nmr-processing - npm Package Compare versions

Comparing version 1.5.2 to 2.0.0

CHANGELOG.md

 # Changelog
 
+## [2.0.0](https://www.github.com/cheminfo/nmr-processing/compare/v1.5.2...v2.0.0) (2021-07-23)
+
+
+### ⚠ BREAKING CHANGES
+
+* use plural name diaIDs instead diaID
+* use plural names signals and js instead of signal and j in ranges
+* use integration instead of integral
+
+### Features
+
+* **prediction:** prediction 2D  ([#68](https://www.github.com/cheminfo/nmr-processing/issues/68)) ([fed091b](https://www.github.com/cheminfo/nmr-processing/commit/fed091b48e21cf29624d7322ddc952d590f16495))
+* predictor returns molecule ([9d7ba24](https://www.github.com/cheminfo/nmr-processing/commit/9d7ba24225aa0fb9a3c4d5fb25f55032c081bdb3))
+* use integration instead of integral ([80ccc25](https://www.github.com/cheminfo/nmr-processing/commit/80ccc25ec21fcb6df5130af40aaf03ce3ea73f17))
+* use plural name diaIDs instead diaID ([8cbcefc](https://www.github.com/cheminfo/nmr-processing/commit/8cbcefc3c3225039cf4f236e2ef908233ccc9ad6))
+* use plural names signals and js instead of signal and j in ranges ([2328a13](https://www.github.com/cheminfo/nmr-processing/commit/2328a13f4084b00927c19ff3ec012c692a00d22a))
+
+
+### Bug Fixes
+
+* database in json format ([9adb6bf](https://www.github.com/cheminfo/nmr-processing/commit/9adb6bfec39eb22b4f238e538cb972462204e2e0))
+
 ### [1.5.2](https://www.github.com/cheminfo/nmr-processing/compare/v1.5.1...v1.5.2) (2021-07-22)
@@ -4,0 +26,0 @@

package.json

 {
   "name": "nmr-processing",
-  "version": "1.5.2",
+  "version": "2.0.0",
   "description": "",
@@ -47,3 +47,3 @@ "main": "lib/index.js",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^7.30.0",
+    "eslint": "^7.31.0",
     "eslint-config-cheminfo": "^5.2.4",
@@ -58,3 +58,3 @@ "esm": "^3.2.25",
     "prettier": "^2.3.2",
-    "rollup": "^2.53.2"
+    "rollup": "^2.53.3"
   },
@@ -79,3 +79,3 @@ "dependencies": {
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^6.7.1",
+    "ml-spectra-processing": "^6.8.0",
     "openchemlib-utils": "^1.2.0",
@@ -82,0 +82,0 @@ "spectrum-generator": "^4.7.1"

src/index.js

@@ -15,2 +15,5 @@ /**
 export * from './prediction/predictCarbon';
+export * from './prediction/predictCOSY';
+export * from './prediction/predictHSQC';
+export * from './prediction/predictHMBC';
 export * from './xyz/xyzAutoPeaksPicking';
@@ -17,0 +20,0 @@ export * from './constants/gyromagneticRatio';

src/peaks/peaksToRanges.js

@@ -8,7 +8,7 @@ // import { Ranges } from 'spectra-data-ranges';
 /**
- * This function clustering peaks and calculate the integral value for each range from the peak list returned from extractPeaks function.
+ * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  * @param {Object} data - spectra data
  * @param {Array} peakList - nmr signals
  * @param {Object} [options={}] - options object with some parameter for GSD, detectSignal functions.
- * @param {Number} [options.integrationSum=100] - Number of hydrogens or some number to normalize the integral data. If it's zero return the absolute integral value
+ * @param {Number} [options.integrationSum=100] - Number of hydrogens or some number to normalize the integration data. If it's zero return the absolute integration value
  * @param {String} [options.integralType='sum'] - option to chose between approx area with peaks or the sum of the points of given range ('sum', 'peaks')
@@ -133,4 +133,4 @@ * @param {Number} [options.frequencyCluster=16] - distance limit to clustering peaks.
       to: signal.integralData.to,
-      integral: signal.integralData.value,
-      signal: [
+      integration: signal.integralData.value,
+      signals: [
         {
@@ -143,9 +143,9 @@ kind: signal.kind || 'signal',
     if (keepPeaks) {
-      ranges[i].signal[0].peak = signal.peaks;
+      ranges[i].signals[0].peak = signal.peaks;
     }
     if (signal.nmrJs) {
-      ranges[i].signal[0].j = signal.nmrJs;
+      ranges[i].signals[0].js = signal.nmrJs;
     }
     if (!signal.asymmetric || signal.multiplicity === 'm') {
-      ranges[i].signal[0].delta = signal.delta1;
+      ranges[i].signals[0].delta = signal.delta1;
     }
@@ -164,3 +164,3 @@ }
  * @param {object} [options = {}]
- * @param {number} [options.integrationSum='100'] - Number of hydrogens or some number to normalize the integration data, If it's zero return the absolute integral value
+ * @param {number} [options.integrationSum='100'] - Number of hydrogens or some number to normalize the integration data, If it's zero return the absolute integration value
  * @param {string} [options.integralType='sum'] - option to chose between approx area with peaks or the sum of the points of given range
@@ -238,3 +238,3 @@ * @param {number} [options.frequencyCluster=16] - distance limit to clustering the peaks.
     peaks = signals[i].peaks;
-    let integral = signals[i].integralData;
+    let integration = signals[i].integralData;
     let chemicalShift = 0;
@@ -251,10 +251,10 @@ let integralPeaks = 0;
     if (integralType === 'sum') {
-      integral.value = xyIntegration(data, {
-        from: integral.from,
-        to: integral.to,
+      integration.value = xyIntegration(data, {
+        from: integration.from,
+        to: integration.to,
       });
     } else {
-      integral.value = integralPeaks;
+      integration.value = integralPeaks;
     }
-    spectrumIntegral += integral.value;
+    spectrumIntegral += integration.value;
   }
@@ -265,4 +265,4 @@
     for (let i = 0; i < signals.length; i++) {
-      let integral = signals[i].integralData;
-      integral.value *= integralFactor;
+      let integration = signals[i].integralData;
+      integration.value *= integralFactor;
     }
@@ -269,0 +269,0 @@ }

src/prediction/predictCarbon.js

 import fetch from 'cross-fetch';
-import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
 import { signalsToRanges } from '../signals/signalsToRanges';
 
-import { createInputJSON } from './utils/createInputJSON';
+import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
+import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
 import { queryByHose } from './utils/queryByHOSE';
@@ -22,18 +22,34 @@
 
+/**
+ * Make a query to a hose code based database to predict carbon chemical shift
+ * @param {Molecule} molecule - openchemlib molecule instance.
+ * @param {object} options
+ * @param {string} options.url - url of a custom database.
+ * @param {object} options.database - custom database, each entry in the levels should has
+ * an array as value [median] or [median, mean, sd, min, max, nb] for statistic purpose.
+ * @param {number} options.maxSphereSize - max level to take into account in the query. If is not specified
+ * the max level in the database will be used.
+ * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
+ */
+
 export async function predictCarbon(molecule, options = {}) {
-  let { levels = [3, 2, 1, 0], url, database } = options;
+  let { url, database } = options;
+
   database = database || (await loadDB(url));
 
-  molecule.addImplicitHydrogens();
-  molecule.addMissingChirality();
-  addDiastereotopicMissingChirality(molecule);
+  const maxLevel = database.length - 1;
 
-  const molfile = molecule.toMolfile();
+  let { maxSphereSize = maxLevel } = options;
 
-  const inputJSON = createInputJSON(molecule, {
-    levels,
-  });
+  if (maxSphereSize > maxLevel) maxSphereSize = maxLevel;
 
-  let predictions = queryByHose(inputJSON, database, {
-    levels,
+  const { groupedDiaIDs, carbonDiaIDs, molfile } = getFilteredIDiaIDs(
+    molecule,
+    {
+      maxSphereSize,
+    },
+  );
+
+  let predictions = queryByHose(carbonDiaIDs, database, {
+    maxSphereSize,
   });
@@ -45,6 +61,7 @@
     molfile,
-    diaIDs: inputJSON.diaIDs.map((e) => e.diaId),
+    diaIDs: flatGroupedDiaIDs(groupedDiaIDs),
     joinedSignals,
     signals,
     ranges: signalsToRanges(joinedSignals),
+    molecule,
   };
@@ -56,9 +73,10 @@ }
   for (const prediction of predictions) {
-    const { atomIDs, nbAtoms, delta, diaIDs } = prediction;
+    const { atomIDs, nbAtoms, delta, diaIDs, statistic } = prediction;
     signals.push({
       delta,
       assignment: atomIDs,
-      diaID: diaIDs,
+      diaIDs: diaIDs,
       nbAtoms,
-      j: [],
+      statistic,
+      js: [],
     });
@@ -72,3 +90,3 @@ }
   for (let signal of signals) {
-    let diaID = signal.diaID[0];
+    let diaID = signal.diaIDs[0];
     if (!joinedSignals[diaID]) {
@@ -75,0 +93,0 @@ joinedSignals[diaID] = JSON.parse(JSON.stringify(signal));

src/prediction/predictProton.js

@@ -17,3 +17,3 @@ import fetch from 'cross-fetch';
  * @param {function} [options.cache] A callback receiving a molfile and the result
- * @return {Promise<Array>}
+ * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
  */
@@ -53,2 +53,3 @@ export async function predictProton(molecule, options = {}) {
     ranges: signalsToRanges(joinedSignals),
+    molecule,
   };
@@ -67,17 +68,17 @@ }
       assignment: [atom],
-      diaID: [diaIDs[atom]],
+      diaIDs: [diaIDs[atom]],
       nbAtoms: 1,
       delta: Number(fields[2]),
-      j: [],
+      js: [],
     };
     for (let i = 0; i < couplings.length; i += 3) {
       let linked = Number(couplings[i] - 1);
-      signal.j.push({
+      signal.js.push({
         coupling: Number(couplings[i + 2]),
         assignment: [linked],
-        diaID: [diaIDs[linked]],
+        diaIDs: [diaIDs[linked]],
         multiplicity: 'd',
         distance: distanceMatrix[atom][linked],
       });
-      signal.j.sort((a, b) => b.coupling - a.coupling);
+      signal.js.sort((a, b) => b.coupling - a.coupling);
     }
@@ -84,0 +85,0 @@ signals.push(signal);

src/prediction/utils/queryByHOSE.js

@@ -1,18 +0,18 @@
-export function queryByHose(input, db, options) {
-  const { levels } = options;
+export function queryByHose(diaIDs, db, options) {
+  const { maxSphereSize } = options;
 
-  levels.sort((a, b) => b - a);
   const toReturn = [];
-  for (const element of input.diaIDs) {
+  for (const element of diaIDs) {
     let res;
-    let k = 0;
-    while (!res && k < levels.length) {
-      if (db[levels[k]]) {
-        res = db[levels[k]][element.hose[levels[k]]];
+    let level;
+    for (let k = maxSphereSize; !res && k >= 0; k--) {
+      if (db[k]) {
+        res = db[k][element.hose[k]];
+        level = k;
       }
-      k++;
     }
+
     if (!res) {
       res = [null];
-      k = 0;
+      level = null;
     }
@@ -25,3 +25,12 @@
       atom.nbAtoms = 1;
-
+      atom.level = level;
+      if (res.length > 1) {
+        atom.statistic = {
+          mean: res[1],
+          sd: res[2],
+          min: res[3],
+          max: res[4],
+          nb: res[5],
+        };
+      }
       toReturn.push(atom);
@@ -28,0 +37,0 @@ }

src/ranges/rangesToACS.js

@@ -98,4 +98,4 @@ import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 
-  if (Array.isArray(range.signal)) {
-    range.signal = range.signal.filter(
+  if (Array.isArray(range.signals)) {
+    range.signals = range.signals.filter(
       (signal) => !uselessKind(signal.kind, options.filter),
@@ -105,4 +105,4 @@ );
 
-  if (Array.isArray(range.signal) && range.signal.length > 0) {
-    let signals = range.signal;
+  if (Array.isArray(range.signals) && range.signals.length > 0) {
+    let signals = range.signals;
     if (signals.length > 1) {
@@ -153,15 +153,15 @@ if (options.ascending === true) {
 function getIntegral(range, options) {
-  let integral = '';
+  let integration = '';
   if (range.pubIntegral) {
-    integral = range.pubIntegral;
-  } else if (range.integral) {
-    integral =
-      range.integral.toFixed(0) + options.nucleus[options.nucleus.length - 1];
+    integration = range.pubIntegral;
+  } else if (range.integration) {
+    integration =
+      range.integration.toFixed(0) + options.nucleus[options.nucleus.length - 1];
   }
-  return integral;
+  return integration;
 }
 
 function pushIntegral(range, parenthesis, options) {
-  let integral = getIntegral(range, options);
-  if (integral.length > 0) parenthesis.push(integral);
+  let integration = getIntegral(range, options);
+  if (integration.length > 0) parenthesis.push(integration);
 }
@@ -221,4 +221,4 @@
 function pushCoupling(signal, parenthesis, options) {
-  if (Array.isArray(signal.j) && signal.j.length > 0) {
-    signal.j.sort(function (a, b) {
+  if (Array.isArray(signal.js) && signal.js.length > 0) {
+    signal.js.sort(function (a, b) {
       return b.coupling - a.coupling;
@@ -228,3 +228,3 @@ });
     let values = [];
-    for (let j of signal.j) {
+    for (let j of signal.js) {
       if (j.coupling !== undefined) {
@@ -231,0 +231,0 @@ values.push(j.coupling.toFixed(options.nbDecimalJ));

src/signal/signalJoinCouplings.js

@@ -21,9 +21,9 @@ import sum from 'ml-array-sum';
 
-  if (!signal.j || signal.j.length < 2) return signal;
+  if (!signal.js || signal.js.length < 2) return signal;
 
   // we group the couplings that are less than the expected tolerance
-  let currentGroup = [signal.j[0]];
+  let currentGroup = [signal.js[0]];
   let groups = [currentGroup];
-  for (let i = 1; i < signal.j.length; i++) {
-    let currentJ = signal.j[i];
+  for (let i = 1; i < signal.js.length; i++) {
+    let currentJ = signal.js[i];
     if (
@@ -40,3 +40,3 @@ currentGroup[currentGroup.length - 1].coupling - currentJ.coupling <
 
-  signal.j = [];
+  signal.js = [];
   for (let group of groups) {
@@ -50,6 +50,6 @@ let coupling = sum(group.map((group) => group.coupling)) / group.length;
     );
-    let diaID = distinctValues(
+    let diaIDs = distinctValues(
       group
-        .filter((group) => group.diaID && group.diaID.length > 0)
-        .map((group) => group.diaID)
+        .filter((group) => group.diaIDs && group.diaIDs.length > 0)
+        .map((group) => group.diaIDs)
         .flat(),
@@ -64,6 +64,6 @@ );
     };
-    if (diaID.length > 0) newJ.diaID = diaID;
+    if (diaIDs.length > 0) newJ.diaIDs = diaIDs;
     if (distances.length === 1 && distances[0]) newJ.distance = distances[0];
     if (assignment.length > 0) newJ.assignment = assignment;
-    signal.j.push(newJ);
+    signal.js.push(newJ);
   }
@@ -70,0 +70,0 @@

src/signal/signalMultiplicityPattern.js

@@ -7,3 +7,3 @@ /**
 export function signalMultiplicityPattern(signal) {
-  let js = signal.j;
+  let js = signal.js;
   let pattern = '';
@@ -10,0 +10,0 @@ if (js && js.length > 0) {

src/signal/signalNormalize.js

 /**
- * Ensure that assignment and diaID are arrays and coupling are sorted
+ * Ensure that assignment and diaIDs are arrays and coupling are sorted
  * @param {object} signal
@@ -12,7 +12,7 @@ * @returns signal
   }
-  if (signal.diaID && !Array.isArray(signal.diaID)) {
-    signal.diaID = [signal.diaID];
+  if (signal.diaIDs && !Array.isArray(signal.diaIDs)) {
+    signal.diaIDs = [signal.diaIDs];
   }
-  if (signal.j) {
-    let couplings = signal.j;
+  if (signal.js) {
+    let couplings = signal.js;
     for (let coupling of couplings) {
@@ -22,9 +22,9 @@ if (coupling.assignment && !Array.isArray(coupling.assignment)) {
       }
-      if (coupling.diaID && !Array.isArray(coupling.diaID)) {
-        coupling.diaID = [coupling.diaID];
+      if (coupling.diaIDs && !Array.isArray(coupling.diaIDs)) {
+        coupling.diaIDs = [coupling.diaIDs];
       }
     }
-    signal.j = signal.j.sort((a, b) => b.coupling - a.coupling);
+    signal.js = signal.js.sort((a, b) => b.coupling - a.coupling);
   }
   return signal;
 }

src/signals/signalsJoin.js

@@ -14,7 +14,7 @@ import mean from 'ml-array-mean';
   for (let signal of signals) {
-    if (!signal.diaID || !signal.diaID.length === 1) return signals;
-    for (let coupling of signal.j) {
+    if (!signal.diaIDs || !signal.diaIDs.length === 1) return signals;
+    for (let coupling of signal.js) {
       if (
-        !coupling.diaID ||
-        !coupling.diaID.length === 1 ||
+        !coupling.diaIDs ||
+        !coupling.diaIDs.length === 1 ||
         coupling.multiplicity !== 'd'
@@ -31,7 +31,7 @@ ) {
     signal = signalNormalize(signal); // we have a copy
-    signal.j = signal.j.sort((a, b) =>
-      a.diaID + a.distance < b.diaID + b.distance ? 1 : -1,
+    signal.js = signal.js.sort((a, b) =>
+      a.diaIDs + a.distance < b.diaIDs + b.distance ? 1 : -1,
     );
-    let id = `${signal.diaID[0]} ${signal.j
-      .map((j) => `${j.diaID[0]} ${j.distance}`)
+    let id = `${signal.diaIDs[0]} ${signal.js
+      .map((j) => `${j.diaIDs[0]} ${j.distance}`)
       .sort()
@@ -51,9 +51,9 @@ .join(' ')}`;
     // joining couplings only if diaID and distance are equal
-    const j = [];
-    for (let i = 0; i < group[0].j.length; i++) {
-      j.push({
-        diaID: group[0].j[i].diaID,
-        distance: group[0].j[i].distance,
-        multiplicity: group[0].j[i].multiplicity,
-        coupling: mean(group.map((item) => item.j[i].coupling)),
+    const js = [];
+    for (let i = 0; i < group[0].js.length; i++) {
+      js.push({
+        diaIDs: group[0].js[i].diaIDs,
+        distance: group[0].js[i].distance,
+        multiplicity: group[0].js[i].multiplicity,
+        coupling: mean(group.map((item) => item.js[i].coupling)),
       });
@@ -65,3 +65,3 @@ }
       delta: mean(group.map((item) => item.delta)),
-      diaID: group[0].diaID,
+      diaIDs: group[0].diaIDs,
       assignment: group
@@ -71,3 +71,3 @@ .map((item) => item.assignment)
         .filter((item) => item),
-      j,
+      js,
     });
@@ -78,4 +78,4 @@ }
       signal = signalNormalize(signalJoinCouplings(signal, { tolerance }));
-      if (signal.j) {
-        signal.multiplicity = signal.j.reduce((multiplicity, jCoupling) => {
+      if (signal.js) {
+        signal.multiplicity = signal.js.reduce((multiplicity, jCoupling) => {
           return `${multiplicity}${jCoupling.multiplicity}`;
@@ -82,0 +82,0 @@ }, '');

src/signals/signalsToRanges.js

@@ -8,3 +8,3 @@ export function signalsToRanges(signals, options = {}) {
     let halfWidth =
-      (signal.original.j || []).reduce(
+      (signal.original.js || []).reduce(
         (total, j) => (total += j.coupling / frequency),
@@ -26,10 +26,10 @@ 0,
         to: signal.to,
-        integral: signal.original.nbAtoms,
-        signal: [signal.original],
+        integration: signal.original.nbAtoms,
+        signals: [signal.original],
       };
       ranges.push(range);
     } else {
-      range.integral += signal.original.nbAtoms;
+      range.integration += signal.original.nbAtoms;
       if (signal.to > range.to) range.to = signal.to;
-      range.signal.push(signal.original);
+      range.signals.push(signal.original);
     }
@@ -36,0 +36,0 @@ }

src/signals/simulation/signalsToSpinSystem.js

@@ -18,3 +18,3 @@ import Matrix from 'ml-matrix';
   for (let i = 0; i < nSpins; i++) {
-    let { assignment: signalAssignment, j: jCoupling } = signals[i];
+    let { assignment: signalAssignment, js: jCoupling } = signals[i];
     for (let k = 0; k < jCoupling.length; k++) {
@@ -21,0 +21,0 @@ let { coupling, assignment } = jCoupling[k];

src/xy/xyAutoRangesPicking.js

@@ -25,3 +25,3 @@ import { peaksFilterImpurities } from '../peaks/peaksFilterImpurities';
  * @param {Boolean} [options.peakPicking.optimize=true] - if it's true adjust an train of gaussian or lorentzian shapes to spectrum.
- * @param {Number}  [options.ranges.integrationSum=100] - Number of hydrogens or some number to normalize the integral data. If it's zero return the absolute integral value
+ * @param {Number}  [options.ranges.integrationSum=100] - Number of hydrogens or some number to normalize the integration data. If it's zero return the absolute integration value
  * @param {String}  [options.ranges.integralType='sum'] - option to chose between approx area with peaks or the sum of the points of given range ('sum', 'peaks')
@@ -37,3 +37,3 @@ * @param {Number}  [options.ranges.frequencyCluster=16] - distance limit to clustering peaks.
  * @param {string}  [options.impurities.error=0.025] - tolerance in ppm to assign a impurity.
- * @returns {array} - Array of ranges with {from, to, integral, signals: [{delta, j, multiplicity, peaks}]}
+ * @returns {array} - Array of ranges with {from, to, integration, signals: [{delta, j, multiplicity, peaks}]}
  */
@@ -40,0 +40,0 @@

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

370286

increased by9.39%

Number of package files

45

increased by15.38%

Lines of code

13368

increased by6.01%

Dependency changes

• Updatedml-spectra-processing@^6.8.0