nmr-processing 7.2.0 → 7.4.1
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/constants/gyromagneticRatio.d.ts +5 -19
- package/lib/constants/gyromagneticRatio.js +0 -1
- package/lib/constants/gyromagneticRatio.js.map +1 -1
- package/lib/index.d.ts +1 -0
- package/lib/index.js +1 -0
- package/lib/index.js.map +1 -1
- package/lib/prediction/utils/predict2D.js +13 -12
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib/signals/signals2DToZ.d.ts +1 -0
- package/lib/signals/signals2DToZ.js +19 -4
- package/lib/signals/signals2DToZ.js.map +1 -1
- package/lib/utilities/getFrequency.d.ts +21 -0
- package/lib/utilities/getFrequency.js +30 -0
- package/lib/utilities/getFrequency.js.map +1 -0
- package/lib-esm/constants/gyromagneticRatio.js +0 -1
- package/lib-esm/constants/gyromagneticRatio.js.map +1 -1
- package/lib-esm/index.js +1 -0
- package/lib-esm/index.js.map +1 -1
- package/lib-esm/prediction/utils/predict2D.js +13 -12
- package/lib-esm/prediction/utils/predict2D.js.map +1 -1
- package/lib-esm/signals/signals2DToZ.js +19 -4
- package/lib-esm/signals/signals2DToZ.js.map +1 -1
- package/lib-esm/utilities/getFrequency.js +26 -0
- package/lib-esm/utilities/getFrequency.js.map +1 -0
- package/package.json +9 -9
- package/src/constants/gyromagneticRatio.ts +25 -1
- package/src/index.ts +1 -0
- package/src/prediction/utils/predict2D.ts +16 -14
- package/src/signals/signals2DToZ.ts +29 -5
- package/src/utilities/getFrequency.ts +47 -0
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@@ -1,20 +1,6 @@
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export declare
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-
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'3H': number;
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'3He': number;
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'7Li': number;
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'13C': number;
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'14N': number;
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'15N': number;
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'17O': number;
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'19F': number;
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'23Na': number;
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'27Al': number;
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'29Si': number;
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'31P': number;
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'57Fe': number;
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'63Cu': number;
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'67Zn': number;
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'129Xe': number;
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export declare type Nuclei = '1H' | '2H' | '3H' | '3He' | '7Li' | '13C' | '14N' | '15N' | '17O' | '19F' | '23Na' | '27Al' | '29Si' | '31P' | '57Fe' | '63Cu' | '67Zn' | '129Xe';
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declare type GyromagneticRatio = {
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[key in Nuclei]: number;
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};
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export declare const gyromagneticRatio: GyromagneticRatio;
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export {};
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@@ -3,7 +3,6 @@
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// https://en.wikipedia.org/wiki/Gyromagnetic_ratio
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.gyromagneticRatio = void 0;
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// TODO: #13 can we have a better source and more digits ? @jwist
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exports.gyromagneticRatio = {
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'1H': 267.52218744e6,
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'2H': 41.065e6,
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@@ -1 +1 @@
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{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":";AAAA,WAAW;AACX,mDAAmD;;;
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{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":";AAAA,WAAW;AACX,mDAAmD;;;AA4BtC,QAAA,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}
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package/lib/index.d.ts
CHANGED
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@@ -19,6 +19,7 @@ export * from './signals/signalsToXY';
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export * from './signals/signals2DToZ';
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export * from './utilities/resurrect';
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export * from './utilities/rangeFromSignal';
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export * from './utilities/getFrequency';
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export * from './xy/xyAutoPeaksPicking';
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export * from './xy/xyAutoRangesPicking';
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export * from './xyz/xyzAutoZonesPicking';
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package/lib/index.js
CHANGED
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@@ -35,6 +35,7 @@ __exportStar(require("./signals/signalsToXY"), exports);
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__exportStar(require("./signals/signals2DToZ"), exports);
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__exportStar(require("./utilities/resurrect"), exports);
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__exportStar(require("./utilities/rangeFromSignal"), exports);
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__exportStar(require("./utilities/getFrequency"), exports);
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__exportStar(require("./xy/xyAutoPeaksPicking"), exports);
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__exportStar(require("./xy/xyAutoRangesPicking"), exports);
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__exportStar(require("./xyz/xyzAutoZonesPicking"), exports);
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package/lib/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,gEAA8C;AAC9C,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,gEAA8C;AAC9C,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C"}
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@@ -16,7 +16,7 @@ async function predict2D(molecule, options = {}) {
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let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
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molecule.addImplicitHydrogens();
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let diaIDs = (0, openchemlib_utils_1.getGroupedDiastereotopicAtomIDs)(molecule);
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const
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const pathsInfo = (0, openchemlib_utils_1.getPathsInfo)(molecule, {
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fromLabel: from,
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toLabel: to,
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minLength,
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for (let diaID of diaIDs) {
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diaIDswithAtomInfo.push({
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...diaID,
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pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
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});
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}
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const xPrediction = await (0, getPredictions_1.getPredictions)(from, molecule, predictOptions, predictor, predictions);
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}
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let group = {};
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for (const diaID of diaIDswithAtomInfo) {
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const
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if (
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const pathInfo = diaID.pathInfo;
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if (pathInfo.paths.length < 1)
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continue;
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if (!signalsByDiaID.x[
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if (!signalsByDiaID.x[pathInfo.oclID])
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continue;
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const currentPaths =
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const currentPaths = pathInfo.paths;
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for (const path of currentPaths) {
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if (!signalsByDiaID.y[
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if (!signalsByDiaID.y[pathsInfo[path.to].oclID])
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continue;
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let fromToDiaID = {
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x:
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y:
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x: pathInfo,
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y: pathsInfo[path.to],
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};
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const key = `${fromToDiaID.x.oclID}-${fromToDiaID.y.oclID}`;
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if (key === `${
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if (key === `${pathInfo.oclID}-${pathInfo.oclID}` || group[key]) {
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continue;
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}
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let peak = { z: 100 };
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group[key] = signal;
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}
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}
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if (includeDiagonal)
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addSelftCorrelation(group, { paths, signalsByDiaID });
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if (includeDiagonal) {
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addSelftCorrelation(group, { paths: pathsInfo, signalsByDiaID });
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}
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// clusterize signals by distance
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const joinedSignals = Object.values(group);
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const zones = createZones(joinedSignals, { joinDistance, from, to });
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{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":";;;AAAA,yCAA2C;AAC3C,yCAAmC;AAEnC,yDAG2B;AAc3B,2CAAwC;AACxC,qDAAkD;AAsFlD,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;AAMM,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,IAAI,EACF,IAAI,EACJ,EAAE,EACF,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,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,MAAM,GAAG,IAAA,mDAA+B,EAAC,QAAQ,CAAC,CAAC;IAEvD,MAAM,
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{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":";;;AAAA,yCAA2C;AAC3C,yCAAmC;AAEnC,yDAG2B;AAc3B,2CAAwC;AACxC,qDAAkD;AAsFlD,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;AAMM,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,IAAI,EACF,IAAI,EACJ,EAAE,EACF,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,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,MAAM,GAAG,IAAA,mDAA+B,EAAC,QAAQ,CAAC,CAAC;IAEvD,MAAM,SAAS,GAAG,IAAA,gCAAY,EAAC,QAAQ,EAAE;QACvC,SAAS,EAAE,IAAI;QACf,OAAO,EAAE,EAAE;QACX,SAAS;QACT,SAAS;KACV,CAAC,CAAC;IAEH,IAAI,kBAAkB,GAA6C,EAAE,CAAC;IACtE,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,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,IAAA,+BAAc,EACtC,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,IAAA,+BAAc,EAClB,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,CAAC,EAAE,GAAG,EAAE,CAAC;YAC3B,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;YACnC,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,IAAA,qBAAS,EAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AAnID,8BAmIC;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,OAAO,CAAC;AACjB,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,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;QACzB,KAAK,IAAI,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE;YAC3B,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;YAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;YACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;YAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,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@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
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3
3
|
exports.signals2DToZ = void 0;
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4
4
|
const spectrum_generator_1 = require("spectrum-generator");
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5
5
|
function signals2DToZ(signals, options = {}) {
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6
|
-
let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
|
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6
|
+
let { from = -1, to = 12, nbPoints = 512, width = 0.02, factor = 3, } = options;
|
|
7
7
|
const peaks = signals.reduce((acc, { x, y }) => {
|
|
8
8
|
acc.x.push(x.delta);
|
|
9
9
|
acc.y.push(y.delta);
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@@ -11,7 +11,7 @@ function signals2DToZ(signals, options = {}) {
|
|
|
11
11
|
return acc;
|
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12
12
|
}, { x: [], y: [], z: [] });
|
|
13
13
|
width = ensureXYNumber(width);
|
|
14
|
-
return (0, spectrum_generator_1.generateSpectrum2D)(peaks, {
|
|
14
|
+
return (0, spectrum_generator_1.generateSpectrum2D)(mergeClosePeaks(peaks), {
|
|
15
15
|
generator: {
|
|
16
16
|
from: ensureXYNumber(from),
|
|
17
17
|
to: ensureXYNumber(to),
|
|
@@ -19,12 +19,27 @@ function signals2DToZ(signals, options = {}) {
|
|
|
19
19
|
},
|
|
20
20
|
peaks: {
|
|
21
21
|
width,
|
|
22
|
+
factor,
|
|
22
23
|
},
|
|
23
24
|
});
|
|
24
25
|
}
|
|
25
26
|
exports.signals2DToZ = signals2DToZ;
|
|
26
27
|
function ensureXYNumber(input) {
|
|
27
|
-
|
|
28
|
-
|
|
28
|
+
return typeof input !== 'object' ? { x: input, y: input } : { ...input };
|
|
29
|
+
}
|
|
30
|
+
function mergeClosePeaks(peaksIn) {
|
|
31
|
+
let peaks = JSON.parse(JSON.stringify(peaksIn));
|
|
32
|
+
for (let i = 0; i < peaks.x.length; i++) {
|
|
33
|
+
for (let j = i + 1; j < peaks.x.length; j++) {
|
|
34
|
+
if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
|
|
35
|
+
peaks.z[i] += peaks.z[j];
|
|
36
|
+
peaks.x.splice(j, 1);
|
|
37
|
+
peaks.y.splice(j, 1);
|
|
38
|
+
peaks.z.splice(j, 1);
|
|
39
|
+
j--;
|
|
40
|
+
}
|
|
41
|
+
}
|
|
42
|
+
}
|
|
43
|
+
return peaks;
|
|
29
44
|
}
|
|
30
45
|
//# sourceMappingURL=signals2DToZ.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signals2DToZ.js","sourceRoot":"","sources":["../../src/signals/signals2DToZ.ts"],"names":[],"mappings":";;;AAAA,2DAAwD;
|
|
1
|
+
{"version":3,"file":"signals2DToZ.js","sourceRoot":"","sources":["../../src/signals/signals2DToZ.ts"],"names":[],"mappings":";;;AAAA,2DAAwD;AAqCxD,SAAgB,YAAY,CAC1B,OAAsB,EACtB,UAA+B,EAAE;IAEjC,IAAI,EACF,IAAI,GAAG,CAAC,CAAC,EACT,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,GAAG,EACd,KAAK,GAAG,IAAI,EACZ,MAAM,GAAG,CAAC,GACX,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,OAAO,CAAC,MAAM,CAC1B,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;QAChB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAChB,OAAO,GAAG,CAAC;IACb,CAAC,EACD,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CACxB,CAAC;IAEF,KAAK,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC;IAE9B,OAAO,IAAA,uCAAkB,EAAC,eAAe,CAAC,KAAK,CAAC,EAAE;QAChD,SAAS,EAAE;YACT,IAAI,EAAE,cAAc,CAAC,IAAI,CAAC;YAC1B,EAAE,EAAE,cAAc,CAAC,EAAE,CAAC;YACtB,QAAQ,EAAE,cAAc,CAAC,QAAQ,CAAC;SACnC;QACD,KAAK,EAAE;YACL,KAAK;YACL,MAAM;SACP;KACF,CAAC,CAAC;AACL,CAAC;AAnCD,oCAmCC;AAED,SAAS,cAAc,CAAC,KAAwB;IAC9C,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC;AAC3E,CAAC;AAED,SAAS,eAAe,CAAC,OAAqB;IAC5C,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC3C,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC1D,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBACzB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,CAAC,EAAE,CAAC;aACL;SACF;KACF;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
import { Nuclei } from '../constants/gyromagneticRatio';
|
|
2
|
+
export interface ObjervedNucleusData {
|
|
3
|
+
/**
|
|
4
|
+
* nucleus to use as reference in the calculation of frequency
|
|
5
|
+
*/
|
|
6
|
+
nucleus: Nucleus;
|
|
7
|
+
/**
|
|
8
|
+
* frequency of the reference nucleus
|
|
9
|
+
*/
|
|
10
|
+
frequency: number;
|
|
11
|
+
}
|
|
12
|
+
declare type Nucleus = Nuclei | (string & Record<never, never>);
|
|
13
|
+
/**
|
|
14
|
+
* calculate the frequency of a nucleus with respect to a reference nucleus
|
|
15
|
+
*/
|
|
16
|
+
export declare function getFrequency(
|
|
17
|
+
/**
|
|
18
|
+
* nucleus to calculate the frequency
|
|
19
|
+
*/
|
|
20
|
+
nucleus: Nucleus, observedNucleusData: ObjervedNucleusData): number;
|
|
21
|
+
export {};
|
|
@@ -0,0 +1,30 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.getFrequency = void 0;
|
|
4
|
+
const gyromagneticRatio_1 = require("../constants/gyromagneticRatio");
|
|
5
|
+
/**
|
|
6
|
+
* calculate the frequency of a nucleus with respect to a reference nucleus
|
|
7
|
+
*/
|
|
8
|
+
function getFrequency(
|
|
9
|
+
/**
|
|
10
|
+
* nucleus to calculate the frequency
|
|
11
|
+
*/
|
|
12
|
+
nucleus, observedNucleusData) {
|
|
13
|
+
const { nucleus: obsNucleus, frequency } = observedNucleusData;
|
|
14
|
+
checkExistence(nucleus, obsNucleus);
|
|
15
|
+
return ((frequency * gyromagneticRatio_1.gyromagneticRatio[nucleus]) /
|
|
16
|
+
gyromagneticRatio_1.gyromagneticRatio[obsNucleus]);
|
|
17
|
+
}
|
|
18
|
+
exports.getFrequency = getFrequency;
|
|
19
|
+
function checkExistence(...nucleus) {
|
|
20
|
+
let nuclei = [];
|
|
21
|
+
for (const n of nucleus) {
|
|
22
|
+
if (!(n in gyromagneticRatio_1.gyromagneticRatio)) {
|
|
23
|
+
nuclei.push(n);
|
|
24
|
+
}
|
|
25
|
+
}
|
|
26
|
+
if (nuclei.length !== 0) {
|
|
27
|
+
throw new Error(`${nuclei.join(' , ')} is not supported`);
|
|
28
|
+
}
|
|
29
|
+
}
|
|
30
|
+
//# sourceMappingURL=getFrequency.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":";;;AAAA,sEAA2E;AAgB3E;;GAEG;AACH,SAAgB,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,qCAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,qCAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAfD,oCAeC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,qCAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":"AAAA,WAAW;AACX,mDAAmD;
|
|
1
|
+
{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":"AAAA,WAAW;AACX,mDAAmD;AA4BnD,MAAM,CAAC,MAAM,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}
|
package/lib-esm/index.js
CHANGED
|
@@ -19,6 +19,7 @@ export * from './signals/signalsToXY';
|
|
|
19
19
|
export * from './signals/signals2DToZ';
|
|
20
20
|
export * from './utilities/resurrect';
|
|
21
21
|
export * from './utilities/rangeFromSignal';
|
|
22
|
+
export * from './utilities/getFrequency';
|
|
22
23
|
export * from './xy/xyAutoPeaksPicking';
|
|
23
24
|
export * from './xy/xyAutoRangesPicking';
|
|
24
25
|
export * from './xyz/xyzAutoZonesPicking';
|
package/lib-esm/index.js.map
CHANGED
|
@@ -1 +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;
|
|
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"}
|
|
@@ -13,7 +13,7 @@ export async function predict2D(molecule, options = {}) {
|
|
|
13
13
|
let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
14
14
|
molecule.addImplicitHydrogens();
|
|
15
15
|
let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
|
|
16
|
-
const
|
|
16
|
+
const pathsInfo = getPathsInfo(molecule, {
|
|
17
17
|
fromLabel: from,
|
|
18
18
|
toLabel: to,
|
|
19
19
|
minLength,
|
|
@@ -23,7 +23,7 @@ export async function predict2D(molecule, options = {}) {
|
|
|
23
23
|
for (let diaID of diaIDs) {
|
|
24
24
|
diaIDswithAtomInfo.push({
|
|
25
25
|
...diaID,
|
|
26
|
-
|
|
26
|
+
pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
|
|
27
27
|
});
|
|
28
28
|
}
|
|
29
29
|
const xPrediction = await getPredictions(from, molecule, predictOptions, predictor, predictions);
|
|
@@ -50,21 +50,21 @@ export async function predict2D(molecule, options = {}) {
|
|
|
50
50
|
}
|
|
51
51
|
let group = {};
|
|
52
52
|
for (const diaID of diaIDswithAtomInfo) {
|
|
53
|
-
const
|
|
54
|
-
if (
|
|
53
|
+
const pathInfo = diaID.pathInfo;
|
|
54
|
+
if (pathInfo.paths.length < 1)
|
|
55
55
|
continue;
|
|
56
|
-
if (!signalsByDiaID.x[
|
|
56
|
+
if (!signalsByDiaID.x[pathInfo.oclID])
|
|
57
57
|
continue;
|
|
58
|
-
const currentPaths =
|
|
58
|
+
const currentPaths = pathInfo.paths;
|
|
59
59
|
for (const path of currentPaths) {
|
|
60
|
-
if (!signalsByDiaID.y[
|
|
60
|
+
if (!signalsByDiaID.y[pathsInfo[path.to].oclID])
|
|
61
61
|
continue;
|
|
62
62
|
let fromToDiaID = {
|
|
63
|
-
x:
|
|
64
|
-
y:
|
|
63
|
+
x: pathInfo,
|
|
64
|
+
y: pathsInfo[path.to],
|
|
65
65
|
};
|
|
66
66
|
const key = `${fromToDiaID.x.oclID}-${fromToDiaID.y.oclID}`;
|
|
67
|
-
if (key === `${
|
|
67
|
+
if (key === `${pathInfo.oclID}-${pathInfo.oclID}` || group[key]) {
|
|
68
68
|
continue;
|
|
69
69
|
}
|
|
70
70
|
let peak = { z: 100 };
|
|
@@ -80,8 +80,9 @@ export async function predict2D(molecule, options = {}) {
|
|
|
80
80
|
group[key] = signal;
|
|
81
81
|
}
|
|
82
82
|
}
|
|
83
|
-
if (includeDiagonal)
|
|
84
|
-
addSelftCorrelation(group, { paths, signalsByDiaID });
|
|
83
|
+
if (includeDiagonal) {
|
|
84
|
+
addSelftCorrelation(group, { paths: pathsInfo, signalsByDiaID });
|
|
85
|
+
}
|
|
85
86
|
// clusterize signals by distance
|
|
86
87
|
const joinedSignals = Object.values(group);
|
|
87
88
|
const zones = createZones(joinedSignals, { joinDistance, from, to });
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAW,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAEnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,GACb,MAAM,mBAAmB,CAAC;AAc3B,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AAsFlD,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,IAAI,EACF,IAAI,EACJ,EAAE,EACF,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,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,MAAM,GAAG,+BAA+B,CAAC,QAAQ,CAAC,CAAC;IAEvD,MAAM,
|
|
1
|
+
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@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { generateSpectrum2D } from 'spectrum-generator';
|
|
2
2
|
export function signals2DToZ(signals, options = {}) {
|
|
3
|
-
let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
|
|
3
|
+
let { from = -1, to = 12, nbPoints = 512, width = 0.02, factor = 3, } = options;
|
|
4
4
|
const peaks = signals.reduce((acc, { x, y }) => {
|
|
5
5
|
acc.x.push(x.delta);
|
|
6
6
|
acc.y.push(y.delta);
|
|
@@ -8,7 +8,7 @@ export function signals2DToZ(signals, options = {}) {
|
|
|
8
8
|
return acc;
|
|
9
9
|
}, { x: [], y: [], z: [] });
|
|
10
10
|
width = ensureXYNumber(width);
|
|
11
|
-
return generateSpectrum2D(peaks, {
|
|
11
|
+
return generateSpectrum2D(mergeClosePeaks(peaks), {
|
|
12
12
|
generator: {
|
|
13
13
|
from: ensureXYNumber(from),
|
|
14
14
|
to: ensureXYNumber(to),
|
|
@@ -16,11 +16,26 @@ export function signals2DToZ(signals, options = {}) {
|
|
|
16
16
|
},
|
|
17
17
|
peaks: {
|
|
18
18
|
width,
|
|
19
|
+
factor,
|
|
19
20
|
},
|
|
20
21
|
});
|
|
21
22
|
}
|
|
22
23
|
function ensureXYNumber(input) {
|
|
23
|
-
|
|
24
|
-
|
|
24
|
+
return typeof input !== 'object' ? { x: input, y: input } : { ...input };
|
|
25
|
+
}
|
|
26
|
+
function mergeClosePeaks(peaksIn) {
|
|
27
|
+
let peaks = JSON.parse(JSON.stringify(peaksIn));
|
|
28
|
+
for (let i = 0; i < peaks.x.length; i++) {
|
|
29
|
+
for (let j = i + 1; j < peaks.x.length; j++) {
|
|
30
|
+
if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
|
|
31
|
+
peaks.z[i] += peaks.z[j];
|
|
32
|
+
peaks.x.splice(j, 1);
|
|
33
|
+
peaks.y.splice(j, 1);
|
|
34
|
+
peaks.z.splice(j, 1);
|
|
35
|
+
j--;
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
return peaks;
|
|
25
40
|
}
|
|
26
41
|
//# sourceMappingURL=signals2DToZ.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signals2DToZ.js","sourceRoot":"","sources":["../../src/signals/signals2DToZ.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;
|
|
1
|
+
{"version":3,"file":"signals2DToZ.js","sourceRoot":"","sources":["../../src/signals/signals2DToZ.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAqCxD,MAAM,UAAU,YAAY,CAC1B,OAAsB,EACtB,UAA+B,EAAE;IAEjC,IAAI,EACF,IAAI,GAAG,CAAC,CAAC,EACT,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,GAAG,EACd,KAAK,GAAG,IAAI,EACZ,MAAM,GAAG,CAAC,GACX,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,OAAO,CAAC,MAAM,CAC1B,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE;QAChB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;QACpB,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAChB,OAAO,GAAG,CAAC;IACb,CAAC,EACD,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CACxB,CAAC;IAEF,KAAK,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC;IAE9B,OAAO,kBAAkB,CAAC,eAAe,CAAC,KAAK,CAAC,EAAE;QAChD,SAAS,EAAE;YACT,IAAI,EAAE,cAAc,CAAC,IAAI,CAAC;YAC1B,EAAE,EAAE,cAAc,CAAC,EAAE,CAAC;YACtB,QAAQ,EAAE,cAAc,CAAC,QAAQ,CAAC;SACnC;QACD,KAAK,EAAE;YACL,KAAK;YACL,MAAM;SACP;KACF,CAAC,CAAC;AACL,CAAC;AAED,SAAS,cAAc,CAAC,KAAwB;IAC9C,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC;AAC3E,CAAC;AAED,SAAS,eAAe,CAAC,OAAqB;IAC5C,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC3C,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC1D,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBACzB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBACrB,CAAC,EAAE,CAAC;aACL;SACF;KACF;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
import { gyromagneticRatio } from '../constants/gyromagneticRatio';
|
|
2
|
+
/**
|
|
3
|
+
* calculate the frequency of a nucleus with respect to a reference nucleus
|
|
4
|
+
*/
|
|
5
|
+
export function getFrequency(
|
|
6
|
+
/**
|
|
7
|
+
* nucleus to calculate the frequency
|
|
8
|
+
*/
|
|
9
|
+
nucleus, observedNucleusData) {
|
|
10
|
+
const { nucleus: obsNucleus, frequency } = observedNucleusData;
|
|
11
|
+
checkExistence(nucleus, obsNucleus);
|
|
12
|
+
return ((frequency * gyromagneticRatio[nucleus]) /
|
|
13
|
+
gyromagneticRatio[obsNucleus]);
|
|
14
|
+
}
|
|
15
|
+
function checkExistence(...nucleus) {
|
|
16
|
+
let nuclei = [];
|
|
17
|
+
for (const n of nucleus) {
|
|
18
|
+
if (!(n in gyromagneticRatio)) {
|
|
19
|
+
nuclei.push(n);
|
|
20
|
+
}
|
|
21
|
+
}
|
|
22
|
+
if (nuclei.length !== 0) {
|
|
23
|
+
throw new Error(`${nuclei.join(' , ')} is not supported`);
|
|
24
|
+
}
|
|
25
|
+
}
|
|
26
|
+
//# sourceMappingURL=getFrequency.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAU,MAAM,gCAAgC,CAAC;AAgB3E;;GAEG;AACH,MAAM,UAAU,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,iBAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,iBAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,iBAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "7.
|
|
3
|
+
"version": "7.4.1",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -41,18 +41,18 @@
|
|
|
41
41
|
"@types/jest": "^27.4.1",
|
|
42
42
|
"cheminfo-build": "^1.1.11",
|
|
43
43
|
"cheminfo-types": "^1.1.0",
|
|
44
|
-
"eslint": "^8.
|
|
45
|
-
"eslint-config-cheminfo-typescript": "^10.
|
|
44
|
+
"eslint": "^8.11.0",
|
|
45
|
+
"eslint-config-cheminfo-typescript": "^10.4.0",
|
|
46
46
|
"jest": "^27.5.1",
|
|
47
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
48
48
|
"md5": "^2.3.0",
|
|
49
49
|
"ml-array-median": "^1.1.6",
|
|
50
50
|
"nmr-xy-testdata": "^0.5.1",
|
|
51
51
|
"openchemlib": "^7.4.3",
|
|
52
|
-
"prettier": "^2.
|
|
52
|
+
"prettier": "^2.6.1",
|
|
53
53
|
"rimraf": "^3.0.2",
|
|
54
|
-
"ts-jest": "^27.1.
|
|
55
|
-
"typescript": "^4.6.
|
|
54
|
+
"ts-jest": "^27.1.4",
|
|
55
|
+
"typescript": "^4.6.3"
|
|
56
56
|
},
|
|
57
57
|
"dependencies": {
|
|
58
58
|
"binary-search": "^1.3.6",
|
|
@@ -63,7 +63,7 @@
|
|
|
63
63
|
"ml-array-rescale": "^1.3.7",
|
|
64
64
|
"ml-array-sequential-fill": "^1.1.8",
|
|
65
65
|
"ml-array-sum": "^1.1.6",
|
|
66
|
-
"ml-gsd": "^10.
|
|
66
|
+
"ml-gsd": "^10.2.0",
|
|
67
67
|
"ml-hclust": "^3.1.0",
|
|
68
68
|
"ml-levenberg-marquardt": "^4.1.0",
|
|
69
69
|
"ml-matrix": "^6.9.0",
|
|
@@ -72,10 +72,10 @@
|
|
|
72
72
|
"ml-peak-shape-generator": "^4.1.1",
|
|
73
73
|
"ml-simple-clustering": "^0.1.0",
|
|
74
74
|
"ml-sparse-matrix": "^2.1.0",
|
|
75
|
-
"ml-spectra-processing": "^11.
|
|
75
|
+
"ml-spectra-processing": "^11.1.0",
|
|
76
76
|
"ml-tree-set": "^0.1.1",
|
|
77
77
|
"nmr-correlation": "^2.2.5",
|
|
78
|
-
"openchemlib-utils": "^1.
|
|
78
|
+
"openchemlib-utils": "^1.10.0",
|
|
79
79
|
"spectrum-generator": "^8.0.0"
|
|
80
80
|
}
|
|
81
81
|
}
|
|
@@ -3,7 +3,31 @@
|
|
|
3
3
|
|
|
4
4
|
// TODO: #13 can we have a better source and more digits ? @jwist
|
|
5
5
|
|
|
6
|
-
export
|
|
6
|
+
export type Nuclei =
|
|
7
|
+
| '1H'
|
|
8
|
+
| '2H'
|
|
9
|
+
| '3H'
|
|
10
|
+
| '3He'
|
|
11
|
+
| '7Li'
|
|
12
|
+
| '13C'
|
|
13
|
+
| '14N'
|
|
14
|
+
| '15N'
|
|
15
|
+
| '17O'
|
|
16
|
+
| '19F'
|
|
17
|
+
| '23Na'
|
|
18
|
+
| '27Al'
|
|
19
|
+
| '29Si'
|
|
20
|
+
| '31P'
|
|
21
|
+
| '57Fe'
|
|
22
|
+
| '63Cu'
|
|
23
|
+
| '67Zn'
|
|
24
|
+
| '129Xe';
|
|
25
|
+
|
|
26
|
+
type GyromagneticRatio = {
|
|
27
|
+
[key in Nuclei]: number;
|
|
28
|
+
};
|
|
29
|
+
|
|
30
|
+
export const gyromagneticRatio: GyromagneticRatio = {
|
|
7
31
|
'1H': 267.52218744e6,
|
|
8
32
|
'2H': 41.065e6,
|
|
9
33
|
'3H': 285.3508e6,
|
package/src/index.ts
CHANGED
|
@@ -25,6 +25,7 @@ export * from './signals/signals2DToZ';
|
|
|
25
25
|
|
|
26
26
|
export * from './utilities/resurrect';
|
|
27
27
|
export * from './utilities/rangeFromSignal';
|
|
28
|
+
export * from './utilities/getFrequency';
|
|
28
29
|
|
|
29
30
|
export * from './xy/xyAutoPeaksPicking';
|
|
30
31
|
export * from './xy/xyAutoRangesPicking';
|
|
@@ -97,7 +97,7 @@ export interface Predictions {
|
|
|
97
97
|
}
|
|
98
98
|
|
|
99
99
|
type GroupDiastereotopicAtomIDsWithAtomInfo = GroupDiastereotopicAtomIDs & {
|
|
100
|
-
|
|
100
|
+
pathInfo: PathInfo;
|
|
101
101
|
};
|
|
102
102
|
|
|
103
103
|
type PredictHMBCOptionsWithFromTo = MakeMandatory<
|
|
@@ -139,7 +139,7 @@ export async function predict2D(
|
|
|
139
139
|
|
|
140
140
|
let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
|
|
141
141
|
|
|
142
|
-
const
|
|
142
|
+
const pathsInfo = getPathsInfo(molecule, {
|
|
143
143
|
fromLabel: from,
|
|
144
144
|
toLabel: to,
|
|
145
145
|
minLength,
|
|
@@ -150,7 +150,9 @@ export async function predict2D(
|
|
|
150
150
|
for (let diaID of diaIDs) {
|
|
151
151
|
diaIDswithAtomInfo.push({
|
|
152
152
|
...diaID,
|
|
153
|
-
|
|
153
|
+
pathInfo: JSON.parse(
|
|
154
|
+
JSON.stringify(pathsInfo[diaID.atoms[0]]),
|
|
155
|
+
) as PathInfo,
|
|
154
156
|
});
|
|
155
157
|
}
|
|
156
158
|
|
|
@@ -192,26 +194,25 @@ export async function predict2D(
|
|
|
192
194
|
signalsByDiaID[axis][signal.diaIDs[0]] = signal;
|
|
193
195
|
}
|
|
194
196
|
}
|
|
195
|
-
|
|
196
197
|
let group: { [key: string]: NMRSignal2D } = {};
|
|
197
198
|
for (const diaID of diaIDswithAtomInfo) {
|
|
198
|
-
const
|
|
199
|
-
if (
|
|
199
|
+
const pathInfo = diaID.pathInfo;
|
|
200
|
+
if (pathInfo.paths.length < 1) continue;
|
|
200
201
|
|
|
201
|
-
if (!signalsByDiaID.x[
|
|
202
|
+
if (!signalsByDiaID.x[pathInfo.oclID]) continue;
|
|
202
203
|
|
|
203
|
-
const currentPaths =
|
|
204
|
+
const currentPaths = pathInfo.paths;
|
|
204
205
|
for (const path of currentPaths) {
|
|
205
|
-
if (!signalsByDiaID.y[
|
|
206
|
+
if (!signalsByDiaID.y[pathsInfo[path.to].oclID]) continue;
|
|
206
207
|
|
|
207
208
|
let fromToDiaID: { [key: string]: AtomInfo } = {
|
|
208
|
-
x:
|
|
209
|
-
y:
|
|
209
|
+
x: pathInfo,
|
|
210
|
+
y: pathsInfo[path.to],
|
|
210
211
|
};
|
|
211
212
|
|
|
212
213
|
const key = `${fromToDiaID.x.oclID}-${fromToDiaID.y.oclID}`;
|
|
213
214
|
|
|
214
|
-
if (key === `${
|
|
215
|
+
if (key === `${pathInfo.oclID}-${pathInfo.oclID}` || group[key]) {
|
|
215
216
|
continue;
|
|
216
217
|
}
|
|
217
218
|
|
|
@@ -226,12 +227,13 @@ export async function predict2D(
|
|
|
226
227
|
}
|
|
227
228
|
|
|
228
229
|
signal.peaks = [peak];
|
|
229
|
-
|
|
230
230
|
group[key] = signal as NMRSignal2D;
|
|
231
231
|
}
|
|
232
232
|
}
|
|
233
233
|
|
|
234
|
-
if (includeDiagonal)
|
|
234
|
+
if (includeDiagonal) {
|
|
235
|
+
addSelftCorrelation(group, { paths: pathsInfo, signalsByDiaID });
|
|
236
|
+
}
|
|
235
237
|
|
|
236
238
|
// clusterize signals by distance
|
|
237
239
|
const joinedSignals = Object.values(group);
|
|
@@ -26,6 +26,7 @@ interface Signals2DToZOptions {
|
|
|
26
26
|
* @default 0.02
|
|
27
27
|
*/
|
|
28
28
|
width?: number | XYNumber;
|
|
29
|
+
factor?: number | XYNumber;
|
|
29
30
|
}
|
|
30
31
|
|
|
31
32
|
export interface Peak2DSeries {
|
|
@@ -38,7 +39,13 @@ export function signals2DToZ(
|
|
|
38
39
|
signals: NMRSignal2D[],
|
|
39
40
|
options: Signals2DToZOptions = {},
|
|
40
41
|
) {
|
|
41
|
-
let {
|
|
42
|
+
let {
|
|
43
|
+
from = -1,
|
|
44
|
+
to = 12,
|
|
45
|
+
nbPoints = 512,
|
|
46
|
+
width = 0.02,
|
|
47
|
+
factor = 3,
|
|
48
|
+
} = options;
|
|
42
49
|
|
|
43
50
|
const peaks = signals.reduce<Peak2DSeries>(
|
|
44
51
|
(acc, { x, y }) => {
|
|
@@ -51,7 +58,8 @@ export function signals2DToZ(
|
|
|
51
58
|
);
|
|
52
59
|
|
|
53
60
|
width = ensureXYNumber(width);
|
|
54
|
-
|
|
61
|
+
|
|
62
|
+
return generateSpectrum2D(mergeClosePeaks(peaks), {
|
|
55
63
|
generator: {
|
|
56
64
|
from: ensureXYNumber(from),
|
|
57
65
|
to: ensureXYNumber(to),
|
|
@@ -59,11 +67,27 @@ export function signals2DToZ(
|
|
|
59
67
|
},
|
|
60
68
|
peaks: {
|
|
61
69
|
width,
|
|
70
|
+
factor,
|
|
62
71
|
},
|
|
63
72
|
});
|
|
64
73
|
}
|
|
65
74
|
|
|
66
|
-
function ensureXYNumber(input: number | XYNumber)
|
|
67
|
-
|
|
68
|
-
|
|
75
|
+
function ensureXYNumber(input: number | XYNumber) {
|
|
76
|
+
return typeof input !== 'object' ? { x: input, y: input } : { ...input };
|
|
77
|
+
}
|
|
78
|
+
|
|
79
|
+
function mergeClosePeaks(peaksIn: Peak2DSeries) {
|
|
80
|
+
let peaks = JSON.parse(JSON.stringify(peaksIn));
|
|
81
|
+
for (let i = 0; i < peaks.x.length; i++) {
|
|
82
|
+
for (let j = i + 1; j < peaks.x.length; j++) {
|
|
83
|
+
if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
|
|
84
|
+
peaks.z[i] += peaks.z[j];
|
|
85
|
+
peaks.x.splice(j, 1);
|
|
86
|
+
peaks.y.splice(j, 1);
|
|
87
|
+
peaks.z.splice(j, 1);
|
|
88
|
+
j--;
|
|
89
|
+
}
|
|
90
|
+
}
|
|
91
|
+
}
|
|
92
|
+
return peaks;
|
|
69
93
|
}
|
|
@@ -0,0 +1,47 @@
|
|
|
1
|
+
import { gyromagneticRatio, Nuclei } from '../constants/gyromagneticRatio';
|
|
2
|
+
|
|
3
|
+
export interface ObjervedNucleusData {
|
|
4
|
+
/**
|
|
5
|
+
* nucleus to use as reference in the calculation of frequency
|
|
6
|
+
*/
|
|
7
|
+
nucleus: Nucleus;
|
|
8
|
+
/**
|
|
9
|
+
* frequency of the reference nucleus
|
|
10
|
+
*/
|
|
11
|
+
frequency: number;
|
|
12
|
+
}
|
|
13
|
+
|
|
14
|
+
//Literal type is extends string and when union it with string we lose the autocomplete and to solve this we distinguish string
|
|
15
|
+
type Nucleus = Nuclei | (string & Record<never, never>);
|
|
16
|
+
|
|
17
|
+
/**
|
|
18
|
+
* calculate the frequency of a nucleus with respect to a reference nucleus
|
|
19
|
+
*/
|
|
20
|
+
export function getFrequency(
|
|
21
|
+
/**
|
|
22
|
+
* nucleus to calculate the frequency
|
|
23
|
+
*/
|
|
24
|
+
nucleus: Nucleus,
|
|
25
|
+
observedNucleusData: ObjervedNucleusData,
|
|
26
|
+
) {
|
|
27
|
+
const { nucleus: obsNucleus, frequency } = observedNucleusData;
|
|
28
|
+
|
|
29
|
+
checkExistence(nucleus, obsNucleus);
|
|
30
|
+
|
|
31
|
+
return (
|
|
32
|
+
(frequency * gyromagneticRatio[nucleus as Nuclei]) /
|
|
33
|
+
gyromagneticRatio[obsNucleus as Nuclei]
|
|
34
|
+
);
|
|
35
|
+
}
|
|
36
|
+
|
|
37
|
+
function checkExistence(...nucleus: Nucleus[]) {
|
|
38
|
+
let nuclei: string[] = [];
|
|
39
|
+
for (const n of nucleus) {
|
|
40
|
+
if (!(n in gyromagneticRatio)) {
|
|
41
|
+
nuclei.push(n);
|
|
42
|
+
}
|
|
43
|
+
}
|
|
44
|
+
if (nuclei.length !== 0) {
|
|
45
|
+
throw new Error(`${nuclei.join(' , ')} is not supported`);
|
|
46
|
+
}
|
|
47
|
+
}
|