nmr-processing 9.9.2 → 10.0.0

package/lib/prediction/predictAll.d.ts

@@ -1,64 +0,0 @@
-import type { Logger } from 'cheminfo-types';
-import type { Molecule } from 'openchemlib/full';
-import type { Prediction1D } from './Prediction1D';
-import { PredictCarbonOptions } from './predictCarbon';
-import { PredictProtonOptions } from './predictProton';
-import type { Predictor } from './utils/predict2D';
-export interface PredictAllOptions {
-    /**
-     * maximum number of bonds to take into account.
-     * @default 1
-     */
-    maxLength?: number;
-    /**
-     * minimum number of bonds to take into account
-     * @default 1
-     */
-    minLength?: number;
-    /**
-     * mono dimensional predictors. The object should has properties with name
-     * equal to "H" and "C".
-     */
-    predictor?: {
-        H?: Predictor;
-        C?: Predictor;
-    };
-    /**
-     *  mono dimensional signal to generate the bidimenionals cross peaks.
-     * The object should has properties with name equal to "H" and "C".
-     */
-    predictOptions?: {
-        H?: PredictProtonOptions;
-        C?: PredictCarbonOptions;
-    };
-    /**
-     * 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;
-    };
-    /**
-     * mono dimensional signal to generate the bidimenionals cross peaks.
-     * 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;
-        C?: Prediction1D;
-    };
-    logger?: Logger;
-}
-export interface PredictedAll {
-    molfile: string;
-    diaIDs: string[];
-    spectra: Record<string, any>;
-}
-/**
- * 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 predictAll(molecule: Molecule, options?: PredictAllOptions): Promise<PredictedAll>;

package/lib/prediction/predictAll.js

@@ -1,82 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.predictAll = 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 getPredictions_1 = require("./utils/getPredictions");
-/**
- * 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 predictAll(molecule, options = {}) {
-    const { logger, predictor = { H: predictProton_1.predictProton, C: predictCarbon_1.predictCarbon }, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
-    const diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule);
-    let { predictions } = options;
-    const protonPrediction = await (0, getPredictions_1.getPredictions)('H', molecule, predictOptions, predictor, predictions);
-    const carbonPrediction = await (0, getPredictions_1.getPredictions)('C', molecule, predictOptions, predictor, predictions);
-    if (!protonPrediction || !carbonPrediction) {
-        throw new Error('predictions are not availaible');
-    }
-    const spectra = {};
-    if (check1DPrediction(protonPrediction)) {
-        spectra.proton = protonPrediction;
-    }
-    if (check1DPrediction(carbonPrediction)) {
-        spectra.carbon = carbonPrediction;
-    }
-    const { molfile } = protonPrediction;
-    predictions = {
-        H: protonPrediction,
-        C: carbonPrediction,
-    };
-    if (spectra.proton) {
-        spectra.cosy = await (0, predictCOSY_1.predictCOSY)(molecule, {
-            predictions,
-            joinDistance,
-        });
-    }
-    else if (logger) {
-        logger.warn('Proton prediction is missing so COSY could not be generated.');
-    }
-    if (spectra.carbon && spectra.proton) {
-        spectra.hsqc = await (0, predictHSQC_1.predictHSQC)(molecule, {
-            predictions,
-            joinDistance,
-        });
-        spectra.hmbc = await (0, predictHMBC_1.predictHMBC)(molecule, {
-            predictions,
-            joinDistance,
-        });
-    }
-    else if (logger) {
-        logger.warn('Carbon and / or proton prediction is missing so HSQC and HMBC could not be generated.');
-    }
-    for (const key in spectra) {
-        delete spectra[key].molfile;
-        delete spectra[key].diaIDs;
-    }
-    return {
-        molfile,
-        diaIDs,
-        spectra,
-    };
-}
-exports.predictAll = predictAll;
-function check1DPrediction(prediction) {
-    if (!prediction)
-        return false;
-    if (prediction.ranges.length === 0)
-        return false;
-    const { signals, diaIDs } = prediction;
-    for (const signal of signals) {
-        const isCorrect = signal.diaIDs?.every((diaID) => diaIDs.includes(diaID));
-        if (!isCorrect)
-            return false;
-    }
-    return true;
-}
-//# sourceMappingURL=predictAll.js.map

package/lib/prediction/predictAll.js.map

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package/lib/prediction/predictAllSpectra.js.map

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

@@ -1,4 +0,0 @@
-import type { Molecule } from 'openchemlib/full';
-import type { Prediction1D } from '../Prediction1D';
-import type { Predictions, PredictOptions, Predictors } from './predict2D';
-export declare function getPredictions(key: string, molecule: Molecule, predictOptions: PredictOptions, predictor?: Predictors, predictions?: Predictions): Promise<Prediction1D | undefined>;

package/lib/prediction/utils/getPredictions.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPredictions = void 0;
-async function getPredictions(key, molecule, predictOptions, predictor, predictions) {
-    let prediction;
-    if (predictions?.[key]) {
-        prediction = predictions[key];
-    }
-    else if (predictor) {
-        const fromPredictor = predictor[key];
-        prediction = fromPredictor
-            ? await fromPredictor(molecule, predictOptions[key])
-            : undefined;
-    }
-    return prediction;
-}
-exports.getPredictions = getPredictions;
-//# sourceMappingURL=getPredictions.js.map

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

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package/lib-esm/prediction/predictAll.js

@@ -1,78 +0,0 @@
-import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
-import { predictCOSY } from './predictCOSY';
-import { predictCarbon } from './predictCarbon';
-import { predictHMBC } from './predictHMBC';
-import { predictHSQC } from './predictHSQC';
-import { predictProton } from './predictProton';
-import { getPredictions } from './utils/getPredictions';
-/**
- * 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 predictAll(molecule, options = {}) {
-    const { logger, predictor = { H: predictProton, C: predictCarbon }, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
-    const diaIDs = getDiastereotopicAtomIDs(molecule);
-    let { predictions } = options;
-    const protonPrediction = await getPredictions('H', molecule, predictOptions, predictor, predictions);
-    const carbonPrediction = await getPredictions('C', molecule, predictOptions, predictor, predictions);
-    if (!protonPrediction || !carbonPrediction) {
-        throw new Error('predictions are not availaible');
-    }
-    const spectra = {};
-    if (check1DPrediction(protonPrediction)) {
-        spectra.proton = protonPrediction;
-    }
-    if (check1DPrediction(carbonPrediction)) {
-        spectra.carbon = carbonPrediction;
-    }
-    const { molfile } = protonPrediction;
-    predictions = {
-        H: protonPrediction,
-        C: carbonPrediction,
-    };
-    if (spectra.proton) {
-        spectra.cosy = await predictCOSY(molecule, {
-            predictions,
-            joinDistance,
-        });
-    }
-    else if (logger) {
-        logger.warn('Proton prediction is missing so COSY could not be generated.');
-    }
-    if (spectra.carbon && spectra.proton) {
-        spectra.hsqc = await predictHSQC(molecule, {
-            predictions,
-            joinDistance,
-        });
-        spectra.hmbc = await predictHMBC(molecule, {
-            predictions,
-            joinDistance,
-        });
-    }
-    else if (logger) {
-        logger.warn('Carbon and / or proton prediction is missing so HSQC and HMBC could not be generated.');
-    }
-    for (const key in spectra) {
-        delete spectra[key].molfile;
-        delete spectra[key].diaIDs;
-    }
-    return {
-        molfile,
-        diaIDs,
-        spectra,
-    };
-}
-function check1DPrediction(prediction) {
-    if (!prediction)
-        return false;
-    if (prediction.ranges.length === 0)
-        return false;
-    const { signals, diaIDs } = prediction;
-    for (const signal of signals) {
-        const isCorrect = signal.diaIDs?.every((diaID) => diaIDs.includes(diaID));
-        if (!isCorrect)
-            return false;
-    }
-    return true;
-}
-//# sourceMappingURL=predictAll.js.map

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

@@ -1 +0,0 @@
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package/lib-esm/prediction/predictAllSpectra.js.map

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

@@ -1,14 +0,0 @@
-export async function getPredictions(key, molecule, predictOptions, predictor, predictions) {
-    let prediction;
-    if (predictions?.[key]) {
-        prediction = predictions[key];
-    }
-    else if (predictor) {
-        const fromPredictor = predictor[key];
-        prediction = fromPredictor
-            ? await fromPredictor(molecule, predictOptions[key])
-            : undefined;
-    }
-    return prediction;
-}
-//# sourceMappingURL=getPredictions.js.map

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

@@ -1 +0,0 @@
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package/src/openchemlib-utils.d.ts

@@ -1,167 +0,0 @@
-declare module 'openchemlib-utils' {
-  import type { Molecule } from 'openchemlib/full';
-
-  export interface GroupDiastereotopicAtomIDs {
-    counter: number;
-    atoms: number[];
-    oclID: string;
-    atomLabel: string;
-  }
-
-  export type GroupedDiastereotopicAtomIDs = GroupDiastereotopicAtomIDs[];
-  function getGroupedDiastereotopicAtomIDs(
-    molecule: Molecule,
-    options?: { atomLabel: string },
-  ): GroupedDiastereotopicAtomIDs;
-
-  interface GetHoseCodesForAtomOptions {
-    minSphereSize?: number;
-    maxSphereSize?: number;
-    kind?: number;
-    /**
-     * Specify is the atom is already tagged
-     * @default false
-     */
-    isTagged?: boolean;
-  }
-
-  type GetHoseCodesFromDiastereotopicIDOptions = GetHoseCodesForAtomOptions;
-
-  function getHoseCodesFromDiastereotopicID(
-    molecule: Molecule,
-    options?: GetHoseCodesFromDiastereotopicIDOptions,
-  ): string[];
-
-  function getHoseCodesForAtom(
-    originalMolecule: Molecule,
-    rootAtom: number,
-    options: GetHoseCodesForAtomOptions,
-  ): string[];
-
-  function ensureHeterotopicChiralBonds(molecule: Molecule): Molecule;
-
-  export interface GetPathsInfoOptions {
-    fromLabel?: string;
-    toLabel?: string;
-    minLength?: number;
-    maxLength?: number;
-  }
-
-  export interface PathInfo extends AtomInfo {
-    paths: HoseCodesForPath[];
-  }
-  function getPathsInfo(
-    molecule: Molecule,
-    options?: GetPathsInfoOptions,
-  ): PathInfo[];
-
-  export interface AtomInfo {
-    oclID: string;
-    x: number;
-    y: number;
-    z: number;
-    abnormalValence: number;
-    charge: number;
-    cipParity: number;
-    color: number;
-    customLabel: string;
-    atomicNo: number;
-    label: string;
-    mass: number;
-    radical: number;
-    ringBondCount: number;
-    ringSize: number;
-    allHydrogens: number;
-    connAtoms: number;
-    allConnAtoms: number;
-    implicitHydrogens: number;
-    isAromatic: boolean;
-    isAllylic: boolean;
-    isStereoCenter: boolean;
-    isRing: boolean;
-    isSmallRing: boolean;
-    isStabilized: boolean;
-    extra: {
-      singleBonds: number;
-      doubleBonds: number;
-      tripleBonds: number;
-      aromaticBonds: number;
-      totalBonds: number;
-      labileHydrogen: boolean;
-      hydrogenOnAtomicNo: number;
-      /**
-       * should be 1 (sp), 2 (sp2) or 3 (sp3)
-       */
-      cnoHybridation: number;
-    };
-  }
-  type AtomsInfo = AtomInfo[];
-  function getAtomsInfo(molecule: Molecule): AtomsInfo;
-
-  export interface Hose {
-    sphere: number;
-    oclID: string;
-  }
-  type Hoses = Hose[];
-
-  export interface HoseCodesForPath {
-    atoms: number[];
-    from: number;
-    to: number;
-    torsion?: number;
-    hoses: Hoses;
-    length: number;
-  }
-
-  function getHoseCodesForPath(
-    molecule: Molecule,
-    from: string,
-    to: string,
-    maxLength: number,
-  ): HoseCodesForPath;
-
-  export interface GetConnectivityMatrixOptions {
-    /**
-     * get the path length between atoms
-     * @default false
-     */
-    pathLength?: boolean;
-    /**
-     * set the nominal mass of the atoms on diagonal
-     * @default false
-     */
-    mass?: boolean;
-    /**
-     * set the atomic number of the atom on diagonal
-     * @default false;
-     */
-    atomicNo?: boolean;
-    /**
-     * set the atomic number of the atom on diagonal
-     * @default false
-     */
-    negativeAtomicNo?: boolean;
-    /**
-     * set 1, 2 or 3 depending if single, double or triple bond
-     * @default false
-     */
-    std?: boolean | number;
-    /**
-     * set 1, 2, 3 or 4 depending if single, double, triple or aromatic  bond
-     * @default false;
-     */
-    stda?: boolean | number;
-  }
-  function getConnectivityMatrix(
-    molecule: Molecule,
-    options?: GetConnectivityMatrixOptions,
-  ): number[][] | Float64Array[];
-
-  function getDiastereotopicAtomIDs(molecule: Molecule): string[];
-
-  function groupDiastereotopicAtomIDs(
-    diaIDs: string[],
-    molecule: Molecule,
-    options?: { atomLabel: string },
-  ): GroupedDiastereotopicAtomIDs;
-}

package/src/prediction/predictAll.ts

@@ -1,157 +0,0 @@
-import type { Logger } from 'cheminfo-types';
-import type { Molecule } from 'openchemlib/full';
-import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
-
-import type { Prediction1D } from './Prediction1D';
-import { predictCOSY } from './predictCOSY';
-import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
-import { predictHMBC } from './predictHMBC';
-import { predictHSQC } from './predictHSQC';
-import { predictProton, PredictProtonOptions } from './predictProton';
-import { getPredictions } from './utils/getPredictions';
-import type { Predictor } from './utils/predict2D';
-
-export interface PredictAllOptions {
-  /**
-   * maximum number of bonds to take into account.
-   * @default 1
-   */
-  maxLength?: number;
-  /**
-   * minimum number of bonds to take into account
-   * @default 1
-   */
-  minLength?: number;
-  /**
-   * mono dimensional predictors. The object should has properties with name
-   * equal to "H" and "C".
-   */
-  predictor?: { H?: Predictor; C?: Predictor };
-  /**
-   *  mono dimensional signal to generate the bidimenionals cross peaks.
-   * The object should has properties with name equal to "H" and "C".
-   */
-  predictOptions?: { H?: PredictProtonOptions; C?: PredictCarbonOptions };
-  /**
-   * 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 };
-  /**
-   * mono dimensional signal to generate the bidimenionals cross peaks.
-   * 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;
-    C?: Prediction1D;
-  };
-  logger?: Logger;
-}
-
-export interface PredictedAll {
-  molfile: string;
-  diaIDs: string[];
-  spectra: Record<string, any>;
-}
-/**
- * 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 predictAll(
-  molecule: Molecule,
-  options: PredictAllOptions = {},
-): Promise<PredictedAll> {
-  const {
-    logger,
-    predictor = { H: predictProton, C: predictCarbon },
-    joinDistance = { H: 0.05, C: 0.5 },
-    predictOptions = {},
-  } = options;
-
-  const diaIDs = getDiastereotopicAtomIDs(molecule);
-  let { predictions } = options;
-
-  const protonPrediction = await getPredictions(
-    'H',
-    molecule,
-    predictOptions,
-    predictor,
-    predictions,
-  );
-
-  const carbonPrediction = await getPredictions(
-    'C',
-    molecule,
-    predictOptions,
-    predictor,
-    predictions,
-  );
-
-  if (!protonPrediction || !carbonPrediction) {
-    throw new Error('predictions are not availaible');
-  }
-
-  const spectra: any = {};
-  if (check1DPrediction(protonPrediction)) {
-    spectra.proton = protonPrediction;
-  }
-  if (check1DPrediction(carbonPrediction)) {
-    spectra.carbon = carbonPrediction;
-  }
-
-  const { molfile } = protonPrediction;
-
-  predictions = {
-    H: protonPrediction,
-    C: carbonPrediction,
-  };
-
-  if (spectra.proton) {
-    spectra.cosy = await predictCOSY(molecule, {
-      predictions,
-      joinDistance,
-    });
-  } else if (logger) {
-    logger.warn('Proton prediction is missing so COSY could not be generated.');
-  }
-
-  if (spectra.carbon && spectra.proton) {
-    spectra.hsqc = await predictHSQC(molecule, {
-      predictions,
-      joinDistance,
-    });
-    spectra.hmbc = await predictHMBC(molecule, {
-      predictions,
-      joinDistance,
-    });
-  } else if (logger) {
-    logger.warn(
-      'Carbon and / or proton prediction is missing so HSQC and HMBC could not be generated.',
-    );
-  }
-
-  for (const key in spectra) {
-    delete spectra[key].molfile;
-    delete spectra[key].diaIDs;
-  }
-
-  return {
-    molfile,
-    diaIDs,
-    spectra,
-  };
-}
-
-function check1DPrediction(prediction?: Prediction1D) {
-  if (!prediction) return false;
-  if (prediction.ranges.length === 0) return false;
-  const { signals, diaIDs } = prediction;
-  for (const signal of signals) {
-    const isCorrect = signal.diaIDs?.every((diaID) => diaIDs.includes(diaID));
-    if (!isCorrect) return false;
-  }
-  return true;
-}

package/src/prediction/utils/getPredictions.ts

@@ -1,24 +0,0 @@
-import type { Molecule } from 'openchemlib/full';
-
-import type { Prediction1D } from '../Prediction1D';
-
-import type { Predictions, PredictOptions, Predictors } from './predict2D';
-
-export async function getPredictions(
-  key: string,
-  molecule: Molecule,
-  predictOptions: PredictOptions,
-  predictor?: Predictors,
-  predictions?: Predictions,
-) {
-  let prediction: Prediction1D | undefined;
-  if (predictions?.[key]) {
-    prediction = predictions[key];
-  } else if (predictor) {
-    const fromPredictor = predictor[key];
-    prediction = fromPredictor
-      ? await fromPredictor(molecule, predictOptions[key])
-      : undefined;
-  }
-  return prediction;
-}