nmr-processing 9.9.2 → 10.0.0

package/lib-esm/prediction/predictCarbon.js

@@ -1,10 +1,9 @@
 import { v4 as generateID } from '@lukeed/uuid';
-import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
 import { setIDs } from '../peaks/util/setIDs';
 import { signalsToRanges } from '../signals/signalsToRanges';
 import { fetchPrediction } from './utils/fetchPrediction';
 import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
-import { isEmptyMolecule } from './utils/isEmptyMolecule';
+import { isMolfileNotEmpty } from './utils/isMolfileNotEmpty';
 import { queryByHose } from './utils/queryByHOSE';
 function checkFromPrediction(signal) {
     if (!signal.atoms)
@@ -18,21 +17,19 @@ function checkFromPrediction(signal) {
  * Make a query to a hose code based database to predict carbon chemical shift
  * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
  */
-export async function predictCarbon(molecule, options = {}) {
-    if (isEmptyMolecule(molecule)) {
+export async function predictCarbon(options) {
+    const { hoses, molfile, database, webserviceURL = 'https://nmr-prediction.service.zakodium.com/v1/predict/carbon', groupedDiaIDs, } = options;
+    if (!database && isMolfileNotEmpty(molfile)) {
+        return fetchPrediction(molfile, { webserviceURL });
+    }
+    else if (!isMolfileNotEmpty(molfile)) {
         return {
-            molfile: molecule.toMolfile(),
             nucleus: '13C',
-            diaIDs: [],
             joinedSignals: [],
             signals: [],
             ranges: [],
-            molecule,
         };
     }
-    const { database, webserviceURL = 'https://nmr-prediction.service.zakodium.com/v1/predict/carbon', diaIDs = getDiastereotopicAtomIDs(molecule), } = options;
-    if (!database)
-        return fetchPrediction(molecule, { webserviceURL });
     if (!database) {
         throw new Error('There is not a database');
     }
@@ -40,9 +37,9 @@ export async function predictCarbon(molecule, options = {}) {
     let { maxSphereSize = maxLevel } = options;
     if (maxSphereSize > maxLevel)
         maxSphereSize = maxLevel;
-    const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
-        maxSphereSize,
-        diaIDs,
+    const carbonDiaIDs = getFilteredIDiaIDs({
+        groupedDiaIDs,
+        hoses,
     });
     const predictions = queryByHose(carbonDiaIDs, database, {
         maxSphereSize,
@@ -50,13 +47,10 @@ export async function predictCarbon(molecule, options = {}) {
     const signals = formatSignals(predictions);
     const joinedSignals = joinSignalByDiaID(signals);
     return {
-        molfile,
         nucleus: '13C',
-        diaIDs,
         joinedSignals,
         signals,
         ranges: signalsToRanges(joinedSignals),
-        molecule,
     };
 }
 function formatSignals(predictions) {

package/lib-esm/prediction/predictCarbon.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/predictHMBC.js

@@ -1,16 +1,12 @@
-import { predictCarbon } from './predictCarbon';
-import { predictProton } from './predictProton';
 import { predict2D } from './utils/predict2D';
-export async function predictHMBC(molecule, options = {}) {
-    const { minLength = 2, maxLength = 3, predictor = { H: predictProton, C: predictCarbon }, predictOptions, predictions, joinDistance = { H: 0.05, C: 0.5 }, } = options;
+export async function predictHMBC(molecule, options) {
+    const { minLength = 2, maxLength = 3, joinDistance = { H: 0.05, C: 0.5 }, } = options;
     return predict2D(molecule, {
+        ...options,
         from: 'H',
         to: 'C',
-        predictor,
         minLength,
         maxLength,
-        predictions,
-        predictOptions,
         joinDistance,
     });
 }

package/lib-esm/prediction/predictHMBC.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictHMBC.js","sourceRoot":"","sources":["../../src/prediction/predictHMBC.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AA6C9C,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,OAA2B;IAE3B,MAAM,EACJ,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,OAAO,SAAS,CAAC,QAAQ,EAAE;QACzB,GAAG,OAAO;QACV,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,YAAY;KACb,CAAC,CAAC;AACL,CAAC"}

package/lib-esm/prediction/predictHSQC.js

@@ -1,20 +1,16 @@
-import { predictCarbon } from './predictCarbon';
-import { predictProton } from './predictProton';
 import { predict2D } from './utils/predict2D';
 /**
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
  * @returns {Promise<object>} - object with molfile, diaIDs, 2D signals joined signals and zones.
  */
-export async function predictHSQC(molecule, options = {}) {
-    const { minLength = 1, maxLength = 1, predictor = { H: predictProton, C: predictCarbon }, predictions, joinDistance = { H: 0.05, C: 0.5 }, predictOptions, } = options;
+export async function predictHSQC(molecule, options) {
+    const { minLength = 1, maxLength = 1, joinDistance = { H: 0.05, C: 0.5 }, } = options;
     return predict2D(molecule, {
+        ...options,
         from: 'H',
         to: 'C',
-        predictor,
         minLength,
         maxLength,
-        predictions,
-        predictOptions,
         joinDistance,
     });
 }

package/lib-esm/prediction/predictHSQC.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictHSQC.js","sourceRoot":"","sources":["../../src/prediction/predictHSQC.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAuC9C;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,OAA2B;IAE3B,MAAM,EACJ,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,OAAO,SAAS,CAAC,QAAQ,EAAE;QACzB,GAAG,OAAO;QACV,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,YAAY;KACb,CAAC,CAAC;AACL,CAAC"}

package/lib-esm/prediction/predictProton.js

@@ -1,27 +1,19 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import fetch from 'cross-fetch';
 import FormData from 'form-data';
-import { ensureHeterotopicChiralBonds, getConnectivityMatrix, getDiastereotopicAtomIDs, } from 'openchemlib-utils';
 import { signalsJoin } from '../signals/signalsJoin';
 import { signalsToRanges } from '../signals/signalsToRanges';
-import { isEmptyMolecule } from './utils/isEmptyMolecule';
-export async function predictProton(molecule, options = {}) {
-    if (isEmptyMolecule(molecule)) {
+import { isMolfileNotEmpty } from './utils/isMolfileNotEmpty';
+export async function predictProton(molfile, options) {
+    if (!isMolfileNotEmpty(molfile)) {
         return {
-            molfile: molecule.toMolfile(),
-            nucleus: '13C',
-            diaIDs: [],
+            nucleus: '1H',
             joinedSignals: [],
             signals: [],
             ranges: [],
-            molecule,
         };
     }
     const { cache } = options;
-    molecule = molecule.getCompactCopy();
-    molecule.addImplicitHydrogens();
-    ensureHeterotopicChiralBonds(molecule);
-    const molfile = molecule.toMolfile();
     let result;
     if (cache) {
         result = cache(molfile);
@@ -39,26 +31,21 @@ export async function predictProton(molecule, options = {}) {
             cache(molfile, result);
         }
     }
-    const { diaIDs = getDiastereotopicAtomIDs(molecule) } = options;
-    const signals = protonParser(result, molecule, diaIDs);
+    const { diaIDs, distanceMatrix } = options;
+    const signals = protonParser(result, { diaIDs, distanceMatrix });
     const joinedSignals = signalsJoin(signals);
     return {
-        molfile,
-        diaIDs,
         nucleus: '1H',
         joinedSignals,
         signals,
         ranges: signalsToRanges(joinedSignals),
-        molecule,
     };
 }
-function protonParser(result, molecule, diaIDs) {
-    if (molecule.getAllAtoms() === 0)
-        return [];
+function protonParser(result, options) {
     if (result.includes('ERR')) {
         throw Error(`Spinus optimization: ${result}`);
     }
-    const distanceMatrix = getConnectivityMatrix(molecule, { pathLength: true });
+    const { diaIDs, distanceMatrix } = options;
     const lines = result.split('\n').filter((line) => line);
     const signals = [];
     for (const line of lines) {

package/lib-esm/prediction/predictProton.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAGjC,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAG7D,OAAO,EAAE,iBAAiB,EAAE,MAAM,2BAA2B,CAAC;AAwB9D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,OAAe,EACf,OAA6B;IAE7B,IAAI,CAAC,iBAAiB,CAAC,OAAO,CAAC,EAAE;QAC/B,OAAO;YACL,OAAO,EAAE,IAAI;YACb,aAAa,EAAE,EAAE;YACjB,OAAO,EAAE,EAAE;YACX,MAAM,EAAE,EAAE;SACX,CAAC;KACH;IACD,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAE1B,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC3C,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,CAAC,CAAC;IACjE,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;KACvC,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,OAAyD;IAEzD,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,MAAM,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC3C,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACxD,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC1C,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACnC,MAAM,MAAM,GAAgB;YAC1B,EAAE,EAAE,UAAU,EAAE;YAChB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACxC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/lib-esm/prediction/{predictAllSpectra.js → predictSpectra.js}

@@ -1,11 +1,10 @@
 import { signals2DToZ } from '../signals/signals2DToZ';
 import { signalsToXY } from '../signals/signalsToXY';
 import { getFrequency } from '../utilities/getFrequency';
-import { predictAll } from './predictAll';
+import { predict } from './predict';
 export async function predictAllSpectra(molecule, options = {}) {
     const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
-    const predictions = await predictAll(molecule, predictionOptions);
-    const { molfile, spectra } = predictions;
+    const { spectra } = await predict(molecule, predictionOptions);
     const oneDOptions = {
         ...{
             proton: { from: 0, to: 14 },
@@ -51,7 +50,10 @@ export async function predictAllSpectra(molecule, options = {}) {
                 break;
         }
     }
-    return { spectra: newSpectra, molecules: [{ molfile }] };
+    return {
+        spectra: newSpectra,
+        molecules: [{ molfile: molecule.toMolfile() }],
+    };
 }
 function get2DSpectrum(prediction, options) {
     const { signals, zones, nuclei } = prediction;
@@ -118,4 +120,4 @@ function calculateFrequency(nucleus, frequency) {
         })}`;
     }
 }
-//# sourceMappingURL=predictAllSpectra.js.map
+//# sourceMappingURL=predictSpectra.js.map

package/lib-esm/prediction/predictSpectra.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"predictSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictSpectra.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAsB,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACzE,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAEzD,OAAO,EAAqB,OAAO,EAAE,MAAM,WAAW,CAAC;AA8BvD,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,QAAkB,EAClB,UAAoC,EAAE;IAEtC,MAAM,EACJ,UAAU,EAAE,iBAAiB,GAAG,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAuB,EAC3E,UAAU,EAAE,iBAAiB,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,OAAO,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAE/D,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE;YAC5B,QAAQ,EAAE,KAAK;YACf,SAAS,EAAE,CAAC;SACb;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,IAAI,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE;YAChE,EAAE,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE;YAC1D,QAAQ,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE;SAC/B;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,MAAM,UAAU,GAAU,EAAE,CAAC;IAC7B,KAAK,MAAM,UAAU,IAAI,OAAO,EAAE;QAChC,QAAQ,UAAU,EAAE;YAClB,KAAK,QAAQ,CAAC;YACd,KAAK,QAAQ,CAAC,CAAC;gBACb,UAAU,CAAC,IAAI,CACb,aAAa,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;oBACjC,QAAQ,EAAE,WAAW,CAAC,QAAQ;oBAC9B,SAAS,EAAE,WAAW,CAAC,SAAS;oBAChC,GAAG,WAAW,CAAC,UAAU,CAAC;oBAC1B,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC,CAAC;gBACX,UAAU,CAAC,IAAI,CACb,aAAa,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;oBACjC,GAAG,WAAW;oBACd,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD;gBACE,MAAM;SACT;KACF;IAED,OAAO;QACL,OAAO,EAAE,UAAU;QACnB,SAAS,EAAE,CAAC,EAAE,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC;KAC/C,CAAC;AACJ,CAAC;AAOD,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC;IAC9C,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAEzD,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC;IACjC,MAAM,SAAS,GAAG,kBAAkB,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;IAE5D,MAAM,aAAa,GAAG,YAAY,CAAC,OAAO,EAAE;QAC1C,GAAG,OAAO;QACV,KAAK;QACL,MAAM,EAAE,CAAC;KACV,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG;QACf,IAAI,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,aAAa,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE;QAC/C,IAAI,EAAE;YACJ,OAAO,EAAE,MAAM;YACf,eAAe,EAAE,SAAS;YAC1B,aAAa,EAAE,SAAS;YACxB,aAAa,EAAE,UAAU;YACzB,UAAU,EAAE,IAAI;SACjB;QACD,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACzB,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,UAAU,CAAC,OAAiB;IACnC,OAAO,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC;AACnE,CAAC;AAID,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,SAAS,GAAG,GAAG,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAChD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC;IACxC,MAAM,aAAa,GAAG,kBAAkB,CAAC,OAAO,EAAE,SAAS,CAAW,CAAC;IACvE,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,OAAO,EAAE;QACpC,GAAG,OAAO;QACV,SAAS,EAAE,aAAa;KACzB,CAAC,CAAC;IACH,MAAM,QAAQ,GAAG;QACf,oDAAoD;QACpD,IAAI,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE;QACvD,IAAI,EAAE;YACJ,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,SAAS,EAAE,CAAC;YACZ,SAAS,EAAE,KAAK;YAChB,eAAe,EAAE,aAAa;YAC9B,aAAa,EAAE,aAAa;YAC5B,aAAa,EAAE,YAAY;YAC3B,UAAU;YACV,IAAI,EAAE,IAAI;SACX;QACD,MAAM,EAAE,EAAE,MAAM,EAAE,UAAU,CAAC,MAAM,EAAE;KACtC,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,kBAAkB,CACzB,OAA0B,EAC1B,SAAiB;IAEjB,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE;QAC/B,OAAO,YAAY,CAAC,OAAO,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAC;KAC5D;SAAM,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,EAAE;QACpC,OAAO,GAAG,SAAS,IAAI,SAAS,EAAE,CAAC;KACpC;SAAM;QACL,OAAO,GAAG,SAAS,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC9C,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC;YACnB,SAAS;SACV,CAAC,EAAE,CAAC;KACN;AACH,CAAC"}

package/lib-esm/prediction/utils/fetchPrediction.js

@@ -1,21 +1,26 @@
 import fetch from 'cross-fetch';
-export async function fetchPrediction(molecule, options) {
+import { isMolfileNotEmpty } from './isMolfileNotEmpty';
+export async function fetchPrediction(molfile, options) {
+    if (!isMolfileNotEmpty(molfile)) {
+        return {
+            nucleus: '13C',
+            joinedSignals: [],
+            signals: [],
+            ranges: [],
+        };
+    }
     const { webserviceURL } = options;
     const response = await fetch(webserviceURL, {
         headers: {
             accept: 'application/json',
             'content-type': 'application/json',
         },
-        body: JSON.stringify({ molfile: molecule.toMolfile() }),
+        body: JSON.stringify({ molfile }),
         method: 'POST',
     });
     if (response.status >= 400) {
         throw new Error(response.statusText);
     }
-    const prediction = (await response.json()).data;
-    prediction.molecule = molecule
-        .getOCL()
-        .Molecule.fromMolfile(prediction.molfile);
-    return prediction;
+    return (await response.json()).data;
 }
 //# sourceMappingURL=fetchPrediction.js.map

package/lib-esm/prediction/utils/fetchPrediction.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/utils/getFilteredIDiaIDs.js

@@ -1,29 +1,16 @@
-import { getHoseCodesFromDiastereotopicID, ensureHeterotopicChiralBonds, groupDiastereotopicAtomIDs, } from 'openchemlib-utils';
-export function getFilteredIDiaIDs(molecule, options) {
-    const { maxSphereSize, diaIDs } = options;
-    molecule.addImplicitHydrogens();
-    molecule.addMissingChirality();
-    ensureHeterotopicChiralBonds(molecule);
-    const molfile = molecule.toMolfile();
-    const groupedDiaIDs = groupDiastereotopicAtomIDs(diaIDs, molecule, {
-        atomLabel: 'C',
-    });
-    const carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
+export function getFilteredIDiaIDs(options) {
+    const { groupedDiaIDs, hoses } = options;
+    const carbonDiaIDs = groupedDiaIDs
+        .filter((group) => group.atomLabel === 'C')
+        .sort((a, b) => {
         if (a.atomLabel === b.atomLabel) {
             return b.counter - a.counter;
         }
         return a.atomLabel < b.atomLabel ? 1 : -1;
     });
-    const OCL = molecule.getOCL();
     for (const diaId of carbonDiaIDs) {
-        diaId.hose = getHoseCodesFromDiastereotopicID(OCL.Molecule.fromIDCode(diaId.oclID), {
-            maxSphereSize,
-        });
+        diaId.hose = hoses[diaId.atoms[0]];
     }
-    const toReturn = {
-        molfile,
-        carbonDiaIDs: carbonDiaIDs,
-    };
-    return toReturn;
+    return carbonDiaIDs;
 }
 //# sourceMappingURL=getFilteredIDiaIDs.js.map

package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/utils/isMolfileNotEmpty.js

@@ -0,0 +1,8 @@
+import { Molecule } from 'openchemlib/full';
+import { isEmptyMolecule } from './isEmptyMolecule';
+export function isMolfileNotEmpty(molFile) {
+    if (!molFile?.match(/V[23]0/))
+        return false;
+    return !isEmptyMolecule(Molecule.fromMolfile(molFile));
+}
+//# sourceMappingURL=isMolfileNotEmpty.js.map

package/lib-esm/prediction/utils/isMolfileNotEmpty.js.map

@@ -0,0 +1 @@
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package/lib-esm/prediction/utils/predict2D.js

@@ -1,39 +1,36 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { agnes } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
-import { getGroupedDiastereotopicAtomIDs, getPathsInfo, groupDiastereotopicAtomIDs, } from 'openchemlib-utils';
+import { Molecule } from 'openchemlib/full';
 import { setIDs } from '../../peaks/util/setIDs';
 import { getNuclei } from './getNuclei';
-import { getPredictions } from './getPredictions';
 function checkFromTo(options) {
     if (!options.from || !options.to) {
         throw new Error('options from and to are mandatory');
     }
 }
-export async function predict2D(molecule, options = {}) {
+export async function predict2D(molecule, options) {
     checkFromTo(options);
     molecule.addImplicitHydrogens();
-    const { from, to, diaIDs, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
-    const pathsInfo = getPathsInfo(molecule, {
+    const { from, to, diaIDs, groupedDiaIDs, minLength = 0, maxLength, predictions, distanceMatrix, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
+    const pathsInfo = getPossibleCorrelations({
+        molecule,
         fromLabel: from,
         toLabel: to,
+        diaIDs,
+        distanceMatrix,
         minLength,
         maxLength,
     });
-    const groupedDiaIDS = diaIDs
-        ? groupDiastereotopicAtomIDs(diaIDs, molecule)
-        : getGroupedDiastereotopicAtomIDs(molecule);
     const diaIDswithAtomInfo = [];
-    for (const diaID of groupedDiaIDS) {
+    for (const diaID of groupedDiaIDs) {
         diaIDswithAtomInfo.push({
             ...diaID,
             pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
         });
     }
-    const xPrediction = await getPredictions(from, molecule, predictOptions, predictor, predictions);
-    const yPrediction = from === to
-        ? xPrediction
-        : await getPredictions(to, molecule, predictOptions, predictor, predictions);
+    const yPrediction = predictions[to];
+    const xPrediction = predictions[from];
     if (!xPrediction || !yPrediction) {
         throw new Error('predictions are not availaible');
     }
@@ -85,21 +82,47 @@ export async function predict2D(molecule, options = {}) {
         }
     }
     if (includeDiagonal) {
-        addSelftCorrelation(group, { paths: pathsInfo, signalsByDiaID });
+        addSelfCorrelation(group, { paths: pathsInfo, signalsByDiaID });
     }
     // clusterize signals by distance
     const joinedSignals = Object.values(group);
     const zones = createZones(joinedSignals, { joinDistance, from, to });
     return {
-        molfile: molecule.toMolfile(),
-        diaIDs: spectra.x.diaIDs,
         nuclei: getNuclei({ from, to }),
         joinedSignals,
         signals: splitSignals(joinedSignals),
         zones,
-        molecule,
     };
 }
+function getPossibleCorrelations(options) {
+    const { fromLabel, toLabel, distanceMatrix, molecule, diaIDs, minLength, maxLength, } = options;
+    const fromAtomicNumber = Molecule.getAtomicNoFromLabel(fromLabel);
+    const toAtomicNumber = Molecule.getAtomicNoFromLabel(toLabel);
+    const atomPathInfo = [];
+    for (let from = 0; from < molecule.getAllAtoms(); from++) {
+        const toSave = {
+            oclID: diaIDs[from],
+            paths: [],
+        };
+        for (let to = 0; to < molecule.getAllAtoms(); to++) {
+            if (from === to)
+                continue;
+            if (molecule.getAtomicNo(to) !== toAtomicNumber)
+                continue;
+            if (molecule.getAtomicNo(from) !== fromAtomicNumber)
+                continue;
+            const pathLength = distanceMatrix[from][to];
+            if (pathLength >= minLength && pathLength <= maxLength) {
+                toSave.paths.push({
+                    from,
+                    to,
+                });
+            }
+        }
+        atomPathInfo.push(toSave);
+    }
+    return atomPathInfo;
+}
 function splitSignals(joinedSignals) {
     const signals = [];
     for (const signal of joinedSignals) {
@@ -114,7 +137,7 @@ function splitSignals(joinedSignals) {
     }
     return setIDs(signals);
 }
-function addSelftCorrelation(group, options) {
+function addSelfCorrelation(group, options) {
     const { paths = [], signalsByDiaID } = options;
     for (const atom of paths) {
         if (atom.paths.length < 1)

package/lib-esm/prediction/utils/predict2D.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/utils/queryByHOSE.js.map

@@ -1 +1 @@
-{"version":3,"file":"queryByHOSE.js","sourceRoot":"","sources":["../../../src/prediction/utils/queryByHOSE.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,WAAW,CACzB,MAA6B,EAC7B,EAAqB,EACrB,OAAkC;IAElC,MAAM,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAElC,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,KAAK,MAAM,OAAO,IAAI,MAAM,EAAE;QAC5B,IAAI,GAAG,CAAC;QACR,IAAI,KAAK,GAAG,IAAI,CAAC;QACjB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;YAC/C,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE;gBACT,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC7B,KAAK,GAAG,CAAC,CAAC;aACX;SACF;QAED,KAAK,MAAM,UAAU,IAAI,OAAO,CAAC,KAAK,EAAE;YACtC,MAAM,IAAI,GAAG;gBACX,MAAM,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;gBACvB,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI;gBAC1B,KAAK,EAAE,CAAC,UAAU,CAAC;gBACnB,OAAO,EAAE,CAAC;gBACV,KAAK;gBACL,SAAS,EACP,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC;oBACnB,CAAC,CAAC;wBACE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;wBACZ,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;wBACV,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;wBACX,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;wBACX,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;qBACX;oBACH,CAAC,CAAC,SAAS;aAChB,CAAC;YACF,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrB;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC"}
+{"version":3,"file":"queryByHOSE.js","sourceRoot":"","sources":["../../../src/prediction/utils/queryByHOSE.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,WAAW,CACzB,MAAW,EACX,EAAqB,EACrB,OAAkC;IAElC,MAAM,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAElC,MAAM,QAAQ,GAAG,EAAE,CAAC;IACpB,KAAK,MAAM,OAAO,IAAI,MAAM,EAAE;QAC5B,IAAI,GAAG,CAAC;QACR,IAAI,KAAK,GAAG,IAAI,CAAC;QACjB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;YAC/C,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE;gBACT,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC7B,KAAK,GAAG,CAAC,CAAC;aACX;SACF;QAED,KAAK,MAAM,UAAU,IAAI,OAAO,CAAC,KAAK,EAAE;YACtC,MAAM,IAAI,GAAG;gBACX,MAAM,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;gBACvB,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI;gBAC1B,KAAK,EAAE,CAAC,UAAU,CAAC;gBACnB,OAAO,EAAE,CAAC;gBACV,KAAK;gBACL,SAAS,EACP,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC;oBACnB,CAAC,CAAC;wBACE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;wBACZ,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;wBACV,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;wBACX,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;wBACX,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;qBACX;oBACH,CAAC,CAAC,SAAS;aAChB,CAAC;YACF,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;SACrB;KACF;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/lib-esm/prediction/utils/shouldPredict.js

@@ -0,0 +1,11 @@
+export function shouldPredict(key, options) {
+    if (key in options)
+        return true;
+    const heteroRequired = 'hsqc' in options || 'hmbc' in options;
+    return key === 'C'
+        ? heteroRequired
+        : key === 'H'
+            ? heteroRequired || 'cosy' in options
+            : false;
+}
+//# sourceMappingURL=shouldPredict.js.map

package/lib-esm/prediction/utils/shouldPredict.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"shouldPredict.js","sourceRoot":"","sources":["../../../src/prediction/utils/shouldPredict.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,aAAa,CAC3B,GAAwC,EACxC,OAAsC;IAEtC,IAAI,GAAG,IAAI,OAAO;QAAE,OAAO,IAAI,CAAC;IAChC,MAAM,cAAc,GAAG,MAAM,IAAI,OAAO,IAAI,MAAM,IAAI,OAAO,CAAC;IAC9D,OAAO,GAAG,KAAK,GAAG;QAChB,CAAC,CAAC,cAAc;QAChB,CAAC,CAAC,GAAG,KAAK,GAAG;YACb,CAAC,CAAC,cAAc,IAAI,MAAM,IAAI,OAAO;YACrC,CAAC,CAAC,KAAK,CAAC;AACZ,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.9.2",
+  "version": "10.0.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -58,7 +58,6 @@
     "@lukeed/uuid": "^2.0.1",
     "@types/lodash": "^4.14.196",
     "binary-search": "^1.3.6",
-    "brukerconverter": "^6.1.4",
     "cross-fetch": "^4.0.0",
     "form-data": "^4.0.0",
     "gyromagnetic-ratio": "^1.0.0",
@@ -82,7 +81,7 @@
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
     "nmredata": "^0.9.2",
-    "openchemlib-utils": "^4.0.0",
+    "openchemlib-utils": "^4.2.1",
     "spectrum-generator": "^8.0.8"
   }
 }

package/src/assignment/get13CAssignments.ts

@@ -1,12 +1,8 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { Molecule } from 'openchemlib/full';
-import { ensureHeterotopicChiralBonds } from 'openchemlib-utils';
 
-import { NMRRange, NMRRangeWithIntegration } from '..';
-import {
-  predictCarbon,
-  PredictCarbonOptions,
-} from '../prediction/predictCarbon';
+import { NMRRange, NMRRangeWithIntegration, predict } from '..';
+import { PredictCarbonOptions } from '../prediction/predictCarbon';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 
 import type {
@@ -81,8 +77,13 @@ export async function get13CAssignments(
     throw new Error('It is needed a OCL molecule instance to assign');
   }
 
-  ensureHeterotopicChiralBonds(molecule);
-  const { joinedSignals } = await predictCarbon(molecule, predictionOptions);
+  const { spectra } = await predict(molecule, {
+    predictOptions: {
+      C: predictionOptions,
+    },
+  });
+
+  const joinedSignals = spectra.carbon?.joinedSignals || [];
 
   checkAtomsAndDiaIDs(joinedSignals);
   const copyRanges = checkIntegration(ranges);