nmr-processing 7.4.3 → 8.2.0

package/lib/xyz/util/formatZone.d.ts

@@ -0,0 +1,3 @@
+import { NMRSignal2D } from '../NMRSignal2D';
+import { NMRZone } from '../NMRZone';
+export declare function formatZones(signals: NMRSignal2D[]): NMRZone[];

package/lib/xyz/util/formatZone.js

@@ -0,0 +1,38 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.formatZones = void 0;
+function formatZones(signals) {
+    let zones = [];
+    for (const signal of signals) {
+        let minMax1 = [Number.MAX_VALUE, 0];
+        let minMax2 = [Number.MAX_VALUE, 0];
+        for (const peak of signal.peaks || []) {
+            if (peak.minX < minMax1[0]) {
+                minMax1[0] = peak.minX;
+            }
+            if (peak.maxX > minMax1[1]) {
+                minMax1[1] = peak.maxX;
+            }
+            if (peak.minY < minMax2[0]) {
+                minMax2[0] = peak.minY;
+            }
+            if (peak.maxY > minMax2[1]) {
+                minMax2[1] = peak.maxY;
+            }
+        }
+        zones.push({
+            x: {
+                from: minMax1[0],
+                to: minMax1[1],
+            },
+            y: {
+                from: minMax2[0],
+                to: minMax2[1],
+            },
+            signals: [signal],
+        });
+    }
+    return zones;
+}
+exports.formatZones = formatZones;
+//# sourceMappingURL=formatZone.js.map

package/lib/xyz/util/formatZone.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"formatZone.js","sourceRoot":"","sources":["../../../src/xyz/util/formatZone.ts"],"names":[],"mappings":";;;AAGA,SAAgB,WAAW,CAAC,OAAsB;IAChD,IAAI,KAAK,GAAc,EAAE,CAAC;IAC1B,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,OAAO,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QACpC,IAAI,OAAO,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,IAAI,EAAE,EAAE;YACrC,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;YACD,IAAI,IAAI,CAAC,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;aACxB;SACF;QACD,KAAK,CAAC,IAAI,CAAC;YACT,CAAC,EAAE;gBACD,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC;gBAChB,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC;aACf;YACD,CAAC,EAAE;gBACD,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC;gBAChB,EAAE,EAAE,OAAO,CAAC,CAAC,CAAC;aACf;YACD,OAAO,EAAE,CAAC,MAAM,CAAC;SAClB,CAAC,CAAC;KACJ;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAhCD,kCAgCC"}

package/lib/xyz/xyzAutoZonesPicking.d.ts

@@ -1,4 +1,3 @@
-import { NMRZone } from '..';
 import type { GetKernelOptions } from '../peaks/util/getKernel';
 export interface Data2D {
     z: number[][] | Float64Array[];
@@ -62,7 +61,7 @@ export interface XYZAutoZonesPickingOptions {
      */
     kernel?: GetKernelOptions;
 }
-export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): NMRZone[];
+export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): import("./NMRZone").NMRZone[];
 /**
  * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
  * of many 2D-peaks, and it has some additional information related to the NMR spectrum.

package/lib/xyz/xyzAutoZonesPicking.js

@@ -34,6 +34,7 @@ const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
 const determineRealTop_1 = require("../peaks/util/determineRealTop");
 const getKernel_1 = require("../peaks/util/getKernel");
 const PeakOptimizer = __importStar(require("../peaks/util/peakOptimizer"));
+const formatZone_1 = require("./util/formatZone");
 const smallFilter = [
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
     [0, 1, 4, 7, 7, 7, 4, 1, 0],
@@ -107,42 +108,9 @@ function xyzAutoZonesPicking(spectraData, options) {
     if (enhanceSymmetry) {
         signals = PeakOptimizer.enhanceSymmetry(signals);
     }
-    return formatZones(signals);
+    return (0, formatZone_1.formatZones)(signals);
 }
 exports.xyzAutoZonesPicking = xyzAutoZonesPicking;
-function formatZones(signals) {
-    let zones = [];
-    for (const signal of signals) {
-        let minMax1 = [Number.MAX_VALUE, 0];
-        let minMax2 = [Number.MAX_VALUE, 0];
-        for (const peak of signal.peaks || []) {
-            if (peak.minX < minMax1[0]) {
-                minMax1[0] = peak.minX;
-            }
-            if (peak.maxX > minMax1[1]) {
-                minMax1[1] = peak.maxX;
-            }
-            if (peak.minY < minMax2[0]) {
-                minMax2[0] = peak.minY;
-            }
-            if (peak.maxY > minMax2[1]) {
-                minMax2[1] = peak.maxY;
-            }
-        }
-        zones.push({
-            x: {
-                from: minMax1[0],
-                to: minMax1[1],
-            },
-            y: {
-                from: minMax2[0],
-                to: minMax2[1],
-            },
-            signals: [signal],
-        });
-    }
-    return zones;
-}
 const createSignals2D = (peaks, options) => {
     let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
     let [nucleusX, nucleusY] = nuclei;

package/lib/xyz/xyzAutoZonesPicking.js.map

@@ -1 +1 @@
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package/lib/xyz/xyzJResAnalyzer.d.ts

@@ -19,6 +19,11 @@ interface XYZJResAnalyzerOptions extends CompilePatternOptions {
      * @default 0
      */
     reference?: number;
+    /**
+     * if it is true returns zones instead of signals 2D
+     * @default false
+     */
+    getZones?: boolean;
 }
-export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): NMRSignal2D[];
+export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): NMRSignal2D[] | import("./NMRZone").NMRZone[];
 export {};

package/lib/xyz/xyzJResAnalyzer.js

@@ -6,25 +6,26 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.xyzJResAnalyzer = void 0;
 const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
 const jAnalyzer_1 = __importDefault(require("../peaks/util/jAnalyzer"));
+const formatZone_1 = require("./util/formatZone");
 function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
     }, } = options;
-    let temporalSignals = compilePattern(signals, {
+    let temporalSignals = compilePattern([...signals], {
         observedFrequencies,
         tolerances,
         nuclei,
         jAnalyzer,
     });
     //check if the signal are symmetric around the reference
-    let result = [];
+    let signals2D = [];
     for (const tempSignal of temporalSignals) {
         let delta = tempSignal.y.delta;
         if (Math.abs(delta - reference) > referenceMaxShiftError)
             continue;
-        result.push(tempSignal);
+        signals2D.push(tempSignal);
     }
-    return result;
+    return getZones ? (0, formatZone_1.formatZones)(signals2D) : signals2D;
 }
 exports.xyzJResAnalyzer = xyzJResAnalyzer;
 function compilePattern(signals, options) {
@@ -74,9 +75,9 @@ function compilePattern(signals, options) {
             }
             if (peaksO.length > 0) {
                 peaksO.reverse();
-                let ranges = createSignals2D(peaksO, signalOptions);
-                for (const range of ranges) {
-                    newSignals.push(range);
+                let signals2D = createSignals2D(peaksO, signalOptions);
+                for (const signal of signals2D) {
+                    newSignals.push(signal);
                 }
             }
         }

package/lib/xyz/xyzJResAnalyzer.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/getAssignments.js

@@ -4,7 +4,7 @@ import { checkIDs } from './utils/getAssignment/checkIDs';
 import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
 import getWorkFlow from './utils/getAssignment/getWorkFlow';
 export 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-esm/assignment/getAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iCAAiC,EAAE,MAAM,mBAAmB,CAAC;AAQtE,OAAO,EAEL,gBAAgB,GAEjB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAC;AAC1D,OAAO,EAAE,yBAAyB,EAAE,MAAM,iDAAiD,CAAC;AAC5F,OAAO,WAAW,MAAM,mCAAmC,CAAC;AA0E5D,MAAM,CAAC,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,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,yBAAyB,CACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,WAAW,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,gBAAgB,CAAC;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"}

package/lib-esm/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,OAAO,UAAU,MAAM,eAAe,CAAC;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD,MAAM,UAAU,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,eAAe,CAAC,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;AAED,MAAM,UAAU,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;AAED,MAAM,UAAU,MAAM,CAAmC,IAAO;IAC9D,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,OAAO,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;QAC3C,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;SAC1C;KACF;IACD,MAAM,CAAC,IAAI,CAAC,CAAC;IACb,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/databases/getDatabase.js

@@ -1,12 +1,22 @@
 import { fetch } from 'cross-fetch';
 import { resurrectRange } from '../utilities/resurrectRange';
-export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
+export 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 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 = {

package/lib-esm/databases/getDatabase.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAEpC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAI7D,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG,EAC5G,UAKI,EAAE;IAEN,MAAM,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEnC,IAAI,GAAG,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE;QAC9B,GAAG,GAAG,kDAAkD,iBAAiB,CACvE,GAAG,CACJ,oBAAoB,CAAC;KACvB;IAED,IAAI,MAAM,CAAC;IACX,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;IAClC,QAAQ,MAAM,EAAE;QACd,KAAK,KAAK;YACR,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;YAC1C,MAAM;QACR,KAAK,MAAM;YACT,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAC/B,MAAM;QACR;YACE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC9C;IAED,MAAM,OAAO,GAAG,EAAE,CAAC;IAEnB,KAAK,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;QAC5B,MAAM,MAAM,GAAqB;YAC/B,MAAM,EAAE,EAAE;YACV,OAAO,EAAE,EAAE;YACX,OAAO,EAAE,EAAE;YACX,QAAQ,EAAE,EAAE;YACZ,KAAK,EAAE,EAAE;YACT,IAAI,EAAE,EAAE;YACR,MAAM,EAAE,EAAE;SACX,CAAC;QACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACpC,QAAQ,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACvB,KAAK,QAAQ;oBACX,MAAM,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,UAAU;oBACb,MAAM,CAAC,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC1B,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,KAAK;wBAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,IAAI;wBAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzD,MAAM;gBACR,KAAK,QAAQ,CAAC,CAAC;oBACb,MAAM,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBACtC,IAAI,KAAK;wBAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBACrC,MAAM;iBACP;gBACD;oBACE,MAAM,IAAI,KAAK,CAAC,wBAAwB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;aAC9D;SACF;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,GAAG,CAAC,OAAO,CAAC,4BAA4B,EAAE,SAAS,CAAC,CAAC;AAC9D,CAAC;AAED,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,MAAM,GAAG,IAAI;SAChB,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAE9E,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACxB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAC7B,OAAO;QACL,MAAM;QACN,KAAK;QACL,IAAI;KACL,CAAC;AACJ,CAAC"}

package/lib-esm/index.js

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';
@@ -27,4 +27,6 @@ export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
+export * from './peaks/solventSuppression';
+export * from './ranges/markSolventSignal';
 //# sourceMappingURL=index.js.map

package/lib-esm/index.js.map

@@ -1 +1 @@
-{"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"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,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;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC"}

package/lib-esm/peaks/peaksToRanges.js

@@ -176,7 +176,7 @@ export function peaksToRanges(data, peakList, options = {}) {
  * @return {array} nmr signals
  * @private
  */
-function detectSignals(data, peakList, options = {}) {
+export function detectSignals(data, peakList, options = {}) {
     let { integrationSum = 100, integralType = 'sum', frequencyCluster = 16, frequency = 400, nucleus = '1H', } = options;
     let signal1D = assignSignal(peakList[0], frequency, nucleus);
     let peaks;

package/lib-esm/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib-esm/peaks/solventSuppression.js

@@ -0,0 +1,151 @@
+import { linearSumAssignment } from 'linear-sum-assignment';
+import { Matrix } from 'ml-matrix';
+import { gaussianFct } from 'ml-peak-shape-generator';
+import { xFindClosestIndex, xMaxValue } from 'ml-spectra-processing';
+import { addDummySignals } from '../signals/addDummySignals';
+import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
+import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
+export function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList].sort((a, b) => a.x - b.x);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
+    for (const solventSignal of solvent) {
+        let solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        solventXYPeaks.sort((a, b) => a.x - b.x);
+        let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
+        let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - solventZoneExtension);
+        if (upIndex === lowIndex)
+            continue;
+        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const { peaks: shiftedSolventPeaks, delta: currentDelta } = 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 = gaussianFct(Math.abs(solventSignal.delta - currentDelta), 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const maxAmplitude = xMaxValue(amplitudeResiduals);
+        const maxDelta = xMaxValue(deltaResiduals);
+        const maxPosition = xMaxValue(positionResiduals);
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        let score = [];
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                1 -
+                positionResiduals[i] / maxPosition) /
+                3;
+            score.push(value);
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        if (minScore < 0) {
+            new Error('There is not a correct match with the pattern');
+            return peaks;
+        }
+        const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = linearSumAssignment(diff, {
+            maximaze: false,
+        });
+        if (gain < 0) {
+            new Error('The gain is below to zero');
+            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;
+}
+function getSolventPeaks(signal, options = {}) {
+    let signals = addDummySignals([signal]);
+    let spinSystem = signalsToSpinSystem(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = 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.
+    let deltaPPM = peak.x - solventSignal.delta;
+    if (solventXYPeaks.length > 1 && solventXYPeaks.length % 2 === 0) {
+        deltaPPM += solventXYPeaks[0].x;
+    }
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    let currentDelta = 0;
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+        currentDelta += shiftedSolventPeak.x;
+    }
+    return {
+        peaks: shiftedSolventPeaks,
+        delta: currentDelta / shiftedSolventPeaks.length,
+    };
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = linearSumAssignment(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 getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new 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-esm/peaks/solventSuppression.js.map

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package/lib-esm/peaks/util/jAnalyzer.js

@@ -8,11 +8,12 @@ let maxErrorIter1 = 2.5; // Hz
 let maxErrorIter2 = 1; // Hz
 let jAxisKeys = { jAxis: 'x', intensity: 'intensity' };
 function checkSignalForCompilePattern(signal) {
-    if (!signal.symRank) {
+    if (!('symRank' in signal)) {
         throw new Error('Internal error, symRank was not calculated');
     }
-    if (!signal.mask)
+    if (!('mask' in signal)) {
         throw new Error('Internal Error, mask was not added');
+    }
 }
 export default {
     /**