nmr-processing 8.0.0 → 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

@@ -0,0 +1 @@
+{"version":3,"file":"simulateXYPeaks.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulateXYPeaks.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,eAAe,CAAC;AACzC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,WAAW,CAAC;AAGxC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAIhD,OAAO,cAAc,MAAM,kBAAkB,CAAC;AAE9C,MAAM,UAAU,GAAG,IAAI,CAAC;AAwCxB,MAAM,UAAU,eAAe;AAC7B;;GAEG;AACH,UAAsB,EACtB,UAA6B,EAAE;IAE/B,IAAI,EACF,SAAS,GAAG,CAAC,EACb,cAAc,GAAG,CAAC,EAClB,SAAS,EAAE,YAAY,GAAG,GAAG,GAC9B,GAAG,OAAO,CAAC;IAEZ,MAAM,cAAc,GAAG,UAAU,CAAC,cAAc,CAAC,KAAK,EAAE,CAAC;IACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC9C,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC;KACtD;IAED,MAAM,YAAY,GAAG,UAAU,CAAC,YAAY,CAAC;IAE7C,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,MAAM,OAAO,IAAI,UAAU,CAAC,QAAQ,EAAE;QACzC,IAAI,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CACxC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CACrC,CAAC;QAEF,IAAI,MAAM,GAAG,CAAC,CAAC;QACf,IAAI,IAAI,GAAG,CAAC,CAAC;QACb,IAAI,WAAW,GAAa,EAAE,CAAC;QAC/B,IAAI,WAAW,GAAa,EAAE,CAAC;QAC/B,IAAI,OAAO,CAAC,MAAM,GAAG,cAAc,EAAE;YACnC,6EAA6E;YAC7E,2CAA2C;YAC3C,uEAAuE;YACvE,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,OAAO,OAAO,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC;gBAAC,CAAC;YAC7B,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;YAC3B,WAAW,CAAC,IAAI,CAAC,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC;YACzC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACvC,IAAI,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;oBAClB,IAAI,EAAE,GAAG,UAAU,CAAC,iBAAiB,CAAC,GAAG,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;oBACrE,IAAI,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC;oBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE;wBACpC,WAAW,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;wBACtC,WAAW,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBACtB;iBACF;aACF;YAED,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAClC,IAAI,GAAG,WAAW,CAAC,MAAM,CAAC;YAC1B,MAAM,GAAG,CAAC,CAAC;YAEX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;gBAC7B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aACrB;SACF;aAAM;YACL,MAAM,WAAW,GAAG,cAAc,CAChC,cAAc,EACd,UAAU,CAAC,iBAAiB,EAC5B,YAAY,EACZ,UAAU,CAAC,YAAY,EACvB,WAAW,CACZ,CAAC;YACF,MAAM,OAAO,GAAG,WAAW,CAAC,IAAI,CAAC;YACjC,uDAAuD;YACvD,+CAA+C;YAC/C,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,WAAW,CAAC,CAAC;YACjC,MAAM,CAAC,GAAG,GAAG,CAAC,iBAAiB,CAAC;YAChC,MAAM,KAAK,GAAG,GAAG,CAAC,eAAe,CAAC;YAClC,MAAM,gBAAgB,GAAG,IAAI,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC5D,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC;YAC/B,MAAM,GAAG,CAAC,CAAC;YACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;gBAChC,MAAM,CAAC,GAAG,cAAc,CAAC,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBAEvD,IAAI,IAAI,GAAG,CAAC,CAAC;gBACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;oBAC1B,IAAI,IAAI,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBACtC;gBACD,MAAM,CAAC,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBAEjC,IAAI,GAAG,CAAC,CAAC;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;oBACpC,IAAI,IAAI,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBACtC;gBACD,MAAM,CAAC,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBACjC,MAAM,OAAO,GAAG,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC;gBAC5D,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;oBACnB,gBAAgB,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;oBAClD,MAAM,EAAE,CAAC;iBACV;qBAAM;oBACL,gBAAgB,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC/C;aACF;YAED,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC3C,gBAAgB,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;gBAC1C,IAAI,CAAC,GAAG,CAAC,EAAE;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;wBAClC,IAAI,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAC1B,IAAI,OAAO,KAAK,CAAC,EAAE;4BACjB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC;yBAC5C;qBACF;iBACF;gBACD,OAAO,CAAC,CAAC;YACX,CAAC,CAAC,CAAC;YAEH,IAAI,MAAM,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC;YAC3B,gBAAgB,CAAC,cAAc,CAAC,CAAC,CAAS,EAAE,CAAS,EAAE,CAAS,EAAE,EAAE;gBAClE,IAAI,CAAC,GAAG,CAAC,EAAE;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;wBAClC,IAAI,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;wBAC1B,IAAI,OAAO,KAAK,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC;yBAC9C;qBACF;iBACF;gBACD,OAAO,CAAC,CAAC;YACX,CAAC,CAAC,CAAC;YACH,MAAM,EAAE,GAAG,CAAC,CAAC,SAAS,EAAE,CAAC;YAEzB,KAAK,GAAG,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YACvB,MAAM,WAAW,GAAG,IAAI,YAAY,CAAC,KAAK,CAAC,SAAS,EAAE,EAAE;gBACtD,SAAS,EAAE,UAAU;aACtB,CAAC,CAAC;YACH,YAAY,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC;YAEtC,MAAM,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACzB,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,SAAS,EAAE,EAAE;gBACxD,SAAS,EAAE,UAAU;aACtB,CAAC,CAAC;YACH,YAAY,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;gBACtC,OAAO,CAAC,CAAC;YACX,CAAC,CAAC,CAAC;YACH,YAAY,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC;YACvC,YAAY,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;gBACtC,IAAI,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;gBAC1B,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC3C,GAAG,IAAI,GAAG,CAAC;gBAEX,IAAI,IAAI,GAAG,CAAC;gBACZ,IAAI,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;gBAClC,IAAI,QAAQ,GAAG,YAAY,CACzB,WAAW,EACX,OAAO,EACP,CAAC,CAAS,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAChC,CAAC;gBACF,IAAI,QAAQ,GAAG,CAAC,EAAE;oBAChB,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,OAAO,CAAC,CAAC;oBAC9C,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;iBAC3C;qBAAM;oBACL,WAAW,CAAC,QAAQ,CAAC,IAAI,GAAG,CAAC;iBAC9B;YACH,CAAC,CAAC,CAAC;SACJ;QAED,MAAM,OAAO,GAAG,WAAW,CAAC,MAAM,CAAC;QAEnC,IAAI,OAAO,GAAG,CAAC,EAAE;YACf,MAAM,IAAI,IAAI,CAAC;YACf,MAAM,IAAI,GAAG,SAAS,GAAG,EAAE,CAAC;YAC5B,IAAI,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;YAC7B,IAAI,IAAI,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;YAC1B,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;gBAChC,IAAI,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,GAAG,OAAO,GAAG,KAAK,CAAC,GAAG,IAAI,EAAE;oBACrD,IAAI,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC;oBACvB,OAAO,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC;oBAC1B,KAAK,EAAE,CAAC;iBACT;qBAAM;oBACL,OAAO,CAAC,IAAI,CAAC;wBACX,CAAC,EAAE,CAAC,OAAO,GAAG,KAAK,GAAG,YAAY;wBAClC,CAAC,EAAE,IAAI,GAAG,MAAM;qBACjB,CAAC,CAAC;oBACH,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;oBACzB,IAAI,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC;oBACtB,KAAK,GAAG,CAAC,CAAC;iBACX;aACF;YAED,OAAO,CAAC,IAAI,CAAC;gBACX,CAAC,EAAE,CAAC,OAAO,GAAG,KAAK,GAAG,YAAY;gBAClC,CAAC,EAAE,IAAI,GAAG,MAAM;aACjB,CAAC,CAAC;SACJ;KACF;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,YAAY,CAAC,CAAe,EAAE,GAAW;IAChD,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3B,IAAI,CAAC,GAAG,CAAC;YAAE,OAAO,CAAC,CAAC;QACpB,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG;YAAE,OAAO,CAAC,CAAC;QACjC,OAAO,CAAC,CAAC;IACX,CAAC,CAAC,CAAC;AACL,CAAC;AACD;;;;;;;;GAQG;AACH,SAAS,cAAc,CACrB,cAAwB,EACxB,iBAAkC,EAClC,YAAsB,EACtB,SAA0B,EAC1B,OAAiB;IAEjB,IAAI,OAAO,GAAG,CAAC,CAAC;IAChB,KAAK,MAAM,OAAO,IAAI,OAAO,EAAE;QAC7B,OAAO,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC;KAClC;IAED,MAAM,UAAU,GAAG,IAAI,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAEtD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE;QAC7C,IAAI,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;QAErB,MAAM,CAAC,GAAG,cAAc,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC;QAE1C,IAAI,EAAE,EAAE,EAAE,CAAC;QACX,IAAI,IAAI,GAAG,CAAC,CAAC;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE;YAC5B,IAAI,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;SAClC;QACD,EAAE,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAE5B,IAAI,GAAG,CAAC,CAAC;QACT,KAAK,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC7C,IAAI,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;SAClC;QACD,EAAE,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAE5B,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;QAChC,MAAM,QAAQ,GAAG,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC;QAC/D,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;QACpC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,OAAO,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;YAChD,MAAM,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YACxB,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC7B,MAAM,CAAC,GAAG,cAAc,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC;gBAE1C,IAAI,EAAE,EAAE,EAAE,CAAC;gBACX,IAAI,IAAI,GAAG,CAAC,CAAC;gBACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAC7B,IAAI,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;iBAClC;gBACD,EAAE,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBAE5B,IAAI,GAAG,CAAC,CAAC;gBACT,KAAK,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC9C,IAAI,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;iBAClC;gBACD,EAAE,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;gBAE5B,MAAM,KAAK,GAAG,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC;qBACnC,gBAAgB,CAAC,EAAE,CAAC;qBACpB,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CAAC;gBACvD,KAAK,CAAC,GAAG,CACP,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC;qBACrB,gBAAgB,CAAC,EAAE,CAAC;qBACpB,GAAG,CAAC,CAAC,CAAC,CAAC;qBACP,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CACvD,CAAC;gBACF,KAAK,CAAC,GAAG,CACP,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC;qBACrB,gBAAgB,CAAC,EAAE,CAAC;qBACpB,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CACvD,CAAC;gBAEF,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aAC5D;SACF;KACF;IACD,OAAO,UAAU,CAAC;AACpB,CAAC"}

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": "8.0.0",
+  "version": "8.1.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -58,7 +58,9 @@
     "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",
@@ -76,6 +78,6 @@
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.2.5",
     "openchemlib-utils": "^1.11.0",
-    "spectrum-generator": "^8.0.1"
+    "spectrum-generator": "^8.0.2"
   }
 }

package/src/index.ts

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

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;
 }

package/src/peaks/solventSuppression.ts

@@ -0,0 +1,186 @@
+import { PointXY } from 'cheminfo-types';
+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 { NMRSignal1D } from '../signals/NMRSignal1D';
+import { addDummySignals } from '../signals/addDummySignals';
+import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
+import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
+
+import { NMRPeak1D } from './NMRPeak1D';
+
+export function solventSuppression(
+  peakList: NMRPeak1D[],
+  solvent: NMRSignal1D[],
+  options: any = {},
+) {
+  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: NMRSignal1D,
+  options: { frequency?: number; maxClusterSize?: number } = {},
+) {
+  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: PointXY,
+  solventSignal: any,
+  solventXYPeaks: PointXY[],
+) {
+  const shiftedSolventPeaks: PointXY[] = 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: PointXY[], nearPeaks: PointXY[]) {
+  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: PointXY[]) {
+  return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
+}
+
+function getDiffMatrix(rows: PointXY[], columns: PointXY[]) {
+  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;
+}

package/src/peaks/util/jAnalyzer.ts

@@ -29,7 +29,7 @@ interface IntergralData {
   to: number;
 }
 
-export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
+export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
   intensity: number;
 };
 

package/src/ranges/rangesToXY.ts

@@ -49,13 +49,21 @@ function checkForSignals(
     if (!range.signals) throw new Error('range has not signals');
   }
 }
+
+const defaultFromTo = (nucleus = '') => {
+  switch (nucleus.toUpperCase()) {
+    case '13C':
+      return { from: -5, to: 206 };
+    default:
+      return { from: -0.5, to: 10.5 };
+  }
+};
+
 export function rangesToXY(ranges: NMRRange[], options: any = {}) {
   checkForSignals(ranges);
   let {
     frequency = 400,
     lineWidth = 1,
-    from = 0,
-    to = 10,
     nbPoints = 16 * 1024,
     shape = { kind: 'gaussian' },
   } = options;
@@ -66,9 +74,10 @@ export function rangesToXY(ranges: NMRRange[], options: any = {}) {
     }
   };
 
+  const { from, to } = getFromTo(ranges, options);
   const spectrumOptions = {
-    from,
     to,
+    from,
     nbPoints,
     shape,
     lineWidth,
@@ -139,7 +148,7 @@ function peaksOfMultiplet(delta: number, options: any) {
   const {
     frequency,
     lineWidth,
-    intensities = [1, 2, 5, 4, 5, 3, 4, 2, 1],
+    intensities = [1, 2, 5, 4, 5, 7, 5, 4, 5, 2, 1],
   } = options;
 
   const lineWidthPpm = lineWidth / frequency;
@@ -182,3 +191,23 @@ function normalizeSpectrum(
     }
   }
 }
+
+function getFromTo(ranges: NMRRange[], options: any) {
+  const { from: defaultFrom, to: defaultTo } = defaultFromTo(options.nucleus);
+
+  let rangesFrom = Number.MAX_SAFE_INTEGER;
+  let rangesTo = Number.MIN_SAFE_INTEGER;
+  for (const range of ranges) {
+    for (const signal of range.signals || []) {
+      if (rangesFrom > signal.delta) rangesFrom = signal.delta;
+      if (rangesTo < signal.delta) rangesTo = signal.delta;
+    }
+  }
+
+  const {
+    from = Math.min(rangesFrom - 0.5, defaultFrom),
+    to = Math.max(rangesTo + 0.5, defaultTo),
+  } = options;
+
+  return { from, to };
+}

package/src/signals/addDummySignals.ts

@@ -0,0 +1,77 @@
+import { couplingPatterns } from '../constants/couplingPatterns';
+
+import { NMRSignal1D } from './NMRSignal1D';
+import type { Jcoupling } from './jcoupling';
+
+export function addDummySignals(signals: NMRSignal1D[]) {
+  let newSignals: NMRSignal1D[] = JSON.parse(JSON.stringify(signals));
+
+  signals.forEach((signal, s) => {
+    const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
+
+    let { newCouplings, tempSignals } = checkCouplings(
+      jCouplings,
+      newSignals,
+      signalAssignment,
+    );
+
+    if (tempSignals.length > 0) newSignals.push(...tempSignals);
+
+    newSignals[s].js = newCouplings;
+    newSignals[s].atoms = signalAssignment;
+  });
+
+  return newSignals.sort((a, b) => a.delta - b.delta);
+}
+
+function checkCouplings(
+  jCouplings: Jcoupling[],
+  signals: NMRSignal1D[],
+  signalAssignment: number[],
+) {
+  let newSignalAssignment = signals.length - 1;
+  let tempSignals: NMRSignal1D[] = [];
+  const newCouplings = jCouplings.reduce<Jcoupling[]>(
+    (newCouplings, jCoupling) => {
+      const { atoms = [], multiplicity, coupling } = jCoupling;
+      if (atoms.length === 0) {
+        if (coupling && multiplicity) {
+          let tempCouplings: Jcoupling[] = [];
+          const nbLinks = couplingPatterns.indexOf(multiplicity);
+          for (let i = 0; i < nbLinks; i++) {
+            newSignalAssignment++;
+            tempCouplings.push({
+              coupling,
+              atoms: [newSignalAssignment],
+            });
+            tempSignals.push(
+              formatSignal(coupling, [newSignalAssignment], signalAssignment),
+            );
+          }
+        } else {
+          newCouplings.push(jCoupling);
+        }
+      }
+      return newCouplings;
+    },
+    [],
+  );
+  return { newCouplings, tempSignals };
+}
+
+function formatSignal(
+  coupling: number,
+  newSignalAssignment: number[],
+  signalAssignment: number[],
+) {
+  return {
+    delta: 100000,
+    atoms: newSignalAssignment,
+    js: [
+      {
+        coupling,
+        atoms: signalAssignment,
+      },
+    ],
+  };
+}