react-cheminfo 0.27.0 → 0.29.0

package/lib/ir/core/bandAssignments.js

@@ -0,0 +1,305 @@
+/**
+ * The correlation table: which vibration a band at a given wavenumber may be.
+ *
+ * This is the infrared analogue of a fragment set — what a producer *claims*
+ * about a spectrum — with one difference that shapes the whole design: a mass
+ * fragment claims one m/z, while a vibration claims a **range**, and the ranges
+ * overlap heavily on purpose. A band at 1715 cm⁻¹ is an ester, an aldehyde, a
+ * ketone and a carboxylic acid until something else decides between them, and a
+ * table that returned one answer there would be inventing chemistry.
+ *
+ * The ranges are the conventional teaching values, rounded to the tens that a
+ * printed table uses. They are deliberately not narrowed to look precise: a
+ * conjugated ketone really does absorb below an unconjugated one, and a table
+ * that excluded it would read as ruling the ketone out.
+ */
+/**
+ * The table, in ascending order of the low end of each range.
+ *
+ * Ordered so that a reader scanning it moves along the axis, and so that the
+ * fingerprint region below 1500 cm⁻¹ — where assignments are least decisive —
+ * sits together at the top rather than being interleaved with the diagnostic
+ * stretches above it.
+ */
+export const BAND_ASSIGNMENTS = [
+    {
+        id: 'c-br-stretch',
+        group: 'alkyl bromide',
+        vibration: 'C–Br stretch',
+        from: 500,
+        to: 600,
+        strength: 'S',
+    },
+    {
+        id: 'c-cl-stretch',
+        group: 'alkyl chloride',
+        vibration: 'C–Cl stretch',
+        from: 600,
+        to: 800,
+        strength: 'S',
+    },
+    {
+        id: 'aromatic-ch-oop',
+        group: 'arene',
+        vibration: 'C–H out-of-plane bend',
+        from: 690,
+        to: 900,
+        strength: 'S',
+        note: 'How many bands, and where, is what tells a substitution pattern apart',
+    },
+    {
+        id: 'alkene-ch-oop',
+        group: 'alkene',
+        vibration: '=C–H out-of-plane bend',
+        from: 890,
+        to: 990,
+        strength: 'S',
+        note: 'A terminal vinyl gives two, near 910 and 990',
+    },
+    {
+        id: 'c-o-stretch',
+        group: 'alcohol, ether, ester',
+        vibration: 'C–O stretch',
+        from: 1000,
+        to: 1300,
+        strength: 'S',
+        note: 'Strong and broad; an ester shows two, the higher one near 1200',
+    },
+    {
+        id: 'c-f-stretch',
+        group: 'alkyl fluoride',
+        vibration: 'C–F stretch',
+        from: 1000,
+        to: 1400,
+        strength: 'S',
+    },
+    {
+        id: 'c-n-stretch',
+        group: 'amine, amide',
+        vibration: 'C–N stretch',
+        from: 1080,
+        to: 1360,
+        strength: 'm',
+    },
+    {
+        id: 'nitro-symmetric',
+        group: 'nitro',
+        vibration: 'N–O symmetric stretch',
+        from: 1300,
+        to: 1390,
+        strength: 'S',
+        note: 'Never alone: the asymmetric partner sits near 1500–1560',
+    },
+    {
+        id: 'oh-bend',
+        group: 'alcohol',
+        vibration: 'O–H bend',
+        from: 1330,
+        to: 1430,
+        strength: 'm',
+    },
+    {
+        id: 'alkane-ch-bend',
+        group: 'alkane',
+        vibration: 'C–H bend',
+        from: 1370,
+        to: 1470,
+        strength: 'm',
+        note: 'A gem-dimethyl splits the 1380 band in two',
+    },
+    {
+        id: 'aromatic-cc-stretch',
+        group: 'arene',
+        vibration: 'C=C aromatic stretch',
+        from: 1450,
+        to: 1600,
+        strength: 'm',
+        note: 'Usually a pair, near 1500 and 1600',
+    },
+    {
+        id: 'nitro-asymmetric',
+        group: 'nitro',
+        vibration: 'N–O asymmetric stretch',
+        from: 1500,
+        to: 1560,
+        strength: 'S',
+    },
+    {
+        id: 'nh-bend',
+        group: 'amine, amide',
+        vibration: 'N–H bend',
+        from: 1550,
+        to: 1640,
+        strength: 'm',
+    },
+    {
+        id: 'alkene-cc-stretch',
+        group: 'alkene',
+        vibration: 'C=C stretch',
+        from: 1620,
+        to: 1680,
+        strength: 'w',
+        note: 'Weak, and absent altogether on a symmetric alkene',
+    },
+    {
+        id: 'amide-co-stretch',
+        group: 'amide',
+        vibration: 'C=O stretch',
+        from: 1630,
+        to: 1690,
+        strength: 'S',
+        note: 'The lowest carbonyl there is; look for N–H above 3300 to confirm',
+    },
+    {
+        id: 'acid-co-stretch',
+        group: 'carboxylic acid',
+        vibration: 'C=O stretch',
+        from: 1700,
+        to: 1725,
+        strength: 'S',
+        note: 'Confirmed by the very broad O–H between 2500 and 3300',
+    },
+    {
+        id: 'ketone-co-stretch',
+        group: 'ketone',
+        vibration: 'C=O stretch',
+        from: 1705,
+        to: 1725,
+        strength: 'S',
+        note: 'Conjugation drops it by about 30; a strained ring raises it',
+    },
+    {
+        id: 'aldehyde-co-stretch',
+        group: 'aldehyde',
+        vibration: 'C=O stretch',
+        from: 1720,
+        to: 1740,
+        strength: 'S',
+        note: 'Confirmed by the C–H pair near 2720 and 2820',
+    },
+    {
+        id: 'ester-co-stretch',
+        group: 'ester',
+        vibration: 'C=O stretch',
+        from: 1735,
+        to: 1750,
+        strength: 'S',
+        note: 'Confirmed by the strong C–O between 1000 and 1300',
+    },
+    {
+        id: 'acid-chloride-co-stretch',
+        group: 'acid chloride',
+        vibration: 'C=O stretch',
+        from: 1770,
+        to: 1815,
+        strength: 'S',
+    },
+    {
+        id: 'anhydride-co-stretch',
+        group: 'anhydride',
+        vibration: 'C=O stretch',
+        from: 1740,
+        to: 1830,
+        strength: 'S',
+        note: 'Two bands, about 60 apart, which is what names it',
+    },
+    {
+        id: 'nitrile-stretch',
+        group: 'nitrile',
+        vibration: 'C≡N stretch',
+        from: 2210,
+        to: 2260,
+        strength: 'm',
+        note: 'Sharp, and in a region almost nothing else occupies',
+    },
+    {
+        id: 'alkyne-cc-stretch',
+        group: 'alkyne',
+        vibration: 'C≡C stretch',
+        from: 2100,
+        to: 2260,
+        strength: 'w',
+        note: 'Weak, and absent on a symmetric internal alkyne',
+    },
+    {
+        id: 'aldehyde-ch-stretch',
+        group: 'aldehyde',
+        vibration: 'C–H stretch',
+        from: 2695,
+        to: 2830,
+        strength: 'm',
+        note: 'The diagnostic pair near 2720 and 2820',
+    },
+    {
+        id: 'acid-oh-stretch',
+        group: 'carboxylic acid',
+        vibration: 'O–H stretch',
+        from: 2500,
+        to: 3300,
+        strength: 'S',
+        note: 'Very broad — it runs under the C–H bands rather than beside them',
+    },
+    {
+        id: 'alkane-ch-stretch',
+        group: 'alkane',
+        vibration: 'C–H stretch',
+        from: 2850,
+        to: 3000,
+        strength: 'S',
+        note: 'Below 3000, which is what separates it from an alkene C–H',
+    },
+    {
+        id: 'alkene-ch-stretch',
+        group: 'alkene',
+        vibration: '=C–H stretch',
+        from: 3000,
+        to: 3100,
+        strength: 'm',
+        note: 'Above 3000, and never alone: the C=C sits near 1650',
+    },
+    {
+        id: 'aromatic-ch-stretch',
+        group: 'arene',
+        vibration: 'C–H stretch',
+        from: 3000,
+        to: 3100,
+        strength: 'm',
+    },
+    {
+        id: 'alkyne-ch-stretch',
+        group: 'alkyne',
+        vibration: '≡C–H stretch',
+        from: 3260,
+        to: 3330,
+        strength: 'S',
+        note: 'Sharp, where an O–H in the same place is broad',
+    },
+    {
+        id: 'alcohol-oh-stretch',
+        group: 'alcohol',
+        vibration: 'O–H stretch',
+        from: 3200,
+        to: 3600,
+        strength: 'S',
+        note: 'Broad when hydrogen bonded, which is nearly always',
+    },
+    {
+        id: 'nh-stretch',
+        group: 'amine, amide',
+        vibration: 'N–H stretch',
+        from: 3300,
+        to: 3500,
+        strength: 'm',
+        note: 'A primary amine gives two bands, a secondary one',
+    },
+    {
+        id: 'free-oh-stretch',
+        group: 'alcohol',
+        vibration: 'O–H stretch, not hydrogen bonded',
+        from: 3580,
+        to: 3650,
+        strength: 'm',
+        note: 'Sharp, and only in a dilute or gas-phase spectrum',
+    },
+];
+//# sourceMappingURL=bandAssignments.js.map

package/lib/ir/core/bandAssignments.js.map

@@ -0,0 +1 @@
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package/lib/ir/core/bandLabelPlan.d.ts

@@ -0,0 +1,93 @@
+/**
+ * Where every band's mark and label go, worked out before anything is drawn.
+ *
+ * Kept apart from the component because it is the part worth testing: which
+ * bands get a label, which way their lines stack, how far a crowded label may
+ * slide from the band it names, and which are dropped rather than drawn
+ * somewhere misleading. All of that is arithmetic over numbers, and none of it
+ * needs a DOM.
+ */
+import type { PlotRect } from '../../chart/core/chartGeometry.ts';
+import type { ChartScale } from '../../chart/core/chartScale.ts';
+import type { AssignedBand } from './assignBands.ts';
+import type { IrBand } from './irBand.ts';
+import type { IrMode } from './irSpectrum.ts';
+/** One band, and where everything about it is drawn. */
+export interface BandLabelPlan {
+    /** The band itself. */
+    band: IrBand;
+    /** Where its tip sits horizontally, in user units of the SVG. */
+    tipX: number;
+    /** Where its tip sits vertically. */
+    tipY: number;
+    /**
+     * Where its label is centred, `NaN` when the label was dropped for having
+     * been slid too far from the band to belong to it.
+     */
+    labelX: number;
+    /** The baseline of each line of the label, in the order the lines are given. */
+    baselines: Float64Array;
+    /** What the label says, farthest line from the band first. */
+    lines: string[];
+}
+/** What the plan is worked out from. */
+export interface BandLabelPlanOptions {
+    /** The bands to name, with whatever the table said about them. */
+    assigned: readonly AssignedBand[];
+    /** Where the plot sits inside the SVG. */
+    plot: PlotRect;
+    /** The wavenumber axis as it is currently zoomed. */
+    xScale: ChartScale;
+    /** The value axis as it is currently zoomed. */
+    yScale: ChartScale;
+    /** Which value axis is being drawn, which decides which way labels stack. */
+    mode: IrMode;
+    /**
+     * Whether each label names the assignment as well as the wavenumber.
+     *
+     * The assignment is the longer line by far — `carboxylic acid C=O stretch`
+     * against `1710` — so a chart showing a dozen bands is legible with the
+     * wavenumbers alone and unreadable with both.
+     * @default false
+     */
+    showAssignments?: boolean;
+    /**
+     * At most how many bands to name.
+     *
+     * Marks are drawn on every band regardless; this only bounds the labels, since
+     * a mark costs three pixels and a two-line label costs sixty.
+     * @default 12
+     */
+    limit?: number;
+}
+/**
+ * Work out where every band's label goes.
+ *
+ * Only the bands inside the window are considered, so a zoom into one region
+ * gives its bands the whole width to be named in rather than sharing it with the
+ * hundred outside the plot.
+ *
+ * The strongest bands win the labels when there are more than `limit`, because a
+ * strong band is the one a reader is looking for; but they come back in ascending
+ * wavenumber — the order `pickBands` returns and the order a band table lists —
+ * rather than in the order they were chosen. Which is right to left on screen,
+ * since the axis is drawn backwards; nothing depends on it, because the declutter
+ * sweep sorts by pixel itself.
+ * @param options - The bands, the axes and how much to say.
+ * @returns One plan per band that is inside the window, in axis order.
+ */
+export declare function planBandLabels(options: BandLabelPlanOptions): BandLabelPlan[];
+/**
+ * How wide a label is taken to be while it is being spaced out.
+ *
+ * A wavenumber is four digits and an assignment is far wider, but the width used
+ * for spacing is the wavenumber's: spacing on the longer line would push every
+ * label so far apart that only three fit, and an assignment is only ever shown
+ * when a handful of bands are named.
+ */
+export declare const LABEL_WIDTH = 34;
+/** The clear space kept between two neighbouring labels. */
+export declare const LABEL_GAP = 6;
+/** How far the mark reaches from the tip of a band, in pixels. */
+export declare const BAND_MARK: 10;
+//# sourceMappingURL=bandLabelPlan.d.ts.map

package/lib/ir/core/bandLabelPlan.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/bandLabelPlan.js

@@ -0,0 +1,104 @@
+/**
+ * Where every band's mark and label go, worked out before anything is drawn.
+ *
+ * Kept apart from the component because it is the part worth testing: which
+ * bands get a label, which way their lines stack, how far a crowded label may
+ * slide from the band it names, and which are dropped rather than drawn
+ * somewhere misleading. All of that is arithmetic over numbers, and none of it
+ * needs a DOM.
+ */
+import { layoutAnnotationBoxes } from "../../chart/core/boxLayout.js";
+import { chartPixel } from "../../chart/core/chartScale.js";
+import { PEAK_LABEL } from "../../chart/core/chartTheme.js";
+import { labelStackBaselines } from "../../chart/core/labelStack.js";
+import { bandLabel } from "./assignBands.js";
+import { formatWavenumber } from "./irFormat.js";
+import { bandsPointDown } from "./irMode.js";
+/**
+ * Work out where every band's label goes.
+ *
+ * Only the bands inside the window are considered, so a zoom into one region
+ * gives its bands the whole width to be named in rather than sharing it with the
+ * hundred outside the plot.
+ *
+ * The strongest bands win the labels when there are more than `limit`, because a
+ * strong band is the one a reader is looking for; but they come back in ascending
+ * wavenumber — the order `pickBands` returns and the order a band table lists —
+ * rather than in the order they were chosen. Which is right to left on screen,
+ * since the axis is drawn backwards; nothing depends on it, because the declutter
+ * sweep sorts by pixel itself.
+ * @param options - The bands, the axes and how much to say.
+ * @returns One plan per band that is inside the window, in axis order.
+ */
+export function planBandLabels(options) {
+    const { assigned, plot, xScale, yScale, mode, showAssignments = false, limit = 12, } = options;
+    const inside = [];
+    for (const entry of assigned) {
+        const pixelX = chartPixel(xScale, entry.band.wavenumber);
+        if (!Number.isFinite(pixelX))
+            continue;
+        if (pixelX < plot.left || pixelX > plot.right)
+            continue;
+        inside.push(entry);
+    }
+    const named = inside.length <= limit
+        ? inside
+        : inside
+            .toSorted((first, second) => second.band.absorbance - first.band.absorbance)
+            .slice(0, limit)
+            .toSorted((first, second) => first.band.wavenumber - second.band.wavenumber);
+    const centres = new Float64Array(named.length);
+    for (let index = 0; index < named.length; index++) {
+        centres[index] = chartPixel(xScale, named[index].band.wavenumber);
+    }
+    const placed = layoutAnnotationBoxes(centres, [plot.left, plot.right], LABEL_WIDTH, LABEL_GAP);
+    const down = bandsPointDown(mode);
+    const plans = new Array(named.length);
+    for (let index = 0; index < named.length; index++) {
+        const entry = named[index];
+        const lines = labelLines(entry, showAssignments);
+        const tipY = chartPixel(yScale, mode === 'absorbance' ? entry.band.absorbance : entry.band.transmittance);
+        plans[index] = {
+            band: entry.band,
+            tipX: centres[index],
+            tipY,
+            labelX: placed[index],
+            // The stack hangs away from the baseline: below the tip of a transmittance
+            // band, which dips downwards, and above the tip of an absorbance one.
+            baselines: labelStackBaselines(tipY, lines.length, [plot.top, plot.bottom], down),
+            lines,
+        };
+    }
+    return plans;
+}
+/**
+ * How wide a label is taken to be while it is being spaced out.
+ *
+ * A wavenumber is four digits and an assignment is far wider, but the width used
+ * for spacing is the wavenumber's: spacing on the longer line would push every
+ * label so far apart that only three fit, and an assignment is only ever shown
+ * when a handful of bands are named.
+ */
+export const LABEL_WIDTH = 34;
+/** The clear space kept between two neighbouring labels. */
+export const LABEL_GAP = 6;
+/** How far the mark reaches from the tip of a band, in pixels. */
+export const BAND_MARK = PEAK_LABEL.topMark;
+/**
+ * What one band's label says.
+ * @param entry - The band and whatever the table said about it.
+ * @param showAssignments - Whether to name the assignment as well.
+ * @returns The lines, farthest from the band first, never empty.
+ */
+function labelLines(entry, showAssignments) {
+    const lines = [formatWavenumber(entry.band.wavenumber)];
+    if (!showAssignments)
+        return lines;
+    const label = bandLabel(entry);
+    // The assignment goes nearest the band, under the wavenumber, so the eye
+    // travels from the mark to what it is claimed to be.
+    if (label !== null)
+        lines.push(label);
+    return lines;
+}
+//# sourceMappingURL=bandLabelPlan.js.map

package/lib/ir/core/bandLabelPlan.js.map

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package/lib/ir/core/detectIrFormat.d.ts

@@ -0,0 +1,23 @@
+/**
+ * Which reader a dropped infrared file belongs to, decided from the file itself.
+ *
+ * The extension is the least reliable thing about a spectrum file: instruments
+ * export JCAMP as `.txt`, LIMS systems rename everything to `.dat`, and a user
+ * pasting into a text box has no extension at all. So the content decides and
+ * the name is consulted only when the content stayed silent.
+ */
+import type { IrFormat } from './irSpectrum.ts';
+/**
+ * Decide what a dropped file is, from its first bytes and only then its name.
+ *
+ * Returns `'unknown'` rather than guessing `'text'` for the two cases the
+ * readers cannot survive: nothing at all, and bytes that are plainly not text.
+ * Handing either to the text reader produces an empty spectrum and a message
+ * about missing columns, which sends whoever dropped the file looking in the
+ * wrong place.
+ * @param data - The file, or the pasted text.
+ * @param fileName - Its name, when it has one.
+ * @returns The format, or `'unknown'` when nothing in the file names one.
+ */
+export declare function detectIrFormat(data: Uint8Array | string, fileName?: string): IrFormat | 'unknown';
+//# sourceMappingURL=detectIrFormat.d.ts.map

package/lib/ir/core/detectIrFormat.d.ts.map

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