nmr-processing 7.4.2 → 8.1.0

package/lib-esm/signals/simulation/simulateXYPeaks.js

@@ -0,0 +1,239 @@
+import binarySearch from 'binary-search';
+import { Matrix, EVD } from 'ml-matrix';
+import { SparseMatrix } from 'ml-sparse-matrix';
+import getPauliMatrix from './getPauliMatrix';
+const smallValue = 1e-2;
+export function simulateXYPeaks(
+/**
+ * The SpinSystem object to be simulated
+ */
+spinSystem, options = {}) {
+    let { lineWidth = 1, maxClusterSize = 8, frequency: frequencyMHz = 400, } = options;
+    const chemicalShifts = spinSystem.chemicalShifts.slice();
+    for (let i = 0; i < chemicalShifts.length; i++) {
+        chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
+    }
+    const multiplicity = spinSystem.multiplicity;
+    const xyPeaks = [];
+    for (const cluster of spinSystem.clusters) {
+        let clusterFake = cluster.map((cluster) => cluster < 0 ? -cluster - 1 : cluster);
+        let weight = 1;
+        let sumI = 0;
+        let frequencies = [];
+        let intensities = [];
+        if (cluster.length > maxClusterSize) {
+            // This is a single spin, but the cluster exceeds the maxClusterSize criteria
+            // we use the simple multiplicity algorithm
+            // Add the central peak. It will be split with every single J coupling.
+            let index = 0;
+            while (cluster[index++] < 0)
+                ;
+            index = cluster[index - 1];
+            frequencies.push(-chemicalShifts[index]);
+            for (let i = 0; i < cluster.length; i++) {
+                if (cluster[i] < 0) {
+                    let jc = spinSystem.couplingConstants.get(index, clusterFake[i]) / 2;
+                    let currentSize = frequencies.length;
+                    for (let j = 0; j < currentSize; j++) {
+                        frequencies.push(frequencies[j] + jc);
+                        frequencies[j] -= jc;
+                    }
+                }
+            }
+            frequencies.sort((a, b) => a - b);
+            sumI = frequencies.length;
+            weight = 1;
+            for (let i = 0; i < sumI; i++) {
+                intensities.push(1);
+            }
+        }
+        else {
+            const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, multiplicity, spinSystem.connectivity, clusterFake);
+            const hamSize = hamiltonian.rows;
+            // TODO: add support for sparse matrix in matrix types.
+            // @ts-expect-error sparse matrix not supported
+            const evd = new EVD(hamiltonian);
+            const V = evd.eigenvectorMatrix;
+            const diagB = evd.realEigenvalues;
+            const assignmentMatrix = new SparseMatrix(hamSize, hamSize);
+            const multLen = cluster.length;
+            weight = 0;
+            for (let n = 0; n < multLen; n++) {
+                const L = getPauliMatrix(multiplicity[clusterFake[n]]);
+                let temp = 1;
+                for (let j = 0; j < n; j++) {
+                    temp *= multiplicity[clusterFake[j]];
+                }
+                const A = SparseMatrix.eye(temp);
+                temp = 1;
+                for (let j = n + 1; j < multLen; j++) {
+                    temp *= multiplicity[clusterFake[j]];
+                }
+                const B = SparseMatrix.eye(temp);
+                const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
+                if (cluster[n] >= 0) {
+                    assignmentMatrix.add(tempMat.mul(cluster[n] + 1));
+                    weight++;
+                }
+                else {
+                    assignmentMatrix.add(tempMat.mul(cluster[n]));
+                }
+            }
+            let rhoip = Matrix.zeros(hamSize, hamSize);
+            assignmentMatrix.forEachNonZero((i, j, v) => {
+                if (v > 0) {
+                    for (let k = 0; k < V.columns; k++) {
+                        let element = V.get(j, k);
+                        if (element !== 0) {
+                            rhoip.set(i, k, rhoip.get(i, k) + element);
+                        }
+                    }
+                }
+                return v;
+            });
+            let rhoip2 = rhoip.clone();
+            assignmentMatrix.forEachNonZero((i, j, v) => {
+                if (v < 0) {
+                    for (let k = 0; k < V.columns; k++) {
+                        let element = V.get(j, k);
+                        if (element !== 0) {
+                            rhoip2.set(i, k, rhoip2.get(i, k) + element);
+                        }
+                    }
+                }
+                return v;
+            });
+            const tV = V.transpose();
+            rhoip = tV.mmul(rhoip);
+            const sparseRhoip = new SparseMatrix(rhoip.to2DArray(), {
+                threshold: smallValue,
+            });
+            triuTimesAbs(sparseRhoip, smallValue);
+            rhoip2 = tV.mmul(rhoip2);
+            const sparseRhoip2 = new SparseMatrix(rhoip2.to2DArray(), {
+                threshold: smallValue,
+            });
+            sparseRhoip2.forEachNonZero((i, j, v) => {
+                return v;
+            });
+            triuTimesAbs(sparseRhoip2, smallValue);
+            sparseRhoip2.forEachNonZero((i, j, v) => {
+                let val = rhoip.get(i, j);
+                val = Math.min(Math.abs(val), Math.abs(v));
+                val *= val;
+                sumI += val;
+                let valFreq = diagB[i] - diagB[j];
+                let insertIn = binarySearch(frequencies, valFreq, (a, b) => a - b);
+                if (insertIn < 0) {
+                    frequencies.splice(-1 - insertIn, 0, valFreq);
+                    intensities.splice(-1 - insertIn, 0, val);
+                }
+                else {
+                    intensities[insertIn] += val;
+                }
+            });
+        }
+        const numFreq = frequencies.length;
+        if (numFreq > 0) {
+            weight /= sumI;
+            const diff = lineWidth / 64;
+            let valFreq = frequencies[0];
+            let inte = intensities[0];
+            let count = 1;
+            for (let i = 1; i < numFreq; i++) {
+                if (Math.abs(frequencies[i] - valFreq / count) < diff) {
+                    inte += intensities[i];
+                    valFreq += frequencies[i];
+                    count++;
+                }
+                else {
+                    xyPeaks.push({
+                        x: -valFreq / count / frequencyMHz,
+                        y: inte * weight,
+                    });
+                    valFreq = frequencies[i];
+                    inte = intensities[i];
+                    count = 1;
+                }
+            }
+            xyPeaks.push({
+                x: -valFreq / count / frequencyMHz,
+                y: inte * weight,
+            });
+        }
+    }
+    return xyPeaks;
+}
+function triuTimesAbs(A, val) {
+    A.forEachNonZero((i, j, v) => {
+        if (i > j)
+            return 0;
+        if (Math.abs(v) <= val)
+            return 0;
+        return v;
+    });
+}
+/**
+ * Create a hamiltonian matrix for the given spinsystem
+ * @param {Array} chemicalShifts - An array containing the chemical shift in Hz
+ * @param {Array} couplingConstants - An array containing the coupling constants in Hz
+ * @param {Array} multiplicity - An array specifiying the multiplicities of each scalar coupling
+ * @param {Array} conMatrix - A one step connectivity matrix for the given spin system
+ * @param {Array} cluster - An binary array specifiying the spins to be considered for this hamiltonial
+ * @return {object}
+ */
+function getHamiltonian(chemicalShifts, couplingConstants, multiplicity, conMatrix, cluster) {
+    let hamSize = 1;
+    for (const element of cluster) {
+        hamSize *= multiplicity[element];
+    }
+    const clusterHam = new SparseMatrix(hamSize, hamSize);
+    for (let pos = 0; pos < cluster.length; pos++) {
+        let n = cluster[pos];
+        const L = getPauliMatrix(multiplicity[n]);
+        let A1, B1;
+        let temp = 1;
+        for (let i = 0; i < pos; i++) {
+            temp *= multiplicity[cluster[i]];
+        }
+        A1 = SparseMatrix.eye(temp);
+        temp = 1;
+        for (let i = pos + 1; i < cluster.length; i++) {
+            temp *= multiplicity[cluster[i]];
+        }
+        B1 = SparseMatrix.eye(temp);
+        const alpha = chemicalShifts[n];
+        const kronProd = A1.kroneckerProduct(L.z).kroneckerProduct(B1);
+        clusterHam.add(kronProd.mul(alpha));
+        for (let pos2 = 0; pos2 < cluster.length; pos2++) {
+            const k = cluster[pos2];
+            if (conMatrix.get(n, k) === 1) {
+                const S = getPauliMatrix(multiplicity[k]);
+                let A2, B2;
+                let temp = 1;
+                for (let i = 0; i < pos2; i++) {
+                    temp *= multiplicity[cluster[i]];
+                }
+                A2 = SparseMatrix.eye(temp);
+                temp = 1;
+                for (let i = pos2 + 1; i < cluster.length; i++) {
+                    temp *= multiplicity[cluster[i]];
+                }
+                B2 = SparseMatrix.eye(temp);
+                const kron1 = A1.kroneckerProduct(L.x)
+                    .kroneckerProduct(B1)
+                    .mmul(A2.kroneckerProduct(S.x).kroneckerProduct(B2));
+                kron1.add(A1.kroneckerProduct(L.y)
+                    .kroneckerProduct(B1)
+                    .mul(-1)
+                    .mmul(A2.kroneckerProduct(S.y).kroneckerProduct(B2)));
+                kron1.add(A1.kroneckerProduct(L.z)
+                    .kroneckerProduct(B1)
+                    .mmul(A2.kroneckerProduct(S.z).kroneckerProduct(B2)));
+                clusterHam.add(kron1.mul(couplingConstants.get(n, k) / 2));
+            }
+        }
+    }
+    return clusterHam;
+}
+//# sourceMappingURL=simulateXYPeaks.js.map

package/lib-esm/signals/simulation/simulateXYPeaks.js.map

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package/lib-esm/utilities/getFrequency.js

@@ -1,4 +1,4 @@
-import { gyromagneticRatio } from '../constants/gyromagneticRatio';
+import { gyromagneticRatio } from 'gyromagnetic-ratio';
 /**
  * calculate the frequency of a nucleus with respect to a reference nucleus
  */

package/lib-esm/utilities/getFrequency.js.map

@@ -1 +1 @@
-{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAU,MAAM,gCAAgC,CAAC;AAgB3E;;GAEG;AACH,MAAM,UAAU,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,iBAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,iBAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,iBAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}
+{"version":3,"file":"getFrequency.js","sourceRoot":"","sources":["../../src/utilities/getFrequency.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAU,MAAM,oBAAoB,CAAC;AAgB/D;;GAEG;AACH,MAAM,UAAU,YAAY;AAC1B;;GAEG;AACH,OAAgB,EAChB,mBAAwC;IAExC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,GAAG,mBAAmB,CAAC;IAE/D,cAAc,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IAEpC,OAAO,CACL,CAAC,SAAS,GAAG,iBAAiB,CAAC,OAAiB,CAAC,CAAC;QAClD,iBAAiB,CAAC,UAAoB,CAAC,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,cAAc,CAAC,GAAG,OAAkB;IAC3C,IAAI,MAAM,GAAa,EAAE,CAAC;IAC1B,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE;QACvB,IAAI,CAAC,CAAC,CAAC,IAAI,iBAAiB,CAAC,EAAE;YAC7B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SAChB;KACF;IACD,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,MAAM,IAAI,KAAK,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;KAC3D;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "7.4.2",
+  "version": "8.1.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,44 +38,46 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^27.4.1",
+    "@types/jest": "^27.5.0",
     "cheminfo-build": "^1.1.11",
     "cheminfo-types": "^1.1.0",
-    "eslint": "^8.11.0",
+    "eslint": "^8.14.0",
     "eslint-config-cheminfo-typescript": "^10.4.0",
-    "jest": "^27.5.1",
+    "jest": "^28.0.3",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "ml-array-median": "^1.1.6",
     "nmr-xy-testdata": "^0.5.1",
     "openchemlib": "^7.4.3",
-    "prettier": "^2.6.1",
+    "prettier": "^2.6.2",
     "rimraf": "^3.0.2",
-    "ts-jest": "^27.1.4",
-    "typescript": "^4.6.3"
+    "ts-jest": "^28.0.1",
+    "typescript": "^4.6.4"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
     "cross-fetch": "^3.1.5",
     "form-data": "^4.0.0",
+    "gyromagnetic-ratio": "^1.0.0",
     "is-any-array": "^2.0.0",
+    "linear-sum-assignment": "^1.0.3",
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sequential-fill": "^1.1.8",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^10.2.0",
+    "ml-gsd": "^11.2.0",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
-    "ml-matrix": "^6.9.0",
+    "ml-matrix": "^6.10.0",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
     "ml-peak-shape-generator": "^4.1.1",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^11.1.0",
+    "ml-spectra-processing": "^11.5.0",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.2.5",
-    "openchemlib-utils": "^1.10.0",
-    "spectrum-generator": "^8.0.0"
+    "openchemlib-utils": "^1.11.0",
+    "spectrum-generator": "^8.0.2"
   }
 }

package/src/assignment/getAssignments.ts

@@ -19,23 +19,22 @@ import getWorkFlow from './utils/getAssignment/getWorkFlow';
 export interface SpectraData1D {
   id?: string;
   ranges: NMRRange[];
-  info?: any;
+  info: any;
 }
 
 export interface SpectraData2D {
   id?: string;
   zones: NMRZone[];
-  info?: any;
+  /**
+   * object with information about the spectrum, it is mandatory at the moment
+   * to generate correlations.
+   */
+  info: any;
 }
 
 export type SpectraData = SpectraData1D | SpectraData2D;
 
 export interface GetAutoAssignmentInput {
-  /**
-   * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
-   */
-  atoms?: { [key: string]: number };
-
   spectra: SpectraData[];
   /**
    * Instance of Molecule
@@ -96,7 +95,7 @@ export async function getAssignments(
   let {
     restrictionByCS = {},
     justAssign,
-    minScore = 1,
+    minScore = 0.01,
     maxSolutions = 10,
     nbAllowedUnAssigned,
     timeout = 6000,
@@ -119,11 +118,11 @@ export async function getAssignments(
   addDiastereotopicMissingChirality(molecule);
 
   const spectra = checkIDs(input.spectra);
-
   const { targets, correlations } = getTargetsAndCorrelations(
     spectra,
     correlationOptions,
   );
+
   const { assignmentOrder } = getWorkFlow(correlations, justAssign);
 
   const solutions = await buildAssignments({

package/src/assignment/utils/getAssignment/buildAssignments.ts

@@ -159,10 +159,13 @@ export async function buildAssignments(props: BuildAssignmentInput) {
       checkNMRSignal1D(joinedSignals);
 
       if (!predictions[atomType]) predictions[atomType] = {};
+
+      let totalHydrogens = 0;
       for (let prediction of joinedSignals) {
         const diaID = prediction.diaIDs[0];
         const index = prediction.atoms[0];
         const allHydrogens = getAllHydrogens[atomType](molecule, index);
+        totalHydrogens += prediction.nbAtoms * allHydrogens;
         predictions[atomType][diaID] = {
           ...prediction,
           diaIDIndex: index,
@@ -171,6 +174,9 @@ export async function buildAssignments(props: BuildAssignmentInput) {
           pathLength: pathLengthMatrix[index] as number[],
         };
       }
+      for (let diaID in predictions[atomType]) {
+        predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
+      }
       infoByAtomType[atomType] = {
         nSources: joinedSignals.length,
         currentIndex: 0,

package/src/assignment/utils/getAssignment/checkIDs.ts

@@ -13,16 +13,16 @@ export function checkIDs(input: SpectraData[] = []): SpectraDataWithIds[] {
   let inputClone = JSON.parse(JSON.stringify(input)) as SpectraData[];
   let spectra: SpectraDataWithIds[] = [];
   for (const spectraData of inputClone) {
+    if (!('info' in spectraData)) {
+      throw new Error(
+        'each spectrum should contain info properties with nucleus information',
+      );
+    }
+
     const { info, id } = spectraData;
     if (isSpectraData1D(spectraData)) {
-      let data = addIDs(spectraData.ranges) as NMRRangeWithIds[];
-      for (const element of data) {
-        const { integration } = element;
-        for (let signal of element.signals || []) {
-          if (!signal.integration) signal.integration = integration;
-        }
-      }
-      spectra.push({ id, info, ranges: data });
+      let ranges = addIDs(spectraData.ranges) as NMRRangeWithIds[];
+      spectra.push({ id, info, ranges });
     } else {
       let data = addIDs(spectraData.zones) as NMRZoneWithIds[];
       spectra.push({ id, info, zones: data });

package/src/assignment/utils/getAssignment/formatData.ts

@@ -25,12 +25,48 @@ export function formatData(
   let inputClone = JSON.parse(JSON.stringify(input)) as SpectraDataWithIds[];
   let spectra: SpectraDataFormatted[] = [];
   for (const spectraData of inputClone) {
-    const { info } = spectraData;
+    const { id, info } = spectraData;
     if (isSpectraData1D(spectraData)) {
-      spectra.push({ info, ranges: { values: spectraData.ranges } });
+      const ranges = rescaleIntegration({
+        id,
+        info,
+        ranges: spectraData.ranges,
+      });
+      spectra.push({ id, info, ranges: { values: ranges } });
     } else {
-      spectra.push({ info, zones: { values: spectraData.zones } });
+      spectra.push({ id, info, zones: { values: spectraData.zones } });
     }
   }
   return spectra;
 }
+
+function rescaleIntegration(spectrum: SpectraData1DWithIds): NMRRangeWithIds[] {
+  if (spectrum.info.nucleus !== '1H') return spectrum.ranges;
+
+  let totalIntegration = spectrum.ranges.reduce(
+    (total, range) => (range.integration ? total + range.integration : total),
+    0,
+  );
+
+  for (let range of spectrum.ranges) {
+    if (range.integration) {
+      range.integration *= 100 / totalIntegration;
+      if (range.signals) {
+        const totalSignalIntegration = range.signals.reduce(
+          (total, signal) =>
+            signal.integration ? total + signal.integration : total,
+          0,
+        );
+        for (let signal of range.signals) {
+          if (signal.integration) {
+            signal.integration *= range.integration / totalSignalIntegration;
+          } else {
+            signal.integration = range.integration;
+          }
+        }
+      }
+    }
+  }
+
+  return spectrum.ranges;
+}

package/src/assignment/utils/getAssignment/partialScore.ts

@@ -114,9 +114,9 @@ export function partialScore(partial: Partial, props: PartialScoreOptions) {
       }
     }
   }
+
   for (const group of targetByIntegral) {
     const { integration, atomType } = group;
-
     if (integration === undefined || isNaN(integration)) continue;
 
     let total = 0;
@@ -128,7 +128,7 @@ export function partialScore(partial: Partial, props: PartialScoreOptions) {
         if (atomType === atomOfPrediction) total += prediction.allHydrogens;
       }
     }
-    if (total - integration >= 0.5) {
+    if (total - integration >= 5) {
       return 0;
     }
   }

package/src/databases/getDatabase.ts

@@ -6,16 +6,33 @@ import { DatabaseNMREntry } from './DatabaseNMREntry';
 
 export async function getDatabase(
   url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing',
+  options: {
+    /**
+     * @default 'tsv'
+     */
+    format?: 'tsv' | 'json';
+  } = {},
 ) {
+  const { format = 'tsv' } = options;
+
   if (url.includes('google.com')) {
     url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(
       url,
     )}/export?format=tsv`;
   }
 
+  let parsed;
   const response = await fetch(url);
-  const result = await response.text();
-  const parsed = parseData(result);
+  switch (format) {
+    case 'tsv':
+      parsed = parseData(await response.text());
+      break;
+    case 'json':
+      parsed = await response.json();
+      break;
+    default:
+      throw new Error('unknown database format');
+  }
 
   const results = [];
 

package/src/index.ts

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 
@@ -38,7 +38,7 @@ export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 
 export type { NMRSignal1D } from './signals/NMRSignal1D';
-export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
+export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';

package/src/peaks/NMRPeak1D.ts

@@ -3,6 +3,5 @@ import type { Shape1D } from 'ml-peak-shape-generator';
 
 export interface NMRPeak1D extends PeakXYWidth {
   kind?: string;
-  fwhm?: number;
   shape?: Shape1D;
 }