nmr-processing 9.3.0 → 9.3.1-pre.1669649322
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/lib/apodization/shapes/WindowFunctions.d.ts +1 -1
- package/lib/assignment/get13CAssignments.d.ts +1 -1
- package/lib/assignment/get1HAssignments.d.ts +3 -3
- package/lib/assignment/getAssignments.d.ts +2 -2
- package/lib/assignment/nmrAssigment.d.ts +3 -3
- package/lib/assignment/utils/createMapPossibleAssignments.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/buildAssignments.d.ts +4 -4
- package/lib/assignment/utils/getAssignment/formatData.d.ts +1 -1
- package/lib/peaks/peaksFilterImpurities.d.ts +1 -1
- package/lib/peaks/peaksToRanges.d.ts +1 -1
- package/lib/peaks/peaksToRanges.js +20 -19
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/util/convertWidth.d.ts +1 -1
- package/lib/peaks/util/convertWidthToHz.d.ts +1 -1
- package/lib/prediction/Prediction1D.d.ts +1 -1
- package/lib/prediction/dataStructure.d.ts +1 -1
- package/lib/prediction/predictAll.d.ts +1 -1
- package/lib/prediction/predictAll.js +4 -1
- package/lib/prediction/predictAll.js.map +1 -1
- package/lib/prediction/predictAllSpectra.d.ts +1 -1
- package/lib/prediction/predictCOSY.d.ts +1 -1
- package/lib/prediction/predictCarbon.d.ts +6 -2
- package/lib/prediction/predictCarbon.js +5 -4
- package/lib/prediction/predictCarbon.js.map +1 -1
- package/lib/prediction/predictHMBC.d.ts +1 -1
- package/lib/prediction/predictHSQC.d.ts +1 -1
- package/lib/prediction/predictProton.d.ts +6 -2
- package/lib/prediction/predictProton.js +1 -1
- package/lib/prediction/predictProton.js.map +1 -1
- package/lib/prediction/utils/fetchPrediction.d.ts +1 -1
- package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +3 -4
- package/lib/prediction/utils/getFilteredIDiaIDs.js +5 -6
- package/lib/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
- package/lib/prediction/utils/getPredictions.d.ts +1 -1
- package/lib/prediction/utils/predict2D.d.ts +6 -2
- package/lib/prediction/utils/predict2D.js +3 -3
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib/signals/optimization/getInternalSignals.d.ts +3 -3
- package/lib/signals/optimization/getSumOfShapes.d.ts +1 -1
- package/lib/signals/optimizeSignals.d.ts +1 -1
- package/lib/signals/signalsJoin.d.ts +3 -3
- package/lib/signals/signalsToRanges.d.ts +1 -1
- package/lib/signals/utils/jAnalyzer.d.ts +2 -2
- package/lib/utilities/MakeMandatory.d.ts +1 -1
- package/lib/utilities/getFrequency.d.ts +1 -1
- package/lib/utilities/hasProperty.d.ts +1 -1
- package/lib/xy/xyAutoPeaksPicking.d.ts +1 -1
- package/lib/xy/xyAutoPeaksPicking.js +4 -1
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib/xyz/xyzAutoZonesPicking.d.ts +2 -2
- package/lib-esm/peaks/peaksToRanges.js +20 -19
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/prediction/predictAll.js +4 -1
- package/lib-esm/prediction/predictAll.js.map +1 -1
- package/lib-esm/prediction/predictCarbon.js +5 -4
- package/lib-esm/prediction/predictCarbon.js.map +1 -1
- package/lib-esm/prediction/predictProton.js +1 -1
- package/lib-esm/prediction/predictProton.js.map +1 -1
- package/lib-esm/prediction/utils/getFilteredIDiaIDs.js +6 -7
- package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
- package/lib-esm/prediction/utils/predict2D.js +4 -4
- package/lib-esm/prediction/utils/predict2D.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +4 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +7 -7
- package/src/assignment/get13CAssignments.ts +1 -1
- package/src/assignment/get1HAssignments.ts +1 -1
- package/src/assignment/getAssignments.ts +1 -1
- package/src/assignment/utils/getAssignment/buildAssignments.ts +1 -1
- package/src/openchemlib-utils.d.ts +6 -1
- package/src/peaks/peaksToRanges.ts +23 -19
- package/src/prediction/Prediction1D.ts +1 -1
- package/src/prediction/predictAll.ts +5 -3
- package/src/prediction/predictAllSpectra.ts +1 -1
- package/src/prediction/predictCOSY.ts +1 -1
- package/src/prediction/predictCarbon.ts +17 -9
- package/src/prediction/predictHMBC.ts +1 -1
- package/src/prediction/predictHSQC.ts +1 -1
- package/src/prediction/predictProton.ts +6 -2
- package/src/prediction/utils/fetchPrediction.ts +1 -1
- package/src/prediction/utils/getFilteredIDiaIDs.ts +13 -13
- package/src/prediction/utils/getPredictions.ts +1 -1
- package/src/prediction/utils/predict2D.ts +12 -6
- package/src/utilities/hasProperty.ts +1 -1
- package/src/xy/xyAutoPeaksPicking.ts +5 -1
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@@ -14,8 +14,8 @@ export interface InternalSignal {
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fromIndexCoupling: number;
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toIndexCoupling: number;
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}
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export
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export type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling';
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export type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
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signal?: Signal;
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shape?: Shape1D;
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index?: number;
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@@ -35,7 +35,7 @@ export interface GetInternalSignalsOptions {
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shape?: Shape1D;
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parameters?: ParametersFromOptions;
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}
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-
export
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+
export type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
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fwhm: number;
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};
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export declare function getInternalSignals(data: DataXY, signals: Signal[], minMaxY: Record<string, number>, options: GetInternalSignalsOptions): {
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@@ -1,4 +1,4 @@
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1
1
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import { InternalSignal } from './getInternalSignals';
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import { SignalsToPointXYOptions } from './signalsToPointXY';
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-
export
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3
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+
export type SumOfShapes = (parameters: number[]) => (x: number) => number;
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export declare function getSumOfShapes(internalSignals: InternalSignal[], options: SignalsToPointXYOptions): (parameters: number[]) => (currentX: number) => number;
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@@ -4,7 +4,7 @@ import { NMRPeak1D } from '../peaks/NMRPeak1D';
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import { NMRSignal1D } from './NMRSignal1D';
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import { ParametersFromOptions, Shape1DWithFWHM } from './optimization/getInternalSignals';
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type ParametersFromSignal = Record<string, Record<string, number>>;
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export interface Signal extends NMRSignal1D {
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intensity?: number;
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shape?: Shape1D;
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@@ -9,9 +9,9 @@ export interface SignalsJoinOptions {
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*/
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}
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type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'multiplicity' | 'diaIDs' | 'pathLength'>;
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type Signal1DWidthDiaID = MakeMandatory<NMRSignal1D, 'diaIDs'>;
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type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthDiaID, 'js'> & {
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js: JcouplingFromPrediction[];
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@@ -13,6 +13,6 @@ interface SignalsToRangesOptions {
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*/
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}
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|
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type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals' | 'id'>;
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export declare function signalsToRanges(signals: NMRSignal1D[], options?: SignalsToRangesOptions): RangeFullfiled[];
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export {};
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@@ -10,7 +10,7 @@ interface IntergralData {
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to: number;
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}
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export
|
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export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
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intensity: number;
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};
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export interface SignalIntern {
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@@ -37,7 +37,7 @@ export interface SignalIntern {
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peaks: Peak1DIntern[];
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}
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|
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+
type SignalInternMandatory = MakeMandatory<SignalIntern, 'symRank' | 'mask' | 'peaksComp'>;
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|
export interface OpitonsCompilePatter {
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jAxisKey?: JAxisKeys;
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}
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@@ -9,7 +9,7 @@ export interface ObjervedNucleusData {
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9
9
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*/
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10
|
frequency: number;
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11
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}
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|
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|
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|
+
type Nucleus = Nuclei | (string & Record<never, never>);
|
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/**
|
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14
|
* calculate the frequency of a nucleus with respect to a reference nucleus
|
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*/
|
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@@ -42,5 +42,5 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
|
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*/
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frequency: number;
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|
}
|
|
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|
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export
|
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|
+
export type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
|
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|
export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];
|
|
@@ -6,7 +6,10 @@ const ml_spectra_processing_1 = require("ml-spectra-processing");
|
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6
6
|
const convertWidthToHz_1 = require("../peaks/util/convertWidthToHz");
|
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7
7
|
function xyAutoPeaksPicking(data, options) {
|
|
8
8
|
const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
|
|
9
|
-
|
|
9
|
+
let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
|
|
10
|
+
// we can consider a peak with of 0.5 Hz for the windowSize
|
|
11
|
+
let ws = Math.max(Math.round(pointsPerHz / 2), 5);
|
|
12
|
+
const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
|
|
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13
|
if (data.x.length < windowSize)
|
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11
14
|
return [];
|
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12
15
|
if (from !== undefined && to !== undefined) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAUgB;AAEhB,iEAI+B;AAG/B,qEAAkE;AAgElE,SAAgB,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAUgB;AAEhB,iEAI+B;AAG/B,qEAAkE;AAgElE,SAAgB,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,WAAW,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1D,2DAA2D;IAC3D,IAAI,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAElD,MAAM,EAAE,UAAU,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErE,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,IAAA,iCAAS,EAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,SAAS;QACT,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,QAAQ,SAAS,EAAE;QACjB,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;SAC1C;QACD,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;SACvD;QACD,KAAK,MAAM,CAAC,CAAC;YACX,OAAO;gBACL,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC;gBACpC,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC;aAClD,CAAC;SACH;QACD,OAAO,CAAC,CAAC;YACP,MAAM,SAAS,GAAU,SAAS,CAAC;YACnC,4EAA4E;YAC5E,MAAM,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;SAClD;KACF;AACH,CAAC;AAzED,gDAyEC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,MAA4B,EAC5B,cAAkC;IAElC,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;IAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;IACnC,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,SAAS,EACT,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,IAAA,YAAG,EAAC,IAAI,EAAE;QACtB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,IAAA,iBAAQ,EAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;IAE3D,MAAM,QAAQ,GAAG,UAAU;QACzB,CAAC,CAAC,IAAA,uBAAc,EAAC,QAAQ,EAAE;YACvB,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC;IAEvC,OAAO,IAAA,mCAAgB,EACrB,QAAQ;QACN,CAAC,CAAC,IAAA,sBAAa,EAAC,IAAI,EAAE,QAAQ,EAAE;YAC5B,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,EACZ,EAAE,SAAS,EAAE,CACd,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,IAAA,qCAAa,EAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,IAAA,uCAAe,EAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAyC;IAEzC,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;IACxC,OAAO;QACL,EAAE;QACF,CAAC;QACD,CAAC;QACD,KAAK;QACL,KAAK;KACN,CAAC;AACJ,CAAC"}
|
|
@@ -65,8 +65,8 @@ export interface XYZAutoZonesPickingOptions {
|
|
|
65
65
|
*/
|
|
66
66
|
kernel?: GetKernelOptions;
|
|
67
67
|
}
|
|
68
|
-
export
|
|
69
|
-
export
|
|
68
|
+
export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<NMRSignal2D<T>, 'id'>;
|
|
69
|
+
export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
|
|
70
70
|
export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): NMRZoneWithID[];
|
|
71
71
|
/**
|
|
72
72
|
* This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
|
|
@@ -108,17 +108,7 @@ export function peaksToRanges(data, peakList, options = {}) {
|
|
|
108
108
|
}
|
|
109
109
|
}
|
|
110
110
|
// it was a updateIntegrals function.
|
|
111
|
-
|
|
112
|
-
let sumObserved = 0;
|
|
113
|
-
for (const signal of signals) {
|
|
114
|
-
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
115
|
-
}
|
|
116
|
-
if (sumObserved !== integrationSum) {
|
|
117
|
-
sumIntegral = integrationSum / sumObserved;
|
|
118
|
-
for (const signal of signals) {
|
|
119
|
-
signal.integralData.value *= sumIntegral;
|
|
120
|
-
}
|
|
121
|
-
}
|
|
111
|
+
updateIntegration(signals, integrationSum);
|
|
122
112
|
}
|
|
123
113
|
signals.sort((a, b) => {
|
|
124
114
|
return b.delta - a.delta;
|
|
@@ -143,7 +133,6 @@ export function peaksToRanges(data, peakList, options = {}) {
|
|
|
143
133
|
delta: signal.delta,
|
|
144
134
|
kind: signal.kind || 'signal',
|
|
145
135
|
multiplicity: signal.multiplicity,
|
|
146
|
-
integration: signal.integralData.value,
|
|
147
136
|
};
|
|
148
137
|
if (keepPeaks) {
|
|
149
138
|
signalResult.peaks = signal.peaks.map((peak) => {
|
|
@@ -185,7 +174,6 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
185
174
|
let peaks;
|
|
186
175
|
let signals = [];
|
|
187
176
|
let prevPeak = { x: Number.MIN_SAFE_INTEGER };
|
|
188
|
-
let spectrumIntegral = 0;
|
|
189
177
|
frequencyCluster /= frequency;
|
|
190
178
|
for (const peak of peakList) {
|
|
191
179
|
if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
|
|
@@ -231,14 +219,9 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
231
219
|
else {
|
|
232
220
|
integration.value = integralPeaks;
|
|
233
221
|
}
|
|
234
|
-
spectrumIntegral += integration.value;
|
|
235
222
|
}
|
|
236
223
|
if (integrationSum > 0) {
|
|
237
|
-
|
|
238
|
-
for (let signal of signals) {
|
|
239
|
-
let integration = signal.integralData;
|
|
240
|
-
integration.value *= integralFactor;
|
|
241
|
-
}
|
|
224
|
+
updateIntegration(signals, integrationSum);
|
|
242
225
|
}
|
|
243
226
|
return signals;
|
|
244
227
|
}
|
|
@@ -249,4 +232,22 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
249
232
|
function computeArea(peak, frequency) {
|
|
250
233
|
return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
|
|
251
234
|
}
|
|
235
|
+
/**
|
|
236
|
+
* update the integration Values
|
|
237
|
+
* @param signals
|
|
238
|
+
* @param integrationSum
|
|
239
|
+
*/
|
|
240
|
+
function updateIntegration(signals, integrationSum) {
|
|
241
|
+
let sumIntegral = 0;
|
|
242
|
+
let sumObserved = 0;
|
|
243
|
+
for (const signal of signals) {
|
|
244
|
+
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
245
|
+
}
|
|
246
|
+
if (sumObserved !== integrationSum) {
|
|
247
|
+
sumIntegral = integrationSum / sumObserved;
|
|
248
|
+
for (const signal of signals) {
|
|
249
|
+
signal.integralData.value *= sumIntegral;
|
|
250
|
+
}
|
|
251
|
+
}
|
|
252
|
+
}
|
|
252
253
|
//# sourceMappingURL=peaksToRanges.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
1
2
|
import { predictCOSY } from './predictCOSY';
|
|
2
3
|
import { predictCarbon } from './predictCarbon';
|
|
3
4
|
import { predictHMBC } from './predictHMBC';
|
|
@@ -10,6 +11,8 @@ import { getPredictions } from './utils/getPredictions';
|
|
|
10
11
|
*/
|
|
11
12
|
export async function predictAll(molecule, options = {}) {
|
|
12
13
|
let { from = 'H', to = 'C', predictor = { H: predictProton, C: predictCarbon }, predictions, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
|
|
14
|
+
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
15
|
+
console.log('entra correction');
|
|
13
16
|
const xPrediction = await getPredictions(from, molecule, predictOptions, predictor, predictions);
|
|
14
17
|
const yPrediction = await getPredictions(to, molecule, predictOptions, predictor, predictions);
|
|
15
18
|
if (!xPrediction || !yPrediction) {
|
|
@@ -19,7 +22,7 @@ export async function predictAll(molecule, options = {}) {
|
|
|
19
22
|
H: xPrediction,
|
|
20
23
|
C: yPrediction,
|
|
21
24
|
};
|
|
22
|
-
const { molfile
|
|
25
|
+
const { molfile } = xPrediction;
|
|
23
26
|
const spectra = {
|
|
24
27
|
proton: predictions.H,
|
|
25
28
|
carbon: predictions.C,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,wBAAwB,EAAmC,MAAM,mBAAmB,CAAC;AAE9F,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAmDxD;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,QAAkB,EAClB,UAA6B,EAAE;IAE/B,IAAI,EACF,IAAI,GAAG,GAAG,EACV,EAAE,GAAG,GAAG,EACR,SAAS,GAAG,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE,aAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GAAG,EAAE,GACpB,GAAG,OAAO,CAAC;IAEZ,MAAM,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,CAAA;IAC/B,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,WAAW,GAAG;QACZ,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,EAAE,OAAO,EAAE,GAAG,WAAW,CAAC;IAEhC,MAAM,OAAO,GAAQ;QACnB,MAAM,EAAE,WAAW,CAAC,CAAC;QACrB,MAAM,EAAE,WAAW,CAAC,CAAC;KACtB,CAAC;IAEF,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IAEH,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE;QACzB,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC;QAC5B,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;KAC5B;IAED,OAAO;QACL,OAAO;QACP,MAAM;QACN,GAAG,OAAO;KACX,CAAC;AACJ,CAAC"}
|
|
@@ -3,9 +3,9 @@ import fetch from 'cross-fetch';
|
|
|
3
3
|
import { setIDs } from '../peaks/util/setIDs';
|
|
4
4
|
import { signalsToRanges } from '../signals/signalsToRanges';
|
|
5
5
|
import { fetchPrediction } from './utils/fetchPrediction';
|
|
6
|
-
import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
|
|
7
6
|
import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
|
|
8
7
|
import { queryByHose } from './utils/queryByHOSE';
|
|
8
|
+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
9
9
|
const cache = {};
|
|
10
10
|
async function loadDB(url = 'https://www.lactame.com/lib/nmr-processing-data/20210711/carbon.js') {
|
|
11
11
|
if (cache[url]) {
|
|
@@ -29,7 +29,7 @@ function checkFromPrediction(signal) {
|
|
|
29
29
|
* @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
|
|
30
30
|
*/
|
|
31
31
|
export async function predictCarbon(molecule, options = {}) {
|
|
32
|
-
let { url, database, webserviceURL } = options;
|
|
32
|
+
let { url, database, webserviceURL, diaIDs = getDiastereotopicAtomIDs(molecule), } = options;
|
|
33
33
|
if (webserviceURL) {
|
|
34
34
|
return fetchPrediction(molecule, { webserviceURL });
|
|
35
35
|
}
|
|
@@ -42,8 +42,9 @@ export async function predictCarbon(molecule, options = {}) {
|
|
|
42
42
|
let { maxSphereSize = maxLevel } = options;
|
|
43
43
|
if (maxSphereSize > maxLevel)
|
|
44
44
|
maxSphereSize = maxLevel;
|
|
45
|
-
const {
|
|
45
|
+
const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
|
|
46
46
|
maxSphereSize,
|
|
47
|
+
diaIDs,
|
|
47
48
|
});
|
|
48
49
|
let predictions = queryByHose(carbonDiaIDs, database, {
|
|
49
50
|
maxSphereSize,
|
|
@@ -53,7 +54,7 @@ export async function predictCarbon(molecule, options = {}) {
|
|
|
53
54
|
return {
|
|
54
55
|
molfile,
|
|
55
56
|
nucleus: '13C',
|
|
56
|
-
diaIDs
|
|
57
|
+
diaIDs,
|
|
57
58
|
joinedSignals,
|
|
58
59
|
signals,
|
|
59
60
|
ranges: signalsToRanges(joinedSignals),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAGhC,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAK7D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;
|
|
1
|
+
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAGhC,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAK7D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAc,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAC9D,OAAO,EAAE,wBAAwB,EAAE,MAAM,mBAAmB,CAAC;AAE7D,MAAM,KAAK,GAAyC,EAAE,CAAC;AAEvD,KAAK,UAAU,MAAM,CACnB,GAAG,GAAG,oEAAoE;IAE1E,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;QACd,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;KACnB;IACD,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;IAClC,MAAM,QAAQ,GAAsB,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;IAC1D,KAAK,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC;IACtB,OAAO,QAAQ,CAAC;AAClB,CAAC;AAkCD,SAAS,mBAAmB,CAC1B,MAAmB;IAEnB,IAAI,CAAC,MAAM,CAAC,KAAK;QAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;IACzD,IAAI,CAAC,MAAM,CAAC,MAAM;QAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;IAC3D,IAAI,CAAC,MAAM,CAAC,OAAO;QAAE,MAAM,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAC;AAC/D,CAAC;AACD;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,IAAI,EACF,GAAG,EACH,QAAQ,EACR,aAAa,EACb,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,GAC5C,GAAG,OAAO,CAAC;IAEZ,IAAI,aAAa,EAAE;QACjB,OAAO,eAAe,CAAC,QAAQ,EAAE,EAAE,aAAa,EAAE,CAAC,CAAC;KACrD;IAED,IAAI,CAAC,QAAQ;QAAE,QAAQ,GAAG,MAAM,MAAM,CAAC,GAAG,CAAC,CAAC;IAE5C,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC5C;IAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC;IAErC,IAAI,EAAE,aAAa,GAAG,QAAQ,EAAE,GAAG,OAAO,CAAC;IAE3C,IAAI,aAAa,GAAG,QAAQ;QAAE,aAAa,GAAG,QAAQ,CAAC;IAEvD,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,kBAAkB,CAAC,QAAQ,EAAE;QAC7D,aAAa;QACb,MAAM;KACP,CAAC,CAAC;IAEH,IAAI,WAAW,GAAG,WAAW,CAAC,YAAY,EAAE,QAAQ,EAAE;QACpD,aAAa;KACd,CAAC,CAAC;IAEH,MAAM,OAAO,GAAG,aAAa,CAAC,WAAW,CAAC,CAAC;IAC3C,MAAM,aAAa,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAC;IACjD,OAAO;QACL,OAAO;QACP,OAAO,EAAE,KAAK;QACd,MAAM;QACN,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,aAAa,CAAC,WAAyB;IAC9C,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,UAAU,CAAC;QAChE,MAAM,MAAM,GAAG;YACb,EAAE,EAAE,UAAU,EAAE;YAChB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,KAAK;YACL,MAAM;YACN,YAAY,EAAE,GAAG;YACjB,OAAO;YACP,SAAS;YACT,EAAE,EAAE,EAAE;SACP,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,MAAqB,CAAC,CAAC;KACrC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,OAAsB;IAC/C,IAAI,aAAa,GAA8C,EAAE,CAAC;IAClE,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;QAC1B,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC5B,IAAI,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAC7B,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,EAAE;YACzB,aAAa,CAAC,KAAK,CAAC,GAAG,IAAI,CAAC,KAAK,CAC/B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CACG,CAAC;SAC7B;aAAM;YACL,aAAa,CAAC,KAAK,CAAC,CAAC,OAAO,IAAI,MAAM,CAAC,OAAO,CAAC;YAC/C,aAAa,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;SAClD;KACF;IACD,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC,CAAC;AAC9C,CAAC"}
|
|
@@ -27,7 +27,7 @@ export async function predictProton(molecule, options = {}) {
|
|
|
27
27
|
cache(molfile, result);
|
|
28
28
|
}
|
|
29
29
|
}
|
|
30
|
-
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
30
|
+
const { diaIDs = getDiastereotopicAtomIDs(molecule) } = options;
|
|
31
31
|
const signals = protonParser(result, molecule, diaIDs);
|
|
32
32
|
const joinedSignals = signalsJoin(signals);
|
|
33
33
|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;
|
|
1
|
+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAsB7D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,EAAE,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,EAAE,GAAG,OAAO,CAAC;IAChE,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACvD,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO;QACP,MAAM;QACN,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,QAAkB,EAClB,MAAgB;IAEhB,IAAI,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,IAAI,cAAc,GAAG,qBAAqB,CAAC,QAAQ,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3E,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACtD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE;QACtB,IAAI,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,IAAI,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,GAAgB;YACxB,EAAE,EAAE,UAAU,EAAE;YAChB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,IAAI,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,14 +1,14 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { getHoseCodesFromDiastereotopicID, addDiastereotopicMissingChirality, groupDiasterotopicAtomIDs, } from 'openchemlib-utils';
|
|
2
2
|
export function getFilteredIDiaIDs(molecule, options) {
|
|
3
|
-
const { maxSphereSize } = options;
|
|
3
|
+
const { maxSphereSize, diaIDs } = options;
|
|
4
4
|
molecule.addImplicitHydrogens();
|
|
5
5
|
molecule.addMissingChirality();
|
|
6
6
|
addDiastereotopicMissingChirality(molecule);
|
|
7
7
|
const molfile = molecule.toMolfile();
|
|
8
|
-
let groupedDiaIDs =
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
8
|
+
let groupedDiaIDs = groupDiasterotopicAtomIDs(diaIDs, molecule, {
|
|
9
|
+
atomLabel: 'C',
|
|
10
|
+
});
|
|
11
|
+
let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
|
|
12
12
|
if (a.atomLabel === b.atomLabel) {
|
|
13
13
|
return b.counter - a.counter;
|
|
14
14
|
}
|
|
@@ -23,7 +23,6 @@ export function getFilteredIDiaIDs(molecule, options) {
|
|
|
23
23
|
let toReturn = {
|
|
24
24
|
molfile,
|
|
25
25
|
carbonDiaIDs: carbonDiaIDs,
|
|
26
|
-
groupedDiaIDs,
|
|
27
26
|
};
|
|
28
27
|
return toReturn;
|
|
29
28
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":"AACA,OAAO,
|
|
1
|
+
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":"AACA,OAAO,EAEL,gCAAgC,EAChC,iCAAiC,EACjC,yBAAyB,GAC1B,MAAM,mBAAmB,CAAC;AAS3B,MAAM,UAAU,kBAAkB,CAChC,QAAkB,EAClB,OAAoD;IAEpD,MAAM,EAAE,aAAa,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IAE1C,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,QAAQ,CAAC,mBAAmB,EAAE,CAAC;IAC/B,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,aAAa,GAAG,yBAAyB,CAAC,MAAM,EAAE,QAAQ,EAAE;QAC9D,SAAS,EAAE,GAAG;KACf,CAAC,CAAC;IAEH,IAAI,YAAY,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QAC7C,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,EAAE;YAC/B,OAAO,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC;SAC9B;QACD,OAAO,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC5C,CAAC,CAAQ,CAAC;IAEV,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC;IAC9B,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE;QAChC,KAAK,CAAC,IAAI,GAAG,gCAAgC,CAC3C,GAAG,CAAC,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,CAAC,EACpC;YACE,aAAa;SACd,CACF,CAAC;KACH;IAED,IAAI,QAAQ,GAAG;QACb,OAAO;QACP,YAAY,EAAE,YAAqC;KACpD,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import { agnes } from 'ml-hclust';
|
|
3
3
|
import { Matrix } from 'ml-matrix';
|
|
4
|
-
import { getGroupedDiastereotopicAtomIDs, getPathsInfo, } from 'openchemlib-utils';
|
|
4
|
+
import { getGroupedDiastereotopicAtomIDs, getPathsInfo, groupDiasterotopicAtomIDs, } from 'openchemlib-utils';
|
|
5
5
|
import { setIDs } from '../../peaks/util/setIDs';
|
|
6
6
|
import { getNuclei } from './getNuclei';
|
|
7
7
|
import { getPredictions } from './getPredictions';
|
|
@@ -12,17 +12,17 @@ function checkFromTo(options) {
|
|
|
12
12
|
}
|
|
13
13
|
export async function predict2D(molecule, options = {}) {
|
|
14
14
|
checkFromTo(options);
|
|
15
|
-
let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
16
15
|
molecule.addImplicitHydrogens();
|
|
17
|
-
let diaIDs =
|
|
16
|
+
let { from, to, diaIDs, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
18
17
|
const pathsInfo = getPathsInfo(molecule, {
|
|
19
18
|
fromLabel: from,
|
|
20
19
|
toLabel: to,
|
|
21
20
|
minLength,
|
|
22
21
|
maxLength,
|
|
23
22
|
});
|
|
23
|
+
const groupedDiaIDS = diaIDs ? groupDiasterotopicAtomIDs(diaIDs, molecule) : getGroupedDiastereotopicAtomIDs(molecule);
|
|
24
24
|
let diaIDswithAtomInfo = [];
|
|
25
|
-
for (let diaID of
|
|
25
|
+
for (let diaID of groupedDiaIDS) {
|
|
26
26
|
diaIDswithAtomInfo.push({
|
|
27
27
|
...diaID,
|
|
28
28
|
pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,EAAE,KAAK,EAAW,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAEnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,
|
|
1
|
+
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,EAAE,KAAK,EAAW,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAEnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,EACZ,yBAAyB,GAC1B,MAAM,mBAAmB,CAAC;AAO3B,OAAO,EAAE,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAQjD,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AA0FlD,SAAS,WAAW,CAClB,OAAyB;IAEzB,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;AACH,CAAC;AAMD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,EACF,IAAI,EACJ,EAAE,EACF,MAAM,EACN,SAAS,GAAG,CAAC,EACb,SAAS,EACT,cAAc,GAAG,EAAE,EACnB,WAAW,EACX,SAAS,EACT,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,eAAe,GAAG,KAAK,GACxB,GAAG,OAAO,CAAC;IAEZ,MAAM,SAAS,GAAG,YAAY,CAAC,QAAQ,EAAE;QACvC,SAAS,EAAE,IAAI;QACf,OAAO,EAAE,EAAE;QACX,SAAS;QACT,SAAS;KACV,CAAC,CAAC;IAEH,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,CAAC,yBAAyB,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,+BAA+B,CAAC,QAAQ,CAAC,CAAA;IAEtH,IAAI,kBAAkB,GAA6C,EAAE,CAAC;IACtE,KAAK,IAAI,KAAK,IAAI,aAAa,EAAE;QAC/B,kBAAkB,CAAC,IAAI,CAAC;YACtB,GAAG,KAAK;YACR,QAAQ,EAAE,IAAI,CAAC,KAAK,CAClB,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAC9B;SACd,CAAC,CAAC;KACJ;IAED,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GACf,IAAI,KAAK,EAAE;QACT,CAAC,CAAC,WAAW;QACb,CAAC,CAAC,MAAM,cAAc,CAClB,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAER,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,MAAM,OAAO,GAAoC;QAC/C,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,cAAc,GAAoB;QACtC,CAAC,EAAE,EAAE;QACL,CAAC,EAAE,EAAE;KACN,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,cAAc,EAAE;QACjC,KAAK,MAAM,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE;YAChD,IAAI,CAAC,MAAM,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;YAC7D,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC;SACjD;KACF;IACD,IAAI,KAAK,GAAmC,EAAE,CAAC;IAC/C,KAAK,MAAM,KAAK,IAAI,kBAAkB,EAAE;QACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;QAChC,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAExC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;YAAE,SAAS;QAEhD,MAAM,YAAY,GAAG,QAAQ,CAAC,KAAK,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE;YAC/B,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC;gBAAE,SAAS;YAE1D,IAAI,WAAW,GAAgC;gBAC7C,CAAC,EAAE,QAAQ;gBACX,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;aACtB,CAAC;YAEF,MAAM,GAAG,GAAG,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,IAAI,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;YAE5D,IAAI,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;gBAC/D,SAAS;aACV;YAED,IAAI,IAAI,GAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC;YAC7C,IAAI,MAAM,GAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;YACrD,KAAK,IAAI,IAAI,IAAI,WAAW,EAAE;gBAC5B,IAAI,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC;gBACpC,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;aACxD;YAED,MAAM,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC;YACtB,KAAK,CAAC,GAAG,CAAC,GAAG,MAAqB,CAAC;SACpC;KACF;IAED,IAAI,eAAe,EAAE;QACnB,mBAAmB,CAAC,KAAK,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,EAAE,CAAC,CAAC;KAClE;IAED,iCAAiC;IACjC,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC3C,MAAM,KAAK,GAAG,WAAW,CAAC,aAAa,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IAErE,OAAO;QACL,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE;QAC7B,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM;QACxB,MAAM,EAAE,SAAS,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CAAC,aAA4B;IAChD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,MAAM,IAAI,aAAa,EAAE;QAClC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;YACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;gBACxC,IAAI,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;gBACnD,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aACzB;SACF;KACF;IACD,OAAO,MAAM,CAAC,OAAO,CAAC,CAAC;AACzB,CAAC;AAMD,SAAS,mBAAmB,CAC1B,KAAqC,EACrC,OAAmC;IAEnC,MAAM,EAAE,KAAK,GAAG,EAAE,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC/C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAEpC,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;QACvB,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC;YAAE,SAAS;QACvC,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,KAAK,EAAE,CAAC;YAAE,SAAS;QAEzC,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;QAEnC,IAAI,IAAI,GAAQ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|
|
@@ -3,7 +3,10 @@ import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processin
|
|
|
3
3
|
import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
|
|
4
4
|
export function xyAutoPeaksPicking(data, options) {
|
|
5
5
|
const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
|
|
6
|
-
|
|
6
|
+
let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
|
|
7
|
+
// we can consider a peak with of 0.5 Hz for the windowSize
|
|
8
|
+
let ws = Math.max(Math.round(pointsPerHz / 2), 5);
|
|
9
|
+
const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
|
|
7
10
|
if (data.x.length < windowSize)
|
|
8
11
|
return [];
|
|
9
12
|
if (from !== undefined && to !== undefined) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EACL,GAAG,EACH,aAAa,EACb,cAAc,EAMd,QAAQ,GACT,MAAM,QAAQ,CAAC;AAEhB,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAgElE,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;
|
|
1
|
+
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