser
+ * rather than the reader.
+ */
+import { useWindowVirtualizer } from '@tanstack/react-virtual';
+import { useCallback, useState } from 'react';
+import { rowSpacers } from "../core/rowSpacers.js";
+/**
+ * Draw only the rows the page is showing, however long the list is.
+ *
+ * The rows are measured against the window, so the list only has to say how far
+ * down the page it begins — which is what the virtualiser calls its scroll
+ * margin, and what `measureList` reports.
+ *
+ * That position is read in a ref callback rather than in an effect, which is
+ * how `useChartSize` reads a box for the same reason: the node is the only
+ * thing the measurement needs, so it is taken the moment React has one and
+ * taken again whenever it hands over another. A filter that cuts a thousand
+ * rows to fifty changes how tall the list is and not where it starts, so there
+ * is nothing to remeasure when the count moves.
+ * @param count - How many rows the list holds.
+ * @param estimatedRowHeight - What one row is worth until one has been drawn.
+ * @returns The rows to draw, the spacers standing in for the others, and the
+ * ref the list reports its position through.
+ */
+export function useVirtualWindowRows(count, estimatedRowHeight) {
+    const [scrollMargin, setScrollMargin] = useState(0);
+    const measureList = useCallback((node) => {
+        if (node === null)
+            return;
+        setScrollMargin(node.getBoundingClientRect().top + window.scrollY);
+    }, []);
+    const virtualizer = useWindowVirtualizer({
+        count,
+        estimateSize: () => estimatedRowHeight,
+        overscan: OVERSCAN,
+        scrollMargin,
+    });
+    const drawn = virtualizer.getVirtualItems();
+    const indices = new Array(drawn.length);
+    for (let position = 0; position < drawn.length; position++) {
+        indices[position] = drawn[position].index;
+    }
+    return {
+        indices,
+        ...rowSpacers(drawn, virtualizer.getTotalSize()),
+        measure: virtualizer.measureElement,
+        measureList,
+    };
+}
+/**
+ * How many rows are drawn beyond each end of the window.
+ *
+ * The same reasoning as `useVirtualRows`, and the same number: enough that a
+ * wheel gesture never reaches the edge of what was drawn before the next render
+ * has run.
+ */
+const OVERSCAN = 12;
+//# sourceMappingURL=useVirtualWindowRows.js.map

package/lib/panel/ui/useVirtualWindowRows.js.map

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

@@ -0,0 +1,56 @@
+/**
+ * How a set of conformers divides itself between its minima at a temperature.
+ *
+ * Each conformer in the list is one minimum of the surface, so the share of
+ * molecules sitting in it is its Boltzmann factor over the sum of them all.
+ * Mirror-image conformers are separate entries and therefore counted twice,
+ * which is right: they are two distinct microstates, and that is what makes
+ * butane two-thirds gauche at room temperature rather than one-half.
+ *
+ * What this is not: a free energy. The weights come from a single energy per
+ * conformer, with no vibrational entropy, no zero-point energy and no solvent,
+ * so a share is the shape of the answer rather than the answer. It is also only
+ * as good as the energies handed to it — see {@link boltzmannConfidence}, which
+ * is what a table showing these shares says out loud.
+ */
+/** Room temperature, in kelvin, and what a share is quoted at unless asked otherwise. */
+export declare const ROOM_TEMPERATURE = 300;
+/**
+ * The gas constant in kcal/(mol·K), matching MMFF94's own energy unit.
+ *
+ * At {@link ROOM_TEMPERATURE} this makes RT 0.596 kcal/mol, so a conformer one
+ * kcal/mol up is populated about a fifth as much as the lowest.
+ */
+export declare const GAS_CONSTANT = 0.001987204259;
+/**
+ * The share of molecules in each conformer at thermal equilibrium.
+ *
+ * The energies are taken relative to whichever is lowest, so they may be
+ * absolute or already relative. A conformer whose energy is unknown takes no
+ * share and is left out of the sum: it cannot be placed on the surface, and
+ * spreading the remainder over the others is a smaller lie than inventing a
+ * weight for it.
+ * @param energies - One energy per conformer in kcal/mol, `null` where unknown.
+ * @param temperature - Temperature in kelvin.
+ * @default ROOM_TEMPERATURE
+ * @returns One share per conformer, from 0 to 1 and summing to 1 over the ones
+ * that have an energy; `null` wherever the energy was `null`.
+ */
+export declare function boltzmannShares(energies: ReadonlyArray<number | null>, temperature?: number): Array<number | null>;
+/**
+ * The factor a share is uncertain by, given how well the energies behind it are
+ * known.
+ *
+ * A population is exponential in the energy gap, so an error in a relative
+ * energy is an error in a share by `exp(error / RT)` — and RT is 0.596 kcal/mol
+ * at {@link ROOM_TEMPERATURE}. A force field that ranks conformers to within
+ * about 1.5 kcal/mol therefore places a population to within a factor of
+ * roughly twelve, which is why a share read off one is a shape and not a
+ * number.
+ * @param energyError - The typical error of a relative energy, kcal/mol.
+ * @param temperature - Temperature in kelvin.
+ * @default ROOM_TEMPERATURE
+ * @returns The multiplicative factor, at least 1.
+ */
+export declare function boltzmannConfidence(energyError: number, temperature?: number): number;
+//# sourceMappingURL=conformerBoltzmann.d.ts.map

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

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package/lib/structure/core/conformerBoltzmann.js

@@ -0,0 +1,96 @@
+/**
+ * How a set of conformers divides itself between its minima at a temperature.
+ *
+ * Each conformer in the list is one minimum of the surface, so the share of
+ * molecules sitting in it is its Boltzmann factor over the sum of them all.
+ * Mirror-image conformers are separate entries and therefore counted twice,
+ * which is right: they are two distinct microstates, and that is what makes
+ * butane two-thirds gauche at room temperature rather than one-half.
+ *
+ * What this is not: a free energy. The weights come from a single energy per
+ * conformer, with no vibrational entropy, no zero-point energy and no solvent,
+ * so a share is the shape of the answer rather than the answer. It is also only
+ * as good as the energies handed to it — see {@link boltzmannConfidence}, which
+ * is what a table showing these shares says out loud.
+ */
+/** Room temperature, in kelvin, and what a share is quoted at unless asked otherwise. */
+export const ROOM_TEMPERATURE = 300;
+/**
+ * The gas constant in kcal/(mol·K), matching MMFF94's own energy unit.
+ *
+ * At {@link ROOM_TEMPERATURE} this makes RT 0.596 kcal/mol, so a conformer one
+ * kcal/mol up is populated about a fifth as much as the lowest.
+ */
+export const GAS_CONSTANT = 0.001_987_204_259;
+/**
+ * The share of molecules in each conformer at thermal equilibrium.
+ *
+ * The energies are taken relative to whichever is lowest, so they may be
+ * absolute or already relative. A conformer whose energy is unknown takes no
+ * share and is left out of the sum: it cannot be placed on the surface, and
+ * spreading the remainder over the others is a smaller lie than inventing a
+ * weight for it.
+ * @param energies - One energy per conformer in kcal/mol, `null` where unknown.
+ * @param temperature - Temperature in kelvin.
+ * @default ROOM_TEMPERATURE
+ * @returns One share per conformer, from 0 to 1 and summing to 1 over the ones
+ * that have an energy; `null` wherever the energy was `null`.
+ */
+export function boltzmannShares(energies, temperature = ROOM_TEMPERATURE) {
+    const shares = new Array(energies.length).fill(null);
+    if (energies.length === 0)
+        return shares;
+    let lowest = Number.POSITIVE_INFINITY;
+    for (const energy of energies) {
+        if (energy !== null && Number.isFinite(energy) && energy < lowest) {
+            lowest = energy;
+        }
+    }
+    if (lowest === Number.POSITIVE_INFINITY)
+        return shares;
+    // Measured from the lowest, so every exponent is at most zero and the sum
+    // cannot overflow however far apart the energies are.
+    const rt = GAS_CONSTANT * temperature;
+    if (!(rt > 0))
+        return shares;
+    const factors = new Array(energies.length).fill(null);
+    let total = 0;
+    for (let index = 0; index < energies.length; index++) {
+        const energy = energies[index] ?? null;
+        if (energy === null || !Number.isFinite(energy))
+            continue;
+        const factor = Math.exp(-(energy - lowest) / rt);
+        factors[index] = factor;
+        total += factor;
+    }
+    if (total === 0)
+        return shares;
+    for (let index = 0; index < factors.length; index++) {
+        const factor = factors[index] ?? null;
+        if (factor !== null)
+            shares[index] = factor / total;
+    }
+    return shares;
+}
+/**
+ * The factor a share is uncertain by, given how well the energies behind it are
+ * known.
+ *
+ * A population is exponential in the energy gap, so an error in a relative
+ * energy is an error in a share by `exp(error / RT)` — and RT is 0.596 kcal/mol
+ * at {@link ROOM_TEMPERATURE}. A force field that ranks conformers to within
+ * about 1.5 kcal/mol therefore places a population to within a factor of
+ * roughly twelve, which is why a share read off one is a shape and not a
+ * number.
+ * @param energyError - The typical error of a relative energy, kcal/mol.
+ * @param temperature - Temperature in kelvin.
+ * @default ROOM_TEMPERATURE
+ * @returns The multiplicative factor, at least 1.
+ */
+export function boltzmannConfidence(energyError, temperature = ROOM_TEMPERATURE) {
+    const rt = GAS_CONSTANT * temperature;
+    if (!(rt > 0) || !Number.isFinite(energyError) || energyError <= 0)
+        return 1;
+    return Math.exp(energyError / rt);
+}
+//# sourceMappingURL=conformerBoltzmann.js.map

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

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

@@ -0,0 +1,69 @@
+/**
+ * Which energy of a conformer a reader is being shown.
+ *
+ * A refined conformer carries two of everything — what the force field said and
+ * what the better method said afterwards — and a table that mixes them is a
+ * ranking of nothing. So every column reads through one of these, and they all
+ * take the same ranking.
+ */
+import type { ConformerRanking } from './conformers.ts';
+/**
+ * What a refinement has to say for an energy column to read it.
+ *
+ * The structural minimum rather than the whole `ConformerRefinement`, so a site
+ * that carries its conformers in a shape of its own — positions instead of a
+ * molfile, say — can still be read by the same helpers and drawn by the same
+ * table.
+ */
+export interface ConformerRowRefinement {
+    /** The rank this conformer held before the refinement reordered the set. */
+    forceFieldId: number;
+    /** Total energy at the relaxed geometry, kcal/mol. */
+    energy: number;
+    /** Energy above the most stable refined conformer, kcal/mol. */
+    relativeEnergy: number;
+}
+/**
+ * The least a conformer must carry to be ranked and drawn.
+ *
+ * `Conformer` from `react-cheminfo/conformers` satisfies it, and so does any
+ * per-site record that keeps the same three numbers.
+ */
+export interface ConformerRow {
+    /** 1-based rank in the set, most stable first. */
+    id: number;
+    /** Total force-field energy in kcal/mol, `null` when not computed. */
+    energy: number | null;
+    /** Energy above the most stable conformer, `null` without an energy. */
+    relativeEnergy: number | null;
+    /**
+     * What a better method said, once the set has been refined.
+     * @default null
+     */
+    refinement?: ConformerRowRefinement | null;
+}
+/**
+ * The energy above the most stable conformer, in the ranking asked for.
+ * @param conformer - The conformer to read.
+ * @param ranking - Which method's energies to read.
+ * @default 'force-field'
+ * @returns kcal/mol above the lowest, or `null` when that method produced none.
+ */
+export declare function relativeEnergyOf(conformer: ConformerRow, ranking?: ConformerRanking): number | null;
+/**
+ * The total energy, in the ranking asked for, so the two columns of a row
+ * describe one method.
+ * @param conformer - The conformer to read.
+ * @param ranking - Which method's energies to read.
+ * @default 'force-field'
+ * @returns kcal/mol, or `null` when that method produced none.
+ */
+export declare function totalEnergyOf(conformer: ConformerRow, ranking?: ConformerRanking): number | null;
+/**
+ * The ranking a set should be read in: refined once anything has been refined,
+ * the force field's until then.
+ * @param conformers - The set to inspect.
+ * @returns `'refined'` when at least one conformer carries a refinement.
+ */
+export declare function bestRanking(conformers: readonly ConformerRow[]): ConformerRanking;
+//# sourceMappingURL=conformerEnergy.d.ts.map

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

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

@@ -0,0 +1,47 @@
+/**
+ * Which energy of a conformer a reader is being shown.
+ *
+ * A refined conformer carries two of everything — what the force field said and
+ * what the better method said afterwards — and a table that mixes them is a
+ * ranking of nothing. So every column reads through one of these, and they all
+ * take the same ranking.
+ */
+/**
+ * The energy above the most stable conformer, in the ranking asked for.
+ * @param conformer - The conformer to read.
+ * @param ranking - Which method's energies to read.
+ * @default 'force-field'
+ * @returns kcal/mol above the lowest, or `null` when that method produced none.
+ */
+export function relativeEnergyOf(conformer, ranking = 'force-field') {
+    return ranking === 'refined'
+        ? (conformer.refinement?.relativeEnergy ?? null)
+        : conformer.relativeEnergy;
+}
+/**
+ * The total energy, in the ranking asked for, so the two columns of a row
+ * describe one method.
+ * @param conformer - The conformer to read.
+ * @param ranking - Which method's energies to read.
+ * @default 'force-field'
+ * @returns kcal/mol, or `null` when that method produced none.
+ */
+export function totalEnergyOf(conformer, ranking = 'force-field') {
+    return ranking === 'refined'
+        ? (conformer.refinement?.energy ?? null)
+        : conformer.energy;
+}
+/**
+ * The ranking a set should be read in: refined once anything has been refined,
+ * the force field's until then.
+ * @param conformers - The set to inspect.
+ * @returns `'refined'` when at least one conformer carries a refinement.
+ */
+export function bestRanking(conformers) {
+    for (const conformer of conformers) {
+        if (conformer.refinement != null)
+            return 'refined';
+    }
+    return 'force-field';
+}
+//# sourceMappingURL=conformerEnergy.js.map

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

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

@@ -1,5 +1,8 @@
 export type { AtomLabelPlacement, LabelledMolecule } from './atomLabels.ts';
 export { applyAtomLabels, customAtomLabel } from './atomLabels.ts';
+export { GAS_CONSTANT, ROOM_TEMPERATURE, boltzmannConfidence, boltzmannShares, } from './conformerBoltzmann.ts';
+export type { ConformerRow, ConformerRowRefinement, } from './conformerEnergy.ts';
+export { bestRanking, relativeEnergyOf, totalEnergyOf, } from './conformerEnergy.ts';
 export type { EditorGesture, EditorGuideKey, EditorGuideLink, EditorGuideOptions, EditorGuideScope, EditorGuideSection, } from './editorGuide.ts';
 export { STRUCTURE_EDITOR_DOCS, STRUCTURE_EDITOR_GUIDE, editorGuideSections, editorKeyLabel, } from './editorGuide.ts';
 export type { EditorToolbarAvailability, EditorToolbarButton, } from './editorToolbar.ts';

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

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package/lib/structure/core/index.js

@@ -1,4 +1,6 @@
 export { applyAtomLabels, customAtomLabel } from "./atomLabels.js";
+export { GAS_CONSTANT, ROOM_TEMPERATURE, boltzmannConfidence, boltzmannShares, } from "./conformerBoltzmann.js";
+export { bestRanking, relativeEnergyOf, totalEnergyOf, } from "./conformerEnergy.js";
 export { STRUCTURE_EDITOR_DOCS, STRUCTURE_EDITOR_GUIDE, editorGuideSections, editorKeyLabel, } from "./editorGuide.js";
 export { EDITOR_TOOLBAR_BUTTONS, isEditorToolbarButtonAvailable, } from "./editorToolbar.js";
 export { EDITOR_TOOLBAR_COLUMNS, EDITOR_TOOLBAR_ROWS, editorToolbarButtonAt, editorToolbarButtonBox, } from "./editorToolbarGeometry.js";

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

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package/lib/structure/ui/ConformerTable.d.ts

@@ -0,0 +1,73 @@
+/**
+ * A conformer set, most stable first, as a table one row of which is selected.
+ *
+ * Two sites read the same set for different reasons — one picks the geometry a
+ * calculation runs on, the other reads the ranking itself — so the columns are
+ * a prop rather than a variant. Everything else is the same table: rows ordered
+ * by energy, one selected, the arrows walking it.
+ *
+ * The population column is the reason the ranking matters. A share is
+ * exponential in the energy gap, so it inherits the error of whatever produced
+ * the energies and magnifies it; the caption under the table says which method
+ * that was, and `boltzmannConfidence` says what its error is worth. A table
+ * that prints a force field's populations without that line is stating a
+ * percentage it cannot support.
+ */
+import type { ReactElement } from 'react';
+import type { ConformerRow } from '../core/conformerEnergy.ts';
+import type { ConformerRanking } from '../core/conformers.ts';
+import type { ConformerColumn } from './conformerColumns.ts';
+/** Props of {@link ConformerTable}. */
+export interface ConformerTableProps {
+    /** The set, already ordered most stable first. */
+    conformers: readonly ConformerRow[];
+    /**
+     * Which columns to draw, in order.
+     * @default PICKER_COLUMNS
+     */
+    columns?: readonly ConformerColumn[];
+    /**
+     * Which method's energies every column reads.
+     * @default 'force-field'
+     */
+    ranking?: ConformerRanking;
+    /**
+     * The selected conformer's id, or `null` when none is.
+     * @default null
+     */
+    selectedId?: number | null;
+    /** Called with the id of the row the reader picked. */
+    onSelect?: (id: number) => void;
+    /**
+     * Temperature the shares are quoted at, in kelvin.
+     * @default ROOM_TEMPERATURE
+     */
+    temperature?: number;
+    /**
+     * Accessible name of the table.
+     * @default 'Conformers, most stable first'
+     */
+    label?: string;
+    /**
+     * What the `id` column says for a conformer. A dense table wants the bare
+     * rank; a picker in a narrow column reads better naming the thing.
+     * @default String — the rank on its own
+     */
+    rowName?: (id: number) => string;
+    /**
+     * Headings to use instead of the default ones, per column.
+     * @default undefined — every column keeps its own
+     */
+    columnLabels?: Partial<Record<ConformerColumn, string>>;
+}
+/**
+ * The conformers of a set, as a selectable table.
+ *
+ * The arrows walk the rows once the table has the focus, rather than from
+ * anywhere on the page: a conformer list usually sits beside a drawing surface
+ * or a 3D canvas, both of which read the arrows themselves.
+ * @param props - See {@link ConformerTableProps}.
+ * @returns The table, or `null` when there is nothing to show.
+ */
+export declare function ConformerTable(props: ConformerTableProps): ReactElement | null;
+//# sourceMappingURL=ConformerTable.d.ts.map

package/lib/structure/ui/ConformerTable.d.ts.map

@@ -0,0 +1 @@
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