nmr-processing 7.2.0 → 7.3.0
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.
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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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19
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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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@@ -26,7 +26,7 @@ async function predict2D(molecule, options = {}) {
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for (let diaID of diaIDs) {
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diaIDswithAtomInfo.push({
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...diaID,
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-
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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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@@ -53,21 +53,21 @@ async function predict2D(molecule, options = {}) {
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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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@@ -83,8 +83,9 @@ async function predict2D(molecule, options = {}) {
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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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@@ -1 +1 @@
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1
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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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1
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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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@@ -13,7 +13,7 @@ export 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 = getGroupedDiastereotopicAtomIDs(molecule);
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const
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const pathsInfo = getPathsInfo(molecule, {
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fromLabel: from,
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toLabel: to,
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minLength,
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@@ -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
|
+
{"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,SAAS,GAAG,YAAY,CAAC,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,cAAc,CACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GACf,IAAI,KAAK,EAAE;QACT,CAAC,CAAC,WAAW;QACb,CAAC,CAAC,MAAM,cAAc,CAClB,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAER,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,MAAM,OAAO,GAAoC;QAC/C,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,cAAc,GAAoB;QACtC,CAAC,EAAE,EAAE;QACL,CAAC,EAAE,EAAE;KACN,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,cAAc,EAAE;QACjC,KAAK,MAAM,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE;YAChD,IAAI,CAAC,MAAM,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;YAC7D,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC;SACjD;KACF;IACD,IAAI,KAAK,GAAmC,EAAE,CAAC;IAC/C,KAAK,MAAM,KAAK,IAAI,kBAAkB,EAAE;QACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;QAChC,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAExC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;YAAE,SAAS;QAEhD,MAAM,YAAY,GAAG,QAAQ,CAAC,KAAK,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE;YAC/B,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC;gBAAE,SAAS;YAE1D,IAAI,WAAW,GAAgC;gBAC7C,CAAC,EAAE,QAAQ;gBACX,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;aACtB,CAAC;YAEF,MAAM,GAAG,GAAG,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,IAAI,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;YAE5D,IAAI,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;gBAC/D,SAAS;aACV;YAED,IAAI,IAAI,GAAQ,EAAE,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,SAAS,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CAAC,aAA4B;IAChD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,MAAM,IAAI,aAAa,EAAE;QAClC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;YACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;gBACxC,IAAI,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;gBACnD,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aACzB;SACF;KACF;IACD,OAAO,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,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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "7.
|
|
3
|
+
"version": "7.3.0",
|
|
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",
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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.
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"prettier": "^2.6.1",
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"rimraf": "^3.0.2",
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"ts-jest": "^27.1.
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"typescript": "^4.6.
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"ts-jest": "^27.1.4",
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"typescript": "^4.6.3"
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},
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"dependencies": {
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"binary-search": "^1.3.6",
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@@ -63,7 +63,7 @@
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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": "^10.
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"ml-gsd": "^10.2.0",
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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": "^6.9.0",
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@@ -72,10 +72,10 @@
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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": "^11.1.0",
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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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+
"openchemlib-utils": "^1.10.0",
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"spectrum-generator": "^8.0.0"
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}
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}
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@@ -97,7 +97,7 @@ export interface Predictions {
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}
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type GroupDiastereotopicAtomIDsWithAtomInfo = GroupDiastereotopicAtomIDs & {
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-
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+
pathInfo: PathInfo;
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};
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type PredictHMBCOptionsWithFromTo = MakeMandatory<
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@@ -139,7 +139,7 @@ export async function predict2D(
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let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
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-
const
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+
const pathsInfo = getPathsInfo(molecule, {
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fromLabel: from,
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toLabel: to,
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minLength,
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@@ -150,7 +150,9 @@ export async function predict2D(
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150
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|
for (let diaID of diaIDs) {
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151
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|
diaIDswithAtomInfo.push({
|
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|
...diaID,
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|
-
|
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153
|
+
pathInfo: JSON.parse(
|
|
154
|
+
JSON.stringify(pathsInfo[diaID.atoms[0]]),
|
|
155
|
+
) as PathInfo,
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});
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|
}
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@@ -192,26 +194,25 @@ export async function predict2D(
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|
signalsByDiaID[axis][signal.diaIDs[0]] = signal;
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}
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}
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|
-
|
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|
let group: { [key: string]: NMRSignal2D } = {};
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|
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198
|
for (const diaID of diaIDswithAtomInfo) {
|
|
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|
-
const
|
|
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|
-
if (
|
|
199
|
+
const pathInfo = diaID.pathInfo;
|
|
200
|
+
if (pathInfo.paths.length < 1) continue;
|
|
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201
|
|
|
201
|
-
if (!signalsByDiaID.x[
|
|
202
|
+
if (!signalsByDiaID.x[pathInfo.oclID]) continue;
|
|
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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;
|
|
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|
|
|
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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);
|