nmr-processing 7.3.0 → 7.4.2

package/lib/assignment/getAssignments.d.ts

@@ -77,5 +77,5 @@ export interface GetAssignmentsOptions {
 }
 export declare function getAssignments(input: GetAutoAssignmentInput, options?: GetAssignmentsOptions): Promise<{
     score: w;
-    assignment: import("./utils/getAssignment/checkIDs").SpectraDataWithIds[];
+    assignment: import("./nmrAssigment").SpectraDataWithIds[];
 }[]>;

package/lib/assignment/nmrAssigment.d.ts

@@ -1,28 +1,20 @@
-import { Molecule } from 'openchemlib';
-import type { NMRRange } from '../xy/NMRRange';
-import type { NMRZone } from '../xyz/NMRZone';
-export interface NMRAssignmentType {
-    /**
-     * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
-     */
-    atoms: {
-        [key: string]: number;
-    };
-    /**
-     * Contains the ranges for each nucleus or kind of experiment e.g. { H: [], C: [], apt: [], dept135: []}
-     * the ranges represented with atom label only contain the range from a single pulse experiment or equivalent.
-     */
-    ranges: {
-        [key: string]: NMRRange[];
-    };
-    /**
-     * Contains the zones for each kind of experiment e.g. { H: [], C: [], apt: [], dept135: []};
-     */
-    zones: {
-        [key: string]: NMRZone[];
-    };
-    /**
-     * Instance of Molecule
-     */
-    molecule: Molecule;
+import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
+import { MakeMandatory } from '../utilities/MakeMandatory';
+import type { SpectraData1D, SpectraData2D } from './getAssignments';
+export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
+export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
+export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
+    id: string;
+    signals: Array<NMRSignal2DWithId>;
 }
+export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
+    id: string;
+    signals: Array<NMRSignal1DWithId>;
+}
+export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
+    ranges: NMRRangeWithIds[];
+}
+export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
+    zones: NMRZoneWithIds[];
+}
+export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;

package/lib/assignment/utils/getAssignment/buildAssignments.d.ts

@@ -2,7 +2,7 @@ import { Values } from 'nmr-correlation';
 import { Molecule } from 'openchemlib';
 import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
 import { MakeMandatory } from '../../../utilities/MakeMandatory';
-import { SpectraDataWithIds } from './checkIDs';
+import { SpectraDataWithIds } from '../../nmrAssigment';
 import { TargetsByAtomType } from './getTargetsAndCorrelations';
 export declare type AtomTypes = 'H' | 'C';
 export declare type CurrentAtoms = Array<AtomTypes>;

package/lib/assignment/utils/getAssignment/checkIDs.d.ts

@@ -1,23 +1,6 @@
-import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '../../..';
-import { MakeMandatory } from '../../../utilities/MakeMandatory';
-import type { SpectraData, SpectraData1D, SpectraData2D } from '../../getAssignments';
-export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
-export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
-export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
-    id: string;
-    signals: Array<NMRSignal2DWithId>;
-}
-export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
-    id: string;
-    signals: Array<NMRSignal1DWithId>;
-}
-export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
-    ranges: NMRRangeWithIds[];
-}
-export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
-    zones: NMRZoneWithIds[];
-}
-export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
+import type { NMRRange, NMRZone } from '../../..';
+import type { SpectraData } from '../../getAssignments';
+import type { SpectraDataWithIds, NMRRangeWithIds, NMRZoneWithIds } from '../../nmrAssigment';
 export declare function checkIDs(input?: SpectraData[]): SpectraDataWithIds[];
 export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
 export declare function addIDs(data: NMRRange[] | NMRZone[]): NMRRangeWithIds[] | NMRZoneWithIds[];

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

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/formatData.d.ts

@@ -1,4 +1,4 @@
-import { NMRRangeWithIds, NMRZoneWithIds, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds } from './checkIDs';
+import { NMRRangeWithIds, NMRZoneWithIds, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds } from '../../nmrAssigment';
 interface SpectraData1DFormatted extends Omit<SpectraData1DWithIds, 'ranges'> {
     ranges: {
         values: NMRRangeWithIds[];

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

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/getTargetsAndCorrelations.d.ts

@@ -1,5 +1,5 @@
 import type { Correlation, Link } from 'nmr-correlation';
-import { SpectraDataWithIds } from './checkIDs';
+import { SpectraDataWithIds } from '../../nmrAssigment';
 export interface CorrelationWithIntegration extends Pick<Correlation, 'link' | 'atomType' | 'label' | 'attachment' | 'protonsCount'> {
     integration: number;
     indirectLinks: Array<Link>;

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

@@ -1 +1 @@
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package/lib/constants/gyromagneticRatio.d.ts

@@ -1,20 +1,6 @@
-export declare const gyromagneticRatio: {
-    '1H': number;
-    '2H': number;
-    '3H': number;
-    '3He': number;
-    '7Li': number;
-    '13C': number;
-    '14N': number;
-    '15N': number;
-    '17O': number;
-    '19F': number;
-    '23Na': number;
-    '27Al': number;
-    '29Si': number;
-    '31P': number;
-    '57Fe': number;
-    '63Cu': number;
-    '67Zn': number;
-    '129Xe': number;
+export declare type Nuclei = '1H' | '2H' | '3H' | '3He' | '7Li' | '13C' | '14N' | '15N' | '17O' | '19F' | '23Na' | '27Al' | '29Si' | '31P' | '57Fe' | '63Cu' | '67Zn' | '129Xe';
+declare type GyromagneticRatio = {
+    [key in Nuclei]: number;
 };
+export declare const gyromagneticRatio: GyromagneticRatio;
+export {};

package/lib/constants/gyromagneticRatio.js

@@ -3,7 +3,6 @@
 // https://en.wikipedia.org/wiki/Gyromagnetic_ratio
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.gyromagneticRatio = void 0;
-// TODO: #13 can we have a better source and more digits ? @jwist
 exports.gyromagneticRatio = {
     '1H': 267.52218744e6,
     '2H': 41.065e6,

package/lib/constants/gyromagneticRatio.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":";AAAA,WAAW;AACX,mDAAmD;;;AA4BtC,QAAA,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}

package/lib/index.d.ts

@@ -19,6 +19,7 @@ export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
+export * from './utilities/getFrequency';
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
 export * from './xyz/xyzAutoZonesPicking';
@@ -27,10 +28,12 @@ export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 export type { NMRSignal1D } from './signals/NMRSignal1D';
-export type { NMRSignal2D } from './xyz/NMRSignal2D';
+export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';
 export type { Prediction1D } from './prediction/prediction1D';
 export type { Jcoupling } from './signals/jcoupling';
+export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
 export type { DataBaseLevelStructure, DataBaseStructure, } from './prediction/dataStructure';
+export type { NMRSignal1DWithId, NMRSignal2DWithId, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds, } from './assignment/nmrAssigment';

package/lib/index.js

@@ -35,6 +35,7 @@ __exportStar(require("./signals/signalsToXY"), exports);
 __exportStar(require("./signals/signals2DToZ"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
+__exportStar(require("./utilities/getFrequency"), exports);
 __exportStar(require("./xy/xyAutoPeaksPicking"), exports);
 __exportStar(require("./xy/xyAutoRangesPicking"), exports);
 __exportStar(require("./xyz/xyzAutoZonesPicking"), 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,gEAA8C;AAC9C,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/signals/signals2DToZ.d.ts

@@ -23,6 +23,7 @@ interface Signals2DToZOptions {
      * @default 0.02
      */
     width?: number | XYNumber;
+    factor?: number | XYNumber;
 }
 export interface Peak2DSeries {
     x: number[];

package/lib/signals/signals2DToZ.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.signals2DToZ = void 0;
 const spectrum_generator_1 = require("spectrum-generator");
 function signals2DToZ(signals, options = {}) {
-    let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
+    let { from = -1, to = 12, nbPoints = 512, width = 0.02, factor = 3, } = options;
     const peaks = signals.reduce((acc, { x, y }) => {
         acc.x.push(x.delta);
         acc.y.push(y.delta);
@@ -11,7 +11,7 @@ function signals2DToZ(signals, options = {}) {
         return acc;
     }, { x: [], y: [], z: [] });
     width = ensureXYNumber(width);
-    return (0, spectrum_generator_1.generateSpectrum2D)(peaks, {
+    return (0, spectrum_generator_1.generateSpectrum2D)(mergeClosePeaks(peaks), {
         generator: {
             from: ensureXYNumber(from),
             to: ensureXYNumber(to),
@@ -19,12 +19,27 @@ function signals2DToZ(signals, options = {}) {
         },
         peaks: {
             width,
+            factor,
         },
     });
 }
 exports.signals2DToZ = signals2DToZ;
 function ensureXYNumber(input) {
-    let result = typeof input !== 'object' ? { x: input, y: input } : input;
-    return result;
+    return typeof input !== 'object' ? { x: input, y: input } : { ...input };
+}
+function mergeClosePeaks(peaksIn) {
+    let peaks = JSON.parse(JSON.stringify(peaksIn));
+    for (let i = 0; i < peaks.x.length; i++) {
+        for (let j = i + 1; j < peaks.x.length; j++) {
+            if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
+                peaks.z[i] += peaks.z[j];
+                peaks.x.splice(j, 1);
+                peaks.y.splice(j, 1);
+                peaks.z.splice(j, 1);
+                j--;
+            }
+        }
+    }
+    return peaks;
 }
 //# sourceMappingURL=signals2DToZ.js.map

package/lib/signals/signals2DToZ.js.map

@@ -1 +1 @@
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+{"version":3,"file":"signals2DToZ.js","sourceRoot":"","sources":["../../src/signals/signals2DToZ.ts"],"names":[],"mappings":";;;AAAA,2DAAwD;AAqCxD,SAAgB,YAAY,CAC1B,OAAsB,EACtB,UAA+B,EAAE;IAEjC,IAAI,EACF,IAAI,GAAG,CAAC,CAAC,EACT,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,GAAG,EACd,KAAK,GAAG,IAAI,EACZ,MAAM,GAAG,CAAC,GACX,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,OAAO,CAAC,MAAM,CAC1B,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;QAChB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAChB,OAAO,GAAG,CAAC;IACb,CAAC,EACD,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CACxB,CAAC;IAEF,KAAK,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC;IAE9B,OAAO,IAAA,uCAAkB,EAAC,eAAe,CAAC,KAAK,CAAC,EAAE;QAChD,SAAS,EAAE;YACT,IAAI,EAAE,cAAc,CAAC,IAAI,CAAC;YAC1B,EAAE,EAAE,cAAc,CAAC,EAAE,CAAC;YACtB,QAAQ,EAAE,cAAc,CAAC,QAAQ,CAAC;SACnC;QACD,KAAK,EAAE;YACL,KAAK;YACL,MAAM;SACP;KACF,CAAC,CAAC;AACL,CAAC;AAnCD,oCAmCC;AAED,SAAS,cAAc,CAAC,KAAwB;IAC9C,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC;AAC3E,CAAC;AAED,SAAS,eAAe,CAAC,OAAqB;IAC5C,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC3C,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC1D,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBACzB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,CAAC,EAAE,CAAC;aACL;SACF;KACF;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}

package/lib/utilities/getFrequency.d.ts

@@ -0,0 +1,21 @@
+import { Nuclei } from '../constants/gyromagneticRatio';
+export interface ObjervedNucleusData {
+    /**
+     * nucleus to use as reference in the calculation of frequency
+     */
+    nucleus: Nucleus;
+    /**
+     * frequency of the reference nucleus
+     */
+    frequency: number;
+}
+declare type Nucleus = Nuclei | (string & Record<never, never>);
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+export declare function getFrequency(
+/**
+ * nucleus to calculate the frequency
+ */
+nucleus: Nucleus, observedNucleusData: ObjervedNucleusData): number;
+export {};

package/lib/utilities/getFrequency.js

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getFrequency = void 0;
+const gyromagneticRatio_1 = require("../constants/gyromagneticRatio");
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+function getFrequency(
+/**
+ * nucleus to calculate the frequency
+ */
+nucleus, observedNucleusData) {
+    const { nucleus: obsNucleus, frequency } = observedNucleusData;
+    checkExistence(nucleus, obsNucleus);
+    return ((frequency * gyromagneticRatio_1.gyromagneticRatio[nucleus]) /
+        gyromagneticRatio_1.gyromagneticRatio[obsNucleus]);
+}
+exports.getFrequency = getFrequency;
+function checkExistence(...nucleus) {
+    let nuclei = [];
+    for (const n of nucleus) {
+        if (!(n in gyromagneticRatio_1.gyromagneticRatio)) {
+            nuclei.push(n);
+        }
+    }
+    if (nuclei.length !== 0) {
+        throw new Error(`${nuclei.join(' , ')} is not supported`);
+    }
+}
+//# sourceMappingURL=getFrequency.js.map

package/lib/utilities/getFrequency.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/getAssignment/formatData.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getTargetsAndCorrelations.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAC;AAKvD,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAC1C,OAAO,EAAE,+BAA+B,EAAE,MAAM,mCAAmC,CAAC;AAsBpF,MAAM,UAAU,yBAAyB,CACvC,OAA6B,EAC7B,UAAe,EAAE;IAEjB,gFAAgF;IAChF,8DAA8D;IAE9D,MAAM,EAAE,SAAS,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,OAAO,CAAC;IAErD,MAAM,WAAW,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,oBAAoB,CAAC,WAAW,EAAE;QACjE,SAAS;KACV,CAAC,CAAC;IAEH,IAAI,OAAO,GAAQ,EAAE,CAAC;IACtB,KAAK,MAAM,WAAW,IAAI,YAAY,EAAE;QACtC,IAAI,WAAW,CAAC,MAAM;YAAE,SAAS;QACjC,MAAM,EAAE,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,WAAW,CAAC;QAC/C,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC;YAAE,OAAO,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;QAC/C,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC;QAC1C,IAAI,QAAQ,KAAK,GAAG,EAAE;YACpB,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW;gBACrC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC;SAC1C;aAAM;YACL,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW,GAAG,+BAA+B,CACvE,WAAW,EACX,YAAY,CACb,CAAC;SACH;KACF;IAED,OAAO;QACL,OAAO;QACP,YAAY;KACb,CAAC;AACJ,CAAC"}

package/lib-esm/constants/gyromagneticRatio.js

@@ -1,6 +1,5 @@
 // sources:
 // https://en.wikipedia.org/wiki/Gyromagnetic_ratio
-// TODO: #13 can we have a better source and more digits ? @jwist
 export const gyromagneticRatio = {
     '1H': 267.52218744e6,
     '2H': 41.065e6,

package/lib-esm/constants/gyromagneticRatio.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":"AAAA,WAAW;AACX,mDAAmD;AA4BnD,MAAM,CAAC,MAAM,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}

package/lib-esm/index.js

@@ -19,6 +19,7 @@ export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
+export * from './utilities/getFrequency';
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
 export * from './xyz/xyzAutoZonesPicking';

package/lib-esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,+BAA+B,CAAC;AAC9C,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC"}

package/lib-esm/signals/signals2DToZ.js

@@ -1,6 +1,6 @@
 import { generateSpectrum2D } from 'spectrum-generator';
 export function signals2DToZ(signals, options = {}) {
-    let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
+    let { from = -1, to = 12, nbPoints = 512, width = 0.02, factor = 3, } = options;
     const peaks = signals.reduce((acc, { x, y }) => {
         acc.x.push(x.delta);
         acc.y.push(y.delta);
@@ -8,7 +8,7 @@ export function signals2DToZ(signals, options = {}) {
         return acc;
     }, { x: [], y: [], z: [] });
     width = ensureXYNumber(width);
-    return generateSpectrum2D(peaks, {
+    return generateSpectrum2D(mergeClosePeaks(peaks), {
         generator: {
             from: ensureXYNumber(from),
             to: ensureXYNumber(to),
@@ -16,11 +16,26 @@ export function signals2DToZ(signals, options = {}) {
         },
         peaks: {
             width,
+            factor,
         },
     });
 }
 function ensureXYNumber(input) {
-    let result = typeof input !== 'object' ? { x: input, y: input } : input;
-    return result;
+    return typeof input !== 'object' ? { x: input, y: input } : { ...input };
+}
+function mergeClosePeaks(peaksIn) {
+    let peaks = JSON.parse(JSON.stringify(peaksIn));
+    for (let i = 0; i < peaks.x.length; i++) {
+        for (let j = i + 1; j < peaks.x.length; j++) {
+            if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
+                peaks.z[i] += peaks.z[j];
+                peaks.x.splice(j, 1);
+                peaks.y.splice(j, 1);
+                peaks.z.splice(j, 1);
+                j--;
+            }
+        }
+    }
+    return peaks;
 }
 //# sourceMappingURL=signals2DToZ.js.map

package/lib-esm/signals/signals2DToZ.js.map

@@ -1 +1 @@
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package/lib-esm/utilities/getFrequency.js

@@ -0,0 +1,26 @@
+import { gyromagneticRatio } from '../constants/gyromagneticRatio';
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+export function getFrequency(
+/**
+ * nucleus to calculate the frequency
+ */
+nucleus, observedNucleusData) {
+    const { nucleus: obsNucleus, frequency } = observedNucleusData;
+    checkExistence(nucleus, obsNucleus);
+    return ((frequency * gyromagneticRatio[nucleus]) /
+        gyromagneticRatio[obsNucleus]);
+}
+function checkExistence(...nucleus) {
+    let nuclei = [];
+    for (const n of nucleus) {
+        if (!(n in gyromagneticRatio)) {
+            nuclei.push(n);
+        }
+    }
+    if (nuclei.length !== 0) {
+        throw new Error(`${nuclei.join(' , ')} is not supported`);
+    }
+}
+//# sourceMappingURL=getFrequency.js.map

package/lib-esm/utilities/getFrequency.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "7.3.0",
+  "version": "7.4.2",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",

package/src/assignment/nmrAssigment.ts

@@ -1,24 +1,26 @@
-import { Molecule } from 'openchemlib';
+import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
+import { MakeMandatory } from '../utilities/MakeMandatory';
 
-import type { NMRRange } from '../xy/NMRRange';
-import type { NMRZone } from '../xyz/NMRZone';
+import type { SpectraData1D, SpectraData2D } from './getAssignments';
 
-export interface NMRAssignmentType {
-  /**
-   * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
-   */
-  atoms: { [key: string]: number };
-  /**
-   * Contains the ranges for each nucleus or kind of experiment e.g. { H: [], C: [], apt: [], dept135: []}
-   * the ranges represented with atom label only contain the range from a single pulse experiment or equivalent.
-   */
-  ranges: { [key: string]: NMRRange[] };
-  /**
-   * Contains the zones for each kind of experiment e.g. { H: [], C: [], apt: [], dept135: []};
-   */
-  zones: { [key: string]: NMRZone[] };
-  /**
-   * Instance of Molecule
-   */
-  molecule: Molecule;
+export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
+export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
+
+export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
+  id: string;
+  signals: Array<NMRSignal2DWithId>;
+}
+
+export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
+  id: string;
+  signals: Array<NMRSignal1DWithId>;
 }
+
+export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
+  ranges: NMRRangeWithIds[];
+}
+export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
+  zones: NMRZoneWithIds[];
+}
+
+export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;

package/src/assignment/utils/getAssignment/buildAssignments.ts

@@ -11,9 +11,9 @@ import {
 import { predictCarbon } from '../../../prediction/predictCarbon';
 import { predictProton } from '../../../prediction/predictProton';
 import { MakeMandatory } from '../../../utilities/MakeMandatory';
+import { SpectraDataWithIds } from '../../nmrAssigment';
 import { StoreAssignments } from '../buildAssignments';
 
-import { SpectraDataWithIds } from './checkIDs';
 import {
   createMapPossibleAssignment,
   MapPossibleAssignments,

package/src/assignment/utils/getAssignment/checkIDs.ts

@@ -1,36 +1,14 @@
-import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '../../..';
-import { MakeMandatory } from '../../../utilities/MakeMandatory';
+import type { NMRRange, NMRZone } from '../../..';
+import type { SpectraData } from '../../getAssignments';
 import type {
-  SpectraData,
-  SpectraData1D,
-  SpectraData2D,
-} from '../../getAssignments';
+  SpectraDataWithIds,
+  NMRRangeWithIds,
+  NMRZoneWithIds,
+} from '../../nmrAssigment';
 import generateID from '../generateID';
 
 import { isSpectraData1D } from './isSpectraData1D';
 
-export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
-export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
-
-export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
-  id: string;
-  signals: Array<NMRSignal2DWithId>;
-}
-
-export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
-  id: string;
-  signals: Array<NMRSignal1DWithId>;
-}
-
-export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
-  ranges: NMRRangeWithIds[];
-}
-export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
-  zones: NMRZoneWithIds[];
-}
-
-export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
-
 export function checkIDs(input: SpectraData[] = []): SpectraDataWithIds[] {
   let inputClone = JSON.parse(JSON.stringify(input)) as SpectraData[];
   let spectra: SpectraDataWithIds[] = [];

package/src/assignment/utils/getAssignment/formatData.ts

@@ -4,7 +4,8 @@ import {
   SpectraData1DWithIds,
   SpectraData2DWithIds,
   SpectraDataWithIds,
-} from './checkIDs';
+} from '../../nmrAssigment';
+
 import { isSpectraData1D } from './isSpectraData1D';
 
 interface SpectraData1DFormatted extends Omit<SpectraData1DWithIds, 'ranges'> {

package/src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts

@@ -1,7 +1,8 @@
 import { buildCorrelationData } from 'nmr-correlation';
 import type { Correlation, Link } from 'nmr-correlation';
 
-import { SpectraDataWithIds } from './checkIDs';
+import { SpectraDataWithIds } from '../../nmrAssigment';
+
 import { formatData } from './formatData';
 import { getIntegrationOfAttachedProtons } from './getIntegrationOfAttachedProtons';
 

package/src/constants/gyromagneticRatio.ts

@@ -3,7 +3,31 @@
 
 // TODO: #13 can we have a better source and more digits ? @jwist
 
-export const gyromagneticRatio = {
+export type Nuclei =
+  | '1H'
+  | '2H'
+  | '3H'
+  | '3He'
+  | '7Li'
+  | '13C'
+  | '14N'
+  | '15N'
+  | '17O'
+  | '19F'
+  | '23Na'
+  | '27Al'
+  | '29Si'
+  | '31P'
+  | '57Fe'
+  | '63Cu'
+  | '67Zn'
+  | '129Xe';
+
+type GyromagneticRatio = {
+  [key in Nuclei]: number;
+};
+
+export const gyromagneticRatio: GyromagneticRatio = {
   '1H': 267.52218744e6,
   '2H': 41.065e6,
   '3H': 285.3508e6,

package/src/index.ts

@@ -25,6 +25,7 @@ export * from './signals/signals2DToZ';
 
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
+export * from './utilities/getFrequency';
 
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
@@ -37,13 +38,21 @@ export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 
 export type { NMRSignal1D } from './signals/NMRSignal1D';
-export type { NMRSignal2D } from './xyz/NMRSignal2D';
+export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';
 export type { Prediction1D } from './prediction/prediction1D';
 export type { Jcoupling } from './signals/jcoupling';
+export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
 export type {
   DataBaseLevelStructure,
   DataBaseStructure,
 } from './prediction/dataStructure';
+export type {
+  NMRSignal1DWithId,
+  NMRSignal2DWithId,
+  SpectraData1DWithIds,
+  SpectraData2DWithIds,
+  SpectraDataWithIds,
+} from './assignment/nmrAssigment';

package/src/signals/signals2DToZ.ts

@@ -26,6 +26,7 @@ interface Signals2DToZOptions {
    * @default 0.02
    */
   width?: number | XYNumber;
+  factor?: number | XYNumber;
 }
 
 export interface Peak2DSeries {
@@ -38,7 +39,13 @@ export function signals2DToZ(
   signals: NMRSignal2D[],
   options: Signals2DToZOptions = {},
 ) {
-  let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
+  let {
+    from = -1,
+    to = 12,
+    nbPoints = 512,
+    width = 0.02,
+    factor = 3,
+  } = options;
 
   const peaks = signals.reduce<Peak2DSeries>(
     (acc, { x, y }) => {
@@ -51,7 +58,8 @@ export function signals2DToZ(
   );
 
   width = ensureXYNumber(width);
-  return generateSpectrum2D(peaks, {
+
+  return generateSpectrum2D(mergeClosePeaks(peaks), {
     generator: {
       from: ensureXYNumber(from),
       to: ensureXYNumber(to),
@@ -59,11 +67,27 @@ export function signals2DToZ(
     },
     peaks: {
       width,
+      factor,
     },
   });
 }
 
-function ensureXYNumber(input: number | XYNumber): XYNumber {
-  let result = typeof input !== 'object' ? { x: input, y: input } : input;
-  return result;
+function ensureXYNumber(input: number | XYNumber) {
+  return typeof input !== 'object' ? { x: input, y: input } : { ...input };
+}
+
+function mergeClosePeaks(peaksIn: Peak2DSeries) {
+  let peaks = JSON.parse(JSON.stringify(peaksIn));
+  for (let i = 0; i < peaks.x.length; i++) {
+    for (let j = i + 1; j < peaks.x.length; j++) {
+      if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
+        peaks.z[i] += peaks.z[j];
+        peaks.x.splice(j, 1);
+        peaks.y.splice(j, 1);
+        peaks.z.splice(j, 1);
+        j--;
+      }
+    }
+  }
+  return peaks;
 }

package/src/utilities/getFrequency.ts

@@ -0,0 +1,47 @@
+import { gyromagneticRatio, Nuclei } from '../constants/gyromagneticRatio';
+
+export interface ObjervedNucleusData {
+  /**
+   * nucleus to use as reference in the calculation of frequency
+   */
+  nucleus: Nucleus;
+  /**
+   * frequency of the reference nucleus
+   */
+  frequency: number;
+}
+
+//Literal type is extends string and when union it with string we lose the autocomplete and to solve this we distinguish string
+type Nucleus = Nuclei | (string & Record<never, never>);
+
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+export function getFrequency(
+  /**
+   * nucleus to calculate the frequency
+   */
+  nucleus: Nucleus,
+  observedNucleusData: ObjervedNucleusData,
+) {
+  const { nucleus: obsNucleus, frequency } = observedNucleusData;
+
+  checkExistence(nucleus, obsNucleus);
+
+  return (
+    (frequency * gyromagneticRatio[nucleus as Nuclei]) /
+    gyromagneticRatio[obsNucleus as Nuclei]
+  );
+}
+
+function checkExistence(...nucleus: Nucleus[]) {
+  let nuclei: string[] = [];
+  for (const n of nucleus) {
+    if (!(n in gyromagneticRatio)) {
+      nuclei.push(n);
+    }
+  }
+  if (nuclei.length !== 0) {
+    throw new Error(`${nuclei.join(' , ')} is not supported`);
+  }
+}