nmr-processing 9.7.5 → 9.7.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/lib/index.d.ts +1 -0
- package/lib/prediction/predictAll.d.ts +1 -1
- package/lib/signals/signalsToXY.js +2 -5
- package/lib/signals/signalsToXY.js.map +1 -1
- package/lib/signals/simulation/signalsToSpinSystem.js +3 -23
- package/lib/signals/simulation/signalsToSpinSystem.js.map +1 -1
- package/lib/signals/simulation/simulate1D.d.ts +1 -5
- package/lib/signals/simulation/simulate1D.js +5 -6
- package/lib/signals/simulation/simulate1D.js.map +1 -1
- package/lib/signals/simulation/simulateXYPeaks.d.ts +1 -1
- package/lib/signals/simulation/simulateXYPeaks.js +8 -6
- package/lib/signals/simulation/simulateXYPeaks.js.map +1 -1
- package/lib/signals/simulation/splitSpinSystem.d.ts +1 -1
- package/lib/signals/simulation/splitSpinSystem.js +3 -1
- package/lib/signals/simulation/splitSpinSystem.js.map +1 -1
- package/lib/signals/spinSystem.d.ts +18 -3
- package/lib/signals/utils/ensureSpinSystemProps.d.ts +9 -0
- package/lib/signals/utils/ensureSpinSystemProps.js +35 -0
- package/lib/signals/utils/ensureSpinSystemProps.js.map +1 -0
- package/lib-esm/signals/signalsToXY.js +1 -1
- package/lib-esm/signals/signalsToXY.js.map +1 -1
- package/lib-esm/signals/simulation/signalsToSpinSystem.js +3 -20
- package/lib-esm/signals/simulation/signalsToSpinSystem.js.map +1 -1
- package/lib-esm/signals/simulation/simulate1D.js +3 -5
- package/lib-esm/signals/simulation/simulate1D.js.map +1 -1
- package/lib-esm/signals/simulation/simulateXYPeaks.js +8 -6
- package/lib-esm/signals/simulation/simulateXYPeaks.js.map +1 -1
- package/lib-esm/signals/simulation/splitSpinSystem.js +3 -1
- package/lib-esm/signals/simulation/splitSpinSystem.js.map +1 -1
- package/lib-esm/signals/utils/ensureSpinSystemProps.js +28 -0
- package/lib-esm/signals/utils/ensureSpinSystemProps.js.map +1 -0
- package/package.json +1 -1
- package/src/index.ts +1 -0
- package/src/prediction/predictAll.ts +1 -1
- package/src/signals/signalsToXY.ts +1 -1
- package/src/signals/simulation/signalsToSpinSystem.ts +3 -25
- package/src/signals/simulation/simulate1D.ts +4 -6
- package/src/signals/simulation/simulateXYPeaks.ts +9 -6
- package/src/signals/simulation/splitSpinSystem.ts +3 -1
- package/src/signals/spinSystem.ts +18 -3
- package/src/signals/utils/ensureSpinSystemProps.ts +41 -0
package/lib/index.d.ts
CHANGED
|
@@ -82,6 +82,7 @@ export type { NMRRange } from './xy/NMRRange';
|
|
|
82
82
|
export type { NMRZone } from './xyz/NMRZone';
|
|
83
83
|
export type { NMRPeak1D } from './peaks/NMRPeak1D';
|
|
84
84
|
export type { Prediction1D } from './prediction/Prediction1D';
|
|
85
|
+
export type { Prediction2D } from './prediction/Prediction2D';
|
|
85
86
|
export type { Jcoupling } from './signals/Jcoupling';
|
|
86
87
|
export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
|
|
87
88
|
export type { DataBaseLevelStructure, DataBaseStructure, } from './prediction/dataStructure';
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib/full';
|
|
2
1
|
import type { Logger } from 'cheminfo-types';
|
|
2
|
+
import type { Molecule } from 'openchemlib/full';
|
|
3
3
|
import type { Prediction1D } from './Prediction1D';
|
|
4
4
|
import { PredictCarbonOptions } from './predictCarbon';
|
|
5
5
|
import { PredictProtonOptions } from './predictProton';
|
|
@@ -1,12 +1,9 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
3
|
exports.signalsToXY = void 0;
|
|
7
4
|
const ml_spectra_processing_1 = require("ml-spectra-processing");
|
|
8
5
|
const signalsToSpinSystem_1 = require("./simulation/signalsToSpinSystem");
|
|
9
|
-
const simulate1D_1 =
|
|
6
|
+
const simulate1D_1 = require("./simulation/simulate1D");
|
|
10
7
|
const splitSpinSystem_1 = require("./simulation/splitSpinSystem");
|
|
11
8
|
function checkForMandatory(signals) {
|
|
12
9
|
for (const signal of signals) {
|
|
@@ -41,7 +38,7 @@ function signalsToXY(signals, options = {}) {
|
|
|
41
38
|
frequency,
|
|
42
39
|
maxClusterSize,
|
|
43
40
|
});
|
|
44
|
-
let spectrum = (0, simulate1D_1.
|
|
41
|
+
let spectrum = (0, simulate1D_1.simulate1D)(spinSystem, {
|
|
45
42
|
frequency,
|
|
46
43
|
from,
|
|
47
44
|
to,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalsToXY.js","sourceRoot":"","sources":["../../src/signals/signalsToXY.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"signalsToXY.js","sourceRoot":"","sources":["../../src/signals/signalsToXY.ts"],"names":[],"mappings":";;;AACA,iEAAgF;AAMhF,0EAAuE;AACvE,wDAAqD;AACrD,kEAA+D;AA8C/D,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,4DAA4D;QAC5D,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;QACzD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,EAAE,EAAE;YACzB,uDAAuD;YACvD,IAAI,CAAC,CAAC,CAAC,KAAK;gBAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;SACrD;KACF;AACH,CAAC;AAED;;GAEG;AACH,SAAgB,WAAW,CACzB,OAAsB,EACtB,UAA8B,EAAE;IAEhC,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,IAAI,EACF,SAAS,GAAG,GAAG,EACf,KAAK,GAAG;QACN,IAAI,EAAE,UAAU;KACjB,EACD,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,SAAS,GAAG,CAAC,EACb,QAAQ,GAAG,EAAE,GAAG,IAAI,EACpB,QAAQ,GAAG,GAAG,EACd,cAAc,GAAG,CAAC,GACnB,GAAG,OAAO,CAAC;IAEZ,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;QACxB,OAAO;YACL,CAAC,EAAE,IAAA,uCAAe,EAAC,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;YAChD,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;SAC1C,CAAC;KACH;IAED,IAAI,UAAU,GAAG,IAAA,yCAAmB,EAAC,OAAO,CAAC,CAAC;IAE9C,UAAU,CAAC,QAAQ,GAAG,IAAA,iCAAe,EAAC,UAAU,EAAE;QAChD,SAAS;QACT,cAAc;KACf,CAAC,CAAC;IAEH,IAAI,QAAQ,GAAG,IAAA,uBAAU,EAAC,UAAU,EAAE;QACpC,SAAS;QACT,IAAI;QACJ,EAAE;QACF,QAAQ;QACR,SAAS;QACT,cAAc;QACd,KAAK;KACN,CAAC,CAAC;IAEH,IAAI,QAAQ,IAAI,IAAA,oCAAY,EAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;QAC9C,QAAQ,CAAC,CAAC,GAAG,IAAA,gCAAQ,EAAC,QAAQ,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAC;KACtD;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC;AA/CD,kCA+CC"}
|
|
@@ -1,11 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
3
|
exports.signalsToSpinSystem = void 0;
|
|
7
4
|
const ml_matrix_1 = require("ml-matrix");
|
|
8
|
-
const
|
|
5
|
+
const ensureSpinSystemProps_1 = require("../utils/ensureSpinSystemProps");
|
|
9
6
|
function checkForMandatory(signals) {
|
|
10
7
|
for (const signal of signals) {
|
|
11
8
|
if (!signal.js)
|
|
@@ -22,12 +19,10 @@ function signalsToSpinSystem(signals) {
|
|
|
22
19
|
checkForMandatory(signals);
|
|
23
20
|
const nSpins = signals.length;
|
|
24
21
|
const chemicalShifts = new Array(nSpins);
|
|
25
|
-
const multiplicity = new Array(nSpins);
|
|
26
22
|
const couplingConstants = ml_matrix_1.Matrix.zeros(nSpins, nSpins);
|
|
27
23
|
//create a list of assignments
|
|
28
24
|
const ids = {};
|
|
29
25
|
for (let i = 0; i < nSpins; i++) {
|
|
30
|
-
multiplicity[i] = 2;
|
|
31
26
|
chemicalShifts[i] = signals[i].delta;
|
|
32
27
|
const index = signals[i].atoms[0];
|
|
33
28
|
ids[index] = i;
|
|
@@ -43,25 +38,10 @@ function signalsToSpinSystem(signals) {
|
|
|
43
38
|
couplingConstants.set(ids[toIndex], ids[fromIndex], coupling);
|
|
44
39
|
}
|
|
45
40
|
}
|
|
46
|
-
|
|
47
|
-
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
48
|
-
for (let j = i; j < couplingConstants.columns; j++) {
|
|
49
|
-
if (couplingConstants.get(i, j) === 0) {
|
|
50
|
-
connectivity.set(i, j, 0);
|
|
51
|
-
connectivity.set(j, i, 0);
|
|
52
|
-
}
|
|
53
|
-
}
|
|
54
|
-
}
|
|
55
|
-
let clusters = (0, ml_simple_clustering_1.default)(connectivity.to2DArray(), {
|
|
56
|
-
out: 'indexes',
|
|
57
|
-
});
|
|
58
|
-
return {
|
|
59
|
-
clusters,
|
|
41
|
+
return (0, ensureSpinSystemProps_1.ensureSpinSystemProps)({
|
|
60
42
|
couplingConstants,
|
|
61
43
|
chemicalShifts,
|
|
62
|
-
|
|
63
|
-
connectivity,
|
|
64
|
-
};
|
|
44
|
+
});
|
|
65
45
|
}
|
|
66
46
|
exports.signalsToSpinSystem = signalsToSpinSystem;
|
|
67
47
|
//# sourceMappingURL=signalsToSpinSystem.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalsToSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/signalsToSpinSystem.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"signalsToSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/signalsToSpinSystem.ts"],"names":[],"mappings":";;;AAAA,yCAAmC;AAMnC,0EAAuE;AAYvE,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;QACzD,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,CAAC,KAAK;gBAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;SAC7D;KACF;AACH,CAAC;AAED,SAAgB,mBAAmB,CAAC,OAAsB;IACxD,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAC9B,MAAM,cAAc,GAAa,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC;IACnD,MAAM,iBAAiB,GAAG,kBAAM,CAAC,KAAK,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvD,8BAA8B;IAC9B,MAAM,GAAG,GAAQ,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,cAAc,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;QACrC,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAClC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;KAChB;IACD,4BAA4B;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,IAAI,EAAE,KAAK,EAAE,gBAAgB,EAAE,EAAE,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC5D,MAAM,SAAS,GAAG,gBAAgB,CAAC,CAAC,CAAC,CAAC;QACtC,KAAK,MAAM,SAAS,IAAI,SAAS,EAAE;YACjC,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC;YACpC,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YACzB,iBAAiB,CAAC,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,GAAG,CAAC,OAAO,CAAC,EAAE,QAAQ,CAAC,CAAC;YAC9D,iBAAiB,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,SAAS,CAAC,EAAE,QAAQ,CAAC,CAAC;SAC/D;KACF;IAED,OAAO,IAAA,6CAAqB,EAAC;QAC3B,iBAAiB;QACjB,cAAc;KACf,CAAC,CAAC;AACL,CAAC;AA5BD,kDA4BC"}
|
|
@@ -4,8 +4,4 @@ import type { Simulate1DOptions } from './simulateXYPeaks';
|
|
|
4
4
|
/**
|
|
5
5
|
* This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
|
|
6
6
|
*/
|
|
7
|
-
export
|
|
8
|
-
/**
|
|
9
|
-
* The SpinSystem object to be simulated
|
|
10
|
-
*/
|
|
11
|
-
spinSystem: SpinSystem, options?: Simulate1DOptions): DataXY;
|
|
7
|
+
export declare function simulate1D(spinSystemInput: SpinSystem, options?: Simulate1DOptions): DataXY;
|
|
@@ -1,18 +1,17 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.simulate1D = void 0;
|
|
3
4
|
const spectrum_generator_1 = require("spectrum-generator");
|
|
4
5
|
const simulateXYPeaks_1 = require("./simulateXYPeaks");
|
|
6
|
+
const ensureSpinSystemProps_1 = require("../utils/ensureSpinSystemProps");
|
|
5
7
|
/**
|
|
6
8
|
* This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
|
|
7
9
|
*/
|
|
8
|
-
function simulate1D(
|
|
9
|
-
/**
|
|
10
|
-
* The SpinSystem object to be simulated
|
|
11
|
-
*/
|
|
12
|
-
spinSystem, options = {}) {
|
|
10
|
+
function simulate1D(spinSystemInput, options = {}) {
|
|
13
11
|
let { lineWidth = 1, frequency: frequencyMHz = 400, from = 0, to = 10, nbPoints = 1024, shape = {
|
|
14
12
|
kind: 'gaussian',
|
|
15
13
|
}, } = options;
|
|
14
|
+
const spinSystem = (0, ensureSpinSystemProps_1.ensureSpinSystemProps)(spinSystemInput);
|
|
16
15
|
let peakWidth = lineWidth / frequencyMHz;
|
|
17
16
|
const xyPeaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem, options);
|
|
18
17
|
return (0, spectrum_generator_1.generateSpectrum)(xyPeaks, {
|
|
@@ -27,5 +26,5 @@ spinSystem, options = {}) {
|
|
|
27
26
|
},
|
|
28
27
|
});
|
|
29
28
|
}
|
|
30
|
-
exports.
|
|
29
|
+
exports.simulate1D = simulate1D;
|
|
31
30
|
//# sourceMappingURL=simulate1D.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":";;;AACA,2DAAsD;AAKtD,uDAAoD;AACpD,0EAAuE;AAEvE;;GAEG;AACH,SAAgB,UAAU,CACxB,eAA2B,EAC3B,UAA6B,EAAE;IAE/B,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,EAAE,YAAY,GAAG,GAAG,EAC7B,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,IAAI,EACf,KAAK,GAAG;QACN,IAAI,EAAE,UAAU;KACjB,GACF,GAAG,OAAO,CAAC;IAEZ,MAAM,UAAU,GAAG,IAAA,6CAAqB,EAAC,eAAe,CAAC,CAAC;IAC1D,IAAI,SAAS,GAAG,SAAS,GAAG,YAAY,CAAC;IAEzC,MAAM,OAAO,GAAG,IAAA,iCAAe,EAAC,UAAU,EAAE,OAAO,CAAC,CAAC;IAErD,OAAO,IAAA,qCAAgB,EAAC,OAAO,EAAE;QAC/B,SAAS,EAAE;YACT,IAAI;YACJ,EAAE;YACF,QAAQ;SACT;QACD,WAAW,EAAE;YACX,KAAK;YACL,KAAK,EAAE,SAAS;SACjB;KACF,CAAC,CAAC;AACL,CAAC;AA/BD,gCA+BC"}
|
|
@@ -8,18 +8,20 @@ const binary_search_1 = __importDefault(require("binary-search"));
|
|
|
8
8
|
const ml_matrix_1 = require("ml-matrix");
|
|
9
9
|
const ml_sparse_matrix_1 = require("ml-sparse-matrix");
|
|
10
10
|
const getPauliMatrix_1 = __importDefault(require("./getPauliMatrix"));
|
|
11
|
+
const ensureSpinSystemProps_1 = require("../utils/ensureSpinSystemProps");
|
|
11
12
|
const smallValue = 1e-2;
|
|
12
13
|
function simulateXYPeaks(
|
|
13
14
|
/**
|
|
14
15
|
* The SpinSystem object to be simulated
|
|
15
16
|
*/
|
|
16
|
-
|
|
17
|
+
spinSystemInput, options = {}) {
|
|
17
18
|
let { lineWidth = 1, maxClusterSize = 8, frequency: frequencyMHz = 400, } = options;
|
|
19
|
+
const spinSystem = (0, ensureSpinSystemProps_1.ensureSpinSystemProps)(spinSystemInput);
|
|
18
20
|
const chemicalShifts = spinSystem.chemicalShifts.slice();
|
|
19
21
|
for (let i = 0; i < chemicalShifts.length; i++) {
|
|
20
22
|
chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
|
|
21
23
|
}
|
|
22
|
-
const
|
|
24
|
+
const levels = spinSystem.levels;
|
|
23
25
|
const xyPeaks = [];
|
|
24
26
|
for (const cluster of spinSystem.clusters) {
|
|
25
27
|
let clusterFake = cluster.map((cluster) => cluster < 0 ? -cluster - 1 : cluster);
|
|
@@ -54,7 +56,7 @@ spinSystem, options = {}) {
|
|
|
54
56
|
}
|
|
55
57
|
}
|
|
56
58
|
else {
|
|
57
|
-
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants,
|
|
59
|
+
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, levels, spinSystem.connectivity, clusterFake);
|
|
58
60
|
const hamSize = hamiltonian.rows;
|
|
59
61
|
// TODO: add support for sparse matrix in matrix types.
|
|
60
62
|
// @ts-expect-error sparse matrix not supported
|
|
@@ -65,15 +67,15 @@ spinSystem, options = {}) {
|
|
|
65
67
|
const multLen = cluster.length;
|
|
66
68
|
weight = 0;
|
|
67
69
|
for (let n = 0; n < multLen; n++) {
|
|
68
|
-
const L = (0, getPauliMatrix_1.default)(
|
|
70
|
+
const L = (0, getPauliMatrix_1.default)(levels[clusterFake[n]]);
|
|
69
71
|
let temp = 1;
|
|
70
72
|
for (let j = 0; j < n; j++) {
|
|
71
|
-
temp *=
|
|
73
|
+
temp *= levels[clusterFake[j]];
|
|
72
74
|
}
|
|
73
75
|
const A = ml_sparse_matrix_1.SparseMatrix.eye(temp);
|
|
74
76
|
temp = 1;
|
|
75
77
|
for (let j = n + 1; j < multLen; j++) {
|
|
76
|
-
temp *=
|
|
78
|
+
temp *= levels[clusterFake[j]];
|
|
77
79
|
}
|
|
78
80
|
const B = ml_sparse_matrix_1.SparseMatrix.eye(temp);
|
|
79
81
|
const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"simulateXYPeaks.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulateXYPeaks.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAyC;AACzC,yCAAwC;AAGxC,uDAAgD;AAIhD,sEAA8C;
|
|
1
|
+
{"version":3,"file":"simulateXYPeaks.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulateXYPeaks.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAyC;AACzC,yCAAwC;AAGxC,uDAAgD;AAIhD,sEAA8C;AAC9C,0EAAuE;AAEvE,MAAM,UAAU,GAAG,IAAI,CAAC;AAwCxB,SAAgB,eAAe;AAC7B;;GAEG;AACH,eAA2B,EAC3B,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,UAAU,GAAG,IAAA,6CAAqB,EAAC,eAAe,CAAC,CAAC;IAE1D,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,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC;IAEjC,MAAM,OAAO,GAAoC,EAAE,CAAC;IACpD,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;QACF,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,MAAM,EACN,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,eAAG,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,+BAAY,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,IAAA,wBAAc,EAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBAEjD,IAAI,IAAI,GAAG,CAAC,CAAC;gBACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;oBAC1B,IAAI,IAAI,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChC;gBACD,MAAM,CAAC,GAAG,+BAAY,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,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChC;gBACD,MAAM,CAAC,GAAG,+BAAY,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;YACD,IAAI,KAAK,GAAG,kBAAM,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,+BAAY,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,+BAAY,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,IAAA,uBAAY,EACzB,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;QACnC,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,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;AACjD,CAAC;AA7LD,0CA6LC;AAED,SAAS,YAAY,CAAC,CAAe,EAAE,GAAW;IAChD,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3B,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,+BAAY,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,IAAA,wBAAc,EAAC,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,+BAAY,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,+BAAY,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,IAAA,wBAAc,EAAC,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,+BAAY,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,+BAAY,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"}
|
|
@@ -9,4 +9,4 @@ export interface SplitSpinSystemOptions {
|
|
|
9
9
|
*/
|
|
10
10
|
maxClusterSize?: number;
|
|
11
11
|
}
|
|
12
|
-
export declare function splitSpinSystem(
|
|
12
|
+
export declare function splitSpinSystem(spinSystemInput: SpinSystem, options?: SplitSpinSystemOptions): any[];
|
|
@@ -3,7 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.splitSpinSystem = void 0;
|
|
4
4
|
const ml_hclust_1 = require("ml-hclust");
|
|
5
5
|
const ml_matrix_1 = require("ml-matrix");
|
|
6
|
-
|
|
6
|
+
const ensureSpinSystemProps_1 = require("../utils/ensureSpinSystemProps");
|
|
7
|
+
function splitSpinSystem(spinSystemInput, options = {}) {
|
|
8
|
+
const spinSystem = (0, ensureSpinSystemProps_1.ensureSpinSystemProps)(spinSystemInput);
|
|
7
9
|
let { chemicalShifts, couplingConstants, connectivity } = spinSystem;
|
|
8
10
|
let { frequency = 400, maxClusterSize = 8 } = options;
|
|
9
11
|
let betas = calculateBetas(chemicalShifts, couplingConstants, frequency);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"splitSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/splitSpinSystem.ts"],"names":[],"mappings":";;;AAAA,yCAAkC;AAElC,yCAAmC;
|
|
1
|
+
{"version":3,"file":"splitSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/splitSpinSystem.ts"],"names":[],"mappings":";;;AAAA,yCAAkC;AAElC,yCAAmC;AAGnC,0EAAuE;AAavE,SAAgB,eAAe,CAC7B,eAA2B,EAC3B,UAAkC,EAAE;IAEpC,MAAM,UAAU,GAAG,IAAA,6CAAqB,EAAC,eAAe,CAAC,CAAC;IAC1D,IAAI,EAAE,cAAc,EAAE,iBAAiB,EAAE,YAAY,EAAE,GAAG,UAAU,CAAC;IACrE,IAAI,EAAE,SAAS,GAAG,GAAG,EAAE,cAAc,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;IACtD,IAAI,KAAK,GAAG,cAAc,CAAC,cAAc,EAAE,iBAAiB,EAAE,SAAS,CAAC,CAAC;IACzE,IAAI,YAAY,GAAG,IAAA,iBAAK,EAAC,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,gBAAgB,EAAE,IAAI,EAAE,CAAC,CAAC;IAC9E,IAAI,WAAW,GAAsB,EAAE,CAAC;IACxC,IAAI,MAAM,GAAG,cAAc,CAAC,MAAM,CAAC;IACnC,YAAY,CAAC,YAAY,EAAE,WAAW,EAAE;QACtC,cAAc;QACd,KAAK,EAAE,KAAK;QACZ,MAAM;QACN,YAAY;KACb,CAAC,CAAC;IACH,IAAI,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,cAAc,CAAC,CAAC;IAChE,IAAI,SAAS,GAAG,cAAc,CAAC,MAAM,CAAC;IACtC,IAAI,QAAQ,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAC;IACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;QAClC,QAAQ,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;QACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;YAC/B,IAAI,OAAO,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACnC,IAAI,OAAO,KAAK,CAAC;gBAAE,SAAS;YAC5B,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC9C;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC;AA9BD,0CA8BC;AASD,SAAS,YAAY,CACnB,OAAgB,EAChB,WAA8B,EAC9B,OAA4B;IAE5B,IAAI,EAAE,cAAc,EAAE,KAAK,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAC;IAC9D,IAAI,CAAC,KAAK,IAAI,OAAO,CAAC,IAAI,IAAI,cAAc,EAAE;QAC5C,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,MAAM,CAAC,CAAC,CAAC;KACzD;SAAM;QACL,KAAK,IAAI,KAAK,IAAI,OAAO,CAAC,QAAQ,EAAE;YAClC,IAAI,KAAK,CAAC,IAAI,IAAI,cAAc,EAAE;gBAChC,IAAI,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,MAAM,CAAC,CAAC;gBAClD,2EAA2E;gBAC3E,IAAI,KAAK,GAAG,CAAC,CAAC;gBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/B,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;wBACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;4BAC/B,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gCACpD,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gCAChB,KAAK,EAAE,CAAC;6BACT;yBACF;wBACD,KAAK,EAAE,CAAC;qBACT;iBACF;gBACD,IAAI,KAAK,IAAI,cAAc,EAAE;oBAC3B,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;iBAC3B;qBAAM,IAAI,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE;oBAC1B,YAAY,CAAC,KAAK,EAAE,WAAW,EAAE;wBAC/B,cAAc;wBACd,KAAK,EAAE,IAAI;wBACX,MAAM;wBACN,YAAY;qBACb,CAAC,CAAC;iBACJ;qBAAM;oBACL,iGAAiG;oBACjG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;oBACzB,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;iBAC3B;aACF;iBAAM;gBACL,YAAY,CAAC,KAAK,EAAE,WAAW,EAAE;oBAC/B,cAAc;oBACd,KAAK,EAAE,KAAK;oBACZ,MAAM;oBACN,YAAY;iBACb,CAAC,CAAC;aACJ;SACF;KACF;AACH,CAAC;AAED,SAAS,cAAc,CACrB,cAAwB,EACxB,iBAAyB,EACzB,SAAiB;IAEjB,IAAI,KAAK,GAAG,iBAAiB,CAAC,IAAI,CAAC;IACnC,IAAI,QAAQ,GAAG,iBAAiB,CAAC,OAAO,CAAC;IACzC,IAAI,KAAK,GAAG,kBAAM,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IACvC,2GAA2G;IAC3G,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;YACjC,IAAI,OAAO,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAC1C,IAAI,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,IAAI,KAAK,GACP,CAAC;oBACD,IAAI,CAAC,GAAG,CACN,OAAO,GAAG,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,CAChE,CAAC;gBACJ,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;gBACvB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;aACxB;iBAAM,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,OAAO,KAAK,CAAC,CAAC,EAAE;gBACtC,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;gBACnB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;aACpB;SACF;KACF;IACD,OAAO,KAAK,CAAC,SAAS,EAAE,CAAC;AAC3B,CAAC;AAED,SAAS,aAAa,CAAC,IAAuB,EAAE,cAAsB;IACpE,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;QACzC,IAAI,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACvB,IAAI,SAAS,GAAG,QAAQ,CAAC,MAAM,CAAC;QAChC,IAAI,KAAK,GAAG,CAAC,CAAC;QAEd,kCAAkC;QAClC,OAAO,KAAK,GAAG,SAAS,IAAI,QAAQ,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC;YAAC,CAAC;QACtD,IAAI,KAAK,IAAI,SAAS;YAAE,SAAS;QAEjC,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7C,IAAI,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;YACvB,gCAAgC;YAChC,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,IAAI,MAAM,GAAG,CAAC,CAAC;YACf,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,EAAE,KAAK,EAAE,EAAE;gBAC9C,IAAI,QAAQ,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;oBAAE,MAAM,EAAE,CAAC;gBACvD,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC;oBAAE,KAAK,EAAE,CAAC;aAC7D;YAED,IAAI,MAAM,GAAG,CAAC,IAAI,KAAK,IAAI,cAAc,EAAE;gBACzC,qCAAqC;gBACrC,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,EAAE,KAAK,EAAE,EAAE;oBAC9C,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;qBACrB;yBAAM,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;wBAC1D,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;qBACtB;iBACF;gBACD,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;aACnB;SACF;KACF;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,UAAU,CAAC,OAAiB,EAAE,MAAc;IACnD,IAAI,OAAO,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC;IACrC,KAAK,IAAI,CAAC,IAAI,OAAO,EAAE;QACrB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;KAChB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,8 +1,23 @@
|
|
|
1
1
|
import type { Matrix } from 'ml-matrix';
|
|
2
2
|
export interface SpinSystem {
|
|
3
|
-
|
|
3
|
+
/**
|
|
4
|
+
* isolated clusters from a similarity/connectivity matrix
|
|
5
|
+
*/
|
|
6
|
+
clusters?: number[][];
|
|
7
|
+
/**
|
|
8
|
+
* Matrix of coupling values between spins.
|
|
9
|
+
*/
|
|
4
10
|
couplingConstants: Matrix;
|
|
11
|
+
/**
|
|
12
|
+
* Array of chemical shifts of the spin system
|
|
13
|
+
*/
|
|
5
14
|
chemicalShifts: number[];
|
|
6
|
-
|
|
7
|
-
|
|
15
|
+
/**
|
|
16
|
+
* Array of degree of freedom of the spin, it is usually an array of 2.
|
|
17
|
+
*/
|
|
18
|
+
levels?: number[];
|
|
19
|
+
/**
|
|
20
|
+
* Binary matrix based on the coupling constants.
|
|
21
|
+
*/
|
|
22
|
+
connectivity?: Matrix;
|
|
8
23
|
}
|
|
@@ -0,0 +1,9 @@
|
|
|
1
|
+
import Matrix from 'ml-matrix';
|
|
2
|
+
import { SpinSystem } from '../spinSystem';
|
|
3
|
+
export declare function ensureSpinSystemProps(spinSystem: SpinSystem): {
|
|
4
|
+
clusters: number[][];
|
|
5
|
+
couplingConstants: Matrix;
|
|
6
|
+
chemicalShifts: number[];
|
|
7
|
+
levels: any[];
|
|
8
|
+
connectivity: Matrix;
|
|
9
|
+
};
|
|
@@ -0,0 +1,35 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
+
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
+
};
|
|
5
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
+
exports.ensureSpinSystemProps = void 0;
|
|
7
|
+
const ml_matrix_1 = __importDefault(require("ml-matrix"));
|
|
8
|
+
const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
|
|
9
|
+
function ensureSpinSystemProps(spinSystem) {
|
|
10
|
+
const { couplingConstants } = spinSystem;
|
|
11
|
+
const { clusters, levels = new Array(couplingConstants.rows).fill(2), connectivity = connectivityMatrixFromCouplingMatrix(couplingConstants), } = spinSystem;
|
|
12
|
+
return {
|
|
13
|
+
levels,
|
|
14
|
+
clusters: clusters ||
|
|
15
|
+
(0, ml_simple_clustering_1.default)(connectivity.to2DArray(), {
|
|
16
|
+
out: 'indexes',
|
|
17
|
+
}),
|
|
18
|
+
connectivity,
|
|
19
|
+
...spinSystem,
|
|
20
|
+
};
|
|
21
|
+
}
|
|
22
|
+
exports.ensureSpinSystemProps = ensureSpinSystemProps;
|
|
23
|
+
function connectivityMatrixFromCouplingMatrix(couplingConstants) {
|
|
24
|
+
const connectivity = ml_matrix_1.default.ones(couplingConstants.rows, couplingConstants.rows);
|
|
25
|
+
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
26
|
+
for (let j = i; j < couplingConstants.columns; j++) {
|
|
27
|
+
if (couplingConstants.get(i, j) === 0) {
|
|
28
|
+
connectivity.set(i, j, 0);
|
|
29
|
+
connectivity.set(j, i, 0);
|
|
30
|
+
}
|
|
31
|
+
}
|
|
32
|
+
}
|
|
33
|
+
return connectivity;
|
|
34
|
+
}
|
|
35
|
+
//# sourceMappingURL=ensureSpinSystemProps.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ensureSpinSystemProps.js","sourceRoot":"","sources":["../../../src/signals/utils/ensureSpinSystemProps.ts"],"names":[],"mappings":";;;;;;AAAA,0DAA+B;AAE/B,gFAAoD;AAEpD,SAAgB,qBAAqB,CAAC,UAAsB;IAC1D,MAAM,EAAE,iBAAiB,EAAE,GAAG,UAAU,CAAC;IAEzC,MAAM,EACJ,QAAQ,EACR,MAAM,GAAG,IAAI,KAAK,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAClD,YAAY,GAAG,oCAAoC,CAAC,iBAAiB,CAAC,GACvE,GAAG,UAAU,CAAC;IAEf,OAAO;QACL,MAAM;QACN,QAAQ,EACN,QAAQ;YACR,IAAA,8BAAgB,EAAC,YAAY,CAAC,SAAS,EAAE,EAAE;gBACzC,GAAG,EAAE,SAAS;aACf,CAAC;QACJ,YAAY;QACZ,GAAG,UAAU;KACd,CAAC;AACJ,CAAC;AAnBD,sDAmBC;AAED,SAAS,oCAAoC,CAAC,iBAAyB;IACrE,MAAM,YAAY,GAAG,mBAAM,CAAC,IAAI,CAC9B,iBAAiB,CAAC,IAAI,EACtB,iBAAiB,CAAC,IAAI,CACvB,CAAC;IACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE;QAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;YAClD,IAAI,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE;gBACrC,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;gBAC1B,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;aAC3B;SACF;KACF;IAED,OAAO,YAAY,CAAC;AACtB,CAAC"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { xSequentialFill, xRescale, xIsMonotonic } from 'ml-spectra-processing';
|
|
2
2
|
import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
|
|
3
|
-
import simulate1D from './simulation/simulate1D';
|
|
3
|
+
import { simulate1D } from './simulation/simulate1D';
|
|
4
4
|
import { splitSpinSystem } from './simulation/splitSpinSystem';
|
|
5
5
|
function checkForMandatory(signals) {
|
|
6
6
|
for (const signal of signals) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalsToXY.js","sourceRoot":"","sources":["../../src/signals/signalsToXY.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAC;AAMhF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,UAAU,MAAM,yBAAyB,CAAC;
|
|
1
|
+
{"version":3,"file":"signalsToXY.js","sourceRoot":"","sources":["../../src/signals/signalsToXY.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAC;AAMhF,OAAO,EAAE,mBAAmB,EAAE,MAAM,kCAAkC,CAAC;AACvE,OAAO,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AA8C/D,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,4DAA4D;QAC5D,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;QACzD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,EAAE,EAAE;YACzB,uDAAuD;YACvD,IAAI,CAAC,CAAC,CAAC,KAAK;gBAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;SACrD;KACF;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,OAAsB,EACtB,UAA8B,EAAE;IAEhC,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,IAAI,EACF,SAAS,GAAG,GAAG,EACf,KAAK,GAAG;QACN,IAAI,EAAE,UAAU;KACjB,EACD,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,SAAS,GAAG,CAAC,EACb,QAAQ,GAAG,EAAE,GAAG,IAAI,EACpB,QAAQ,GAAG,GAAG,EACd,cAAc,GAAG,CAAC,GACnB,GAAG,OAAO,CAAC;IAEZ,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;QACxB,OAAO;YACL,CAAC,EAAE,eAAe,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;YAChD,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;SAC1C,CAAC;KACH;IAED,IAAI,UAAU,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC;IAE9C,UAAU,CAAC,QAAQ,GAAG,eAAe,CAAC,UAAU,EAAE;QAChD,SAAS;QACT,cAAc;KACf,CAAC,CAAC;IAEH,IAAI,QAAQ,GAAG,UAAU,CAAC,UAAU,EAAE;QACpC,SAAS;QACT,IAAI;QACJ,EAAE;QACF,QAAQ;QACR,SAAS;QACT,cAAc;QACd,KAAK;KACN,CAAC,CAAC;IAEH,IAAI,QAAQ,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;QAC9C,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,CAAC;KACtD;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { Matrix } from 'ml-matrix';
|
|
2
|
-
import
|
|
2
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
3
3
|
function checkForMandatory(signals) {
|
|
4
4
|
for (const signal of signals) {
|
|
5
5
|
if (!signal.js)
|
|
@@ -16,12 +16,10 @@ export function signalsToSpinSystem(signals) {
|
|
|
16
16
|
checkForMandatory(signals);
|
|
17
17
|
const nSpins = signals.length;
|
|
18
18
|
const chemicalShifts = new Array(nSpins);
|
|
19
|
-
const multiplicity = new Array(nSpins);
|
|
20
19
|
const couplingConstants = Matrix.zeros(nSpins, nSpins);
|
|
21
20
|
//create a list of assignments
|
|
22
21
|
const ids = {};
|
|
23
22
|
for (let i = 0; i < nSpins; i++) {
|
|
24
|
-
multiplicity[i] = 2;
|
|
25
23
|
chemicalShifts[i] = signals[i].delta;
|
|
26
24
|
const index = signals[i].atoms[0];
|
|
27
25
|
ids[index] = i;
|
|
@@ -37,24 +35,9 @@ export function signalsToSpinSystem(signals) {
|
|
|
37
35
|
couplingConstants.set(ids[toIndex], ids[fromIndex], coupling);
|
|
38
36
|
}
|
|
39
37
|
}
|
|
40
|
-
|
|
41
|
-
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
42
|
-
for (let j = i; j < couplingConstants.columns; j++) {
|
|
43
|
-
if (couplingConstants.get(i, j) === 0) {
|
|
44
|
-
connectivity.set(i, j, 0);
|
|
45
|
-
connectivity.set(j, i, 0);
|
|
46
|
-
}
|
|
47
|
-
}
|
|
48
|
-
}
|
|
49
|
-
let clusters = simpleClustering(connectivity.to2DArray(), {
|
|
50
|
-
out: 'indexes',
|
|
51
|
-
});
|
|
52
|
-
return {
|
|
53
|
-
clusters,
|
|
38
|
+
return ensureSpinSystemProps({
|
|
54
39
|
couplingConstants,
|
|
55
40
|
chemicalShifts,
|
|
56
|
-
|
|
57
|
-
connectivity,
|
|
58
|
-
};
|
|
41
|
+
});
|
|
59
42
|
}
|
|
60
43
|
//# sourceMappingURL=signalsToSpinSystem.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalsToSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/signalsToSpinSystem.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;
|
|
1
|
+
{"version":3,"file":"signalsToSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/signalsToSpinSystem.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAMnC,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAYvE,SAAS,iBAAiB,CACxB,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QACnD,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;QACzD,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,EAAE,EAAE;YACjC,IAAI,CAAC,SAAS,CAAC,KAAK;gBAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;SAC7D;KACF;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,OAAsB;IACxD,iBAAiB,CAAC,OAAO,CAAC,CAAC;IAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAC9B,MAAM,cAAc,GAAa,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC;IACnD,MAAM,iBAAiB,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvD,8BAA8B;IAC9B,MAAM,GAAG,GAAQ,EAAE,CAAC;IACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,cAAc,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;QACrC,MAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAClC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;KAChB;IACD,4BAA4B;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,IAAI,EAAE,KAAK,EAAE,gBAAgB,EAAE,EAAE,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC5D,MAAM,SAAS,GAAG,gBAAgB,CAAC,CAAC,CAAC,CAAC;QACtC,KAAK,MAAM,SAAS,IAAI,SAAS,EAAE;YACjC,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC;YACpC,MAAM,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YACzB,iBAAiB,CAAC,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,GAAG,CAAC,OAAO,CAAC,EAAE,QAAQ,CAAC,CAAC;YAC9D,iBAAiB,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,SAAS,CAAC,EAAE,QAAQ,CAAC,CAAC;SAC/D;KACF;IAED,OAAO,qBAAqB,CAAC;QAC3B,iBAAiB;QACjB,cAAc;KACf,CAAC,CAAC;AACL,CAAC"}
|
|
@@ -1,16 +1,14 @@
|
|
|
1
1
|
import { generateSpectrum } from 'spectrum-generator';
|
|
2
2
|
import { simulateXYPeaks } from './simulateXYPeaks';
|
|
3
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
3
4
|
/**
|
|
4
5
|
* This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
|
|
5
6
|
*/
|
|
6
|
-
export
|
|
7
|
-
/**
|
|
8
|
-
* The SpinSystem object to be simulated
|
|
9
|
-
*/
|
|
10
|
-
spinSystem, options = {}) {
|
|
7
|
+
export function simulate1D(spinSystemInput, options = {}) {
|
|
11
8
|
let { lineWidth = 1, frequency: frequencyMHz = 400, from = 0, to = 10, nbPoints = 1024, shape = {
|
|
12
9
|
kind: 'gaussian',
|
|
13
10
|
}, } = options;
|
|
11
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
14
12
|
let peakWidth = lineWidth / frequencyMHz;
|
|
15
13
|
const xyPeaks = simulateXYPeaks(spinSystem, options);
|
|
16
14
|
return generateSpectrum(xyPeaks, {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAKtD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;
|
|
1
|
+
{"version":3,"file":"simulate1D.js","sourceRoot":"","sources":["../../../src/signals/simulation/simulate1D.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AAKtD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACpD,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE;;GAEG;AACH,MAAM,UAAU,UAAU,CACxB,eAA2B,EAC3B,UAA6B,EAAE;IAE/B,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,EAAE,YAAY,GAAG,GAAG,EAC7B,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,IAAI,EACf,KAAK,GAAG;QACN,IAAI,EAAE,UAAU;KACjB,GACF,GAAG,OAAO,CAAC;IAEZ,MAAM,UAAU,GAAG,qBAAqB,CAAC,eAAe,CAAC,CAAC;IAC1D,IAAI,SAAS,GAAG,SAAS,GAAG,YAAY,CAAC;IAEzC,MAAM,OAAO,GAAG,eAAe,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC;IAErD,OAAO,gBAAgB,CAAC,OAAO,EAAE;QAC/B,SAAS,EAAE;YACT,IAAI;YACJ,EAAE;YACF,QAAQ;SACT;QACD,WAAW,EAAE;YACX,KAAK;YACL,KAAK,EAAE,SAAS;SACjB;KACF,CAAC,CAAC;AACL,CAAC"}
|
|
@@ -2,18 +2,20 @@ import binarySearch from 'binary-search';
|
|
|
2
2
|
import { Matrix, EVD } from 'ml-matrix';
|
|
3
3
|
import { SparseMatrix } from 'ml-sparse-matrix';
|
|
4
4
|
import getPauliMatrix from './getPauliMatrix';
|
|
5
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
5
6
|
const smallValue = 1e-2;
|
|
6
7
|
export function simulateXYPeaks(
|
|
7
8
|
/**
|
|
8
9
|
* The SpinSystem object to be simulated
|
|
9
10
|
*/
|
|
10
|
-
|
|
11
|
+
spinSystemInput, options = {}) {
|
|
11
12
|
let { lineWidth = 1, maxClusterSize = 8, frequency: frequencyMHz = 400, } = options;
|
|
13
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
12
14
|
const chemicalShifts = spinSystem.chemicalShifts.slice();
|
|
13
15
|
for (let i = 0; i < chemicalShifts.length; i++) {
|
|
14
16
|
chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
|
|
15
17
|
}
|
|
16
|
-
const
|
|
18
|
+
const levels = spinSystem.levels;
|
|
17
19
|
const xyPeaks = [];
|
|
18
20
|
for (const cluster of spinSystem.clusters) {
|
|
19
21
|
let clusterFake = cluster.map((cluster) => cluster < 0 ? -cluster - 1 : cluster);
|
|
@@ -48,7 +50,7 @@ spinSystem, options = {}) {
|
|
|
48
50
|
}
|
|
49
51
|
}
|
|
50
52
|
else {
|
|
51
|
-
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants,
|
|
53
|
+
const hamiltonian = getHamiltonian(chemicalShifts, spinSystem.couplingConstants, levels, spinSystem.connectivity, clusterFake);
|
|
52
54
|
const hamSize = hamiltonian.rows;
|
|
53
55
|
// TODO: add support for sparse matrix in matrix types.
|
|
54
56
|
// @ts-expect-error sparse matrix not supported
|
|
@@ -59,15 +61,15 @@ spinSystem, options = {}) {
|
|
|
59
61
|
const multLen = cluster.length;
|
|
60
62
|
weight = 0;
|
|
61
63
|
for (let n = 0; n < multLen; n++) {
|
|
62
|
-
const L = getPauliMatrix(
|
|
64
|
+
const L = getPauliMatrix(levels[clusterFake[n]]);
|
|
63
65
|
let temp = 1;
|
|
64
66
|
for (let j = 0; j < n; j++) {
|
|
65
|
-
temp *=
|
|
67
|
+
temp *= levels[clusterFake[j]];
|
|
66
68
|
}
|
|
67
69
|
const A = SparseMatrix.eye(temp);
|
|
68
70
|
temp = 1;
|
|
69
71
|
for (let j = n + 1; j < multLen; j++) {
|
|
70
|
-
temp *=
|
|
72
|
+
temp *= levels[clusterFake[j]];
|
|
71
73
|
}
|
|
72
74
|
const B = SparseMatrix.eye(temp);
|
|
73
75
|
const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
|
|
@@ -1 +1 @@
|
|
|
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;
|
|
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;AAC9C,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,MAAM,UAAU,GAAG,IAAI,CAAC;AAwCxB,MAAM,UAAU,eAAe;AAC7B;;GAEG;AACH,eAA2B,EAC3B,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,UAAU,GAAG,qBAAqB,CAAC,eAAe,CAAC,CAAC;IAE1D,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,MAAM,GAAG,UAAU,CAAC,MAAM,CAAC;IAEjC,MAAM,OAAO,GAAoC,EAAE,CAAC;IACpD,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;QACF,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,MAAM,EACN,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,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gBAEjD,IAAI,IAAI,GAAG,CAAC,CAAC;gBACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;oBAC1B,IAAI,IAAI,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChC;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,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChC;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;YACD,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;QACnC,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,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,YAAY,CAAC,CAAe,EAAE,GAAW;IAChD,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3B,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"}
|
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
import { agnes } from 'ml-hclust';
|
|
2
2
|
import { Matrix } from 'ml-matrix';
|
|
3
|
-
|
|
3
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
4
|
+
export function splitSpinSystem(spinSystemInput, options = {}) {
|
|
5
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
4
6
|
let { chemicalShifts, couplingConstants, connectivity } = spinSystem;
|
|
5
7
|
let { frequency = 400, maxClusterSize = 8 } = options;
|
|
6
8
|
let betas = calculateBetas(chemicalShifts, couplingConstants, frequency);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"splitSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/splitSpinSystem.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AAElC,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;
|
|
1
|
+
{"version":3,"file":"splitSpinSystem.js","sourceRoot":"","sources":["../../../src/signals/simulation/splitSpinSystem.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,WAAW,CAAC;AAElC,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAGnC,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAavE,MAAM,UAAU,eAAe,CAC7B,eAA2B,EAC3B,UAAkC,EAAE;IAEpC,MAAM,UAAU,GAAG,qBAAqB,CAAC,eAAe,CAAC,CAAC;IAC1D,IAAI,EAAE,cAAc,EAAE,iBAAiB,EAAE,YAAY,EAAE,GAAG,UAAU,CAAC;IACrE,IAAI,EAAE,SAAS,GAAG,GAAG,EAAE,cAAc,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;IACtD,IAAI,KAAK,GAAG,cAAc,CAAC,cAAc,EAAE,iBAAiB,EAAE,SAAS,CAAC,CAAC;IACzE,IAAI,YAAY,GAAG,KAAK,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,gBAAgB,EAAE,IAAI,EAAE,CAAC,CAAC;IAC9E,IAAI,WAAW,GAAsB,EAAE,CAAC;IACxC,IAAI,MAAM,GAAG,cAAc,CAAC,MAAM,CAAC;IACnC,YAAY,CAAC,YAAY,EAAE,WAAW,EAAE;QACtC,cAAc;QACd,KAAK,EAAE,KAAK;QACZ,MAAM;QACN,YAAY;KACb,CAAC,CAAC;IACH,IAAI,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,cAAc,CAAC,CAAC;IAChE,IAAI,SAAS,GAAG,cAAc,CAAC,MAAM,CAAC;IACtC,IAAI,QAAQ,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAC;IACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;QAClC,QAAQ,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC;QACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;YAC/B,IAAI,OAAO,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YACnC,IAAI,OAAO,KAAK,CAAC;gBAAE,SAAS;YAC5B,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC9C;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC;AASD,SAAS,YAAY,CACnB,OAAgB,EAChB,WAA8B,EAC9B,OAA4B;IAE5B,IAAI,EAAE,cAAc,EAAE,KAAK,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAC;IAC9D,IAAI,CAAC,KAAK,IAAI,OAAO,CAAC,IAAI,IAAI,cAAc,EAAE;QAC5C,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,MAAM,CAAC,CAAC,CAAC;KACzD;SAAM;QACL,KAAK,IAAI,KAAK,IAAI,OAAO,CAAC,QAAQ,EAAE;YAClC,IAAI,KAAK,CAAC,IAAI,IAAI,cAAc,EAAE;gBAChC,IAAI,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,MAAM,CAAC,CAAC;gBAClD,2EAA2E;gBAC3E,IAAI,KAAK,GAAG,CAAC,CAAC;gBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;oBAC/B,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;wBACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;4BAC/B,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gCACpD,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gCAChB,KAAK,EAAE,CAAC;6BACT;yBACF;wBACD,KAAK,EAAE,CAAC;qBACT;iBACF;gBACD,IAAI,KAAK,IAAI,cAAc,EAAE;oBAC3B,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;iBAC3B;qBAAM,IAAI,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE;oBAC1B,YAAY,CAAC,KAAK,EAAE,WAAW,EAAE;wBAC/B,cAAc;wBACd,KAAK,EAAE,IAAI;wBACX,MAAM;wBACN,YAAY;qBACb,CAAC,CAAC;iBACJ;qBAAM;oBACL,iGAAiG;oBACjG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;oBACzB,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;iBAC3B;aACF;iBAAM;gBACL,YAAY,CAAC,KAAK,EAAE,WAAW,EAAE;oBAC/B,cAAc;oBACd,KAAK,EAAE,KAAK;oBACZ,MAAM;oBACN,YAAY;iBACb,CAAC,CAAC;aACJ;SACF;KACF;AACH,CAAC;AAED,SAAS,cAAc,CACrB,cAAwB,EACxB,iBAAyB,EACzB,SAAiB;IAEjB,IAAI,KAAK,GAAG,iBAAiB,CAAC,IAAI,CAAC;IACnC,IAAI,QAAQ,GAAG,iBAAiB,CAAC,OAAO,CAAC;IACzC,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IACvC,2GAA2G;IAC3G,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;YACjC,IAAI,OAAO,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAC1C,IAAI,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gBAC/C,IAAI,KAAK,GACP,CAAC;oBACD,IAAI,CAAC,GAAG,CACN,OAAO,GAAG,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,CAChE,CAAC;gBACJ,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;gBACvB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC;aACxB;iBAAM,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,OAAO,KAAK,CAAC,CAAC,EAAE;gBACtC,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;gBACnB,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;aACpB;SACF;KACF;IACD,OAAO,KAAK,CAAC,SAAS,EAAE,CAAC;AAC3B,CAAC;AAED,SAAS,aAAa,CAAC,IAAuB,EAAE,cAAsB;IACpE,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;QACzC,IAAI,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACvB,IAAI,SAAS,GAAG,QAAQ,CAAC,MAAM,CAAC;QAChC,IAAI,KAAK,GAAG,CAAC,CAAC;QAEd,kCAAkC;QAClC,OAAO,KAAK,GAAG,SAAS,IAAI,QAAQ,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC;YAAC,CAAC;QACtD,IAAI,KAAK,IAAI,SAAS;YAAE,SAAS;QAEjC,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7C,IAAI,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;YACvB,gCAAgC;YAChC,IAAI,KAAK,GAAG,CAAC,CAAC;YACd,IAAI,MAAM,GAAG,CAAC,CAAC;YACf,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,EAAE,KAAK,EAAE,EAAE;gBAC9C,IAAI,QAAQ,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;oBAAE,MAAM,EAAE,CAAC;gBACvD,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC;oBAAE,KAAK,EAAE,CAAC;aAC7D;YAED,IAAI,MAAM,GAAG,CAAC,IAAI,KAAK,IAAI,cAAc,EAAE;gBACzC,qCAAqC;gBACrC,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,SAAS,EAAE,KAAK,EAAE,EAAE;oBAC9C,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;qBACrB;yBAAM,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;wBAC1D,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;qBACtB;iBACF;gBACD,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;aACnB;SACF;KACF;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,UAAU,CAAC,OAAiB,EAAE,MAAc;IACnD,IAAI,OAAO,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC;IACrC,KAAK,IAAI,CAAC,IAAI,OAAO,EAAE;QACrB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;KAChB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
import Matrix from 'ml-matrix';
|
|
2
|
+
import simpleClustering from 'ml-simple-clustering';
|
|
3
|
+
export function ensureSpinSystemProps(spinSystem) {
|
|
4
|
+
const { couplingConstants } = spinSystem;
|
|
5
|
+
const { clusters, levels = new Array(couplingConstants.rows).fill(2), connectivity = connectivityMatrixFromCouplingMatrix(couplingConstants), } = spinSystem;
|
|
6
|
+
return {
|
|
7
|
+
levels,
|
|
8
|
+
clusters: clusters ||
|
|
9
|
+
simpleClustering(connectivity.to2DArray(), {
|
|
10
|
+
out: 'indexes',
|
|
11
|
+
}),
|
|
12
|
+
connectivity,
|
|
13
|
+
...spinSystem,
|
|
14
|
+
};
|
|
15
|
+
}
|
|
16
|
+
function connectivityMatrixFromCouplingMatrix(couplingConstants) {
|
|
17
|
+
const connectivity = Matrix.ones(couplingConstants.rows, couplingConstants.rows);
|
|
18
|
+
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
19
|
+
for (let j = i; j < couplingConstants.columns; j++) {
|
|
20
|
+
if (couplingConstants.get(i, j) === 0) {
|
|
21
|
+
connectivity.set(i, j, 0);
|
|
22
|
+
connectivity.set(j, i, 0);
|
|
23
|
+
}
|
|
24
|
+
}
|
|
25
|
+
}
|
|
26
|
+
return connectivity;
|
|
27
|
+
}
|
|
28
|
+
//# sourceMappingURL=ensureSpinSystemProps.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ensureSpinSystemProps.js","sourceRoot":"","sources":["../../../src/signals/utils/ensureSpinSystemProps.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,WAAW,CAAC;AAE/B,OAAO,gBAAgB,MAAM,sBAAsB,CAAC;AAEpD,MAAM,UAAU,qBAAqB,CAAC,UAAsB;IAC1D,MAAM,EAAE,iBAAiB,EAAE,GAAG,UAAU,CAAC;IAEzC,MAAM,EACJ,QAAQ,EACR,MAAM,GAAG,IAAI,KAAK,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAClD,YAAY,GAAG,oCAAoC,CAAC,iBAAiB,CAAC,GACvE,GAAG,UAAU,CAAC;IAEf,OAAO;QACL,MAAM;QACN,QAAQ,EACN,QAAQ;YACR,gBAAgB,CAAC,YAAY,CAAC,SAAS,EAAE,EAAE;gBACzC,GAAG,EAAE,SAAS;aACf,CAAC;QACJ,YAAY;QACZ,GAAG,UAAU;KACd,CAAC;AACJ,CAAC;AAED,SAAS,oCAAoC,CAAC,iBAAyB;IACrE,MAAM,YAAY,GAAG,MAAM,CAAC,IAAI,CAC9B,iBAAiB,CAAC,IAAI,EACtB,iBAAiB,CAAC,IAAI,CACvB,CAAC;IACF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE;QAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,iBAAiB,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE;YAClD,IAAI,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE;gBACrC,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;gBAC1B,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;aAC3B;SACF;KACF;IAED,OAAO,YAAY,CAAC;AACtB,CAAC"}
|
package/package.json
CHANGED
package/src/index.ts
CHANGED
|
@@ -99,6 +99,7 @@ export type { NMRRange } from './xy/NMRRange';
|
|
|
99
99
|
export type { NMRZone } from './xyz/NMRZone';
|
|
100
100
|
export type { NMRPeak1D } from './peaks/NMRPeak1D';
|
|
101
101
|
export type { Prediction1D } from './prediction/Prediction1D';
|
|
102
|
+
export type { Prediction2D } from './prediction/Prediction2D';
|
|
102
103
|
export type { Jcoupling } from './signals/Jcoupling';
|
|
103
104
|
export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
|
|
104
105
|
export type {
|
|
@@ -6,7 +6,7 @@ import type { MakeMandatory } from '../utilities/MakeMandatory';
|
|
|
6
6
|
import type { Jcoupling } from './Jcoupling';
|
|
7
7
|
import type { NMRSignal1D } from './NMRSignal1D';
|
|
8
8
|
import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
|
|
9
|
-
import simulate1D from './simulation/simulate1D';
|
|
9
|
+
import { simulate1D } from './simulation/simulate1D';
|
|
10
10
|
import { splitSpinSystem } from './simulation/splitSpinSystem';
|
|
11
11
|
|
|
12
12
|
export interface OptionsSignalsToXY {
|
|
@@ -1,10 +1,10 @@
|
|
|
1
1
|
import { Matrix } from 'ml-matrix';
|
|
2
|
-
import simpleClustering from 'ml-simple-clustering';
|
|
3
2
|
|
|
4
3
|
import type { MakeMandatory } from '../../utilities/MakeMandatory';
|
|
5
4
|
import type { Jcoupling } from '../Jcoupling';
|
|
6
5
|
import type { NMRSignal1D } from '../NMRSignal1D';
|
|
7
6
|
import type { SpinSystem } from '../spinSystem';
|
|
7
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
8
8
|
|
|
9
9
|
interface Ids {
|
|
10
10
|
[index: number]: number;
|
|
@@ -32,12 +32,10 @@ export function signalsToSpinSystem(signals: NMRSignal1D[]): SpinSystem {
|
|
|
32
32
|
checkForMandatory(signals);
|
|
33
33
|
const nSpins = signals.length;
|
|
34
34
|
const chemicalShifts: number[] = new Array(nSpins);
|
|
35
|
-
const multiplicity: number[] = new Array(nSpins);
|
|
36
35
|
const couplingConstants = Matrix.zeros(nSpins, nSpins);
|
|
37
36
|
//create a list of assignments
|
|
38
37
|
const ids: Ids = {};
|
|
39
38
|
for (let i = 0; i < nSpins; i++) {
|
|
40
|
-
multiplicity[i] = 2;
|
|
41
39
|
chemicalShifts[i] = signals[i].delta;
|
|
42
40
|
const index = signals[i].atoms[0];
|
|
43
41
|
ids[index] = i;
|
|
@@ -54,28 +52,8 @@ export function signalsToSpinSystem(signals: NMRSignal1D[]): SpinSystem {
|
|
|
54
52
|
}
|
|
55
53
|
}
|
|
56
54
|
|
|
57
|
-
|
|
58
|
-
couplingConstants.rows,
|
|
59
|
-
couplingConstants.rows,
|
|
60
|
-
);
|
|
61
|
-
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
62
|
-
for (let j = i; j < couplingConstants.columns; j++) {
|
|
63
|
-
if (couplingConstants.get(i, j) === 0) {
|
|
64
|
-
connectivity.set(i, j, 0);
|
|
65
|
-
connectivity.set(j, i, 0);
|
|
66
|
-
}
|
|
67
|
-
}
|
|
68
|
-
}
|
|
69
|
-
|
|
70
|
-
let clusters = simpleClustering(connectivity.to2DArray(), {
|
|
71
|
-
out: 'indexes',
|
|
72
|
-
});
|
|
73
|
-
|
|
74
|
-
return {
|
|
75
|
-
clusters,
|
|
55
|
+
return ensureSpinSystemProps({
|
|
76
56
|
couplingConstants,
|
|
77
57
|
chemicalShifts,
|
|
78
|
-
|
|
79
|
-
connectivity,
|
|
80
|
-
};
|
|
58
|
+
});
|
|
81
59
|
}
|
|
@@ -5,16 +5,13 @@ import type { SpinSystem } from '../spinSystem';
|
|
|
5
5
|
|
|
6
6
|
import type { Simulate1DOptions } from './simulateXYPeaks';
|
|
7
7
|
import { simulateXYPeaks } from './simulateXYPeaks';
|
|
8
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
8
9
|
|
|
9
10
|
/**
|
|
10
11
|
* This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
|
|
11
12
|
*/
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
/**
|
|
15
|
-
* The SpinSystem object to be simulated
|
|
16
|
-
*/
|
|
17
|
-
spinSystem: SpinSystem,
|
|
13
|
+
export function simulate1D(
|
|
14
|
+
spinSystemInput: SpinSystem,
|
|
18
15
|
options: Simulate1DOptions = {},
|
|
19
16
|
): DataXY {
|
|
20
17
|
let {
|
|
@@ -28,6 +25,7 @@ export default function simulate1D(
|
|
|
28
25
|
},
|
|
29
26
|
} = options;
|
|
30
27
|
|
|
28
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
31
29
|
let peakWidth = lineWidth / frequencyMHz;
|
|
32
30
|
|
|
33
31
|
const xyPeaks = simulateXYPeaks(spinSystem, options);
|
|
@@ -7,6 +7,7 @@ import { SparseMatrix } from 'ml-sparse-matrix';
|
|
|
7
7
|
import type { SpinSystem } from '../spinSystem';
|
|
8
8
|
|
|
9
9
|
import getPauliMatrix from './getPauliMatrix';
|
|
10
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
10
11
|
|
|
11
12
|
const smallValue = 1e-2;
|
|
12
13
|
|
|
@@ -52,7 +53,7 @@ export function simulateXYPeaks(
|
|
|
52
53
|
/**
|
|
53
54
|
* The SpinSystem object to be simulated
|
|
54
55
|
*/
|
|
55
|
-
|
|
56
|
+
spinSystemInput: SpinSystem,
|
|
56
57
|
options: Simulate1DOptions = {},
|
|
57
58
|
) {
|
|
58
59
|
let {
|
|
@@ -61,12 +62,14 @@ export function simulateXYPeaks(
|
|
|
61
62
|
frequency: frequencyMHz = 400,
|
|
62
63
|
} = options;
|
|
63
64
|
|
|
65
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
66
|
+
|
|
64
67
|
const chemicalShifts = spinSystem.chemicalShifts.slice();
|
|
65
68
|
for (let i = 0; i < chemicalShifts.length; i++) {
|
|
66
69
|
chemicalShifts[i] = chemicalShifts[i] * frequencyMHz;
|
|
67
70
|
}
|
|
68
71
|
|
|
69
|
-
const
|
|
72
|
+
const levels = spinSystem.levels;
|
|
70
73
|
|
|
71
74
|
const xyPeaks: Array<{ x: number; y: number }> = [];
|
|
72
75
|
for (const cluster of spinSystem.clusters) {
|
|
@@ -107,7 +110,7 @@ export function simulateXYPeaks(
|
|
|
107
110
|
const hamiltonian = getHamiltonian(
|
|
108
111
|
chemicalShifts,
|
|
109
112
|
spinSystem.couplingConstants,
|
|
110
|
-
|
|
113
|
+
levels,
|
|
111
114
|
spinSystem.connectivity,
|
|
112
115
|
clusterFake,
|
|
113
116
|
);
|
|
@@ -121,17 +124,17 @@ export function simulateXYPeaks(
|
|
|
121
124
|
const multLen = cluster.length;
|
|
122
125
|
weight = 0;
|
|
123
126
|
for (let n = 0; n < multLen; n++) {
|
|
124
|
-
const L = getPauliMatrix(
|
|
127
|
+
const L = getPauliMatrix(levels[clusterFake[n]]);
|
|
125
128
|
|
|
126
129
|
let temp = 1;
|
|
127
130
|
for (let j = 0; j < n; j++) {
|
|
128
|
-
temp *=
|
|
131
|
+
temp *= levels[clusterFake[j]];
|
|
129
132
|
}
|
|
130
133
|
const A = SparseMatrix.eye(temp);
|
|
131
134
|
|
|
132
135
|
temp = 1;
|
|
133
136
|
for (let j = n + 1; j < multLen; j++) {
|
|
134
|
-
temp *=
|
|
137
|
+
temp *= levels[clusterFake[j]];
|
|
135
138
|
}
|
|
136
139
|
const B = SparseMatrix.eye(temp);
|
|
137
140
|
const tempMat = A.kroneckerProduct(L.m).kroneckerProduct(B);
|
|
@@ -3,6 +3,7 @@ import type { Cluster } from 'ml-hclust';
|
|
|
3
3
|
import { Matrix } from 'ml-matrix';
|
|
4
4
|
|
|
5
5
|
import type { SpinSystem } from '../spinSystem';
|
|
6
|
+
import { ensureSpinSystemProps } from '../utils/ensureSpinSystemProps';
|
|
6
7
|
|
|
7
8
|
export interface SplitSpinSystemOptions {
|
|
8
9
|
/**
|
|
@@ -16,9 +17,10 @@ export interface SplitSpinSystemOptions {
|
|
|
16
17
|
}
|
|
17
18
|
|
|
18
19
|
export function splitSpinSystem(
|
|
19
|
-
|
|
20
|
+
spinSystemInput: SpinSystem,
|
|
20
21
|
options: SplitSpinSystemOptions = {},
|
|
21
22
|
) {
|
|
23
|
+
const spinSystem = ensureSpinSystemProps(spinSystemInput);
|
|
22
24
|
let { chemicalShifts, couplingConstants, connectivity } = spinSystem;
|
|
23
25
|
let { frequency = 400, maxClusterSize = 8 } = options;
|
|
24
26
|
let betas = calculateBetas(chemicalShifts, couplingConstants, frequency);
|
|
@@ -1,9 +1,24 @@
|
|
|
1
1
|
import type { Matrix } from 'ml-matrix';
|
|
2
2
|
|
|
3
3
|
export interface SpinSystem {
|
|
4
|
-
|
|
4
|
+
/**
|
|
5
|
+
* isolated clusters from a similarity/connectivity matrix
|
|
6
|
+
*/
|
|
7
|
+
clusters?: number[][];
|
|
8
|
+
/**
|
|
9
|
+
* Matrix of coupling values between spins.
|
|
10
|
+
*/
|
|
5
11
|
couplingConstants: Matrix;
|
|
12
|
+
/**
|
|
13
|
+
* Array of chemical shifts of the spin system
|
|
14
|
+
*/
|
|
6
15
|
chemicalShifts: number[];
|
|
7
|
-
|
|
8
|
-
|
|
16
|
+
/**
|
|
17
|
+
* Array of degree of freedom of the spin, it is usually an array of 2.
|
|
18
|
+
*/
|
|
19
|
+
levels?: number[];
|
|
20
|
+
/**
|
|
21
|
+
* Binary matrix based on the coupling constants.
|
|
22
|
+
*/
|
|
23
|
+
connectivity?: Matrix;
|
|
9
24
|
}
|
|
@@ -0,0 +1,41 @@
|
|
|
1
|
+
import Matrix from 'ml-matrix';
|
|
2
|
+
import { SpinSystem } from '../spinSystem';
|
|
3
|
+
import simpleClustering from 'ml-simple-clustering';
|
|
4
|
+
|
|
5
|
+
export function ensureSpinSystemProps(spinSystem: SpinSystem) {
|
|
6
|
+
const { couplingConstants } = spinSystem;
|
|
7
|
+
|
|
8
|
+
const {
|
|
9
|
+
clusters,
|
|
10
|
+
levels = new Array(couplingConstants.rows).fill(2),
|
|
11
|
+
connectivity = connectivityMatrixFromCouplingMatrix(couplingConstants),
|
|
12
|
+
} = spinSystem;
|
|
13
|
+
|
|
14
|
+
return {
|
|
15
|
+
levels,
|
|
16
|
+
clusters:
|
|
17
|
+
clusters ||
|
|
18
|
+
simpleClustering(connectivity.to2DArray(), {
|
|
19
|
+
out: 'indexes',
|
|
20
|
+
}),
|
|
21
|
+
connectivity,
|
|
22
|
+
...spinSystem,
|
|
23
|
+
};
|
|
24
|
+
}
|
|
25
|
+
|
|
26
|
+
function connectivityMatrixFromCouplingMatrix(couplingConstants: Matrix) {
|
|
27
|
+
const connectivity = Matrix.ones(
|
|
28
|
+
couplingConstants.rows,
|
|
29
|
+
couplingConstants.rows,
|
|
30
|
+
);
|
|
31
|
+
for (let i = 0; i < couplingConstants.rows; i++) {
|
|
32
|
+
for (let j = i; j < couplingConstants.columns; j++) {
|
|
33
|
+
if (couplingConstants.get(i, j) === 0) {
|
|
34
|
+
connectivity.set(i, j, 0);
|
|
35
|
+
connectivity.set(j, i, 0);
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
|
+
}
|
|
39
|
+
|
|
40
|
+
return connectivity;
|
|
41
|
+
}
|