nmr-processing 8.0.0 → 8.3.0

package/lib/ranges/markSolventSignal.js

@@ -0,0 +1,107 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.markSolventPeaks = void 0;
+const generateID_1 = __importDefault(require("../assignment/utils/generateID"));
+const checkIDs_1 = require("../assignment/utils/getAssignment/checkIDs");
+const peaksToRanges_1 = require("../peaks/peaksToRanges");
+const solventSuppression_1 = require("../peaks/solventSuppression");
+function markSolventPeaks(input, solventSignals, options = {}) {
+    const { frequency = 400 } = options;
+    const ranges = (0, checkIDs_1.addIDs)([...input]);
+    let peakList = [];
+    for (const range of ranges) {
+        const rangeID = range.id;
+        for (const signal of range.signals || []) {
+            const signalID = signal.id;
+            for (let peak of signal.peaks || []) {
+                peakList.push({
+                    ...peak,
+                    rangeID,
+                    signalID,
+                });
+            }
+        }
+    }
+    const peaks = (0, solventSuppression_1.solventSuppression)(peakList, solventSignals, {
+        markSolventPeaks: true,
+    });
+    const signalsWithSolvent = getSignalIDsWithSolvent(peaks);
+    for (let range of ranges) {
+        if (!range.signals)
+            continue;
+        for (let signal of range.signals) {
+            if (!signalsWithSolvent.includes(signal.id))
+                continue;
+            const signalPeaks = [];
+            const solventSignalPeaks = [];
+            for (let peak of peaks) {
+                if (peak.signalID === signal.id) {
+                    const { signalID, rangeID, ...newPeak } = peak;
+                    if (peak.kind === 'solvent') {
+                        solventSignalPeaks.push(newPeak);
+                    }
+                    else {
+                        signalPeaks.push(newPeak);
+                    }
+                }
+            }
+            const newSignals = signalPeaks.length > 0
+                ? (0, peaksToRanges_1.detectSignals)({ x: [], y: [] }, signalPeaks, {
+                    integralType: 'peak',
+                    frequency,
+                })
+                : [];
+            solventSignalPeaks.sort((a, b) => a.x - b.x);
+            const lowPPMValue = solventSignalPeaks[0].x;
+            const highPPMValue = solventSignalPeaks[solventSignalPeaks.length - 1].x;
+            const newSolventSignals = (0, peaksToRanges_1.detectSignals)({ x: [], y: [] }, solventSignalPeaks, {
+                integralType: 'peak',
+                frequencyCluster: (highPPMValue - lowPPMValue) * frequency,
+                frequency,
+            });
+            range.signals = [
+                ...adaptSignals(newSignals),
+                ...adaptSignals(newSolventSignals),
+                ...range.signals.filter((currSignal) => currSignal.id !== signal.id),
+            ];
+        }
+    }
+    return ranges;
+}
+exports.markSolventPeaks = markSolventPeaks;
+function getSignalIDsWithSolvent(solventPeaks) {
+    const uniqueSignalID = new Set();
+    for (let peak of solventPeaks) {
+        if (peak.kind !== 'solvent')
+            continue;
+        uniqueSignalID.add(peak.signalID);
+    }
+    return Array.from(uniqueSignalID);
+}
+function adaptSignals(signals) {
+    const newSignals = [];
+    for (let signal of signals) {
+        const signalResult = {
+            id: (0, generateID_1.default)(),
+            delta: signal.delta,
+            kind: signal.kind || 'signal',
+            multiplicity: signal.multiplicity,
+            integration: signal.integralData.value,
+        };
+        signalResult.peaks = signal.peaks.map((peak) => {
+            const newResult = {
+                y: peak.intensity,
+                ...peak,
+            };
+            delete newResult.intensity;
+            return newResult;
+        });
+        signalResult.js = signal.nmrJs || [];
+        newSignals.push(signalResult);
+    }
+    return newSignals;
+}
+//# sourceMappingURL=markSolventSignal.js.map

package/lib/ranges/markSolventSignal.js.map

@@ -0,0 +1 @@
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package/lib/ranges/rangesToACS.js

@@ -28,7 +28,12 @@ function rangesToACS(ranges, options = {}) {
         options.nucleus = '1H';
     const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
     const defaultOptions = globalOptions[nucleus];
-    options = Object.assign({}, defaultOptions, { ascending: false, format: 'IMJA' }, options);
+    options = {
+        ...defaultOptions,
+        ascending: false,
+        format: 'IMJA',
+        ...options,
+    };
     ranges = JSON.parse(JSON.stringify(ranges));
     if (options.ascending === true) {
         ranges.sort((a, b) => {
@@ -141,9 +146,8 @@ function getIntegral(range, options) {
         integration = String(range.pubIntegral);
     }
     else if (range.integration) {
-        integration =
-            range.integration.toFixed(0) +
-                options.nucleus[options.nucleus.length - 1];
+        const { nucleus } = options;
+        integration = range.integration.toFixed(0) + nucleus[nucleus.length - 1];
     }
     return integration;
 }

package/lib/ranges/rangesToACS.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":";;;AAAA,uEAAoE;AACpE,mFAAgF;AAIhF,MAAM,aAAa,GAQf;IACF,CAAC,EAAE;QACD,OAAO,EAAE,IAAI;QACb,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;CACF,CAAC;AAmCF,SAAgB,WAAW,CACzB,MAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,CAAC,OAAO,CAAC,OAAO;QAAE,OAAO,CAAC,OAAO,GAAG,IAAI,CAAC;IAC7C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;IACpE,MAAM,cAAc,GAAG,aAAa,CAAC,OAAO,CAAC,CAAC;IAC9C,OAAO,GAAG;QACR,GAAG,cAAc;QACjB,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,MAAM;QACd,GAAG,OAAO;KACX,CAAC;IAEF,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;IAC5C,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;QAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACnB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,OAAO,KAAK,GAAG,KAAK,CAAC;QACvB,CAAC,CAAC,CAAC;KACJ;IAED,IAAI,SAAS,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC3C,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;QAAE,SAAS,IAAI,GAAG,CAAC;IAE3C,OAAO,SAAS,CAAC;AACnB,CAAC;AA3BD,kCA2BC;AAED,SAAS,SAAS,CAAC,MAAkB,EAAE,OAAY;IACjD,IAAI,GAAG,GAAG,kBAAkB,CAAC,OAAO,CAAC,CAAC;IACtC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;QAAE,GAAG,GAAG,IAAI,CAAC;IACjC,MAAM,SAAS,GAAa,EAAE,CAAC;IAC/B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,WAAW,CAAC,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC;YAAE,SAAS;QACtD,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;KACtC;IACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE;QACxB,OAAO,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;KACnC;SAAM;QACL,OAAO,EAAE,CAAC;KACX;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAY;IACtC,MAAM,WAAW,GAAG,EAAE,CAAC;IACvB,IAAI,OAAO,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC;IACtD,IAAI,OAAO,CAAC,OAAO,EAAE;QACnB,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;KAC7C;IACD,IAAI,OAAO,CAAC,iBAAiB,EAAE;QAC7B,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,iBAAiB,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;KACvE;IACD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE;QAC1B,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;KAC/C;SAAM;QACL,OAAO,IAAI,MAAM,CAAC;KACnB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,SAAS,CAAC,KAAe,EAAE,SAAmB,EAAE,OAAY;IACnE,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,WAAW,GAAQ,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,CAAC,CAAC;IAEtC,IAAI,KAAK,CAAC,OAAO,EAAE;QACjB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAClC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,CACtD,CAAC;KACH;IAED,IAAI,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;QAC7C,IAAI,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC;QAC5B,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;YACtB,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;gBAC9B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;oBACpB,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;gBAC3B,CAAC,CAAC,CAAC;aACJ;YACD,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;YAC3D,OAAO,IAAI,KAAK,WAAW,CAAC,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;YAC9C,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;gBAC1B,WAAW,GAAG,EAAE,CAAC;gBACjB,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,EAAE;oBAC9B,OAAO,GAAG,eAAe,CAAC,OAAO,CAAC,CAAC;oBACnC,OAAO,IAAI,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;iBACzD;gBACD,MAAM,KAAK,GAAa;oBACtB,IAAI,EAAE,MAAM,CAAC,gBAAgB;oBAC7B,EAAE,EAAE,MAAM,CAAC,gBAAgB;iBAC5B,CAAC;gBACF,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBAClD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACvE;YACD,OAAO,IAAI,GAAG,CAAC;SAChB;aAAM;YACL,WAAW,GAAG,EAAE,CAAC;YACjB,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,EAAE;gBAClC,OAAO,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;gBAC5D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACvE;iBAAM;gBACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;gBAC3D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,GAAG,CAAC;aAC5D;SACF;KACF;SAAM;QACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;QAC3D,MAAM,MAAM,GAAQ,EAAE,CAAC;QACvB,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;QAClD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;YAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;KACvE;IACD,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,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package/lib/ranges/rangesToXY.js

@@ -13,17 +13,26 @@ function checkForSignals(ranges) {
             throw new Error('range has not signals');
     }
 }
+const defaultFromTo = (nucleus = '') => {
+    switch (nucleus.toUpperCase()) {
+        case '13C':
+            return { from: -5, to: 206 };
+        default:
+            return { from: -0.5, to: 10.5 };
+    }
+};
 function rangesToXY(ranges, options = {}) {
     checkForSignals(ranges);
-    let { frequency = 400, lineWidth = 1, from = 0, to = 10, nbPoints = 16 * 1024, shape = { kind: 'gaussian' }, } = options;
+    let { frequency = 400, lineWidth = 1, nbPoints = 16 * 1024, shape = { kind: 'gaussian' }, } = options;
     const addSpectrum = (a, b) => {
         for (let i = 0; i < nbPoints; i++) {
             a[i] += b[i];
         }
     };
+    const { from, to } = getFromTo(ranges, options);
     const spectrumOptions = {
-        from,
         to,
+        from,
         nbPoints,
         shape,
         lineWidth,
@@ -84,7 +93,7 @@ function broadPeakOrMultipletSpectrum(signals, options = {}) {
     return spectrumGenerator.getSpectrum();
 }
 function peaksOfMultiplet(delta, options) {
-    const { frequency, lineWidth, intensities = [1, 2, 5, 4, 5, 3, 4, 2, 1], } = options;
+    const { frequency, lineWidth, intensities = [1, 2, 5, 4, 5, 7, 5, 4, 5, 2, 1], } = options;
     const lineWidthPpm = lineWidth / frequency;
     const spaceBetweenPeaks = lineWidthPpm * 1.5;
     const peaks = [];
@@ -111,4 +120,19 @@ function normalizeSpectrum(spectrum, signals, options = {}) {
         }
     }
 }
+function getFromTo(ranges, options) {
+    const { from: defaultFrom, to: defaultTo } = defaultFromTo(options.nucleus);
+    let rangesFrom = Number.MAX_SAFE_INTEGER;
+    let rangesTo = Number.MIN_SAFE_INTEGER;
+    for (const range of ranges) {
+        for (const signal of range.signals || []) {
+            if (rangesFrom > signal.delta)
+                rangesFrom = signal.delta;
+            if (rangesTo < signal.delta)
+                rangesTo = signal.delta;
+        }
+    }
+    const { from = Math.min(rangesFrom - 0.5, defaultFrom), to = Math.max(rangesTo + 0.5, defaultTo), } = options;
+    return { from, to };
+}
 //# sourceMappingURL=rangesToXY.js.map

package/lib/ranges/rangesToXY.js.map

@@ -1 +1 @@
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package/lib/signals/addDummySignals.d.ts

@@ -0,0 +1,2 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export declare function addDummySignals(signals: NMRSignal1D[]): NMRSignal1D[];

package/lib/signals/addDummySignals.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addDummySignals = void 0;
+const couplingPatterns_1 = require("../constants/couplingPatterns");
+function addDummySignals(signals) {
+    let newSignals = JSON.parse(JSON.stringify(signals));
+    signals.forEach((signal, s) => {
+        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
+        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
+        if (tempSignals.length > 0)
+            newSignals.push(...tempSignals);
+        newSignals[s].js = newCouplings;
+        newSignals[s].atoms = signalAssignment;
+    });
+    return newSignals.sort((a, b) => a.delta - b.delta);
+}
+exports.addDummySignals = addDummySignals;
+function checkCouplings(jCouplings, signals, signalAssignment) {
+    let newSignalAssignment = signals.length - 1;
+    let tempSignals = [];
+    const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
+        const { atoms = [], multiplicity, coupling } = jCoupling;
+        if (atoms.length === 0) {
+            if (coupling && multiplicity) {
+                let tempCouplings = [];
+                const nbLinks = couplingPatterns_1.couplingPatterns.indexOf(multiplicity);
+                for (let i = 0; i < nbLinks; i++) {
+                    newSignalAssignment++;
+                    tempCouplings.push({
+                        coupling,
+                        atoms: [newSignalAssignment],
+                    });
+                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
+                }
+            }
+            else {
+                newCouplings.push(jCoupling);
+            }
+        }
+        return newCouplings;
+    }, []);
+    return { newCouplings, tempSignals };
+}
+function formatSignal(coupling, newSignalAssignment, signalAssignment) {
+    return {
+        delta: 100000,
+        atoms: newSignalAssignment,
+        js: [
+            {
+                coupling,
+                atoms: signalAssignment,
+            },
+        ],
+    };
+}
+//# sourceMappingURL=addDummySignals.js.map

package/lib/signals/addDummySignals.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"addDummySignals.js","sourceRoot":"","sources":["../../src/signals/addDummySignals.ts"],"names":[],"mappings":";;;AAAA,oEAAiE;AAKjE,SAAgB,eAAe,CAAC,OAAsB;IACpD,IAAI,UAAU,GAAkB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC;IAEpE,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC5B,MAAM,EAAE,EAAE,EAAE,UAAU,GAAG,EAAE,EAAE,KAAK,EAAE,gBAAgB,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,MAAM,CAAC;QAEtE,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,cAAc,CAChD,UAAU,EACV,UAAU,EACV,gBAAgB,CACjB,CAAC;QAEF,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;YAAE,UAAU,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,CAAC;QAE5D,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,YAAY,CAAC;QAChC,UAAU,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,gBAAgB,CAAC;IACzC,CAAC,CAAC,CAAC;IAEH,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC;AACtD,CAAC;AAnBD,0CAmBC;AAED,SAAS,cAAc,CACrB,UAAuB,EACvB,OAAsB,EACtB,gBAA0B;IAE1B,IAAI,mBAAmB,GAAG,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC;IAC7C,IAAI,WAAW,GAAkB,EAAE,CAAC;IACpC,MAAM,YAAY,GAAG,UAAU,CAAC,MAAM,CACpC,CAAC,YAAY,EAAE,SAAS,EAAE,EAAE;QAC1B,MAAM,EAAE,KAAK,GAAG,EAAE,EAAE,YAAY,EAAE,QAAQ,EAAE,GAAG,SAAS,CAAC;QACzD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;YACtB,IAAI,QAAQ,IAAI,YAAY,EAAE;gBAC5B,IAAI,aAAa,GAAgB,EAAE,CAAC;gBACpC,MAAM,OAAO,GAAG,mCAAgB,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;gBACvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;oBAChC,mBAAmB,EAAE,CAAC;oBACtB,aAAa,CAAC,IAAI,CAAC;wBACjB,QAAQ;wBACR,KAAK,EAAE,CAAC,mBAAmB,CAAC;qBAC7B,CAAC,CAAC;oBACH,WAAW,CAAC,IAAI,CACd,YAAY,CAAC,QAAQ,EAAE,CAAC,mBAAmB,CAAC,EAAE,gBAAgB,CAAC,CAChE,CAAC;iBACH;aACF;iBAAM;gBACL,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aAC9B;SACF;QACD,OAAO,YAAY,CAAC;IACtB,CAAC,EACD,EAAE,CACH,CAAC;IACF,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,CAAC;AACvC,CAAC;AAED,SAAS,YAAY,CACnB,QAAgB,EAChB,mBAA6B,EAC7B,gBAA0B;IAE1B,OAAO;QACL,KAAK,EAAE,MAAM;QACb,KAAK,EAAE,mBAAmB;QAC1B,EAAE,EAAE;YACF;gBACE,QAAQ;gBACR,KAAK,EAAE,gBAAgB;aACxB;SACF;KACF,CAAC;AACJ,CAAC"}

package/lib/signals/hackSignalsToXY.js

@@ -1,61 +1,15 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.hackSignalsToXY = void 0;
-const couplingPatterns_1 = require("../constants/couplingPatterns");
+const addDummySignals_1 = require("./addDummySignals");
 const signalsToXY_1 = require("./signalsToXY");
 /**
  * Create the xy object from an array of 1D signals.
  * @param signals Array of signals with assigned or unassigned couplings.
  */
 function hackSignalsToXY(signals, options = {}) {
-    let newSignals = JSON.parse(JSON.stringify(signals));
-    signals.forEach((signal, s) => {
-        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
-        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
-        if (tempSignals.length > 0)
-            newSignals.push(...tempSignals);
-        newSignals[s].js = newCouplings;
-        newSignals[s].atoms = signalAssignment;
-    });
+    let newSignals = (0, addDummySignals_1.addDummySignals)(signals);
     return (0, signalsToXY_1.signalsToXY)(newSignals, options);
 }
 exports.hackSignalsToXY = hackSignalsToXY;
-function checkCouplings(jCouplings, signals, signalAssignment) {
-    let newSignalAssignment = signals.length - 1;
-    let tempSignals = [];
-    const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
-        const { atoms = [], multiplicity, coupling } = jCoupling;
-        if (atoms.length === 0) {
-            if (coupling && multiplicity) {
-                let tempCouplings = [];
-                const nbLinks = couplingPatterns_1.couplingPatterns.indexOf(multiplicity);
-                for (let i = 0; i < nbLinks; i++) {
-                    newSignalAssignment++;
-                    tempCouplings.push({
-                        coupling,
-                        atoms: [newSignalAssignment],
-                    });
-                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
-                }
-            }
-            else {
-                newCouplings.push(jCoupling);
-            }
-        }
-        return newCouplings;
-    }, []);
-    return { newCouplings, tempSignals };
-}
-function formatSignal(coupling, newSignalAssignment, signalAssignment) {
-    return {
-        delta: 100000,
-        atoms: newSignalAssignment,
-        js: [
-            {
-                coupling,
-                atoms: signalAssignment,
-            },
-        ],
-    };
-}
 //# sourceMappingURL=hackSignalsToXY.js.map

package/lib/signals/hackSignalsToXY.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hackSignalsToXY.js","sourceRoot":"","sources":["../../src/signals/hackSignalsToXY.ts"],"names":[],"mappings":";;;AACA,uDAAoD;AACpD,+CAAgE;AAEhE;;;GAGG;AAEH,SAAgB,eAAe,CAC7B,OAAsB,EACtB,UAA8B,EAAE;IAEhC,IAAI,UAAU,GAAG,IAAA,iCAAe,EAAC,OAAO,CAAC,CAAC;IAC1C,OAAO,IAAA,yBAAW,EAAC,UAAU,EAAE,OAAO,CAAC,CAAC;AAC1C,CAAC;AAND,0CAMC"}

package/lib/signals/simulation/getPauliMatrix.js.map

@@ -1 +1 @@
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package/lib/signals/simulation/simulate1D.d.ts

@@ -1,43 +1,6 @@
 import { DataXY } from 'cheminfo-types';
-import type { Shape1D } from 'ml-peak-shape-generator';
 import type { SpinSystem } from '../spinSystem';
-interface Simulate1DOptions {
-    /**
-     * The linewidth of the output spectrum, expresed in Hz.
-     * @default 1
-     */
-    lineWidth?: number;
-    /**
-     * Maximum number of atoms on each cluster that can be considered to be simulated together. It affects the the quality and speed of the simulation.
-     * @default 8
-     */
-    maxClusterSize?: number;
-    /**
-     * The frequency in Mhz of the fake spectrometer that records the spectrum.
-     * @default 400
-     */
-    frequency?: number;
-    /**
-     * The low limit of the ordinate variable.
-     * @default 0
-     */
-    from?: number;
-    /**
-     * The upper limit of the ordinate variable.
-     * @default 10
-     */
-    to?: number;
-    /**
-     * Number of points of the output spectrum.
-     * @default 16K
-     */
-    nbPoints?: number;
-    /**
-     * Shape options
-     * @default {kind:'gaussian'}
-     */
-    shape?: Shape1D;
-}
+import type { Simulate1DOptions } from './simulateXYPeaks';
 /**
  * This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
  */
@@ -46,4 +9,3 @@ export default function simulate1D(
  * The SpinSystem object to be simulated
  */
 spinSystem: SpinSystem, options?: Simulate1DOptions): DataXY;
-export {};