nmr-processing 8.2.0 → 8.4.0

package/src/ranges/rangesToACS.ts

@@ -72,12 +72,12 @@ export function rangesToACS(
   if (!options.nucleus) options.nucleus = '1H';
   const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
   const defaultOptions = globalOptions[nucleus];
-  options = Object.assign(
-    {},
-    defaultOptions,
-    { ascending: false, format: 'IMJA' },
-    options,
-  );
+  options = {
+    ...defaultOptions,
+    ascending: false,
+    format: 'IMJA',
+    ...options,
+  };
 
   ranges = JSON.parse(JSON.stringify(ranges));
   if (options.ascending === true) {
@@ -188,14 +188,13 @@ function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
   acsRanges.push(strings);
 }
 
-function getIntegral(range: NMRRange, options: any) {
+function getIntegral(range: NMRRange, options: { nucleus: string[] }) {
   let integration = '';
   if (range.pubIntegral) {
     integration = String(range.pubIntegral);
   } else if (range.integration) {
-    integration =
-      range.integration.toFixed(0) +
-      options.nucleus[options.nucleus.length - 1];
+    const { nucleus } = options;
+    integration = range.integration.toFixed(0) + nucleus[nucleus.length - 1];
   }
   return integration;
 }

package/src/signals/signalsJoin.ts

@@ -62,7 +62,7 @@ export function signalsJoin(
     JSON.stringify(signals),
   );
 
-  const groupedSignals: { [index: string]: Signal1DWidthJsAndDiaID[] } = {};
+  const groupedSignals: Record<string, Signal1DWidthJsAndDiaID[]> = {};
 
   for (let signal of copySignals) {
     signal.js = signal.js.sort(localeCompareJcouplingKeys);
@@ -117,12 +117,10 @@ export function signalsJoin(
         ignoreDiaIDs,
       }) as Signal1DWidthJsAndDiaID;
       if (newSignal.js) {
-        newSignal.multiplicity = newSignal.js.reduce(
-          (multiplicity, jCoupling) => {
-            return `${multiplicity}${jCoupling.multiplicity}`;
-          },
-          '',
-        );
+        newSignal.multiplicity =
+          newSignal.js.length > 0
+            ? newSignal.js.map((j) => j.multiplicity).join('')
+            : 's';
       }
       return newSignal;
     })

package/src/signals/simulation/getPauliMatrix.ts

@@ -2,7 +2,7 @@ import { SparseMatrix } from 'ml-sparse-matrix';
 
 function createPauli(mult: number) {
   const spin = (mult - 1) / 2;
-  const prjs = new Array(mult);
+  const prjs: number[] = new Array(mult);
   const temp = new Array(mult);
   for (let i = 0; i < mult; i++) {
     prjs[i] = mult - 1 - i - spin;

package/src/signals/simulation/splitSpinSystem.ts

@@ -80,19 +80,17 @@ function splitCluster(
         }
         if (count <= maxClusterSize) {
           clusterList.push(members);
+        } else if (child.index < 0) {
+          splitCluster(child, clusterList, {
+            maxClusterSize,
+            force: true,
+            nSpins,
+            connectivity,
+          });
         } else {
-          if (child.index < 0) {
-            splitCluster(child, clusterList, {
-              maxClusterSize,
-              force: true,
-              nSpins,
-              connectivity,
-            });
-          } else {
-            // We have to threat this spin alone and use the resurrection algorithm instead of the simulation
-            members[child.index] = 2;
-            clusterList.push(members);
-          }
+          // We have to threat this spin alone and use the resurrection algorithm instead of the simulation
+          members[child.index] = 2;
+          clusterList.push(members);
         }
       } else {
         splitCluster(child, clusterList, {

package/src/utilities/rangeFromSignal.ts

@@ -6,24 +6,32 @@ export interface RangeFromSignalOptions {
    * nucleus
    * @default '1h'
    */
-  nucleus: string;
+  nucleus?: string;
   /**
-   * frequency observed
+   * frequency observedhttps://www.wiley.com/en-us/NMR+Data+Processing-p-9780471039006#content-section
    * @default 400
    */
-  frequency: number;
+  frequency?: number;
+  /**
+   * tolerance to the halfWidth, default depends of the nucleus
+   */
+  tolerance?: number;
 }
 
-export function rangeFromSignal(signal: NMRSignal1D, options: any = {}) {
+export function rangeFromSignal(
+  signal: NMRSignal1D,
+  options: RangeFromSignalOptions,
+) {
   const { nucleus = '1h', frequency = 400 } = options;
   const { tolerance = getTolerance(nucleus) / frequency } = options;
-  let halfWidth =
-    (signal.js || []).reduce((total, j) => {
-      const { coupling, multiplicity = 'd' } = j;
-      return total + (couplingValues[multiplicity] * coupling) / frequency;
-    }, 0) /
-      2 +
-    tolerance;
+
+  let halfWidth = 0;
+  for (const js of signal.js || []) {
+    const { coupling, multiplicity = 'd' } = js;
+    halfWidth += (couplingValues[multiplicity] * coupling) / frequency;
+  }
+
+  halfWidth = tolerance + halfWidth / 2;
   return {
     from: signal.delta - halfWidth,
     to: signal.delta + halfWidth,

package/src/utilities/resurrectRange.ts

@@ -46,13 +46,10 @@ export function resurrectRange(part: string, options: any = {}) {
         signal.delta = from;
         signal.multiplicity = multiplicity;
       }
-    } else {
-      // looks like a real multiplicity, s, d, dd, etc..
-      if (!isARange) {
-        // a complex signal
-        signal.delta = from;
-        signal.multiplicity = multiplicity;
-      }
+    } else if (!isARange) {
+      // a complex signal
+      signal.delta = from;
+      signal.multiplicity = multiplicity;
     }
   }
 

package/src/xy/xyAutoPeaksPicking.ts

@@ -50,6 +50,11 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
    * @default 3
    */
   thresholdFactor?: number;
+  /**
+   * If it is true, it check for negative peaks.
+   * @default true
+   */
+  lookPositive?: boolean;
   /**
    * If it is true, it check for negative peaks.
    * @default false
@@ -82,15 +87,19 @@ export function xyAutoPeaksPicking(
     optimization = { kind: 'lm' },
     broadWidth = 0.25,
     sgOptions = {},
+    lookPositive = true,
     lookNegative = false,
   } = options;
 
   const { windowSize = 9, polynomial = 3 } = sgOptions;
 
+  if (data.x.length < windowSize) return [];
+
+  if (!lookPositive && !lookNegative) return [];
+
   if (from !== undefined && to !== undefined) {
     data = xyExtract(data, { zones: [{ from, to }] });
   }
-  if (data.x.length < windowSize) return [];
 
   const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
 
@@ -109,7 +118,10 @@ export function xyAutoPeaksPicking(
     realTopDetection,
   };
 
-  let peaks = getPeakList(data, getPeakOptions);
+  const peaks = [];
+  if (lookPositive) {
+    peaks.push(...getPeakList(data, getPeakOptions));
+  }
 
   if (lookNegative) {
     getPeakOptions.noiseLevel = cutOff.negative;