fix simulation of only negatives chemical shift

package.json

@@ -86,7 +86,7 @@
     "multiplet-analysis": "^2.1.1",
     "nmr-correlation": "^2.3.3",
     "nmr-load-save": "^0.13.2",
-    "nmr-processing": "^9.7.1",
+    "nmr-processing": "9.7.3-pre.1687951924",
     "nmredata": "^0.9.2",
     "numeral": "^2.0.6",
     "openchemlib": "^8.3.0",

src/component/1d/multiAnalysis/MultiAnalysisRanges.tsx

@@ -1,10 +1,10 @@
+import { AnalysisColumnsTypes, SpectraAnalysisColumns } from 'nmr-load-save';
 import { memo } from 'react';
 
 import { useChartData } from '../../context/ChartContext';
 import { usePanelPreferences } from '../../hooks/usePanelPreferences';
 
 import AnalysisRange from './AnalysisRange';
-import { AnalysisColumnsTypes, SpectraAnalysisColumns } from 'nmr-load-save';
 
 interface MultiAnalysisRangesInnerProps {
   displayerKey: string;

src/component/header/BaseLineCorrectionPanel.tsx

@@ -5,6 +5,7 @@ import * as Yup from 'yup';
 
 import { useDispatch } from '../context/DispatchContext';
 import ActionButtons from '../elements/ActionButtons';
+import { InputStyle } from '../elements/Input';
 import Label from '../elements/Label';
 import Select from '../elements/Select';
 import FormikCheckBox from '../elements/formik/FormikCheckBox';
@@ -14,7 +15,6 @@ import { useFilter } from '../hooks/useFilter';
 
 import { headerLabelStyle } from './Header';
 import { HeaderContainer } from './HeaderContainer';
-import { InputStyle } from '../elements/Input';
 
 interface BaseLineCorrectionInnerPanelProps {
   filter: Filter | null;

src/component/modal/PredictSpectraModal.tsx

@@ -9,6 +9,7 @@ import {
 import { StateMoleculeExtended } from '../../data/molecules/Molecule';
 import { useChartData } from '../context/ChartContext';
 import { useDispatch } from '../context/DispatchContext';
+import { useLogger } from '../context/LoggerContext';
 import Button from '../elements/Button';
 import CheckBox from '../elements/CheckBox';
 import CloseButton from '../elements/CloseButton';
@@ -77,6 +78,7 @@ function PredictSpectraModal({
     });
   }, [predictionPreferences, predictionIndex]);
 
+  const { logger } = useLogger();
   const submitHandler = useCallback(
     (values) => {
       void (async () => {
@@ -96,7 +98,7 @@ function PredictSpectraModal({
           );
 
           try {
-            const data = await predictSpectra(molfile);
+            const data = await predictSpectra(molfile, logger);
             dispatch({
               type: 'PREDICT_SPECTRA',
               payload: {
@@ -114,7 +116,15 @@ function PredictSpectraModal({
         }
       })();
     },
-    [alert, dispatch, isApproved, molecule, onClose, setPredictionPreferences],
+    [
+      alert,
+      dispatch,
+      isApproved,
+      molecule,
+      onClose,
+      logger,
+      setPredictionPreferences,
+    ],
   );
 
   const approveCheckHandler = useCallback((e) => {

src/component/panels/MultipleSpectraAnalysisPanel/preferences/AnalysisTablePreferences.tsx

@@ -1,11 +1,11 @@
 import { useFormikContext } from 'formik';
+import { AnalysisColumnsTypes } from 'nmr-load-save';
 import { useMemo, useCallback } from 'react';
 import { FaPlus, FaTimes } from 'react-icons/fa';
 
 import Button from '../../../elements/Button';
 import ReactTable, { Column } from '../../../elements/ReactTable/ReactTable';
 import FormikInput from '../../../elements/formik/FormikInput';
-import { AnalysisColumnsTypes } from 'nmr-load-save';
 
 const inputStyle = { input: { width: '100%', fontSize: '1.15em' } };
 

src/component/panels/predictionPanel/PredictionPanel.tsx

@@ -9,6 +9,7 @@ import { predictSpectra } from '../../../data/PredictionManager';
 import { StateMoleculeExtended } from '../../../data/molecules/Molecule';
 import { useChartData } from '../../context/ChartContext';
 import { useDispatch } from '../../context/DispatchContext';
+import { useLogger } from '../../context/LoggerContext';
 import Button from '../../elements/Button';
 import NextPrev from '../../elements/NextPrev';
 import { useAlert } from '../../elements/popup/Alert';
@@ -40,6 +41,7 @@ export default function PredictionPanel() {
   } = useChartData();
   const dispatch = useDispatch();
   const alert = useAlert();
+  const { logger } = useLogger();
   const [currentIndex, setCurrentIndex] = useState(0);
   const [molfile, setMolfile] = useState<string | null>(null);
   const [isFlipped, setFlipStatus] = useState(false);
@@ -93,7 +95,7 @@ export default function PredictionPanel() {
         );
 
         try {
-          const data = await predictSpectra(molfile);
+          const data = await predictSpectra(molfile, logger);
           dispatch({
             type: 'PREDICT_SPECTRA',
             payload: {

src/component/reducer/actions/DatabaseActions.ts

@@ -54,12 +54,13 @@ function handleResurrectSpectrumFromRanges(
   action: ResurrectSpectrumFromRangesAction,
 ) {
   const { ranges, info } = action.payload;
-
   const datum = generateSpectrumFromRanges(ranges, info, draft.usedColors);
-  draft.data.push(datum);
-  setDomain(draft, { isYDomainShared: false });
-  setIntegralsYDomain(draft, [datum]);
-  setZoom(draft, { scale: 0.8, spectrumID: datum.id });
+  if (datum) {
+    draft.data.push(datum);
+    setDomain(draft, { isYDomainShared: false });
+    setIntegralsYDomain(draft, [datum]);
+    setZoom(draft, { scale: 0.8, spectrumID: datum.id });
+  }
 }
 
 export { handleResurrectSpectrumFromRanges, handleResurrectSpectrumFromJcamp };

src/component/reducer/actions/IntegralsActions.ts

@@ -89,14 +89,18 @@ function handleAddIntegral(draft: Draft<State>, action: AddIntegralAction) {
     const { x, re } = datum.data;
 
     const shiftX = getShiftX(datum);
-
+    const integration = xyIntegration(
+      { x, y: re },
+      { from, to, reverse: true },
+    );
     const integral = {
       id: v4(),
       originFrom: from - shiftX,
       originTo: to - shiftX,
       from,
       to,
-      absolute: xyIntegration({ x, y: re }, { from, to, reverse: true }), // the real value
+      integral: integration,
+      absolute: integration,
       kind: 'signal',
     };
     datum.integrals.values.push(integral);

src/component/reducer/actions/MoleculeActions.ts

@@ -163,7 +163,6 @@ function handlePredictSpectraFromMolecule(
     molecule,
     action: predictionAction = 'save',
   } = action.payload;
-
   const color = generateColor(false, draft.usedColors['1d']);
   const spectraIds: string[] = [];
   for (const spectrum of generateSpectra(predictedSpectra, options, color)) {

src/component/reducer/actions/SpectrumsActions.ts

@@ -515,9 +515,11 @@ function handleGenerateSpectrumFromPublicationStringHandler(
     publicationString,
     draft.usedColors,
   );
-  draft.data.push(spectrum);
-  setActiveTab(draft);
-  setZoom(draft, { scale: 0.8, spectrumID: spectrum.id });
+  if (spectrum) {
+    draft.data.push(spectrum);
+    setActiveTab(draft);
+    setZoom(draft, { scale: 0.8, spectrumID: spectrum.id });
+  }
 }
 
 //action

src/data/PredictionManager.ts

@@ -1,4 +1,5 @@
 import { v4 } from '@lukeed/uuid';
+import { FifoLogger } from 'fifo-logger';
 import { Spectrum } from 'nmr-load-save';
 import {
   Signal2D,
@@ -37,6 +38,7 @@ export interface PredictionOptions {
     nbPoints: { x: number; y: number };
   };
   spectra: SpectraPredictionOptions;
+  logger?: FifoLogger;
 }
 
 export const defaultPredictionOptions: PredictionOptions = {
@@ -75,10 +77,14 @@ export const FREQUENCIES: Array<{ value: number; label: string }> = [
 
 const baseURL = 'https://nmr-prediction.service.zakodium.com';
 
-export async function predictSpectra(molfile: string): Promise<PredictedAll> {
+export async function predictSpectra(
+  molfile: string,
+  logger: FifoLogger,
+): Promise<PredictedAll> {
   const molecule = OCL.Molecule.fromMolfile(molfile);
 
   return predictAll(molecule, {
+    logger,
     predictOptions: {
       C: {
         webserviceURL: `${baseURL}/v1/predict/carbon`,

src/data/data1d/Spectrum1D/generateSpectrumFromPublicationString.ts

@@ -1,4 +1,3 @@
-import { Spectrum1D } from 'nmr-load-save';
 import { resurrect } from 'nmr-processing';
 
 import { UsedColors } from '../../../types/UsedColors';
@@ -8,7 +7,7 @@
 export function generateSpectrumFromPublicationString(
   publicationString: string,
   usedColors: UsedColors,
-): Spectrum1D {
+) {
   const {
     ranges,
     experiment: { nucleus, solvent },

src/data/data1d/Spectrum1D/ranges/detectSignal.ts

@@ -77,17 +77,22 @@
 
 function joinCouplings(result: any) {
   const { chemShift: delta, js } = result;
+  let jCouplings = js;
+  if (js.length > 1) {
+    try {
+      jCouplings = signalJoinCouplings(
+        {
+          delta,
+          js,
+        },
+        { tolerance: 0.6, ignoreDiaIDs: true },
+      ).js;
+    } catch (error) {
+      reportError(error);
+    }
+  }
   return {
     delta,
-    js:
-      js.length > 1
-        ? signalJoinCouplings(
-            {
-              delta,
-              js,
-            },
-            { tolerance: 0.6, ignoreDiaIDs: true },
-          ).js
-        : js,
+    js: jCouplings,
   };
 }

src/data/data1d/Spectrum1D/ranges/generateSpectrumFromRanges.ts

@@ -16,31 +16,34 @@
   ranges: NMRRange[],
   info: ResurrectSpectrumInfo,
   usedColors: UsedColors,
-): Spectrum1D {
+): Spectrum1D | undefined {
   const { nucleus, solvent, name = null, frequency = 400 } = info;
 
-  const { x, y } = rangesToXY(ranges, {
-    nucleus,
-    frequency,
-    nbPoints: 2 ** 17,
-  });
-
-  const datum = initiateDatum1D(
-    {
-      data: { x, im: null, re: y },
-      info: {
-        nucleus,
-        originFrequency: frequency,
-        baseFrequency: frequency,
-        pulseSequence: '',
-        solvent,
-        isFt: true,
-        name,
+  try {
+    const { x, y } = rangesToXY(ranges, {
+      nucleus,
+      frequency,
+      nbPoints: 2 ** 17,
+    });
+    const datum = initiateDatum1D(
+      {
+        data: { x, im: null, re: y },
+        info: {
+          nucleus,
+          originFrequency: frequency,
+          baseFrequency: frequency,
+          pulseSequence: '',
+          solvent,
+          isFt: true,
+          name,
+        },
+        ranges: { values: ranges, options: { sum: 100 } },
       },
-      ranges: { values: ranges, options: { sum: 100 } },
-    },
-    { usedColors },
-  );
+      { usedColors },
+    );
 
-  return datum;
+    return datum;
+  } catch (error) {
+    reportError(error);
+  }
 }