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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@@ -1 +1 @@
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-
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+
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package/lib/xyz/NMRSignal2D.d.ts
CHANGED
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@@ -1,6 +1,6 @@
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import type { FromTo } from 'cheminfo-types';
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import type { Peak2D } from 'ml-matrix-peaks-finder';
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export interface
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export interface Signal2DProjection {
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nucleus?: string;
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delta: number;
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resolution?: number;
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@@ -8,8 +8,8 @@ export interface Signal2DAxisData {
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diaIDs?: string[];
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}
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export interface NMRSignal2D {
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x:
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y:
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x: Signal2DProjection;
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y: Signal2DProjection;
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j?: {
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pathLength?: number | FromTo;
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};
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@@ -4,7 +4,7 @@ import { checkIDs } from './utils/getAssignment/checkIDs';
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import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
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import getWorkFlow from './utils/getAssignment/getWorkFlow';
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export 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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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iCAAiC,EAAE,MAAM,mBAAmB,CAAC;AAQtE,OAAO,EAEL,gBAAgB,GAEjB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAC;AAC1D,OAAO,EAAE,yBAAyB,EAAE,MAAM,iDAAiD,CAAC;AAC5F,OAAO,WAAW,MAAM,mCAAmC,CAAC;
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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iCAAiC,EAAE,MAAM,mBAAmB,CAAC;AAQtE,OAAO,EAEL,gBAAgB,GAEjB,MAAM,wCAAwC,CAAC;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,gCAAgC,CAAC;AAC1D,OAAO,EAAE,yBAAyB,EAAE,MAAM,iDAAiD,CAAC;AAC5F,OAAO,WAAW,MAAM,mCAAmC,CAAC;AA0E5D,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,yBAAyB,CACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,WAAW,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,gBAAgB,CAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC"}
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@@ -53,10 +53,12 @@ export async function buildAssignments(props) {
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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 = 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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diaIDIndex: index,
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pathLength: pathLengthMatrix[index],
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};
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}
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for (let diaID in predictions[atomType]) {
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predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
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}
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infoByAtomType[atomType] = {
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nSources: joinedSignals.length,
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currentIndex: 0,
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-
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1
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@@ -4,17 +4,13 @@ export function checkIDs(input = []) {
|
|
|
4
4
|
let inputClone = JSON.parse(JSON.stringify(input));
|
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5
5
|
let spectra = [];
|
|
6
6
|
for (const spectraData of inputClone) {
|
|
7
|
+
if (!('info' in spectraData)) {
|
|
8
|
+
throw new Error('each spectrum should contain info properties with nucleus information');
|
|
9
|
+
}
|
|
7
10
|
const { info, id } = spectraData;
|
|
8
11
|
if (isSpectraData1D(spectraData)) {
|
|
9
|
-
let
|
|
10
|
-
|
|
11
|
-
const { integration } = element;
|
|
12
|
-
for (let signal of element.signals || []) {
|
|
13
|
-
if (!signal.integration)
|
|
14
|
-
signal.integration = integration;
|
|
15
|
-
}
|
|
16
|
-
}
|
|
17
|
-
spectra.push({ id, info, ranges: data });
|
|
12
|
+
let ranges = addIDs(spectraData.ranges);
|
|
13
|
+
spectra.push({ id, info, ranges });
|
|
18
14
|
}
|
|
19
15
|
else {
|
|
20
16
|
let data = addIDs(spectraData.zones);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":"AAOA,OAAO,UAAU,MAAM,eAAe,CAAC;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;
|
|
1
|
+
{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":"AAOA,OAAO,UAAU,MAAM,eAAe,CAAC;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD,MAAM,UAAU,QAAQ,CAAC,QAAuB,EAAE;IAChD,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAkB,CAAC;IACpE,IAAI,OAAO,GAAyB,EAAE,CAAC;IACvC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,IAAI,CAAC,CAAC,MAAM,IAAI,WAAW,CAAC,EAAE;YAC5B,MAAM,IAAI,KAAK,CACb,uEAAuE,CACxE,CAAC;SACH;QAED,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,eAAe,CAAC,WAAW,CAAC,EAAE;YAChC,IAAI,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAsB,CAAC;YAC7D,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;SACpC;aAAM;YACL,IAAI,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAqB,CAAC;YACzD,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;SACzC;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,MAAM,CACpB,IAA4B;IAE5B,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAC;QAC/D,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAC;SAC3D;KACF;AACH,CAAC;AAED,MAAM,UAAU,MAAM,CAAC,IAA4B;IACjD,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,OAAO,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;QAC3C,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;SAC1C;KACF;IACD,MAAM,CAAC,IAAI,CAAC,CAAC;IACb,OAAO,IAAI,CAAC;AACd,CAAC"}
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@@ -3,14 +3,41 @@ export function formatData(input = []) {
|
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|
3
3
|
let inputClone = JSON.parse(JSON.stringify(input));
|
|
4
4
|
let spectra = [];
|
|
5
5
|
for (const spectraData of inputClone) {
|
|
6
|
-
const { info } = spectraData;
|
|
6
|
+
const { id, info } = spectraData;
|
|
7
7
|
if (isSpectraData1D(spectraData)) {
|
|
8
|
-
|
|
8
|
+
const ranges = rescaleIntegration({
|
|
9
|
+
id,
|
|
10
|
+
info,
|
|
11
|
+
ranges: spectraData.ranges,
|
|
12
|
+
});
|
|
13
|
+
spectra.push({ id, info, ranges: { values: ranges } });
|
|
9
14
|
}
|
|
10
15
|
else {
|
|
11
|
-
spectra.push({ info, zones: { values: spectraData.zones } });
|
|
16
|
+
spectra.push({ id, info, zones: { values: spectraData.zones } });
|
|
12
17
|
}
|
|
13
18
|
}
|
|
14
19
|
return spectra;
|
|
15
20
|
}
|
|
21
|
+
function rescaleIntegration(spectrum) {
|
|
22
|
+
if (spectrum.info.nucleus !== '1H')
|
|
23
|
+
return spectrum.ranges;
|
|
24
|
+
let totalIntegration = spectrum.ranges.reduce((total, range) => (range.integration ? total + range.integration : total), 0);
|
|
25
|
+
for (let range of spectrum.ranges) {
|
|
26
|
+
if (range.integration) {
|
|
27
|
+
range.integration *= 100 / totalIntegration;
|
|
28
|
+
if (range.signals) {
|
|
29
|
+
const totalSignalIntegration = range.signals.reduce((total, signal) => signal.integration ? total + signal.integration : total, 0);
|
|
30
|
+
for (let signal of range.signals) {
|
|
31
|
+
if (signal.integration) {
|
|
32
|
+
signal.integration *= range.integration / totalSignalIntegration;
|
|
33
|
+
}
|
|
34
|
+
else {
|
|
35
|
+
signal.integration = range.integration;
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
}
|
|
40
|
+
}
|
|
41
|
+
return spectrum.ranges;
|
|
42
|
+
}
|
|
16
43
|
//# 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,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAapD,MAAM,UAAU,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,eAAe,CAAC,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;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 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getTargetsAndCorrelations.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"getTargetsAndCorrelations.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/getTargetsAndCorrelations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAC;AAKvD,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAC1C,OAAO,EAAE,+BAA+B,EAAE,MAAM,mCAAmC,CAAC;AAsBpF,MAAM,UAAU,yBAAyB,CACvC,OAA6B,EAC7B,UAAe,EAAE;IAEjB,gFAAgF;IAChF,8DAA8D;IAE9D,MAAM,EAAE,SAAS,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,OAAO,CAAC;IAErD,MAAM,WAAW,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,oBAAoB,CAAC,WAAW,EAAE;QACjE,SAAS;KACV,CAAC,CAAC;IAEH,IAAI,OAAO,GAAQ,EAAE,CAAC;IACtB,KAAK,MAAM,WAAW,IAAI,YAAY,EAAE;QACtC,IAAI,WAAW,CAAC,MAAM;YAAE,SAAS;QACjC,MAAM,EAAE,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,WAAW,CAAC;QAC/C,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC;YAAE,OAAO,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;QAC/C,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,GAAG,WAAW,CAAC;QAC1C,IAAI,QAAQ,KAAK,GAAG,EAAE;YACpB,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW;gBACrC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC;SAC1C;aAAM;YACL,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW,GAAG,+BAA+B,CACvE,WAAW,EACX,YAAY,CACb,CAAC;SACH;KACF;IAED,OAAO;QACL,OAAO;QACP,YAAY;KACb,CAAC;AACJ,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"partialScore.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/partialScore.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAatD,OAAO,kCAAkC,MAAM,sCAAsC,CAAC;AAmBtF,MAAM,UAAU,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,kCAAkC,CACnC,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,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAatD,OAAO,kCAAkC,MAAM,sCAAsC,CAAC;AAmBtF,MAAM,UAAU,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,kCAAkC,CACnC,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,mBAAmB,CAAC,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,CAA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|
|
@@ -1,12 +1,22 @@
|
|
|
1
1
|
import { fetch } from 'cross-fetch';
|
|
2
2
|
import { resurrectRange } from '../utilities/resurrectRange';
|
|
3
|
-
export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
|
|
3
|
+
export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
|
|
4
|
+
const { format = 'tsv' } = options;
|
|
4
5
|
if (url.includes('google.com')) {
|
|
5
6
|
url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
|
|
6
7
|
}
|
|
8
|
+
let parsed;
|
|
7
9
|
const response = await fetch(url);
|
|
8
|
-
|
|
9
|
-
|
|
10
|
+
switch (format) {
|
|
11
|
+
case 'tsv':
|
|
12
|
+
parsed = parseData(await response.text());
|
|
13
|
+
break;
|
|
14
|
+
case 'json':
|
|
15
|
+
parsed = await response.json();
|
|
16
|
+
break;
|
|
17
|
+
default:
|
|
18
|
+
throw new Error('unknown database format');
|
|
19
|
+
}
|
|
10
20
|
const results = [];
|
|
11
21
|
for (let line of parsed.data) {
|
|
12
22
|
const result = {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAEpC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAI7D,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG;
|
|
1
|
+
{"version":3,"file":"getDatabase.js","sourceRoot":"","sources":["../../src/databases/getDatabase.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AAEpC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAI7D,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,GAAG,GAAG,sGAAsG,EAC5G,UAKI,EAAE;IAEN,MAAM,EAAE,MAAM,GAAG,KAAK,EAAE,GAAG,OAAO,CAAC;IAEnC,IAAI,GAAG,CAAC,QAAQ,CAAC,YAAY,CAAC,EAAE;QAC9B,GAAG,GAAG,kDAAkD,iBAAiB,CACvE,GAAG,CACJ,oBAAoB,CAAC;KACvB;IAED,IAAI,MAAM,CAAC;IACX,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;IAClC,QAAQ,MAAM,EAAE;QACd,KAAK,KAAK;YACR,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC;YAC1C,MAAM;QACR,KAAK,MAAM;YACT,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAC/B,MAAM;QACR;YACE,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC9C;IAED,MAAM,OAAO,GAAG,EAAE,CAAC;IAEnB,KAAK,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;QAC5B,MAAM,MAAM,GAAqB;YAC/B,MAAM,EAAE,EAAE;YACV,OAAO,EAAE,EAAE;YACX,OAAO,EAAE,EAAE;YACX,QAAQ,EAAE,EAAE;YACZ,KAAK,EAAE,EAAE;YACT,IAAI,EAAE,EAAE;YACR,MAAM,EAAE,EAAE;SACX,CAAC;QACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACpC,QAAQ,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACvB,KAAK,QAAQ;oBACX,MAAM,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,SAAS;oBACZ,MAAM,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzB,MAAM;gBACR,KAAK,UAAU;oBACb,MAAM,CAAC,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC1B,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,KAAK;wBAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM;gBACR,KAAK,MAAM;oBACT,IAAI,MAAM,CAAC,IAAI;wBAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;oBACzD,MAAM;gBACR,KAAK,QAAQ,CAAC,CAAC;oBACb,MAAM,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBACtC,IAAI,KAAK;wBAAE,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBACrC,MAAM;iBACP;gBACD;oBACE,MAAM,IAAI,KAAK,CAAC,wBAAwB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;aAC9D;SACF;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,GAAG,CAAC,OAAO,CAAC,4BAA4B,EAAE,SAAS,CAAC,CAAC;AAC9D,CAAC;AAED,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,MAAM,GAAG,IAAI;SAChB,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAE9E,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACxB,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAC7B,OAAO;QACL,MAAM;QACN,KAAK;QACL,IAAI;KACL,CAAC;AACJ,CAAC"}
|
|
@@ -1,36 +1,122 @@
|
|
|
1
|
+
import { signals2DToZ } from '../signals/signals2DToZ';
|
|
1
2
|
import { signalsToXY } from '../signals/signalsToXY';
|
|
3
|
+
import { getFrequency } from '../utilities/getFrequency';
|
|
2
4
|
import { predictAll } from './predictAll';
|
|
3
|
-
/**
|
|
4
|
-
* This function will generate an object compatible with NMR-ium
|
|
5
|
-
*
|
|
6
|
-
* @param molecule
|
|
7
|
-
* @param options
|
|
8
|
-
*/
|
|
9
5
|
export async function predictAllSpectra(molecule, options = {}) {
|
|
10
|
-
const
|
|
6
|
+
const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
|
|
7
|
+
const predictions = await predictAll(molecule, predictionOptions);
|
|
11
8
|
const spectra = [];
|
|
12
9
|
const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
|
|
13
|
-
|
|
10
|
+
const oneDOptions = {
|
|
11
|
+
...{
|
|
12
|
+
proton: { from: 0, to: 14 },
|
|
13
|
+
carbon: { from: 0, to: 200 },
|
|
14
|
+
nbPoints: 4098,
|
|
15
|
+
lineWidth: 0.03,
|
|
16
|
+
},
|
|
17
|
+
...(simulationOptions.oneD || {}),
|
|
18
|
+
};
|
|
19
|
+
const twoDOptions = {
|
|
20
|
+
...{
|
|
21
|
+
from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
|
|
22
|
+
to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
|
|
23
|
+
nbPoints: { x: 1024, y: 1024 },
|
|
24
|
+
},
|
|
25
|
+
...(simulationOptions.twoD || {}),
|
|
26
|
+
};
|
|
27
|
+
for (const experiment in predictions) {
|
|
28
|
+
switch (experiment) {
|
|
29
|
+
case 'carbon':
|
|
30
|
+
case 'proton': {
|
|
31
|
+
spectra.push(get1DSpectrum(predictions[experiment], {
|
|
32
|
+
nbPoints: oneDOptions.nbPoints,
|
|
33
|
+
lineWidth: oneDOptions.lineWidth,
|
|
34
|
+
...oneDOptions[experiment],
|
|
35
|
+
experiment,
|
|
36
|
+
frequency: simulationOptions.frequency,
|
|
37
|
+
}));
|
|
38
|
+
break;
|
|
39
|
+
}
|
|
40
|
+
case 'cosy':
|
|
41
|
+
case 'hsqc':
|
|
42
|
+
case 'hmbc': {
|
|
43
|
+
spectra.push(get2DSpectrum(predictions[experiment], {
|
|
44
|
+
...twoDOptions,
|
|
45
|
+
experiment,
|
|
46
|
+
frequency: simulationOptions.frequency,
|
|
47
|
+
}));
|
|
48
|
+
break;
|
|
49
|
+
}
|
|
50
|
+
default:
|
|
51
|
+
break;
|
|
52
|
+
}
|
|
53
|
+
}
|
|
14
54
|
return result;
|
|
15
55
|
}
|
|
16
|
-
function
|
|
17
|
-
const {
|
|
56
|
+
function get2DSpectrum(prediction, options) {
|
|
57
|
+
const { signals, zones, nuclei } = prediction;
|
|
58
|
+
const { frequency: baseFrequency, experiment } = options;
|
|
59
|
+
const width = get2DWidth(nuclei);
|
|
60
|
+
const frequency = calculateFrequency(nuclei, baseFrequency);
|
|
61
|
+
const spectrumData = signals2DToZ(signals, {
|
|
62
|
+
...options,
|
|
63
|
+
width,
|
|
64
|
+
factor: 3,
|
|
65
|
+
});
|
|
66
|
+
const spectrum = {
|
|
67
|
+
data: { ...spectrumData, noise: 0.01 },
|
|
68
|
+
info: {
|
|
69
|
+
nucleus: nuclei,
|
|
70
|
+
originFrequency: frequency,
|
|
71
|
+
baseFrequency: frequency,
|
|
72
|
+
pulseSequence: experiment,
|
|
73
|
+
experiment: '2d',
|
|
74
|
+
},
|
|
75
|
+
zones: { values: zones },
|
|
76
|
+
};
|
|
77
|
+
return spectrum;
|
|
78
|
+
}
|
|
79
|
+
function get2DWidth(nucleus) {
|
|
80
|
+
return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
|
|
81
|
+
}
|
|
82
|
+
function get1DSpectrum(prediction, options) {
|
|
83
|
+
const { frequency = 400, experiment } = options;
|
|
84
|
+
const { signals, nucleus } = prediction;
|
|
85
|
+
const realFrequency = calculateFrequency(nucleus, frequency);
|
|
86
|
+
const { x, y } = signalsToXY(signals, {
|
|
87
|
+
...options,
|
|
88
|
+
frequency: realFrequency,
|
|
89
|
+
});
|
|
18
90
|
const spectrum = {
|
|
19
|
-
id: '',
|
|
20
91
|
// todo Array.from is temporary for the developement
|
|
21
92
|
data: { x: Array.from(x), re: Array.from(y), im: null },
|
|
22
93
|
info: {
|
|
23
94
|
nucleus: prediction.nucleus,
|
|
24
95
|
dimension: 1,
|
|
25
|
-
originFrequency:
|
|
26
|
-
baseFrequency:
|
|
96
|
+
originFrequency: realFrequency,
|
|
97
|
+
baseFrequency: realFrequency,
|
|
27
98
|
pulseSequence: 'prediction',
|
|
28
|
-
experiment
|
|
99
|
+
experiment,
|
|
29
100
|
isFt: true,
|
|
30
101
|
},
|
|
31
|
-
|
|
32
|
-
//ranges: { values: prediction.ranges },
|
|
102
|
+
ranges: { values: prediction.ranges },
|
|
33
103
|
};
|
|
34
104
|
return spectrum;
|
|
35
105
|
}
|
|
106
|
+
function calculateFrequency(nucleus, frequency) {
|
|
107
|
+
if (typeof nucleus === 'string') {
|
|
108
|
+
return getFrequency(nucleus, { nucleus: '1H', frequency });
|
|
109
|
+
}
|
|
110
|
+
else {
|
|
111
|
+
if (nucleus[0] === nucleus[1]) {
|
|
112
|
+
return `${frequency},${frequency}`;
|
|
113
|
+
}
|
|
114
|
+
else {
|
|
115
|
+
return `${frequency},${getFrequency(nucleus[1], {
|
|
116
|
+
nucleus: nucleus[0],
|
|
117
|
+
frequency,
|
|
118
|
+
})}`;
|
|
119
|
+
}
|
|
120
|
+
}
|
|
121
|
+
}
|
|
36
122
|
//# sourceMappingURL=predictAllSpectra.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictAllSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictAllSpectra.ts"],"names":[],"mappings":"
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "8.0.0",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
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"module": "./lib-esm/index.js",
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},
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"homepage": "https://github.com/cheminfo/nmr-processing#readme",
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"devDependencies": {
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"@types/jest": "^27.
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"@types/jest": "^27.5.0",
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"cheminfo-build": "^1.1.11",
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"cheminfo-types": "^1.1.0",
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"eslint": "^8.
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"eslint": "^8.14.0",
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"eslint-config-cheminfo-typescript": "^10.4.0",
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"jest": "^
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"jest": "^28.0.3",
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"jest-matcher-deep-close-to": "^3.0.2",
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"md5": "^2.3.0",
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"ml-array-median": "^1.1.6",
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"nmr-xy-testdata": "^0.5.1",
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"openchemlib": "^7.4.3",
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"prettier": "^2.6.
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"prettier": "^2.6.2",
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"rimraf": "^3.0.2",
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"ts-jest": "^
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"typescript": "^4.6.
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"ts-jest": "^28.0.1",
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"typescript": "^4.6.4"
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},
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"dependencies": {
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"binary-search": "^1.3.6",
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"ml-array-rescale": "^1.3.7",
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"ml-array-sequential-fill": "^1.1.8",
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"ml-array-sum": "^1.1.6",
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"ml-gsd": "^
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"ml-gsd": "^11.2.0",
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"ml-hclust": "^3.1.0",
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"ml-levenberg-marquardt": "^4.1.0",
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"ml-matrix": "^6.
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"ml-matrix": "^6.10.0",
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"ml-matrix-convolution": "^1.0.0",
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"ml-matrix-peaks-finder": "^1.0.0",
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"ml-peak-shape-generator": "^4.1.1",
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"ml-simple-clustering": "^0.1.0",
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"ml-sparse-matrix": "^2.1.0",
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"ml-spectra-processing": "^11.
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"ml-spectra-processing": "^11.5.0",
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"ml-tree-set": "^0.1.1",
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"nmr-correlation": "^2.2.5",
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"openchemlib-utils": "^1.
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"spectrum-generator": "^8.0.
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"openchemlib-utils": "^1.11.0",
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"spectrum-generator": "^8.0.1"
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}
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}
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@@ -19,23 +19,22 @@ import getWorkFlow from './utils/getAssignment/getWorkFlow';
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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 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?: { [key: string]: number };
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spectra: SpectraData[];
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/**
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* Instance of Molecule
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@@ -96,7 +95,7 @@ export async function getAssignments(
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let {
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restrictionByCS = {},
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justAssign,
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minScore =
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minScore = 0.01,
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maxSolutions = 10,
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nbAllowedUnAssigned,
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timeout = 6000,
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|
@@ -119,11 +118,11 @@ export async function getAssignments(
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|
addDiastereotopicMissingChirality(molecule);
|
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|
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|
const spectra = checkIDs(input.spectra);
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|
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|
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|
const { targets, correlations } = getTargetsAndCorrelations(
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spectra,
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|
correlationOptions,
|
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);
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|
const { assignmentOrder } = getWorkFlow(correlations, justAssign);
|
|
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|
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|
const solutions = await buildAssignments({
|
|
@@ -1,24 +1,26 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
|
|
2
|
+
import { MakeMandatory } from '../utilities/MakeMandatory';
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|
2
3
|
|
|
3
|
-
import type {
|
|
4
|
-
import type { NMRZone } from '../xyz/NMRZone';
|
|
4
|
+
import type { SpectraData1D, SpectraData2D } from './getAssignments';
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|
5
5
|
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6
|
-
export
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-
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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: []};
|
|
18
|
-
*/
|
|
19
|
-
zones: { [key: string]: NMRZone[] };
|
|
20
|
-
/**
|
|
21
|
-
* Instance of Molecule
|
|
22
|
-
*/
|
|
23
|
-
molecule: Molecule;
|
|
6
|
+
export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
|
|
7
|
+
export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
|
|
8
|
+
|
|
9
|
+
export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
|
|
10
|
+
id: string;
|
|
11
|
+
signals: Array<NMRSignal2DWithId>;
|
|
12
|
+
}
|
|
13
|
+
|
|
14
|
+
export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
|
|
15
|
+
id: string;
|
|
16
|
+
signals: Array<NMRSignal1DWithId>;
|
|
24
17
|
}
|
|
18
|
+
|
|
19
|
+
export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
|
|
20
|
+
ranges: NMRRangeWithIds[];
|
|
21
|
+
}
|
|
22
|
+
export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
|
|
23
|
+
zones: NMRZoneWithIds[];
|
|
24
|
+
}
|
|
25
|
+
|
|
26
|
+
export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
|