nmr-processing 9.9.1 → 9.9.3-pre.1691757604

package/lib/assignment/get13CAssignments.js

@@ -2,8 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.get13CAssignments = void 0;
 const uuid_1 = require("@lukeed/uuid");
-const openchemlib_utils_1 = require("openchemlib-utils");
-const predictCarbon_1 = require("../prediction/predictCarbon");
+const __1 = require("..");
 const buildAssignments_1 = require("./utils/oneDimensionalAssignment/buildAssignments");
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
@@ -27,8 +26,12 @@ async function get13CAssignments(ranges, molecule, options = {}) {
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }
-    (0, openchemlib_utils_1.ensureHeterotopicChiralBonds)(molecule);
-    const { joinedSignals } = await (0, predictCarbon_1.predictCarbon)(molecule, predictionOptions);
+    const { spectra } = await (0, __1.predict)(molecule, {
+        predictOptions: {
+            C: predictionOptions,
+        },
+    });
+    const joinedSignals = spectra.carbon?.joinedSignals || [];
     checkAtomsAndDiaIDs(joinedSignals);
     const copyRanges = checkIntegration(ranges);
     const targets = {};

package/lib/assignment/get13CAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/get1HAssignments.js

@@ -2,8 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.get1HAssignments = void 0;
 const uuid_1 = require("@lukeed/uuid");
-const openchemlib_utils_1 = require("openchemlib-utils");
-const predictProton_1 = require("../prediction/predictProton");
+const __1 = require("..");
 const buildAssignments_1 = require("./utils/oneDimensionalAssignment/buildAssignments");
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
@@ -27,9 +26,12 @@ async function get1HAssignments(ranges, molecule, options = {}) {
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }
-    molecule.addImplicitHydrogens();
-    (0, openchemlib_utils_1.ensureHeterotopicChiralBonds)(molecule);
-    const { joinedSignals } = await (0, predictProton_1.predictProton)(molecule, predictionOptions);
+    const { spectra } = await (0, __1.predict)(molecule, {
+        predictOptions: {
+            H: predictionOptions,
+        },
+    });
+    const joinedSignals = spectra.proton?.joinedSignals || [];
     checkForIntegration(ranges);
     checkAtomsAndDiaIDs(joinedSignals);
     const targets = {};

package/lib/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/generalAssignment/buildAssignments.d.ts

@@ -1,6 +1,8 @@
 import { Values } from 'nmr-correlation';
 import type { Molecule } from 'openchemlib/full';
-import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
+import { PredictCarbonOptions } from '../../../prediction/predictCarbon';
+import { PredictProtonOptions } from '../../../prediction/predictProton';
+import { NMRSignal1D } from '../../../signals/NMRSignal1D';
 import { MakeMandatory } from '../../../utilities/MakeMandatory';
 import { SpectraDataWithIds } from '../../nmrAssigment';
 import { TargetsByAtomType } from './getTargetsAndCorrelations';

package/lib/assignment/utils/generalAssignment/buildAssignments.js

@@ -6,8 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.buildAssignments = exports.getAllHydrogens = void 0;
 const ml_tree_set_1 = __importDefault(require("ml-tree-set"));
 const openchemlib_utils_1 = require("openchemlib-utils");
-const predictCarbon_1 = require("../../../prediction/predictCarbon");
-const predictProton_1 = require("../../../prediction/predictProton");
+const predict_1 = require("../../../prediction/predict");
 const createMapPossibleAssignment_1 = require("./createMapPossibleAssignment");
 const exploreTree_1 = require("./exploreTree");
 const isSpectraData1D_1 = require("./isSpectraData1D");
@@ -15,7 +14,6 @@ const searchIndices_1 = require("./searchIndices");
 const comparator = (a, b) => {
     return b.score - a.score;
 };
-const predictor = { H: predictProton_1.predictProton, C: predictCarbon_1.predictCarbon };
 function checkNMRSignal1D(signals) {
     const keys = [
         'nbAtoms',
@@ -49,11 +47,15 @@ async function buildAssignments(props) {
     let diaIDPeerPossibleAssignment = {};
     for (const atomTypesToPredict of assignmentOrder) {
         for (const atomType of atomTypesToPredict) {
-            const options = predictionOptions[atomType];
+            const options = {};
+            options[atomType] = predictionOptions[atomType];
             const predictedSignals = inputPrediction[atomType];
-            const { joinedSignals } = predictedSignals
-                ? { joinedSignals: predictedSignals }
-                : await predictor[atomType](molecule, options);
+            const joinedSignals = await getJoinedSignals({
+                molecule,
+                predictedSignals,
+                options,
+                atomType,
+            });
             checkNMRSignal1D(joinedSignals);
             if (!predictions[atomType])
                 predictions[atomType] = {};
@@ -209,4 +211,13 @@ function fillPartial(nSources, value = null) {
     }
     return partial;
 }
+async function getJoinedSignals(input) {
+    const { molecule, predictedSignals, options, atomType } = input;
+    if (predictedSignals)
+        return predictedSignals;
+    const { spectra } = await (0, predict_1.predict)(molecule, {
+        predictOptions: options,
+    });
+    return spectra[atomType === 'C' ? 'carbon' : 'proton']?.joinedSignals || [];
+}
 //# sourceMappingURL=buildAssignments.js.map

package/lib/assignment/utils/generalAssignment/buildAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"buildAssignments.js","sourceRoot":"","sources":["../../../../src/assignment/utils/generalAssignment/buildAssignments.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAkC;AAGlC,yDAA0D;AAE1D,yDAGqC;AAQrC,+EAGuC;AACvC,+CAAgE;AAEhE,uDAAoD;AACpD,mDAAgD;AAEhD,MAAM,UAAU,GAAG,CAAC,CAAqB,EAAE,CAAqB,EAAE,EAAE;IAClE,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;AAC3B,CAAC,CAAC;AAwCF,SAAS,gBAAgB,CACvB,OAAsB;IAEtB,MAAM,IAAI,GAA0C;QAClD,SAAS;QACT,QAAQ;QACR,OAAO;KACR,CAAC;IACF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE;YACtB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC;gBAAE,MAAM,IAAI,KAAK,CAAC,YAAY,GAAG,iBAAiB,CAAC,CAAC;SACrE;KACF;AACH,CAAC;AAsBY,QAAA,eAAe,GAAG;IAC7B,CAAC,EAAE,CAAC,CAAW,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC;IACnD,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC;CACX,CAAC;AAEK,KAAK,UAAU,gBAAgB,CAAC,KAA2B;IAChE,MAAM,EACJ,OAAO,EACP,QAAQ,EACR,eAAe,EACf,OAAO,EACP,QAAQ,EACR,mBAAmB,GAAG,EAAE,EACxB,YAAY,EACZ,YAAY,EACZ,eAAe,EACf,iBAAiB,EACjB,WAAW,EAAE,eAAe,GAAG,EAAE,EACjC,OAAO,GACR,GAAG,KAAK,CAAC;IAEV,MAAM,eAAe,GAAG,QAAQ,CAAC;IAEjC,IAAI,KAAK,GAAqB;QAC5B,SAAS,EAAE,IAAI,qBAAO,CAAC,UAAU,CAAC;QAClC,UAAU,EAAE,CAAC;KACd,CAAC;IAEF,MAAM,gBAAgB,GAAG,IAAA,yCAAqB,EAAC,QAAQ,EAAE;QACvD,UAAU,EAAE,IAAI;KACjB,CAAC,CAAC;IAEH,MAAM,cAAc,GAAmB,EAAE,CAAC;IAC1C,MAAM,WAAW,GAA0B,EAAE,CAAC;IAC9C,IAAI,qBAAqB,GAA2B,EAAE,CAAC;IACvD,IAAI,2BAA2B,GAAgC,EAAE,CAAC;IAElE,KAAK,MAAM,kBAAkB,IAAI,eAAe,EAAE;QAChD,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE;YACzC,MAAM,OAAO,GAAkC,EAAE,CAAC;YAClD,OAAO,CAAC,QAAQ,CAAC,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YAChD,MAAM,gBAAgB,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;YACnD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC;gBAC3C,QAAQ;gBACR,gBAAgB;gBAChB,OAAO;gBACP,QAAQ;aACT,CAAC,CAAC;YAEH,gBAAgB,CAAC,aAAa,CAAC,CAAC;YAEhC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC;gBAAE,WAAW,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;YAEvD,IAAI,cAAc,GAAG,CAAC,CAAC;YACvB,KAAK,MAAM,UAAU,IAAI,aAAa,EAAE;gBACtC,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;gBACnC,MAAM,KAAK,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gBAClC,MAAM,YAAY,GAAG,uBAAe,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;gBAChE,cAAc,IAAI,UAAU,CAAC,OAAO,GAAG,YAAY,CAAC;gBACpD,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,GAAG;oBAC7B,GAAG,UAAU;oBACb,UAAU,EAAE,KAAK;oBACjB,YAAY,EAAE,UAAU,CAAC,OAAO,GAAG,YAAY;oBAC/C,YAAY,EAAE,YAAY;oBAC1B,UAAU,EAAE,gBAAgB,CAAC,KAAK,CAAa;iBAChD,CAAC;aACH;YACD,KAAK,MAAM,KAAK,IAAI,WAAW,CAAC,QAAQ,CAAC,EAAE;gBACzC,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC,YAAY,IAAI,GAAG,GAAG,cAAc,CAAC;aACnE;YACD,cAAc,CAAC,QAAQ,CAAC,GAAG;gBACzB,QAAQ,EAAE,aAAa,CAAC,MAAM;gBAC9B,YAAY,EAAE,CAAC;gBACf,mBAAmB,EAAE,mBAAmB,CAAC,QAAQ,CAAC,IAAI,CAAC;aACxD,CAAC;SACH;QAED,qBAAqB,GAAG,IAAA,yDAA2B,EAAC,qBAAqB,EAAE;YACzE,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,2BAA2B,GAAG,EAAE,CAAC;QACjC,KAAK,MAAM,QAAQ,IAAI,qBAAqB,EAAE;YAC5C,2BAA2B,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAC,IAAI,CACjD,qBAAqB,CAAC,QAAQ,CAAC,CAChC,CAAC;SACH;QAED,MAAM,gBAAgB,GAAG,mBAAmB,CAC1C,KAAK,EACL,cAAc,EACd,kBAAkB,CACnB,CAAC;QAEF,KAAK,GAAG;YACN,SAAS,EAAE,IAAI,qBAAO,CAAC,UAAU,CAAC;YAClC,UAAU,EAAE,CAAC;SACd,CAAC;QAEF,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAE7B,KAAK,MAAM,OAAO,IAAI,gBAAgB,EAAE;YACtC,IAAA,yBAAW,EACT;gBACE,gBAAgB,EAAE,kBAAkB;gBACpC,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,OAAO;gBACP,WAAW;gBACX,YAAY;gBACZ,YAAY;gBACZ,eAAe;gBACf,qBAAqB;gBACrB,2BAA2B;aAC5B,EACD,cAAc,EACd,OAAO,EACP,KAAK,CACN,CAAC;SACH;KACF;IACD,OAAO,mBAAmB,CAAC;QACzB,KAAK;QACL,OAAO;QACP,2BAA2B;QAC3B,OAAO;KACR,CAAC,CAAC;AACL,CAAC;AA7HD,4CA6HC;AASD,SAAS,mBAAmB,CAAC,KAA+B;IAC1D,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,2BAA2B,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IACvE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC;IAC5B,MAAM,WAAW,GAAQ,EAAE,CAAC;IAC5B,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,CAAC;IACtD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,MAAM,gBAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QAC3C,KAAK,MAAM,QAAQ,IAAI,gBAAgB,EAAE;YACvC,MAAM,MAAM,GAAG,gBAAgB,CAAC,QAAQ,CAAC,CAAC;YAC1C,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;gBAC9B,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;gBAChC,IAAI,WAAW,CAAC,QAAQ,CAAC;oBAAE,SAAS;gBACpC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,GAAG,IAAA,6BAAa,EAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;aAChE;SACF;KACF;IAED,MAAM,MAAM,GAAG,EAAE,CAAC;IAClB,KAAK,MAAM,QAAQ,IAAI,SAAS,CAAC,QAAQ,EAAE;QACzC,MAAM,aAAa,GAAG,IAAI,CAAC,KAAK,CAC9B,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CACA,CAAC;QAC1B,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,GAAG,QAAQ,CAAC;QACvC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,UAAU,CAAgB,CAAC;QACzD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;YAChC,MAAM,gBAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC3C,MAAM,sBAAsB,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC;YACpD,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,sBAAsB,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBAClE,MAAM,QAAQ,GAAG,sBAAsB,CAAC,KAAK,CAAC,CAAC;gBAE/C,IAAI,QAAQ,KAAK,GAAG,IAAI,CAAC,QAAQ;oBAAE,SAAS;gBAE5C,MAAM,MAAM,GAAG,gBAAgB,CAAC,QAAQ,CAAC,CAAC;gBAC1C,MAAM,KAAK,GAAG,2BAA2B,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;gBAE3D,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;oBAC9B,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,WAAW,EAAE,GAChD,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;oBAC9B,MAAM,QAAQ,GAAG,aAAa,CAAC,aAAa,CAAC,CAAC;oBAE9C,IAAI,IAAA,iCAAe,EAAC,QAAQ,CAAC,EAAE;wBAC7B,MAAM,EAAE,MAAM,E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package/lib/databases/getDatabase.js

@@ -1,7 +1,10 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getDatabase = void 0;
-const cross_fetch_1 = require("cross-fetch");
+const cross_fetch_1 = __importDefault(require("cross-fetch"));
 const resurrectRange_1 = require("../utilities/resurrectRange");
 async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
     const { format = 'tsv' } = options;
@@ -9,7 +12,7 @@ async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L
         url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
     }
     let parsed;
-    const response = await (0, cross_fetch_1.fetch)(url);
+    const response = await (0, cross_fetch_1.default)(url);
     switch (format) {
         case 'tsv':
             parsed = parseData(await response.text());

package/lib/databases/getDatabase.js.map

@@ -1 +1 @@
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package/lib/index.d.ts

@@ -5,13 +5,6 @@ export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';
 export * from './peaks/peaksToXY';
 export * from './peaks/peakToXY';
-export * from './prediction/predictProton';
-export * from './prediction/predictCarbon';
-export * from './prediction/predictCOSY';
-export * from './prediction/predictHSQC';
-export * from './prediction/predictHMBC';
-export * from './prediction/predictAll';
-export * from './prediction/predictAllSpectra';
 export * from './assignment/get1HAssignments';
 export * from './assignment/get13CAssignments';
 export * from './assignment/getAssignments';
@@ -25,6 +18,8 @@ export * from './signals/signalsToFID';
 export * from './signals/simulation/simulate1D';
 export * from './signal/signalJoinCouplings';
 export * from './signal/signalMultiplicityPattern';
+export * from './prediction/predict';
+export * from './prediction/predictSpectra';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';

package/lib/index.js

@@ -34,13 +34,6 @@ __exportStar(require("./constants/couplingPatterns"), exports);
 __exportStar(require("./peaks/peaksFilterImpurities"), exports);
 __exportStar(require("./peaks/peaksToXY"), exports);
 __exportStar(require("./peaks/peakToXY"), exports);
-__exportStar(require("./prediction/predictProton"), exports);
-__exportStar(require("./prediction/predictCarbon"), exports);
-__exportStar(require("./prediction/predictCOSY"), exports);
-__exportStar(require("./prediction/predictHSQC"), exports);
-__exportStar(require("./prediction/predictHMBC"), exports);
-__exportStar(require("./prediction/predictAll"), exports);
-__exportStar(require("./prediction/predictAllSpectra"), exports);
 __exportStar(require("./assignment/get1HAssignments"), exports);
 __exportStar(require("./assignment/get13CAssignments"), exports);
 __exportStar(require("./assignment/getAssignments"), exports);
@@ -54,6 +47,8 @@ __exportStar(require("./signals/signalsToFID"), exports);
 __exportStar(require("./signals/simulation/simulate1D"), exports);
 __exportStar(require("./signal/signalJoinCouplings"), exports);
 __exportStar(require("./signal/signalMultiplicityPattern"), exports);
+__exportStar(require("./prediction/predict"), exports);
+__exportStar(require("./prediction/predictSpectra"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
 __exportStar(require("./utilities/getFrequency"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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package/lib/prediction/GroupDiastereotopicAtomIDs.d.ts

@@ -0,0 +1,6 @@
+export interface GroupDiastereotopicAtomIDs {
+    counter: number;
+    atoms: number[];
+    oclID: string;
+    atomLabel: string;
+}

package/lib/prediction/GroupDiastereotopicAtomIDs.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=GroupDiastereotopicAtomIDs.js.map

package/lib/prediction/GroupDiastereotopicAtomIDs.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GroupDiastereotopicAtomIDs.js","sourceRoot":"","sources":["../../src/prediction/GroupDiastereotopicAtomIDs.ts"],"names":[],"mappings":""}

package/lib/prediction/Prediction1D.d.ts

@@ -1,12 +1,7 @@
 import type { Molecule } from 'openchemlib/full';
-import type { NMRSignal1D } from '../signals/NMRSignal1D';
-import type { NMRRange } from '../xy/NMRRange';
-export interface Prediction1D {
+import type { PredictionBase1D } from './PredictionBase1D';
+export interface Prediction1D extends PredictionBase1D {
     molfile: string;
     diaIDs: string[];
-    nucleus: string;
-    joinedSignals: NMRSignal1D[];
-    signals: NMRSignal1D[];
-    ranges: NMRRange[];
     molecule: Molecule;
 }

package/lib/prediction/Prediction2D.d.ts

@@ -1,12 +1,7 @@
 import type { Molecule } from 'openchemlib/full';
-import { NMRSignal2D } from '../xyz/NMRSignal2D';
-import { NMRZone } from '../xyz/NMRZone';
-export interface Prediction2D {
+import { PredictionBase2D } from './PredictionBase2D';
+export interface Prediction2D extends PredictionBase2D {
     molfile: string;
     diaIDs: string[];
-    nuclei: string[];
-    joinedSignals: NMRSignal2D[];
-    signals: NMRSignal2D[];
-    zones: NMRZone[];
     molecule: Molecule;
 }

package/lib/prediction/PredictionBase1D.d.ts

@@ -0,0 +1,8 @@
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { NMRRange } from '../xy/NMRRange';
+export interface PredictionBase1D {
+    nucleus: string;
+    joinedSignals: NMRSignal1D[];
+    signals: NMRSignal1D[];
+    ranges: NMRRange[];
+}

package/lib/prediction/PredictionBase1D.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=PredictionBase1D.js.map

package/lib/prediction/PredictionBase1D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"PredictionBase1D.js","sourceRoot":"","sources":["../../src/prediction/PredictionBase1D.ts"],"names":[],"mappings":""}

package/lib/prediction/PredictionBase2D.d.ts

@@ -0,0 +1,8 @@
+import { NMRSignal2D } from '../xyz/NMRSignal2D';
+import { NMRZone } from '../xyz/NMRZone';
+export interface PredictionBase2D {
+    nuclei: string[];
+    joinedSignals: NMRSignal2D[];
+    signals: NMRSignal2D[];
+    zones: NMRZone[];
+}

package/lib/prediction/PredictionBase2D.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=PredictionBase2D.js.map

package/lib/prediction/PredictionBase2D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"PredictionBase2D.js","sourceRoot":"","sources":["../../src/prediction/PredictionBase2D.ts"],"names":[],"mappings":""}

package/lib/prediction/predict.d.ts

@@ -0,0 +1,55 @@
+import type { Logger } from 'cheminfo-types';
+import type { Molecule } from 'openchemlib/full';
+import { PredictionBase1D } from './PredictionBase1D';
+import { PredictionBase2D } from './PredictionBase2D';
+import { PredictCOSYOptions } from './predictCOSY';
+import { PredictCarbonOptions } from './predictCarbon';
+import { PredictHMBCOptions } from './predictHMBC';
+import { PredictHSQCOptions } from './predictHSQC';
+import { PredictProtonOptions } from './predictProton';
+export interface PredictionOptionsByExperiment {
+    H?: Partial<PredictProtonOptions>;
+    C?: Partial<PredictCarbonOptions>;
+    hsqc?: Partial<PredictHSQCOptions>;
+    cosy?: Partial<PredictCOSYOptions>;
+    hmbc?: Partial<PredictHMBCOptions>;
+}
+export interface PredictAllOptions {
+    /**
+     *  mono dimensional signal to generate the bidimenionals cross peaks.
+     * The object should has properties with name equal to "H" and "C".
+     */
+    predictOptions?: PredictionOptionsByExperiment;
+    /**
+     * signals with euclidean distance in ppm less than this it will
+     * joined into a zone.
+     * @default {H:0.05,C:0.5}
+     */
+    joinDistance?: {
+        H: number;
+        C: number;
+    };
+    logger?: Logger;
+}
+export interface PredictedSpectra {
+    proton?: PredictionBase1D;
+    carbon?: PredictionBase1D;
+    cosy?: PredictionBase2D;
+    hsqc?: PredictionBase2D;
+    hmbc?: PredictionBase2D;
+}
+export interface Predicted {
+    molfile: string;
+    molfileWithH: string;
+    hoses: any[];
+    diaIDs: any[] | undefined;
+    groupedDiaIDs: any[];
+    moleculeWithHydrogens: Molecule;
+    distanceMatrix: any[];
+    spectra: PredictedSpectra;
+}
+/**
+ * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
+ * @returns {Promise<object>} - object with molfile, diaIDs, 1D and 2D signals, joined signals, ranges and zones.
+ */
+export declare function predict(molecule: Molecule, options?: PredictAllOptions): Promise<Predicted>;

package/lib/prediction/predict.js

@@ -0,0 +1,113 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.predict = void 0;
+const openchemlib_utils_1 = require("openchemlib-utils");
+const predictCOSY_1 = require("./predictCOSY");
+const predictCarbon_1 = require("./predictCarbon");
+const predictHMBC_1 = require("./predictHMBC");
+const predictHSQC_1 = require("./predictHSQC");
+const predictProton_1 = require("./predictProton");
+const shouldPredict_1 = require("./utils/shouldPredict");
+const toPredict = {
+    cosy: {
+        predictor: predictCOSY_1.predictCOSY,
+        required: ['H'],
+        message: 'Proton prediction is missing so COSY could not be generated.',
+    },
+    hsqc: {
+        predictor: predictHSQC_1.predictHSQC,
+        required: ['H', 'C'],
+        message: 'Carbon and / or proton prediction is missing so HSQC could not be generated.',
+    },
+    hmbc: {
+        predictor: predictHMBC_1.predictHMBC,
+        required: ['H', 'C'],
+        message: 'Carbon and / or proton prediction is missing so HMBC could not be generated.',
+    },
+};
+/**
+ * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
+ * @returns {Promise<object>} - object with molfile, diaIDs, 1D and 2D signals, joined signals, ranges and zones.
+ */
+async function predict(molecule, options = {}) {
+    const { logger, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {
+        H: {},
+        C: {},
+        hsqc: {},
+        hmbc: {},
+        cosy: {},
+    }, } = options;
+    const hoseCodesAndInfo = (0, openchemlib_utils_1.getHoseCodesAndInfo)(molecule, {
+        maxSphereSize: predictOptions?.C?.maxSphereSize,
+    });
+    const { diaIDs = [], moleculeWithHydrogens, hoses, molfileWithH, distanceMatrix, } = hoseCodesAndInfo;
+    const groupedDiaIDs = (0, openchemlib_utils_1.groupDiastereotopicAtomIDs)(diaIDs, moleculeWithHydrogens);
+    const protonPrediction = (0, shouldPredict_1.shouldPredict)('H', predictOptions)
+        ? await (0, predictProton_1.predictProton)(molfileWithH, {
+            ...predictOptions?.H,
+            diaIDs,
+            distanceMatrix,
+        })
+        : undefined;
+    const carbonPrediction = (0, shouldPredict_1.shouldPredict)('C', predictOptions)
+        ? await (0, predictCarbon_1.predictCarbon)({
+            ...predictOptions?.C,
+            molfile: molfileWithH,
+            groupedDiaIDs,
+            hoses,
+        })
+        : undefined;
+    const spectra = {};
+    const predictions = {};
+    if (check1DPrediction(protonPrediction, diaIDs)) {
+        predictions.H = protonPrediction;
+        if ('H' in predictOptions)
+            spectra.proton = protonPrediction;
+    }
+    if (check1DPrediction(carbonPrediction, diaIDs)) {
+        predictions.C = carbonPrediction;
+        if ('C' in predictOptions)
+            spectra.carbon = carbonPrediction;
+    }
+    const optionsTwoD = {
+        predictions,
+        joinDistance,
+        distanceMatrix,
+        groupedDiaIDs,
+        diaIDs,
+    };
+    for (const key in predictOptions) {
+        if (key === 'H' || key === 'C')
+            continue;
+        const { predictor, required, message } = toPredict[key];
+        if (required.every((key) => key in predictions)) {
+            spectra[key] = await predictor(molecule, {
+                ...optionsTwoD,
+                ...predictOptions[key],
+            });
+        }
+        else if (logger) {
+            logger.warn(message);
+        }
+    }
+    return {
+        ...hoseCodesAndInfo,
+        groupedDiaIDs,
+        spectra,
+    };
+}
+exports.predict = predict;
+function check1DPrediction(prediction, diaIDs = []) {
+    if (!prediction)
+        return false;
+    if (prediction.ranges.length === 0)
+        return false;
+    const { signals } = prediction;
+    for (const signal of signals) {
+        const isCorrect = signal.diaIDs?.every((diaID) => diaIDs.includes(diaID));
+        if (!isCorrect)
+            return false;
+    }
+    return true;
+}
+//# sourceMappingURL=predict.js.map

package/lib/prediction/predict.js.map

@@ -0,0 +1 @@
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package/lib/prediction/predictCOSY.d.ts

@@ -1,7 +1,7 @@
 import type { Molecule } from 'openchemlib/full';
-import type { Prediction1D } from './Prediction1D';
+import { GroupDiastereotopicAtomIDs } from './GroupDiastereotopicAtomIDs';
+import type { PredictionBase1D } from './PredictionBase1D';
 import { PredictProtonOptions } from './predictProton';
-import { Predictor } from './utils/predict2D';
 export interface PredictCOSYOptions {
     /**
      * maximum number of bonds to take into account.
@@ -13,13 +13,6 @@ export interface PredictCOSYOptions {
      * @default 2
      */
     minLength?: number;
-    /**
-     * mono dimensional predictors. The object should has properties with name
-     * equal to "H" and "C".
-     */
-    predictor?: {
-        H?: Predictor;
-    };
     /**
      *  mono dimensional signal to generate the bidimenionals cross peaks.
      * The object should has properties with name equal to "H" and "C".
@@ -41,18 +34,27 @@ export interface PredictCOSYOptions {
      * The object should has properties with name equal to "H" and "C".
      * the value of each prediction should be similar that predictProton and predictCarbon.
      */
-    predictions?: {
-        [key: string]: Prediction1D | undefined;
-        H?: Prediction1D;
+    predictions: {
+        [key: string]: PredictionBase1D | undefined;
+        H?: PredictionBase1D;
     };
     /**
      * if true, the self correlation signal will be add to the prediction.
      * @default true
      */
     includeDiagonal?: boolean;
+    /**
+     * diastereotopic atom ids of the molecule.
+     */
+    diaIDs: string[];
+    /**
+     * grouped diastereotopic atom ids of the molecule.
+     */
+    groupedDiaIDs: GroupDiastereotopicAtomIDs[];
+    distanceMatrix: number[][];
 }
 /**
  * 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 declare function predictCOSY(molecule: Molecule, options?: PredictCOSYOptions): Promise<import("./Prediction2D").Prediction2D>;
+export declare function predictCOSY(molecule: Molecule, options: PredictCOSYOptions): Promise<import("./PredictionBase2D").PredictionBase2D>;

package/lib/prediction/predictCOSY.js

@@ -1,24 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.predictCOSY = void 0;
-const predictProton_1 = require("./predictProton");
 const predict2D_1 = require("./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.
  */
-async function predictCOSY(molecule, options = {}) {
-    const { minLength = 2, maxLength = 3, predictions, predictor = { H: predictProton_1.predictProton }, predictOptions, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = true, } = options;
+async function predictCOSY(molecule, options) {
+    const { minLength = 2, maxLength = 3, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = true, } = options;
     return (0, predict2D_1.predict2D)(molecule, {
+        ...options,
         from: 'H',
         to: 'H',
-        predictor,
         minLength,
         maxLength,
         joinDistance,
-        predictions,
         includeDiagonal,
-        predictOptions,
     });
 }
 exports.predictCOSY = predictCOSY;

package/lib/prediction/predictCOSY.js.map

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