nmr-processing 7.4.1 → 8.0.0
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/assignment/getAssignments.d.ts +7 -9
- package/lib/assignment/getAssignments.js +1 -1
- package/lib/assignment/getAssignments.js.map +1 -1
- package/lib/assignment/nmrAssigment.d.ts +19 -27
- package/lib/assignment/utils/getAssignment/buildAssignments.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/buildAssignments.js +5 -0
- package/lib/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
- package/lib/assignment/utils/getAssignment/checkIDs.d.ts +3 -20
- package/lib/assignment/utils/getAssignment/checkIDs.js +5 -9
- package/lib/assignment/utils/getAssignment/checkIDs.js.map +1 -1
- package/lib/assignment/utils/getAssignment/formatData.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/formatData.js +30 -3
- package/lib/assignment/utils/getAssignment/formatData.js.map +1 -1
- package/lib/assignment/utils/getAssignment/getTargetsAndCorrelations.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map +1 -1
- package/lib/assignment/utils/getAssignment/partialScore.js +1 -1
- package/lib/assignment/utils/getAssignment/partialScore.js.map +1 -1
- package/lib/databases/getDatabase.d.ts +6 -1
- package/lib/databases/getDatabase.js +13 -3
- package/lib/databases/getDatabase.js.map +1 -1
- package/lib/index.d.ts +3 -1
- package/lib/prediction/predictAllSpectra.d.ts +22 -4
- package/lib/prediction/predictAllSpectra.js +102 -16
- package/lib/prediction/predictAllSpectra.js.map +1 -1
- package/lib/xyz/NMRSignal2D.d.ts +3 -3
- package/lib-esm/assignment/getAssignments.js +1 -1
- package/lib-esm/assignment/getAssignments.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/buildAssignments.js +5 -0
- package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/checkIDs.js +5 -9
- package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/formatData.js +30 -3
- package/lib-esm/assignment/utils/getAssignment/formatData.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/partialScore.js +1 -1
- package/lib-esm/assignment/utils/getAssignment/partialScore.js.map +1 -1
- package/lib-esm/databases/getDatabase.js +13 -3
- package/lib-esm/databases/getDatabase.js.map +1 -1
- package/lib-esm/prediction/predictAllSpectra.js +102 -16
- package/lib-esm/prediction/predictAllSpectra.js.map +1 -1
- package/package.json +12 -12
- package/src/assignment/getAssignments.ts +8 -9
- package/src/assignment/nmrAssigment.ts +23 -21
- package/src/assignment/utils/getAssignment/buildAssignments.ts +7 -1
- package/src/assignment/utils/getAssignment/checkIDs.ts +14 -36
- package/src/assignment/utils/getAssignment/formatData.ts +41 -4
- package/src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts +2 -1
- package/src/assignment/utils/getAssignment/partialScore.ts +2 -2
- package/src/databases/getDatabase.ts +19 -2
- package/src/index.ts +9 -1
- package/src/prediction/predictAllSpectra.ts +151 -14
- package/src/xyz/NMRSignal2D.ts +3 -3
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@@ -8,21 +8,19 @@ import { AtomTypes, RestrictionByCS } from './utils/getAssignment/buildAssignmen
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export interface SpectraData1D {
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id?: string;
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ranges: NMRRange[];
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info
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info: any;
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}
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export interface SpectraData2D {
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id?: string;
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zones: NMRZone[];
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/**
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* object with information about the spectrum, it is mandatory at the moment
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* to generate correlations.
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*/
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info: any;
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}
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export declare type SpectraData = SpectraData1D | SpectraData2D;
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export interface GetAutoAssignmentInput {
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/**
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* It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
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*/
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atoms?: {
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[key: string]: number;
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};
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spectra: SpectraData[];
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/**
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* Instance of Molecule
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@@ -77,5 +75,5 @@ export interface GetAssignmentsOptions {
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}
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export declare function getAssignments(input: GetAutoAssignmentInput, options?: GetAssignmentsOptions): Promise<{
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score: w;
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assignment: import("./
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assignment: import("./nmrAssigment").SpectraDataWithIds[];
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}[]>;
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@@ -10,7 +10,7 @@ const checkIDs_1 = require("./utils/getAssignment/checkIDs");
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const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
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const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
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async function getAssignments(input, options = {}) {
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let { restrictionByCS = {}, justAssign, minScore =
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let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
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const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
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const molecule = input.molecule;
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if (!molecule)
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@@ -1 +1 @@
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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;
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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}
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@@ -1,28 +1,20 @@
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import {
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import
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import type {
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export
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[key: string]: number;
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};
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/**
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* Contains the ranges for each nucleus or kind of experiment e.g. { H: [], C: [], apt: [], dept135: []}
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* the ranges represented with atom label only contain the range from a single pulse experiment or equivalent.
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*/
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ranges: {
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[key: string]: NMRRange[];
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};
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/**
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* Contains the zones for each kind of experiment e.g. { H: [], C: [], apt: [], dept135: []};
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*/
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zones: {
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[key: string]: NMRZone[];
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};
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/**
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* Instance of Molecule
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*/
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molecule: Molecule;
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import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
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import { MakeMandatory } from '../utilities/MakeMandatory';
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import type { SpectraData1D, SpectraData2D } from './getAssignments';
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export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
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export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
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export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
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id: string;
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signals: Array<NMRSignal2DWithId>;
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}
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export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
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id: string;
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signals: Array<NMRSignal1DWithId>;
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}
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export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
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ranges: NMRRangeWithIds[];
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}
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export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
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zones: NMRZoneWithIds[];
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}
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export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
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@@ -2,7 +2,7 @@ import { Values } from 'nmr-correlation';
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import { Molecule } from 'openchemlib';
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import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
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import { MakeMandatory } from '../../../utilities/MakeMandatory';
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import { SpectraDataWithIds } from '
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import { SpectraDataWithIds } from '../../nmrAssigment';
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import { TargetsByAtomType } from './getTargetsAndCorrelations';
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export declare type AtomTypes = 'H' | 'C';
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export declare type CurrentAtoms = Array<AtomTypes>;
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checkNMRSignal1D(joinedSignals);
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if (!predictions[atomType])
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predictions[atomType] = {};
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let totalHydrogens = 0;
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for (let prediction of joinedSignals) {
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const diaID = prediction.diaIDs[0];
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const index = prediction.atoms[0];
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const allHydrogens = exports.getAllHydrogens[atomType](molecule, index);
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totalHydrogens += prediction.nbAtoms * allHydrogens;
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predictions[atomType][diaID] = {
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...prediction,
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}
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}
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@@ -1,23 +1,6 @@
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import type { NMRRange,
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import {
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import type {
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export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
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export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
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export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
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id: string;
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signals: Array<NMRSignal2DWithId>;
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}
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export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
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id: string;
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signals: Array<NMRSignal1DWithId>;
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}
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export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
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ranges: NMRRangeWithIds[];
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}
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export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
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zones: NMRZoneWithIds[];
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}
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20
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export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
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1
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+
import type { NMRRange, NMRZone } from '../../..';
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2
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+
import type { SpectraData } from '../../getAssignments';
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3
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+
import type { SpectraDataWithIds, NMRRangeWithIds, NMRZoneWithIds } from '../../nmrAssigment';
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21
4
|
export declare function checkIDs(input?: SpectraData[]): SpectraDataWithIds[];
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22
5
|
export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
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23
6
|
export declare function addIDs(data: NMRRange[] | NMRZone[]): NMRRangeWithIds[] | NMRZoneWithIds[];
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@@ -10,17 +10,13 @@ function checkIDs(input = []) {
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10
10
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let inputClone = JSON.parse(JSON.stringify(input));
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11
11
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let spectra = [];
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12
12
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for (const spectraData of inputClone) {
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13
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+
if (!('info' in spectraData)) {
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14
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+
throw new Error('each spectrum should contain info properties with nucleus information');
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15
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+
}
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13
16
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const { info, id } = spectraData;
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14
17
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if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
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let
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-
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-
const { integration } = element;
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18
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-
for (let signal of element.signals || []) {
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if (!signal.integration)
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signal.integration = integration;
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}
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-
}
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23
|
-
spectra.push({ id, info, ranges: data });
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18
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+
let ranges = addIDs(spectraData.ranges);
|
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19
|
+
spectra.push({ id, info, ranges });
|
|
24
20
|
}
|
|
25
21
|
else {
|
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26
22
|
let data = addIDs(spectraData.zones);
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@@ -1 +1 @@
|
|
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1
|
-
{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":";;;;;;AAOA,+DAAuC;AAEvC,uDAAoD;
|
|
1
|
+
{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":";;;;;;AAOA,+DAAuC;AAEvC,uDAAoD;AAEpD,SAAgB,QAAQ,CAAC,QAAuB,EAAE;IAChD,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAkB,CAAC;IACpE,IAAI,OAAO,GAAyB,EAAE,CAAC;IACvC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,IAAI,CAAC,CAAC,MAAM,IAAI,WAAW,CAAC,EAAE;YAC5B,MAAM,IAAI,KAAK,CACb,uEAAuE,CACxE,CAAC;SACH;QAED,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,IAAA,iCAAe,EAAC,WAAW,CAAC,EAAE;YAChC,IAAI,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAsB,CAAC;YAC7D,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;SACpC;aAAM;YACL,IAAI,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAqB,CAAC;YACzD,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;SACzC;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AApBD,4BAoBC;AAED,SAAgB,MAAM,CACpB,IAA4B;IAE5B,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAC;QAC/D,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAC;SAC3D;KACF;AACH,CAAC;AATD,wBASC;AAED,SAAgB,MAAM,CAAC,IAA4B;IACjD,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,OAAO,CAAC,EAAE,GAAG,IAAA,oBAAU,GAAE,CAAC;QAC3C,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,CAAC,EAAE,GAAG,IAAA,oBAAU,GAAE,CAAC;SAC1C;KACF;IACD,MAAM,CAAC,IAAI,CAAC,CAAC;IACb,OAAO,IAAI,CAAC;AACd,CAAC;AATD,wBASC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { NMRRangeWithIds, NMRZoneWithIds, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds } from '
|
|
1
|
+
import { NMRRangeWithIds, NMRZoneWithIds, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds } from '../../nmrAssigment';
|
|
2
2
|
interface SpectraData1DFormatted extends Omit<SpectraData1DWithIds, 'ranges'> {
|
|
3
3
|
ranges: {
|
|
4
4
|
values: NMRRangeWithIds[];
|
|
@@ -6,15 +6,42 @@ function formatData(input = []) {
|
|
|
6
6
|
let inputClone = JSON.parse(JSON.stringify(input));
|
|
7
7
|
let spectra = [];
|
|
8
8
|
for (const spectraData of inputClone) {
|
|
9
|
-
const { info } = spectraData;
|
|
9
|
+
const { id, info } = spectraData;
|
|
10
10
|
if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
|
|
11
|
-
|
|
11
|
+
const ranges = rescaleIntegration({
|
|
12
|
+
id,
|
|
13
|
+
info,
|
|
14
|
+
ranges: spectraData.ranges,
|
|
15
|
+
});
|
|
16
|
+
spectra.push({ id, info, ranges: { values: ranges } });
|
|
12
17
|
}
|
|
13
18
|
else {
|
|
14
|
-
spectra.push({ info, zones: { values: spectraData.zones } });
|
|
19
|
+
spectra.push({ id, info, zones: { values: spectraData.zones } });
|
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15
20
|
}
|
|
16
21
|
}
|
|
17
22
|
return spectra;
|
|
18
23
|
}
|
|
19
24
|
exports.formatData = formatData;
|
|
25
|
+
function rescaleIntegration(spectrum) {
|
|
26
|
+
if (spectrum.info.nucleus !== '1H')
|
|
27
|
+
return spectrum.ranges;
|
|
28
|
+
let totalIntegration = spectrum.ranges.reduce((total, range) => (range.integration ? total + range.integration : total), 0);
|
|
29
|
+
for (let range of spectrum.ranges) {
|
|
30
|
+
if (range.integration) {
|
|
31
|
+
range.integration *= 100 / totalIntegration;
|
|
32
|
+
if (range.signals) {
|
|
33
|
+
const totalSignalIntegration = range.signals.reduce((total, signal) => signal.integration ? total + signal.integration : total, 0);
|
|
34
|
+
for (let signal of range.signals) {
|
|
35
|
+
if (signal.integration) {
|
|
36
|
+
signal.integration *= range.integration / totalSignalIntegration;
|
|
37
|
+
}
|
|
38
|
+
else {
|
|
39
|
+
signal.integration = range.integration;
|
|
40
|
+
}
|
|
41
|
+
}
|
|
42
|
+
}
|
|
43
|
+
}
|
|
44
|
+
}
|
|
45
|
+
return spectrum.ranges;
|
|
46
|
+
}
|
|
20
47
|
//# sourceMappingURL=formatData.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"formatData.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/formatData.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"formatData.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/formatData.ts"],"names":[],"mappings":";;;AAQA,uDAAoD;AAapD,SAAgB,UAAU,CACxB,QAA8B,EAAE;IAEhC,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAyB,CAAC;IAC3E,IAAI,OAAO,GAA2B,EAAE,CAAC;IACzC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,IAAA,iCAAe,EAAC,WAAW,CAAC,EAAE;YAChC,MAAM,MAAM,GAAG,kBAAkB,CAAC;gBAChC,EAAE;gBACF,IAAI;gBACJ,MAAM,EAAE,WAAW,CAAC,MAAM;aAC3B,CAAC,CAAC;YACH,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,CAAC;SACxD;aAAM;YACL,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;SAClE;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAnBD,gCAmBC;AAED,SAAS,kBAAkB,CAAC,QAA8B;IACxD,IAAI,QAAQ,CAAC,IAAI,CAAC,OAAO,KAAK,IAAI;QAAE,OAAO,QAAQ,CAAC,MAAM,CAAC;IAE3D,IAAI,gBAAgB,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,CAC3C,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,EACzE,CAAC,CACF,CAAC;IAEF,KAAK,IAAI,KAAK,IAAI,QAAQ,CAAC,MAAM,EAAE;QACjC,IAAI,KAAK,CAAC,WAAW,EAAE;YACrB,KAAK,CAAC,WAAW,IAAI,GAAG,GAAG,gBAAgB,CAAC;YAC5C,IAAI,KAAK,CAAC,OAAO,EAAE;gBACjB,MAAM,sBAAsB,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CACjD,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,CAChB,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,EACzD,CAAC,CACF,CAAC;gBACF,KAAK,IAAI,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE;oBAChC,IAAI,MAAM,CAAC,WAAW,EAAE;wBACtB,MAAM,CAAC,WAAW,IAAI,KAAK,CAAC,WAAW,GAAG,sBAAsB,CAAC;qBAClE;yBAAM;wBACL,MAAM,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC;qBACxC;iBACF;aACF;SACF;KACF;IAED,OAAO,QAAQ,CAAC,MAAM,CAAC;AACzB,CAAC"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import type { Correlation, Link } from 'nmr-correlation';
|
|
2
|
-
import { SpectraDataWithIds } from '
|
|
2
|
+
import { SpectraDataWithIds } from '../../nmrAssigment';
|
|
3
3
|
export interface CorrelationWithIntegration extends Pick<Correlation, 'link' | 'atomType' | 'label' | 'attachment' | 'protonsCount'> {
|
|
4
4
|
integration: number;
|
|
5
5
|
indirectLinks: Array<Link>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getTargetsAndCorrelations.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts"],"names":[],"mappings":";;;AAAA,qDAAuD;
|
|
1
|
+
{"version":3,"file":"getTargetsAndCorrelations.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts"],"names":[],"mappings":";;;AAAA,qDAAuD;AAKvD,6CAA0C;AAC1C,uFAAoF;AAsBpF,SAAgB,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,IAAA,uBAAU,EAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,IAAA,sCAAoB,EAAC,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,IAAA,iEAA+B,EACvE,WAAW,EACX,YAAY,CACb,CAAC;SACH;KACF;IAED,OAAO;QACL,OAAO;QACP,YAAY;KACb,CAAC;AACJ,CAAC;AAnCD,8DAmCC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"partialScore.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/partialScore.ts"],"names":[],"mappings":";;;;;;AAAA,qDAAsD;AAatD,8GAAsF;AAmBtF,SAAgB,YAAY,CAAC,OAAgB,EAAE,KAA0B;IACvE,MAAM,EACJ,2BAA2B,EAC3B,eAAe,EACf,eAAe,EACf,WAAW,EACX,OAAO,EACP,YAAY,GACb,GAAG,KAAK,CAAC;IAEV,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,qBAAqB,EAAE,GAAG,eAAe,CAAC;IAC1E,IAAI,WAAW,GAAG,CAAC,CAAC;IACpB,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,cAAc,GAA4B,EAAE,CAAC;IACjD,IAAI,wBAAwB,GAAgC,EAAE,CAAC;IAC/D,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,CAAC;IACtD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,IAAI,UAAU,GAAG,CAAC,CAAC;QACnB,MAAM,EAAE,mBAAmB,EAAE,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;QAC1D,MAAM,qBAAqB,GAAsB,EAAE,CAAC;QACpD,MAAM,iBAAiB,GAAG,OAAO,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;QAClD,cAAc,CAAC,QAAQ,CAAC,GAAG,qBAAqB,CAAC;QACjD,wBAAwB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;QACxC,YAAY,IAAI,iBAAiB,CAAC,MAAM,CAAC;QACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACjD,MAAM,QAAQ,GAAG,iBAAiB,CAAC,CAAC,CAAC,CAAC;YACtC,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;gBAChC,wBAAwB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBAC3C,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,EAAE;oBACpC,qBAAqB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;iBACtC;gBACD,qBAAqB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAClC,2BAA2B,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CACzC,CAAC;aACH;YACD,IAAI,QAAQ,KAAK,GAAG;gBAAE,UAAU,EAAE,CAAC;SACpC;QAED,IAAI,UAAU,GAAG,mBAAmB;YAAE,OAAO,CAAC,CAAC;QAC/C,WAAW,IAAI,UAAU,CAAC;KAC3B;IAED,MAAM,oBAAoB,GAAsB,EAAE,CAAC;IACnD,KAAK,MAAM,QAAQ,IAAI,cAAc,EAAE;QACrC,oBAAoB,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;KACxE;IAED,MAAM,0BAA0B,GAAG,MAAM,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;IACvE,IACE,0BAA0B,CAAC,MAAM,CAC/B,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAC5C,CAAC,CACF,KAAK,0BAA0B,CAAC,MAAM,EACvC;QACA,OAAO,CAAC,CAAC;KACV;IAED,MAAM,oBAAoB,GAAG,aAAa,CAAC,IAAI,CAAC,EAAE,EAAE,WAAW,CAAC,CAAC;IACjE,wBAAwB;IACxB,MAAM,gBAAgB,GAIhB,EAAE,CAAC;IAET,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE;QAC9B,IAAI,QAAQ,KAAK,GAAG,IAAI,oBAAoB,CAAC,QAAQ,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACjE,gBAAgB,CAAC,IAAI,CACnB,GAAG,IAAA,4CAAkC,EACnC,oBAAoB,CAAC,QAAQ,CAAC,EAC9B,OAAO,CAAC,QAAQ,CAAC,EACjB,YAAY,CACb,CACF,CAAC;SACH;aAAM;YACL,KAAK,IAAI,QAAQ,IAAI,oBAAoB,CAAC,QAAQ,CAAC,EAAE;gBACnD,gBAAgB,CAAC,IAAI,CAAC;oBACpB,QAAQ;oBACR,SAAS,EAAE,CAAC,QAAQ,CAAC;oBACrB,WAAW,EAAE,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW;iBAC7C,CAAC,CAAC;aACJ;SACF;KACF;
|
|
1
|
+
{"version":3,"file":"partialScore.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/partialScore.ts"],"names":[],"mappings":";;;;;;AAAA,qDAAsD;AAatD,8GAAsF;AAmBtF,SAAgB,YAAY,CAAC,OAAgB,EAAE,KAA0B;IACvE,MAAM,EACJ,2BAA2B,EAC3B,eAAe,EACf,eAAe,EACf,WAAW,EACX,OAAO,EACP,YAAY,GACb,GAAG,KAAK,CAAC;IAEV,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,qBAAqB,EAAE,GAAG,eAAe,CAAC;IAC1E,IAAI,WAAW,GAAG,CAAC,CAAC;IACpB,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,cAAc,GAA4B,EAAE,CAAC;IACjD,IAAI,wBAAwB,GAAgC,EAAE,CAAC;IAC/D,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,CAAC;IACtD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,IAAI,UAAU,GAAG,CAAC,CAAC;QACnB,MAAM,EAAE,mBAAmB,EAAE,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;QAC1D,MAAM,qBAAqB,GAAsB,EAAE,CAAC;QACpD,MAAM,iBAAiB,GAAG,OAAO,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;QAClD,cAAc,CAAC,QAAQ,CAAC,GAAG,qBAAqB,CAAC;QACjD,wBAAwB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;QACxC,YAAY,IAAI,iBAAiB,CAAC,MAAM,CAAC;QACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACjD,MAAM,QAAQ,GAAG,iBAAiB,CAAC,CAAC,CAAC,CAAC;YACtC,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;gBAChC,wBAAwB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBAC3C,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,EAAE;oBACpC,qBAAqB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;iBACtC;gBACD,qBAAqB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAClC,2BAA2B,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CACzC,CAAC;aACH;YACD,IAAI,QAAQ,KAAK,GAAG;gBAAE,UAAU,EAAE,CAAC;SACpC;QAED,IAAI,UAAU,GAAG,mBAAmB;YAAE,OAAO,CAAC,CAAC;QAC/C,WAAW,IAAI,UAAU,CAAC;KAC3B;IAED,MAAM,oBAAoB,GAAsB,EAAE,CAAC;IACnD,KAAK,MAAM,QAAQ,IAAI,cAAc,EAAE;QACrC,oBAAoB,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;KACxE;IAED,MAAM,0BAA0B,GAAG,MAAM,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;IACvE,IACE,0BAA0B,CAAC,MAAM,CAC/B,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAC5C,CAAC,CACF,KAAK,0BAA0B,CAAC,MAAM,EACvC;QACA,OAAO,CAAC,CAAC;KACV;IAED,MAAM,oBAAoB,GAAG,aAAa,CAAC,IAAI,CAAC,EAAE,EAAE,WAAW,CAAC,CAAC;IACjE,wBAAwB;IACxB,MAAM,gBAAgB,GAIhB,EAAE,CAAC;IAET,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE;QAC9B,IAAI,QAAQ,KAAK,GAAG,IAAI,oBAAoB,CAAC,QAAQ,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACjE,gBAAgB,CAAC,IAAI,CACnB,GAAG,IAAA,4CAAkC,EACnC,oBAAoB,CAAC,QAAQ,CAAC,EAC9B,OAAO,CAAC,QAAQ,CAAC,EACjB,YAAY,CACb,CACF,CAAC;SACH;aAAM;YACL,KAAK,IAAI,QAAQ,IAAI,oBAAoB,CAAC,QAAQ,CAAC,EAAE;gBACnD,gBAAgB,CAAC,IAAI,CAAC;oBACpB,QAAQ;oBACR,SAAS,EAAE,CAAC,QAAQ,CAAC;oBACrB,WAAW,EAAE,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW;iBAC7C,CAAC,CAAC;aACJ;SACF;KACF;IAED,KAAK,MAAM,KAAK,IAAI,gBAAgB,EAAE;QACpC,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAC;QACxC,IAAI,WAAW,KAAK,SAAS,IAAI,KAAK,CAAC,WAAW,CAAC;YAAE,SAAS;QAE9D,IAAI,KAAK,GAAG,CAAC,CAAC;QACd,KAAK,IAAI,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE;YACpC,IAAI,cAAc,GAAG,cAAc,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC;YACxD,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE;gBAClC,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAC9C,oBAAoB,CAAC,KAAK,CAAC,CAAC;gBAC9B,IAAI,QAAQ,KAAK,gBAAgB;oBAAE,KAAK,IAAI,UAAU,CAAC,YAAY,CAAC;aACrE;SACF;QACD,IAAI,KAAK,GAAG,WAAW,IAAI,CAAC,EAAE;YAC5B,OAAO,CAAC,CAAC;SACV;KACF;IAED,sBAAsB;IACtB,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,kBAAkB,GAAG,CAAC,CAAC;IAC3B,IAAI,qBAAqB,EAAE;QACzB,kBAAkB,GAAG,CAAC,CAAC;QACvB,KAAK,GAAG,CAAC,CAAC;QACV,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,EAAE;YAC1D,MAAM,mBAAmB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC9C,MAAM,mBAAmB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC9C,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,mBAAmB,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBAC/D,MAAM,QAAQ,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAC;gBAC5C,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;oBAChC,KAAK,EAAE,CAAC;oBACR,IAAI,KAAK,GAAG,2BAA2B,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;oBACzD,IAAI,MAAM,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;oBAC1C,IAAI,MAAM,GAAG,mBAAmB,CAAC,QAAQ,CAAC,CAAC;oBAC3C,IAAI,KAAK,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAC;oBAClC,sBAAsB;oBACtB,iDAAiD;oBACjD,IAAI;oBACJ,IAAI,OAAO,MAAM,CAAC,KAAK,KAAK,WAAW,EAAE;wBACvC,sCAAsC;wBACtC,kBAAkB,IAAI,CAAC,CAAC;qBACzB;yBAAM;wBACL,MAAM,WAAW,GAAG,IAAA,qCAAmB,EAAC,MAAM,CAAC,CAAC;wBAEhD,IAAI,WAAW,KAAK,SAAS,EAAE;4BAC7B,MAAM,IAAI,KAAK,CAAC,2BAA2B,CAAC,CAAC;yBAC9C;wBAED,IAAI,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,WAAW,CAAC,CAAC;wBAChD,IAAI,IAAI,GAAG,KAAK,EAAE;4BAChB,wCAAwC;4BACxC,kBAAkB,IAAI,CAAC,CAAC;yBACzB;6BAAM;4BACL,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,CAAC,CAAC;4BAC9B,kBAAkB,IAAI,CAAC,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC;yBAClD;qBACF;iBACF;aACF;SACF;QACD,IAAI,KAAK,GAAG,CAAC,EAAE;YACb,kBAAkB,IAAI,KAAK,CAAC;SAC7B;KACF;IAED,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,IAAI,cAAc,CAAC,oBAAoB,CAAC,GAAG,CAAC,EAAE;QAC5C,IAAI,aAAa,GAA8B,EAAE,CAAC;QAClD,IAAI,YAAY,GAAkD,EAAE,CAAC;QAErE,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,IAAI,CAChC,wBAAwB,CACV,EAAE;YAChB,YAAY,GAAG,YAAY,CAAC,MAAM,CAChC,wBAAwB,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,CACxE,CAAC;SACH;QAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5C,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAC;YAC/D,MAAM,WAAW,GACf,WAAW,CAAC,SAAS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|
|
@@ -1,2 +1,7 @@
|
|
|
1
1
|
import { DatabaseNMREntry } from './DatabaseNMREntry';
|
|
2
|
-
export declare function getDatabase(url?: string
|
|
2
|
+
export declare function getDatabase(url?: string, options?: {
|
|
3
|
+
/**
|
|
4
|
+
* @default 'tsv'
|
|
5
|
+
*/
|
|
6
|
+
format?: 'tsv' | 'json';
|
|
7
|
+
}): Promise<DatabaseNMREntry[]>;
|
|
@@ -3,13 +3,23 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.getDatabase = void 0;
|
|
4
4
|
const cross_fetch_1 = require("cross-fetch");
|
|
5
5
|
const resurrectRange_1 = require("../utilities/resurrectRange");
|
|
6
|
-
async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
|
|
6
|
+
async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
|
|
7
|
+
const { format = 'tsv' } = options;
|
|
7
8
|
if (url.includes('google.com')) {
|
|
8
9
|
url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
|
|
9
10
|
}
|
|
11
|
+
let parsed;
|
|
10
12
|
const response = await (0, cross_fetch_1.fetch)(url);
|
|
11
|
-
|
|
12
|
-
|
|
13
|
+
switch (format) {
|
|
14
|
+
case 'tsv':
|
|
15
|
+
parsed = parseData(await response.text());
|
|
16
|
+
break;
|
|
17
|
+
case 'json':
|
|
18
|
+
parsed = await response.json();
|
|
19
|
+
break;
|
|
20
|
+
default:
|
|
21
|
+
throw new Error('unknown database format');
|
|
22
|
+
}
|
|
13
23
|
const results = [];
|
|
14
24
|
for (let line of parsed.data) {
|
|
15
25
|
const result = {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":";;;AAAA,6CAAoC;AAEpC,gEAA6D;AAItD,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG;
|
|
1
|
+
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|
package/lib/index.d.ts
CHANGED
|
@@ -28,10 +28,12 @@ export * from './databases/getDatabase';
|
|
|
28
28
|
export * from './databases/carbonImpurities';
|
|
29
29
|
export * from './databases/protonImpurities';
|
|
30
30
|
export type { NMRSignal1D } from './signals/NMRSignal1D';
|
|
31
|
-
export type { NMRSignal2D } from './xyz/NMRSignal2D';
|
|
31
|
+
export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
|
|
32
32
|
export type { NMRRange } from './xy/NMRRange';
|
|
33
33
|
export type { NMRZone } from './xyz/NMRZone';
|
|
34
34
|
export type { NMRPeak1D } from './peaks/NMRPeak1D';
|
|
35
35
|
export type { Prediction1D } from './prediction/prediction1D';
|
|
36
36
|
export type { Jcoupling } from './signals/jcoupling';
|
|
37
|
+
export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
|
|
37
38
|
export type { DataBaseLevelStructure, DataBaseStructure, } from './prediction/dataStructure';
|
|
39
|
+
export type { NMRSignal1DWithId, NMRSignal2DWithId, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds, } from './assignment/nmrAssigment';
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
+
import { FromTo, PointXY } from 'cheminfo-types';
|
|
1
2
|
import type { Molecule } from 'openchemlib';
|
|
2
|
-
import { OptionsSignalsToXY } from '../signals/signalsToXY';
|
|
3
3
|
import { PredictAllOptions } from './predictAll';
|
|
4
4
|
/**
|
|
5
5
|
* This function will generate an object compatible with NMR-ium
|
|
@@ -7,12 +7,30 @@ import { PredictAllOptions } from './predictAll';
|
|
|
7
7
|
* @param molecule
|
|
8
8
|
* @param options
|
|
9
9
|
*/
|
|
10
|
-
|
|
10
|
+
interface OneDOptions {
|
|
11
|
+
proton: FromTo;
|
|
12
|
+
carbon: FromTo;
|
|
13
|
+
nbPoints: number;
|
|
14
|
+
lineWidth: number;
|
|
15
|
+
}
|
|
16
|
+
interface TwoDOptions {
|
|
17
|
+
from: PointXY;
|
|
18
|
+
to: PointXY;
|
|
19
|
+
nbPoints: PointXY;
|
|
20
|
+
}
|
|
21
|
+
interface SimulationOptions {
|
|
22
|
+
frequency: number;
|
|
23
|
+
oneD?: Partial<OneDOptions>;
|
|
24
|
+
twoD?: Partial<TwoDOptions>;
|
|
25
|
+
}
|
|
26
|
+
interface PredictAllSpectraOptions {
|
|
11
27
|
prediction?: PredictAllOptions;
|
|
12
|
-
simulation?:
|
|
13
|
-
}
|
|
28
|
+
simulation?: SimulationOptions;
|
|
29
|
+
}
|
|
30
|
+
export declare function predictAllSpectra(molecule: Molecule, options?: PredictAllSpectraOptions): Promise<{
|
|
14
31
|
spectra: any[];
|
|
15
32
|
molecules: {
|
|
16
33
|
molfile: any;
|
|
17
34
|
}[];
|
|
18
35
|
}>;
|
|
36
|
+
export {};
|
|
@@ -1,40 +1,126 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.predictAllSpectra = void 0;
|
|
4
|
+
const signals2DToZ_1 = require("../signals/signals2DToZ");
|
|
4
5
|
const signalsToXY_1 = require("../signals/signalsToXY");
|
|
6
|
+
const getFrequency_1 = require("../utilities/getFrequency");
|
|
5
7
|
const predictAll_1 = require("./predictAll");
|
|
6
|
-
/**
|
|
7
|
-
* This function will generate an object compatible with NMR-ium
|
|
8
|
-
*
|
|
9
|
-
* @param molecule
|
|
10
|
-
* @param options
|
|
11
|
-
*/
|
|
12
8
|
async function predictAllSpectra(molecule, options = {}) {
|
|
13
|
-
const
|
|
9
|
+
const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
|
|
10
|
+
const predictions = await (0, predictAll_1.predictAll)(molecule, predictionOptions);
|
|
14
11
|
const spectra = [];
|
|
15
12
|
const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
|
|
16
|
-
|
|
13
|
+
const oneDOptions = {
|
|
14
|
+
...{
|
|
15
|
+
proton: { from: 0, to: 14 },
|
|
16
|
+
carbon: { from: 0, to: 200 },
|
|
17
|
+
nbPoints: 4098,
|
|
18
|
+
lineWidth: 0.03,
|
|
19
|
+
},
|
|
20
|
+
...(simulationOptions.oneD || {}),
|
|
21
|
+
};
|
|
22
|
+
const twoDOptions = {
|
|
23
|
+
...{
|
|
24
|
+
from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
|
|
25
|
+
to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
|
|
26
|
+
nbPoints: { x: 1024, y: 1024 },
|
|
27
|
+
},
|
|
28
|
+
...(simulationOptions.twoD || {}),
|
|
29
|
+
};
|
|
30
|
+
for (const experiment in predictions) {
|
|
31
|
+
switch (experiment) {
|
|
32
|
+
case 'carbon':
|
|
33
|
+
case 'proton': {
|
|
34
|
+
spectra.push(get1DSpectrum(predictions[experiment], {
|
|
35
|
+
nbPoints: oneDOptions.nbPoints,
|
|
36
|
+
lineWidth: oneDOptions.lineWidth,
|
|
37
|
+
...oneDOptions[experiment],
|
|
38
|
+
experiment,
|
|
39
|
+
frequency: simulationOptions.frequency,
|
|
40
|
+
}));
|
|
41
|
+
break;
|
|
42
|
+
}
|
|
43
|
+
case 'cosy':
|
|
44
|
+
case 'hsqc':
|
|
45
|
+
case 'hmbc': {
|
|
46
|
+
spectra.push(get2DSpectrum(predictions[experiment], {
|
|
47
|
+
...twoDOptions,
|
|
48
|
+
experiment,
|
|
49
|
+
frequency: simulationOptions.frequency,
|
|
50
|
+
}));
|
|
51
|
+
break;
|
|
52
|
+
}
|
|
53
|
+
default:
|
|
54
|
+
break;
|
|
55
|
+
}
|
|
56
|
+
}
|
|
17
57
|
return result;
|
|
18
58
|
}
|
|
19
59
|
exports.predictAllSpectra = predictAllSpectra;
|
|
20
|
-
function
|
|
21
|
-
const {
|
|
60
|
+
function get2DSpectrum(prediction, options) {
|
|
61
|
+
const { signals, zones, nuclei } = prediction;
|
|
62
|
+
const { frequency: baseFrequency, experiment } = options;
|
|
63
|
+
const width = get2DWidth(nuclei);
|
|
64
|
+
const frequency = calculateFrequency(nuclei, baseFrequency);
|
|
65
|
+
const spectrumData = (0, signals2DToZ_1.signals2DToZ)(signals, {
|
|
66
|
+
...options,
|
|
67
|
+
width,
|
|
68
|
+
factor: 3,
|
|
69
|
+
});
|
|
70
|
+
const spectrum = {
|
|
71
|
+
data: { ...spectrumData, noise: 0.01 },
|
|
72
|
+
info: {
|
|
73
|
+
nucleus: nuclei,
|
|
74
|
+
originFrequency: frequency,
|
|
75
|
+
baseFrequency: frequency,
|
|
76
|
+
pulseSequence: experiment,
|
|
77
|
+
experiment: '2d',
|
|
78
|
+
},
|
|
79
|
+
zones: { values: zones },
|
|
80
|
+
};
|
|
81
|
+
return spectrum;
|
|
82
|
+
}
|
|
83
|
+
function get2DWidth(nucleus) {
|
|
84
|
+
return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
|
|
85
|
+
}
|
|
86
|
+
function get1DSpectrum(prediction, options) {
|
|
87
|
+
const { frequency = 400, experiment } = options;
|
|
88
|
+
const { signals, nucleus } = prediction;
|
|
89
|
+
const realFrequency = calculateFrequency(nucleus, frequency);
|
|
90
|
+
const { x, y } = (0, signalsToXY_1.signalsToXY)(signals, {
|
|
91
|
+
...options,
|
|
92
|
+
frequency: realFrequency,
|
|
93
|
+
});
|
|
22
94
|
const spectrum = {
|
|
23
|
-
id: '',
|
|
24
95
|
// todo Array.from is temporary for the developement
|
|
25
96
|
data: { x: Array.from(x), re: Array.from(y), im: null },
|
|
26
97
|
info: {
|
|
27
98
|
nucleus: prediction.nucleus,
|
|
28
99
|
dimension: 1,
|
|
29
|
-
originFrequency:
|
|
30
|
-
baseFrequency:
|
|
100
|
+
originFrequency: realFrequency,
|
|
101
|
+
baseFrequency: realFrequency,
|
|
31
102
|
pulseSequence: 'prediction',
|
|
32
|
-
experiment
|
|
103
|
+
experiment,
|
|
33
104
|
isFt: true,
|
|
34
105
|
},
|
|
35
|
-
|
|
36
|
-
//ranges: { values: prediction.ranges },
|
|
106
|
+
ranges: { values: prediction.ranges },
|
|
37
107
|
};
|
|
38
108
|
return spectrum;
|
|
39
109
|
}
|
|
110
|
+
function calculateFrequency(nucleus, frequency) {
|
|
111
|
+
if (typeof nucleus === 'string') {
|
|
112
|
+
return (0, getFrequency_1.getFrequency)(nucleus, { nucleus: '1H', frequency });
|
|
113
|
+
}
|
|
114
|
+
else {
|
|
115
|
+
if (nucleus[0] === nucleus[1]) {
|
|
116
|
+
return `${frequency},${frequency}`;
|
|
117
|
+
}
|
|
118
|
+
else {
|
|
119
|
+
return `${frequency},${(0, getFrequency_1.getFrequency)(nucleus[1], {
|
|
120
|
+
nucleus: nucleus[0],
|
|
121
|
+
frequency,
|
|
122
|
+
})}`;
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
}
|
|
40
126
|
//# sourceMappingURL=predictAllSpectra.js.map
|