nmr-processing 7.4.2 → 8.1.0

package/lib-esm/assignment/getAssignments.js

@@ -4,7 +4,7 @@ import { checkIDs } from './utils/getAssignment/checkIDs';
 import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
 import getWorkFlow from './utils/getAssignment/getWorkFlow';
 export async function getAssignments(input, options = {}) {
-    let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
     const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
     const molecule = input.molecule;
     if (!molecule)

package/lib-esm/assignment/getAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/getAssignment/buildAssignments.js

@@ -53,10 +53,12 @@ export async function buildAssignments(props) {
             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,
@@ -65,6 +67,9 @@ export async function buildAssignments(props) {
                     pathLength: pathLengthMatrix[index],
                 };
             }
+            for (let diaID in predictions[atomType]) {
+                predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
+            }
             infoByAtomType[atomType] = {
                 nSources: joinedSignals.length,
                 currentIndex: 0,

package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/utils/getAssignment/checkIDs.js

@@ -4,17 +4,13 @@ export function checkIDs(input = []) {
     let inputClone = JSON.parse(JSON.stringify(input));
     let spectra = [];
     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);
-            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);
+            spectra.push({ id, info, ranges });
         }
         else {
             let data = addIDs(spectraData.zones);

package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map

@@ -1 +1 @@
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+{"version":3,"file":"checkIDs.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/checkIDs.ts"],"names":[],"mappings":"AAOA,OAAO,UAAU,MAAM,eAAe,CAAC;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD,MAAM,UAAU,QAAQ,CAAC,QAAuB,EAAE;IAChD,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAkB,CAAC;IACpE,IAAI,OAAO,GAAyB,EAAE,CAAC;IACvC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,IAAI,CAAC,CAAC,MAAM,IAAI,WAAW,CAAC,EAAE;YAC5B,MAAM,IAAI,KAAK,CACb,uEAAuE,CACxE,CAAC;SACH;QAED,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,eAAe,CAAC,WAAW,CAAC,EAAE;YAChC,IAAI,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAsB,CAAC;YAC7D,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;SACpC;aAAM;YACL,IAAI,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAqB,CAAC;YACzD,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC;SACzC;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,MAAM,CACpB,IAA4B;IAE5B,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAC;QAC/D,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAC;SAC3D;KACF;AACH,CAAC;AAED,MAAM,UAAU,MAAM,CAAC,IAA4B;IACjD,KAAK,MAAM,OAAO,IAAI,IAAI,EAAE;QAC1B,IAAI,CAAC,OAAO,CAAC,EAAE;YAAE,OAAO,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;QAC3C,KAAK,IAAI,MAAM,IAAI,OAAO,CAAC,OAAO,IAAI,EAAE,EAAE;YACxC,IAAI,CAAC,MAAM,CAAC,EAAE;gBAAE,MAAM,CAAC,EAAE,GAAG,UAAU,EAAE,CAAC;SAC1C;KACF;IACD,MAAM,CAAC,IAAI,CAAC,CAAC;IACb,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/assignment/utils/getAssignment/formatData.js

@@ -3,14 +3,41 @@ export function formatData(input = []) {
     let inputClone = JSON.parse(JSON.stringify(input));
     let spectra = [];
     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) {
+    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;
+}
 //# sourceMappingURL=formatData.js.map

package/lib-esm/assignment/utils/getAssignment/formatData.js.map

@@ -1 +1 @@
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+{"version":3,"file":"formatData.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/formatData.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAapD,MAAM,UAAU,UAAU,CACxB,QAA8B,EAAE;IAEhC,IAAI,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAyB,CAAC;IAC3E,IAAI,OAAO,GAA2B,EAAE,CAAC;IACzC,KAAK,MAAM,WAAW,IAAI,UAAU,EAAE;QACpC,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,WAAW,CAAC;QACjC,IAAI,eAAe,CAAC,WAAW,CAAC,EAAE;YAChC,MAAM,MAAM,GAAG,kBAAkB,CAAC;gBAChC,EAAE;gBACF,IAAI;gBACJ,MAAM,EAAE,WAAW,CAAC,MAAM;aAC3B,CAAC,CAAC;YACH,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,CAAC;SACxD;aAAM;YACL,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;SAClE;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,kBAAkB,CAAC,QAA8B;IACxD,IAAI,QAAQ,CAAC,IAAI,CAAC,OAAO,KAAK,IAAI;QAAE,OAAO,QAAQ,CAAC,MAAM,CAAC;IAE3D,IAAI,gBAAgB,GAAG,QAAQ,CAAC,MAAM,CAAC,MAAM,CAC3C,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,EACzE,CAAC,CACF,CAAC;IAEF,KAAK,IAAI,KAAK,IAAI,QAAQ,CAAC,MAAM,EAAE;QACjC,IAAI,KAAK,CAAC,WAAW,EAAE;YACrB,KAAK,CAAC,WAAW,IAAI,GAAG,GAAG,gBAAgB,CAAC;YAC5C,IAAI,KAAK,CAAC,OAAO,EAAE;gBACjB,MAAM,sBAAsB,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CACjD,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,CAChB,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,EACzD,CAAC,CACF,CAAC;gBACF,KAAK,IAAI,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE;oBAChC,IAAI,MAAM,CAAC,WAAW,EAAE;wBACtB,MAAM,CAAC,WAAW,IAAI,KAAK,CAAC,WAAW,GAAG,sBAAsB,CAAC;qBAClE;yBAAM;wBACL,MAAM,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC;qBACxC;iBACF;aACF;SACF;KACF;IAED,OAAO,QAAQ,CAAC,MAAM,CAAC;AACzB,CAAC"}

package/lib-esm/assignment/utils/getAssignment/partialScore.js

@@ -70,7 +70,7 @@ export function partialScore(partial, props) {
                     total += prediction.allHydrogens;
             }
         }
-        if (total - integration >= 0.5) {
+        if (total - integration >= 5) {
             return 0;
         }
     }

package/lib-esm/assignment/utils/getAssignment/partialScore.js.map

@@ -1 +1 @@
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+{"version":3,"file":"partialScore.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/partialScore.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAatD,OAAO,kCAAkC,MAAM,sCAAsC,CAAC;AAmBtF,MAAM,UAAU,YAAY,CAAC,OAAgB,EAAE,KAA0B;IACvE,MAAM,EACJ,2BAA2B,EAC3B,eAAe,EACf,eAAe,EACf,WAAW,EACX,OAAO,EACP,YAAY,GACb,GAAG,KAAK,CAAC;IAEV,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,qBAAqB,EAAE,GAAG,eAAe,CAAC;IAC1E,IAAI,WAAW,GAAG,CAAC,CAAC;IACpB,IAAI,YAAY,GAAG,CAAC,CAAC;IACrB,IAAI,cAAc,GAA4B,EAAE,CAAC;IACjD,IAAI,wBAAwB,GAAgC,EAAE,CAAC;IAC/D,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,CAAC;IACtD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,IAAI,UAAU,GAAG,CAAC,CAAC;QACnB,MAAM,EAAE,mBAAmB,EAAE,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;QAC1D,MAAM,qBAAqB,GAAsB,EAAE,CAAC;QACpD,MAAM,iBAAiB,GAAG,OAAO,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;QAClD,cAAc,CAAC,QAAQ,CAAC,GAAG,qBAAqB,CAAC;QACjD,wBAAwB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;QACxC,YAAY,IAAI,iBAAiB,CAAC,MAAM,CAAC;QACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACjD,MAAM,QAAQ,GAAG,iBAAiB,CAAC,CAAC,CAAC,CAAC;YACtC,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;gBAChC,wBAAwB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBAC3C,IAAI,CAAC,qBAAqB,CAAC,QAAQ,CAAC,EAAE;oBACpC,qBAAqB,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;iBACtC;gBACD,qBAAqB,CAAC,QAAQ,CAAC,CAAC,IAAI,CAClC,2BAA2B,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CACzC,CAAC;aACH;YACD,IAAI,QAAQ,KAAK,GAAG;gBAAE,UAAU,EAAE,CAAC;SACpC;QAED,IAAI,UAAU,GAAG,mBAAmB;YAAE,OAAO,CAAC,CAAC;QAC/C,WAAW,IAAI,UAAU,CAAC;KAC3B;IAED,MAAM,oBAAoB,GAAsB,EAAE,CAAC;IACnD,KAAK,MAAM,QAAQ,IAAI,cAAc,EAAE;QACrC,oBAAoB,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAC,CAAC;KACxE;IAED,MAAM,0BAA0B,GAAG,MAAM,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;IACvE,IACE,0BAA0B,CAAC,MAAM,CAC/B,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAC5C,CAAC,CACF,KAAK,0BAA0B,CAAC,MAAM,EACvC;QACA,OAAO,CAAC,CAAC;KACV;IAED,MAAM,oBAAoB,GAAG,aAAa,CAAC,IAAI,CAAC,EAAE,EAAE,WAAW,CAAC,CAAC;IACjE,wBAAwB;IACxB,MAAM,gBAAgB,GAIhB,EAAE,CAAC;IAET,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE;QAC9B,IAAI,QAAQ,KAAK,GAAG,IAAI,oBAAoB,CAAC,QAAQ,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;YACjE,gBAAgB,CAAC,IAAI,CACnB,GAAG,kCAAkC,CACnC,oBAAoB,CAAC,QAAQ,CAAC,EAC9B,OAAO,CAAC,QAAQ,CAAC,EACjB,YAAY,CACb,CACF,CAAC;SACH;aAAM;YACL,KAAK,IAAI,QAAQ,IAAI,oBAAoB,CAAC,QAAQ,CAAC,EAAE;gBACnD,gBAAgB,CAAC,IAAI,CAAC;oBACpB,QAAQ;oBACR,SAAS,EAAE,CAAC,QAAQ,CAAC;oBACrB,WAAW,EAAE,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,WAAW;iBAC7C,CAAC,CAAC;aACJ;SACF;KACF;IAED,KAAK,MAAM,KAAK,IAAI,gBAAgB,EAAE;QACpC,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAC;QACxC,IAAI,WAAW,KAAK,SAAS,IAAI,KAAK,CAAC,WAAW,CAAC;YAAE,SAAS;QAE9D,IAAI,KAAK,GAAG,CAAC,CAAC;QACd,KAAK,IAAI,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE;YACpC,IAAI,cAAc,GAAG,cAAc,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC;YACxD,KAAK,MAAM,KAAK,IAAI,cAAc,EAAE;gBAClC,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAC9C,oBAAoB,CAAC,KAAK,CAAC,CAAC;gBAC9B,IAAI,QAAQ,KAAK,gBAAgB;oBAAE,KAAK,IAAI,UAAU,CAAC,YAAY,CAAC;aACrE;SACF;QACD,IAAI,KAAK,GAAG,WAAW,IAAI,CAAC,EAAE;YAC5B,OAAO,CAAC,CAAC;SACV;KACF;IAED,sBAAsB;IACtB,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,kBAAkB,GAAG,CAAC,CAAC;IAC3B,IAAI,qBAAqB,EAAE;QACzB,kBAAkB,GAAG,CAAC,CAAC;QACvB,KAAK,GAAG,CAAC,CAAC;QACV,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,EAAE;YAC1D,MAAM,mBAAmB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC9C,MAAM,mBAAmB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC9C,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,mBAAmB,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBAC/D,MAAM,QAAQ,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAC;gBAC5C,IAAI,QAAQ,IAAI,QAAQ,KAAK,GAAG,EAAE;oBAChC,KAAK,EAAE,CAAC;oBACR,IAAI,KAAK,GAAG,2BAA2B,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;oBACzD,IAAI,MAAM,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;oBAC1C,IAAI,MAAM,GAAG,mBAAmB,CAAC,QAAQ,CAAC,CAAC;oBAC3C,IAAI,KAAK,GAAG,WAAW,CAAC,QAAQ,CAAC,CAAC;oBAClC,sBAAsB;oBACtB,iDAAiD;oBACjD,IAAI;oBACJ,IAAI,OAAO,MAAM,CAAC,KAAK,KAAK,WAAW,EAAE;wBACvC,sCAAsC;wBACtC,kBAAkB,IAAI,CAAC,CAAC;qBACzB;yBAAM;wBACL,MAAM,WAAW,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAC;wBAEhD,IAAI,WAAW,KAAK,SAAS,EAAE;4BAC7B,MAAM,IAAI,KAAK,CAAC,2BAA2B,CAAC,CAAC;yBAC9C;wBAED,IAAI,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,WAAW,CAAC,CAAC;wBAChD,IAAI,IAAI,GAAG,KAAK,EAAE;4BAChB,wCAAwC;4BACxC,kBAAkB,IAAI,CAAC,CAAC;yBACzB;6BAAM;4BACL,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,CAAC,CAAC;4BAC9B,kBAAkB,IAAI,CAAC,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC;yBAClD;qBACF;iBACF;aACF;SACF;QACD,IAAI,KAAK,GAAG,CAAC,EAAE;YACb,kBAAkB,IAAI,KAAK,CAAC;SAC7B;KACF;IAED,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,IAAI,cAAc,CAAC,oBAAoB,CAAC,GAAG,CAAC,EAAE;QAC5C,IAAI,aAAa,GAA8B,EAAE,CAAC;QAClD,IAAI,YAAY,GAAkD,EAAE,CAAC;QAErE,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,IAAI,CAChC,wBAAwB,CACV,EAAE;YAChB,YAAY,GAAG,YAAY,CAAC,MAAM,CAChC,wBAAwB,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,CACxE,CAAC;SACH;QAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5C,MAAM,EAAE,QAAQ,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CA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package/lib-esm/databases/getDatabase.js

@@ -1,12 +1,22 @@
 import { fetch } from 'cross-fetch';
 import { resurrectRange } from '../utilities/resurrectRange';
-export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
+export async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
+    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 = [];
     for (let line of parsed.data) {
         const result = {

package/lib-esm/databases/getDatabase.js.map

@@ -1 +1 @@
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package/lib-esm/index.js

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';

package/lib-esm/index.js.map

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package/lib-esm/peaks/solventSuppression.js

@@ -0,0 +1,140 @@
+import linearSumAssignment from 'linear-sum-assignment';
+import { Matrix } from 'ml-matrix';
+import { gaussianFct } from 'ml-peak-shape-generator';
+import { xFindClosestIndex, xMaxValue } from 'ml-spectra-processing';
+import { addDummySignals } from '../signals/addDummySignals';
+import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
+import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
+export function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList];
+    sortAscending(peaks);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false } = options;
+    let solventSignals = solvent; //addDummySignals(solvent);
+    // solventSignals = solventSignals.slice(0, solventSignals.findIndex((signal) => signal.delta > 400));
+    for (const solventSignal of solventSignals) {
+        const solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        sortAscending(solventXYPeaks);
+        let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + 1);
+        let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - 1);
+        if (upIndex === lowIndex)
+            continue;
+        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const shiftedSolventPeaks = getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
+            const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
+            let deltaResidual = 0;
+            let amplitudeResidual = 0;
+            let positionResidual = 0;
+            for (let i = 0; i < closestPeaks.length; i++) {
+                amplitudeResidual += Math.abs(shiftedSolventPeaks[i].y - closestPeaks[i].y);
+                deltaResidual += Math.abs(shiftedSolventPeaks[i].x - closestPeaks[i].x);
+            }
+            if (closestPeaks.length === 0) {
+                deltaResidual = Number.MAX_SAFE_INTEGER;
+                amplitudeResidual = Number.MAX_SAFE_INTEGER;
+                positionResidual = Number.MAX_SAFE_INTEGER;
+            }
+            else {
+                positionResidual = gaussianFct(solventSignal.delta - peak.x, 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const maxAmplitude = xMaxValue(amplitudeResiduals);
+        const maxDelta = xMaxValue(deltaResiduals);
+        const maxPosition = xMaxValue(positionResiduals);
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                (1 - positionResiduals[i]) / maxPosition) /
+                3;
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        const shiftedSolventPeaks = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = linearSumAssignment(diff, {
+            maximaze: false,
+        });
+        if (gain === -1)
+            return peaks;
+        if (markSolventPeaks) {
+            for (let index of rowAssignments) {
+                peaks[index + lowIndex].kind = 'solvent';
+            }
+        }
+        else {
+            rowAssignments.sort((a, b) => b - a);
+            for (let index of rowAssignments) {
+                peaks.splice(index + lowIndex, 1);
+            }
+        }
+    }
+    return peaks;
+}
+function getSolventPeaks(signal, options = {}) {
+    let signals = addDummySignals([signal]);
+    let spinSystem = signalsToSpinSystem(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = simulateXYPeaks(spinSystem);
+    return peaks.filter((peak) => peak.x < 1000);
+}
+function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
+    const shiftedSolventPeaks = JSON.parse(JSON.stringify(solventXYPeaks));
+    // shift x values of solventPeaks to center it to the current peak.
+    const deltaPPM = peak.x - solventSignal.delta;
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+    }
+    return shiftedSolventPeaks;
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = linearSumAssignment(diff, {
+        maximaze: false,
+    });
+    if (gain === -1)
+        return [];
+    const assignmentPeaks = [];
+    let maxValue = Number.MIN_SAFE_INTEGER;
+    for (let index of rowAssignments) {
+        if (maxValue < nearPeaks[index].y)
+            maxValue = nearPeaks[index].y;
+        assignmentPeaks.push({ ...nearPeaks[index] });
+    }
+    assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
+    return assignmentPeaks;
+}
+function sortAscending(peaks) {
+    return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
+}
+function getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new Matrix(nbRows, nbColumns);
+    for (let r = 0; r < nbRows; r++) {
+        for (let c = 0; c < nbColumns; c++) {
+            diff.set(r, c, Math.abs(rows[r].x - columns[c].x));
+        }
+    }
+    return diff;
+}
+//# sourceMappingURL=solventSuppression.js.map

package/lib-esm/peaks/solventSuppression.js.map

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

@@ -1,36 +1,122 @@
+import { signals2DToZ } from '../signals/signals2DToZ';
 import { signalsToXY } from '../signals/signalsToXY';
+import { getFrequency } from '../utilities/getFrequency';
 import { predictAll } from './predictAll';
-/**
- * This function will generate an object compatible with NMR-ium
- *
- * @param molecule
- * @param options
- */
 export async function predictAllSpectra(molecule, options = {}) {
-    const predictions = await predictAll(molecule, options.prediction);
+    const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
+    const predictions = await predictAll(molecule, predictionOptions);
     const spectra = [];
     const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
-    spectra.push(getProton(predictions.proton, options.simulation));
+    const oneDOptions = {
+        ...{
+            proton: { from: 0, to: 14 },
+            carbon: { from: 0, to: 200 },
+            nbPoints: 4098,
+            lineWidth: 0.03,
+        },
+        ...(simulationOptions.oneD || {}),
+    };
+    const twoDOptions = {
+        ...{
+            from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
+            to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
+            nbPoints: { x: 1024, y: 1024 },
+        },
+        ...(simulationOptions.twoD || {}),
+    };
+    for (const experiment in predictions) {
+        switch (experiment) {
+            case 'carbon':
+            case 'proton': {
+                spectra.push(get1DSpectrum(predictions[experiment], {
+                    nbPoints: oneDOptions.nbPoints,
+                    lineWidth: oneDOptions.lineWidth,
+                    ...oneDOptions[experiment],
+                    experiment,
+                    frequency: simulationOptions.frequency,
+                }));
+                break;
+            }
+            case 'cosy':
+            case 'hsqc':
+            case 'hmbc': {
+                spectra.push(get2DSpectrum(predictions[experiment], {
+                    ...twoDOptions,
+                    experiment,
+                    frequency: simulationOptions.frequency,
+                }));
+                break;
+            }
+            default:
+                break;
+        }
+    }
     return result;
 }
-function getProton(prediction, options) {
-    const { x, y } = signalsToXY(prediction.signals, options);
+function get2DSpectrum(prediction, options) {
+    const { signals, zones, nuclei } = prediction;
+    const { frequency: baseFrequency, experiment } = options;
+    const width = get2DWidth(nuclei);
+    const frequency = calculateFrequency(nuclei, baseFrequency);
+    const spectrumData = signals2DToZ(signals, {
+        ...options,
+        width,
+        factor: 3,
+    });
+    const spectrum = {
+        data: { ...spectrumData, noise: 0.01 },
+        info: {
+            nucleus: nuclei,
+            originFrequency: frequency,
+            baseFrequency: frequency,
+            pulseSequence: experiment,
+            experiment: '2d',
+        },
+        zones: { values: zones },
+    };
+    return spectrum;
+}
+function get2DWidth(nucleus) {
+    return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
+}
+function get1DSpectrum(prediction, options) {
+    const { frequency = 400, experiment } = options;
+    const { signals, nucleus } = prediction;
+    const realFrequency = calculateFrequency(nucleus, frequency);
+    const { x, y } = signalsToXY(signals, {
+        ...options,
+        frequency: realFrequency,
+    });
     const spectrum = {
-        id: '',
         // todo Array.from is temporary for the developement
         data: { x: Array.from(x), re: Array.from(y), im: null },
         info: {
             nucleus: prediction.nucleus,
             dimension: 1,
-            originFrequency: 400,
-            baseFrequency: 400,
+            originFrequency: realFrequency,
+            baseFrequency: realFrequency,
             pulseSequence: 'prediction',
-            experiment: 'proton',
+            experiment,
             isFt: true,
         },
-        // todo: currently we disable the ranges because there is no ID
-        //ranges: { values: prediction.ranges },
+        ranges: { values: prediction.ranges },
     };
     return spectrum;
 }
+function calculateFrequency(nucleus, frequency) {
+    if (typeof nucleus === 'string') {
+        return getFrequency(nucleus, { nucleus: '1H', frequency });
+    }
+    else {
+        if (nucleus[0] === nucleus[1]) {
+            return `${frequency},${frequency}`;
+        }
+        else {
+            return `${frequency},${getFrequency(nucleus[1], {
+                nucleus: nucleus[0],
+                frequency,
+            })}`;
+        }
+    }
+}
 //# sourceMappingURL=predictAllSpectra.js.map

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

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