nmr-processing 7.4.2 → 8.1.0

package/lib/assignment/getAssignments.d.ts

@@ -8,21 +8,19 @@ import { AtomTypes, RestrictionByCS } from './utils/getAssignment/buildAssignmen
 export interface SpectraData1D {
     id?: string;
     ranges: NMRRange[];
-    info?: any;
+    info: any;
 }
 export interface SpectraData2D {
     id?: string;
     zones: NMRZone[];
-    info?: any;
+    /**
+     * object with information about the spectrum, it is mandatory at the moment
+     * to generate correlations.
+     */
+    info: any;
 }
 export declare type SpectraData = SpectraData1D | SpectraData2D;
 export interface GetAutoAssignmentInput {
-    /**
-     * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
-     */
-    atoms?: {
-        [key: string]: number;
-    };
     spectra: SpectraData[];
     /**
      * Instance of Molecule

package/lib/assignment/getAssignments.js

@@ -10,7 +10,7 @@ const checkIDs_1 = require("./utils/getAssignment/checkIDs");
 const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
 const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
 async function getAssignments(input, options = {}) {
-    let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
     const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
     const molecule = input.molecule;
     if (!molecule)

package/lib/assignment/getAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}

package/lib/assignment/utils/getAssignment/buildAssignments.js

@@ -59,10 +59,12 @@ async function buildAssignments(props) {
             checkNMRSignal1D(joinedSignals);
             if (!predictions[atomType])
                 predictions[atomType] = {};
+            let totalHydrogens = 0;
             for (let prediction of joinedSignals) {
                 const diaID = prediction.diaIDs[0];
                 const index = prediction.atoms[0];
                 const allHydrogens = exports.getAllHydrogens[atomType](molecule, index);
+                totalHydrogens += prediction.nbAtoms * allHydrogens;
                 predictions[atomType][diaID] = {
                     ...prediction,
                     diaIDIndex: index,
@@ -71,6 +73,9 @@ async function buildAssignments(props) {
                     pathLength: pathLengthMatrix[index],
                 };
             }
+            for (let diaID in predictions[atomType]) {
+                predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
+            }
             infoByAtomType[atomType] = {
                 nSources: joinedSignals.length,
                 currentIndex: 0,

package/lib/assignment/utils/getAssignment/buildAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/checkIDs.js

@@ -10,17 +10,13 @@ function checkIDs(input = []) {
     let inputClone = JSON.parse(JSON.stringify(input));
     let spectra = [];
     for (const spectraData of inputClone) {
+        if (!('info' in spectraData)) {
+            throw new Error('each spectrum should contain info properties with nucleus information');
+        }
         const { info, id } = spectraData;
         if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
-            let data = addIDs(spectraData.ranges);
-            for (const element of data) {
-                const { integration } = element;
-                for (let signal of element.signals || []) {
-                    if (!signal.integration)
-                        signal.integration = integration;
-                }
-            }
-            spectra.push({ id, info, ranges: data });
+            let ranges = addIDs(spectraData.ranges);
+            spectra.push({ id, info, ranges });
         }
         else {
             let data = addIDs(spectraData.zones);

package/lib/assignment/utils/getAssignment/checkIDs.js.map

@@ -1 +1 @@
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+{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":";;;;;;AAOA,+DAAuC;AAEvC,uDAAoD;AAEpD,SAAgB,QAAQ,CAAC,QAAuB,EAAE;IAChD,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAkB,CAAC;IACpE,IAAI,OAAO,GAAyB,EAAE,CAAC;IACvC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,IAAI,CAAC,CAAC,MAAM,IAAI,WAAW,CAAC,EAAE;YAC5B,MAAM,IAAI,KAAK,CACb,uEAAuE,CACxE,CAAC;SACH;QAED,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,IAAA,iCAAe,EAAC,WAAW,CAAC,EAAE;YAChC,IAAI,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAsB,CAAC;YAC7D,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;SACpC;aAAM;YACL,IAAI,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAqB,CAAC;YACzD,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;SACzC;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AApBD,4BAoBC;AAED,SAAgB,MAAM,CACpB,IAA4B;IAE5B,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAC;QAC/D,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAC;SAC3D;KACF;AACH,CAAC;AATD,wBASC;AAED,SAAgB,MAAM,CAAC,IAA4B;IACjD,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,OAAO,CAAC,EAAE,GAAG,IAAA,oBAAU,GAAE,CAAC;QAC3C,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,CAAC,EAAE,GAAG,IAAA,oBAAU,GAAE,CAAC;SAC1C;KACF;IACD,MAAM,CAAC,IAAI,CAAC,CAAC;IACb,OAAO,IAAI,CAAC;AACd,CAAC;AATD,wBASC"}

package/lib/assignment/utils/getAssignment/formatData.js

@@ -6,15 +6,42 @@ function formatData(input = []) {
     let inputClone = JSON.parse(JSON.stringify(input));
     let spectra = [];
     for (const spectraData of inputClone) {
-        const { info } = spectraData;
+        const { id, info } = spectraData;
         if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
-            spectra.push({ info, ranges: { values: spectraData.ranges } });
+            const ranges = rescaleIntegration({
+                id,
+                info,
+                ranges: spectraData.ranges,
+            });
+            spectra.push({ id, info, ranges: { values: ranges } });
         }
         else {
-            spectra.push({ info, zones: { values: spectraData.zones } });
+            spectra.push({ id, info, zones: { values: spectraData.zones } });
         }
     }
     return spectra;
 }
 exports.formatData = formatData;
+function rescaleIntegration(spectrum) {
+    if (spectrum.info.nucleus !== '1H')
+        return spectrum.ranges;
+    let totalIntegration = spectrum.ranges.reduce((total, range) => (range.integration ? total + range.integration : total), 0);
+    for (let range of spectrum.ranges) {
+        if (range.integration) {
+            range.integration *= 100 / totalIntegration;
+            if (range.signals) {
+                const totalSignalIntegration = range.signals.reduce((total, signal) => signal.integration ? total + signal.integration : total, 0);
+                for (let signal of range.signals) {
+                    if (signal.integration) {
+                        signal.integration *= range.integration / totalSignalIntegration;
+                    }
+                    else {
+                        signal.integration = range.integration;
+                    }
+                }
+            }
+        }
+    }
+    return spectrum.ranges;
+}
 //# sourceMappingURL=formatData.js.map

package/lib/assignment/utils/getAssignment/formatData.js.map

@@ -1 +1 @@
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+{"version":3,"file":"formatData.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/formatData.ts"],"names":[],"mappings":";;;AAQA,uDAAoD;AAapD,SAAgB,UAAU,CACxB,QAA8B,EAAE;IAEhC,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAyB,CAAC;IAC3E,IAAI,OAAO,GAA2B,EAAE,CAAC;IACzC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,IAAA,iCAAe,EAAC,WAAW,CAAC,EAAE;YAChC,MAAM,MAAM,GAAG,kBAAkB,CAAC;gBAChC,EAAE;gBACF,IAAI;gBACJ,MAAM,EAAE,WAAW,CAAC,MAAM;aAC3B,CAAC,CAAC;YACH,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,CAAC;SACxD;aAAM;YACL,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;SAClE;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAnBD,gCAmBC;AAED,SAAS,kBAAkB,CAAC,QAA8B;IACxD,IAAI,QAAQ,CAAC,IAAI,CAAC,OAAO,KAAK,IAAI;QAAE,OAAO,QAAQ,CAAC,MAAM,CAAC;IAE3D,IAAI,gBAAgB,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,CAC3C,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,EACzE,CAAC,CACF,CAAC;IAEF,KAAK,IAAI,KAAK,IAAI,QAAQ,CAAC,MAAM,EAAE;QACjC,IAAI,KAAK,CAAC,WAAW,EAAE;YACrB,KAAK,CAAC,WAAW,IAAI,GAAG,GAAG,gBAAgB,CAAC;YAC5C,IAAI,KAAK,CAAC,OAAO,EAAE;gBACjB,MAAM,sBAAsB,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CACjD,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,CAChB,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,EACzD,CAAC,CACF,CAAC;gBACF,KAAK,IAAI,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE;oBAChC,IAAI,MAAM,CAAC,WAAW,EAAE;wBACtB,MAAM,CAAC,WAAW,IAAI,KAAK,CAAC,WAAW,GAAG,sBAAsB,CAAC;qBAClE;yBAAM;wBACL,MAAM,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC;qBACxC;iBACF;aACF;SACF;KACF;IAED,OAAO,QAAQ,CAAC,MAAM,CAAC;AACzB,CAAC"}

package/lib/assignment/utils/getAssignment/partialScore.js

@@ -76,7 +76,7 @@ function partialScore(partial, props) {
                     total += prediction.allHydrogens;
             }
         }
-        if (total - integration >= 0.5) {
+        if (total - integration >= 5) {
             return 0;
         }
     }

package/lib/assignment/utils/getAssignment/partialScore.js.map

@@ -1 +1 @@
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package/lib/databases/getDatabase.d.ts

@@ -1,2 +1,7 @@
 import { DatabaseNMREntry } from './DatabaseNMREntry';
-export declare function getDatabase(url?: string): Promise<DatabaseNMREntry[]>;
+export declare function getDatabase(url?: string, options?: {
+    /**
+     * @default 'tsv'
+     */
+    format?: 'tsv' | 'json';
+}): Promise<DatabaseNMREntry[]>;

package/lib/databases/getDatabase.js

@@ -3,13 +3,23 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getDatabase = void 0;
 const cross_fetch_1 = require("cross-fetch");
 const resurrectRange_1 = require("../utilities/resurrectRange");
-async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
+async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
+    const { format = 'tsv' } = options;
     if (url.includes('google.com')) {
         url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
     }
+    let parsed;
     const response = await (0, cross_fetch_1.fetch)(url);
-    const result = await response.text();
-    const parsed = parseData(result);
+    switch (format) {
+        case 'tsv':
+            parsed = parseData(await response.text());
+            break;
+        case 'json':
+            parsed = await response.json();
+            break;
+        default:
+            throw new Error('unknown database format');
+    }
     const results = [];
     for (let line of parsed.data) {
         const result = {

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package/lib/index.d.ts

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';
@@ -28,7 +28,7 @@ export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 export type { NMRSignal1D } from './signals/NMRSignal1D';
-export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
+export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';

package/lib/index.js

@@ -14,7 +14,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-__exportStar(require("./constants/gyromagneticRatio"), exports);
+__exportStar(require("gyromagnetic-ratio"), exports);
 __exportStar(require("./constants/impurities"), exports);
 __exportStar(require("./constants/couplingPatterns"), exports);
 __exportStar(require("./peaks/peaksFilterImpurities"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C"}

package/lib/peaks/NMRPeak1D.d.ts

@@ -2,6 +2,5 @@ import type { PeakXYWidth } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 export interface NMRPeak1D extends PeakXYWidth {
     kind?: string;
-    fwhm?: number;
     shape?: Shape1D;
 }

package/lib/peaks/solventSuppression.d.ts

@@ -0,0 +1,3 @@
+import { NMRSignal1D } from '../signals/NMRSignal1D';
+import { NMRPeak1D } from './NMRPeak1D';
+export declare function solventSuppression(peakList: NMRPeak1D[], solvent: NMRSignal1D[], options?: any): NMRPeak1D[];

package/lib/peaks/solventSuppression.js

@@ -0,0 +1,147 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.solventSuppression = void 0;
+const linear_sum_assignment_1 = __importDefault(require("linear-sum-assignment"));
+const ml_matrix_1 = require("ml-matrix");
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const addDummySignals_1 = require("../signals/addDummySignals");
+const signalsToSpinSystem_1 = require("../signals/simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("../signals/simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("../signals/simulation/splitSpinSystem");
+function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList];
+    sortAscending(peaks);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false } = options;
+    let solventSignals = solvent; //addDummySignals(solvent);
+    // solventSignals = solventSignals.slice(0, solventSignals.findIndex((signal) => signal.delta > 400));
+    for (const solventSignal of solventSignals) {
+        const solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        sortAscending(solventXYPeaks);
+        let upIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + 1);
+        let lowIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[0].x - 1);
+        if (upIndex === lowIndex)
+            continue;
+        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const shiftedSolventPeaks = getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
+            const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
+            let deltaResidual = 0;
+            let amplitudeResidual = 0;
+            let positionResidual = 0;
+            for (let i = 0; i < closestPeaks.length; i++) {
+                amplitudeResidual += Math.abs(shiftedSolventPeaks[i].y - closestPeaks[i].y);
+                deltaResidual += Math.abs(shiftedSolventPeaks[i].x - closestPeaks[i].x);
+            }
+            if (closestPeaks.length === 0) {
+                deltaResidual = Number.MAX_SAFE_INTEGER;
+                amplitudeResidual = Number.MAX_SAFE_INTEGER;
+                positionResidual = Number.MAX_SAFE_INTEGER;
+            }
+            else {
+                positionResidual = (0, ml_peak_shape_generator_1.gaussianFct)(solventSignal.delta - peak.x, 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const maxAmplitude = (0, ml_spectra_processing_1.xMaxValue)(amplitudeResiduals);
+        const maxDelta = (0, ml_spectra_processing_1.xMaxValue)(deltaResiduals);
+        const maxPosition = (0, ml_spectra_processing_1.xMaxValue)(positionResiduals);
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                (1 - positionResiduals[i]) / maxPosition) /
+                3;
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        const shiftedSolventPeaks = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = (0, linear_sum_assignment_1.default)(diff, {
+            maximaze: false,
+        });
+        if (gain === -1)
+            return peaks;
+        if (markSolventPeaks) {
+            for (let index of rowAssignments) {
+                peaks[index + lowIndex].kind = 'solvent';
+            }
+        }
+        else {
+            rowAssignments.sort((a, b) => b - a);
+            for (let index of rowAssignments) {
+                peaks.splice(index + lowIndex, 1);
+            }
+        }
+    }
+    return peaks;
+}
+exports.solventSuppression = solventSuppression;
+function getSolventPeaks(signal, options = {}) {
+    let signals = (0, addDummySignals_1.addDummySignals)([signal]);
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem);
+    return peaks.filter((peak) => peak.x < 1000);
+}
+function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
+    const shiftedSolventPeaks = JSON.parse(JSON.stringify(solventXYPeaks));
+    // shift x values of solventPeaks to center it to the current peak.
+    const deltaPPM = peak.x - solventSignal.delta;
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+    }
+    return shiftedSolventPeaks;
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = (0, linear_sum_assignment_1.default)(diff, {
+        maximaze: false,
+    });
+    if (gain === -1)
+        return [];
+    const assignmentPeaks = [];
+    let maxValue = Number.MIN_SAFE_INTEGER;
+    for (let index of rowAssignments) {
+        if (maxValue < nearPeaks[index].y)
+            maxValue = nearPeaks[index].y;
+        assignmentPeaks.push({ ...nearPeaks[index] });
+    }
+    assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
+    return assignmentPeaks;
+}
+function sortAscending(peaks) {
+    return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
+}
+function getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new ml_matrix_1.Matrix(nbRows, nbColumns);
+    for (let r = 0; r < nbRows; r++) {
+        for (let c = 0; c < nbColumns; c++) {
+            diff.set(r, c, Math.abs(rows[r].x - columns[c].x));
+        }
+    }
+    return diff;
+}
+//# sourceMappingURL=solventSuppression.js.map

package/lib/peaks/solventSuppression.js.map

@@ -0,0 +1 @@
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package/lib/peaks/util/jAnalyzer.d.ts

@@ -10,7 +10,7 @@ interface IntergralData {
     from: number;
     to: number;
 }
-export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
+export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
     intensity: number;
 };
 export interface SignalIntern {

package/lib/prediction/predictAllSpectra.d.ts

@@ -1,5 +1,5 @@
+import { FromTo, PointXY } from 'cheminfo-types';
 import type { Molecule } from 'openchemlib';
-import { OptionsSignalsToXY } from '../signals/signalsToXY';
 import { PredictAllOptions } from './predictAll';
 /**
  * This function will generate an object compatible with NMR-ium
@@ -7,12 +7,30 @@ import { PredictAllOptions } from './predictAll';
  * @param molecule
  * @param options
  */
-export declare function predictAllSpectra(molecule: Molecule, options?: {
+interface OneDOptions {
+    proton: FromTo;
+    carbon: FromTo;
+    nbPoints: number;
+    lineWidth: number;
+}
+interface TwoDOptions {
+    from: PointXY;
+    to: PointXY;
+    nbPoints: PointXY;
+}
+interface SimulationOptions {
+    frequency: number;
+    oneD?: Partial<OneDOptions>;
+    twoD?: Partial<TwoDOptions>;
+}
+interface PredictAllSpectraOptions {
     prediction?: PredictAllOptions;
-    simulation?: OptionsSignalsToXY;
-}): Promise<{
+    simulation?: SimulationOptions;
+}
+export declare function predictAllSpectra(molecule: Molecule, options?: PredictAllSpectraOptions): Promise<{
     spectra: any[];
     molecules: {
         molfile: any;
     }[];
 }>;
+export {};