nmr-processing 9.9.2 → 10.0.0

package/lib/prediction/utils/predict2D.js

@@ -4,39 +4,36 @@ exports.predict2D = void 0;
 const uuid_1 = require("@lukeed/uuid");
 const ml_hclust_1 = require("ml-hclust");
 const ml_matrix_1 = require("ml-matrix");
-const openchemlib_utils_1 = require("openchemlib-utils");
+const full_1 = require("openchemlib/full");
 const setIDs_1 = require("../../peaks/util/setIDs");
 const getNuclei_1 = require("./getNuclei");
-const getPredictions_1 = require("./getPredictions");
 function checkFromTo(options) {
     if (!options.from || !options.to) {
         throw new Error('options from and to are mandatory');
     }
 }
-async function predict2D(molecule, options = {}) {
+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 = (0, openchemlib_utils_1.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
-        ? (0, openchemlib_utils_1.groupDiastereotopicAtomIDs)(diaIDs, molecule)
-        : (0, openchemlib_utils_1.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 (0, getPredictions_1.getPredictions)(from, molecule, predictOptions, predictor, predictions);
-    const yPrediction = from === to
-        ? xPrediction
-        : await (0, getPredictions_1.getPredictions)(to, molecule, predictOptions, predictor, predictions);
+    const yPrediction = predictions[to];
+    const xPrediction = predictions[from];
     if (!xPrediction || !yPrediction) {
         throw new Error('predictions are not availaible');
     }
@@ -88,22 +85,48 @@ 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: (0, getNuclei_1.getNuclei)({ from, to }),
         joinedSignals,
         signals: splitSignals(joinedSignals),
         zones,
-        molecule,
     };
 }
 exports.predict2D = predict2D;
+function getPossibleCorrelations(options) {
+    const { fromLabel, toLabel, distanceMatrix, molecule, diaIDs, minLength, maxLength, } = options;
+    const fromAtomicNumber = full_1.Molecule.getAtomicNoFromLabel(fromLabel);
+    const toAtomicNumber = full_1.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) {
@@ -118,7 +141,7 @@ function splitSignals(joinedSignals) {
     }
     return (0, setIDs_1.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/prediction/utils/predict2D.js.map

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package/lib/prediction/utils/queryByHOSE.d.ts

@@ -1,5 +1,4 @@
 import type { DataBaseStructure } from '../dataStructure';
-import type { GroupedDiaIDsWithHose } from './getFilteredIDiaIDs';
 export interface Prediction {
     diaIDs: string[];
     delta: number | null;
@@ -14,6 +13,6 @@ export interface Prediction {
         nb: number;
     };
 }
-export declare function queryByHose(diaIDs: GroupedDiaIDsWithHose, db: DataBaseStructure, options: {
+export declare function queryByHose(diaIDs: any, db: DataBaseStructure, options: {
     maxSphereSize: number;
 }): Prediction[];

package/lib/prediction/utils/queryByHOSE.js.map

@@ -1 +1 @@
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+{"version":3,"file":"queryByHOSE.js","sourceRoot":"","sources":["../../../src/prediction/utils/queryByHOSE.ts"],"names":[],"mappings":";;;AAkBA,SAAgB,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;AAxCD,kCAwCC"}

package/lib/prediction/utils/shouldPredict.d.ts

@@ -0,0 +1,2 @@
+import { PredictionOptionsByExperiment } from '../predict';
+export declare function shouldPredict(key: keyof PredictionOptionsByExperiment, options: PredictionOptionsByExperiment): boolean;

package/lib/prediction/utils/shouldPredict.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.shouldPredict = void 0;
+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;
+}
+exports.shouldPredict = shouldPredict;
+//# sourceMappingURL=shouldPredict.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"shouldPredict.js","sourceRoot":"","sources":["../../../src/prediction/utils/shouldPredict.ts"],"names":[],"mappings":";;;AAEA,SAAgB,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;AAXD,sCAWC"}

package/lib-esm/assignment/get13CAssignments.js

@@ -1,6 +1,5 @@
 import { v4 as generateID } from '@lukeed/uuid';
-import { ensureHeterotopicChiralBonds } from 'openchemlib-utils';
-import { predictCarbon, } from '../prediction/predictCarbon';
+import { predict } from '..';
 import { buildAssignments, } from './utils/oneDimensionalAssignment/buildAssignments';
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
@@ -24,8 +23,12 @@ export async function get13CAssignments(ranges, molecule, options = {}) {
     if (!molecule) {
         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);
     const targets = {};

package/lib-esm/assignment/get13CAssignments.js.map

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

@@ -1,6 +1,5 @@
 import { v4 as generateID } from '@lukeed/uuid';
-import { ensureHeterotopicChiralBonds } from 'openchemlib-utils';
-import { predictProton, } from '../prediction/predictProton';
+import { predict } from '..';
 import { buildAssignments, } from './utils/oneDimensionalAssignment/buildAssignments';
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
@@ -24,9 +23,12 @@ export async function get1HAssignments(ranges, molecule, options = {}) {
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }
-    molecule.addImplicitHydrogens();
-    ensureHeterotopicChiralBonds(molecule);
-    const { joinedSignals } = await predictProton(molecule, predictionOptions);
+    const { spectra } = await predict(molecule, {
+        predictOptions: {
+            H: predictionOptions,
+        },
+    });
+    const joinedSignals = spectra.proton?.joinedSignals || [];
     checkForIntegration(ranges);
     checkAtomsAndDiaIDs(joinedSignals);
     const targets = {};

package/lib-esm/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/generalAssignment/buildAssignments.js

@@ -1,7 +1,6 @@
 import TreeSet from 'ml-tree-set';
 import { getConnectivityMatrix } from 'openchemlib-utils';
-import { predictCarbon } from '../../../prediction/predictCarbon';
-import { predictProton } from '../../../prediction/predictProton';
+import { predict, } from '../../../prediction/predict';
 import { createMapPossibleAssignment, } from './createMapPossibleAssignment';
 import { exploreTree } from './exploreTree';
 import { isSpectraData1D } from './isSpectraData1D';
@@ -9,7 +8,6 @@ import { searchIndices } from './searchIndices';
 const comparator = (a, b) => {
     return b.score - a.score;
 };
-const predictor = { H: predictProton, C: predictCarbon };
 function checkNMRSignal1D(signals) {
     const keys = [
         'nbAtoms',
@@ -43,11 +41,15 @@ export 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] = {};
@@ -202,4 +204,13 @@ function fillPartial(nSources, value = null) {
     }
     return partial;
 }
+async function getJoinedSignals(input) {
+    const { molecule, predictedSignals, options, atomType } = input;
+    if (predictedSignals)
+        return predictedSignals;
+    const { spectra } = await predict(molecule, {
+        predictOptions: options,
+    });
+    return spectra[atomType === 'C' ? 'carbon' : 'proton']?.joinedSignals || [];
+}
 //# sourceMappingURL=buildAssignments.js.map

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

@@ -1 +1 @@
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package/lib-esm/index.js

@@ -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-esm/index.js.map

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=GroupDiastereotopicAtomIDs.js.map

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

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

package/lib-esm/prediction/PredictionBase1D.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=PredictionBase1D.js.map

package/lib-esm/prediction/PredictionBase1D.js.map

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

package/lib-esm/prediction/PredictionBase2D.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=PredictionBase2D.js.map

package/lib-esm/prediction/PredictionBase2D.js.map

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

package/lib-esm/prediction/predict.js

@@ -0,0 +1,109 @@
+import { getHoseCodesAndInfo, groupDiastereotopicAtomIDs, } from 'openchemlib-utils';
+import { predictCOSY } from './predictCOSY';
+import { predictCarbon } from './predictCarbon';
+import { predictHMBC } from './predictHMBC';
+import { predictHSQC } from './predictHSQC';
+import { predictProton } from './predictProton';
+import { shouldPredict } from './utils/shouldPredict';
+const toPredict = {
+    cosy: {
+        predictor: predictCOSY,
+        required: ['H'],
+        message: 'Proton prediction is missing so COSY could not be generated.',
+    },
+    hsqc: {
+        predictor: predictHSQC,
+        required: ['H', 'C'],
+        message: 'Carbon and / or proton prediction is missing so HSQC could not be generated.',
+    },
+    hmbc: {
+        predictor: 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.
+ */
+export async function predict(molecule, options = {}) {
+    const { logger, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {
+        H: {},
+        C: {},
+        hsqc: {},
+        hmbc: {},
+        cosy: {},
+    }, } = options;
+    const hoseCodesAndInfo = getHoseCodesAndInfo(molecule, {
+        maxSphereSize: predictOptions?.C?.maxSphereSize,
+    });
+    const { diaIDs = [], moleculeWithHydrogens, hoses, molfileWithH, distanceMatrix, } = hoseCodesAndInfo;
+    const groupedDiaIDs = groupDiastereotopicAtomIDs(diaIDs, moleculeWithHydrogens);
+    const protonPrediction = shouldPredict('H', predictOptions)
+        ? await predictProton(molfileWithH, {
+            ...predictOptions?.H,
+            diaIDs,
+            distanceMatrix,
+        })
+        : undefined;
+    const carbonPrediction = shouldPredict('C', predictOptions)
+        ? await 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,
+    };
+}
+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-esm/prediction/predict.js.map

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package/lib-esm/prediction/predictCOSY.js

@@ -1,21 +1,18 @@
-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 predictCOSY(molecule, options = {}) {
-    const { minLength = 2, maxLength = 3, predictions, predictor = { H: predictProton }, predictOptions, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = true, } = options;
+export async function predictCOSY(molecule, options) {
+    const { minLength = 2, maxLength = 3, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = true, } = options;
     return predict2D(molecule, {
+        ...options,
         from: 'H',
         to: 'H',
-        predictor,
         minLength,
         maxLength,
         joinDistance,
-        predictions,
         includeDiagonal,
-        predictOptions,
     });
 }
 //# sourceMappingURL=predictCOSY.js.map

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

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