nmr-simulation - npm Package Compare versions

Comparing version 0.2.1 to 0.2.2

package.json

		{
		"name": "nmr-simulation",
		"version": "0.2.1",
		"version": "0.2.2",
		"description": "Simulate NMR spectra from spin systems",
		@@ -5,0 +5,0 @@ "main": "src/index.js",

src/index.js

		@@ -5,1 +5,2 @@ 'use strict';
		exports.simulate1D = require('./simulate1D');
		exports.simulate2D = require('./simulate2D');

src/simulate1D.js

		@@ -11,3 +11,2 @@ 'use strict';

		const DEBUG = false;
		const smallValue = 1e-2;
		@@ -231,4 +230,2 @@

		if(DEBUG) console.log("Hamiltonian size: "+hamSize);

		const clusterHam = new SparseMatrix(hamSize, hamSize);
		@@ -235,0 +232,0 @@

src/simulate2D.js

		@@ -1,3 +0,86 @@
		function simulate2d(spinSystem, options) {
		'use strict';

		}
		const Matrix = require('ml-matrix');

		let defOptions = {'H': {frequency: 400, lineWidth: 10}, 'C': {frequency: 100, lineWidth: 10}}

		function simule2DNmrSpectrum(table, options) {
		var i, j;
		const fromLabel = table[0].fromAtomLabel;
		const toLabel = table[0].toLabel;
		const frequencyX = options.frequencyX \|\| defOptions[fromLabel].frequency;
		const frequencyY = options.frequencyY \|\| defOptions[toLabel].frequency;
		var lineWidthX = options.lineWidthX \|\| defOptions[fromLabel].lineWidth;
		var lineWidthY = options.lineWidthY \|\| defOptions[toLabel].lineWidth;

		var sigmaX = lineWidthX / frequencyX;
		var sigmaY = lineWidthY / frequencyY;

		var minX = table[0].fromChemicalShift;
		var maxX = table[0].fromChemicalShift;
		var minY = table[0].toChemicalShift;
		var maxY = table[0].toChemicalShift;
		i = 1;
		while(i < table.length) {
		minX = Math.min(minX, table[i].fromChemicalShift);
		maxX = Math.max(maxX, table[i].fromChemicalShift);
		minY = Math.min(minY, table[i].toChemicalShift);
		maxY = Math.max(maxY, table[i].toChemicalShift);
		i++;
		}

		if(options.firstX !== null && !isNaN(options.firstX))
		minX = options.firstX;
		if(options.firstY !== null && !isNaN(options.firstY))
		minY = options.firstY;
		if(options.lastX !== null && !isNaN(options.lastX))
		maxX = options.lastX
		if(options.lastY !== null && !isNaN(options.lastY))
		maxY = options.lastY;

		var nbPointsX = options.nbPointsX \|\| 512;
		var nbPointsY = options.nbPointsY \|\| 512;

		var spectraMatrix = new Matrix(nbPointsY, nbPointsX).fill(0);
		i = 0;
		while(i < table.length) {
		//parameters.couplingConstant = table[i].j;
		//parameters.pathLength = table[i].pathLength;
		let peak = {
		x: unitsToArrayPoints(table[i].fromChemicalShift, minX, maxX, nbPointsX),
		y: unitsToArrayPoints(table[i].toChemicalShift, minY, maxY, nbPointsY),
		z: table[i].fromAtoms.length + table[i].toAtoms.length,
		widthX: unitsToArrayPoints(sigmaX + minX, minX, maxX, nbPointsX),
		widthY: unitsToArrayPoints(sigmaY+ minY, minY, maxY, nbPointsY)
		}
		addPeak(spectraMatrix, peak);
		i++;
		}
		return spectraMatrix;
		}

		function unitsToArrayPoints(x, from, to, nbPoints) {
		return ((x - from) * nbPoints - 1) / (to - from);
		}

		function addPeak(matrix, peak) {
		var nSigma = 4;
		var fromX = Math.max(0, Math.round(peak.x - peak.widthX * nSigma));
		var toX = Math.min(matrix[0].length - 1, Math.round(peak.x + peak.widthX * nSigma));
		var fromY = Math.max(0, Math.round(peak.y - peak.widthY * nSigma));
		var toY = Math.min(matrix.length - 1, Math.round(peak.y + peak.widthY * nSigma));

		var squareSigmaX = peak.widthX * peak.widthX;
		var squareSigmaY = peak.widthY * peak.widthY;
		for (var j = fromY; j < toY; j++) {
		for (var i = fromX; i < toX; i++) {
		var exponent = Math.pow(peak.x - i, 2) / squareSigmaX +
		Math.pow(peak.y - j, 2) / squareSigmaY;
		var result = 10000 * peak.z * Math.exp( - exponent);
		matrix[j][i] += result;
		}
		}
		}


		module.exports = simule2DNmrSpectrum;

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