@ccp-nc/crystvis-js 0.4.13

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Files changed (100) hide show
  1. package/.eslintrc.json +16 -0
  2. package/.github/workflows/test-mocha.yml +30 -0
  3. package/.vscode/settings.json +4 -0
  4. package/LICENSE +21 -0
  5. package/README.html +1127 -0
  6. package/README.md +76 -0
  7. package/demo/demo.css +30 -0
  8. package/demo/index.html +76 -0
  9. package/demo/main.js +143 -0
  10. package/docs/.nojekyll +0 -0
  11. package/docs-tutorials/Events.md +57 -0
  12. package/docs-tutorials/Queries.md +50 -0
  13. package/fonts/Rubik/OFL.txt +93 -0
  14. package/fonts/Rubik/README.txt +77 -0
  15. package/fonts/Rubik/Rubik-Italic-VariableFont_wght.ttf +0 -0
  16. package/fonts/Rubik/Rubik-VariableFont_wght.ttf +0 -0
  17. package/fonts/Rubik/static/Rubik-Black.ttf +0 -0
  18. package/fonts/Rubik/static/Rubik-BlackItalic.ttf +0 -0
  19. package/fonts/Rubik/static/Rubik-Bold.ttf +0 -0
  20. package/fonts/Rubik/static/Rubik-BoldItalic.ttf +0 -0
  21. package/fonts/Rubik/static/Rubik-ExtraBold.ttf +0 -0
  22. package/fonts/Rubik/static/Rubik-ExtraBoldItalic.ttf +0 -0
  23. package/fonts/Rubik/static/Rubik-Italic.ttf +0 -0
  24. package/fonts/Rubik/static/Rubik-Light.ttf +0 -0
  25. package/fonts/Rubik/static/Rubik-LightItalic.ttf +0 -0
  26. package/fonts/Rubik/static/Rubik-Medium.ttf +0 -0
  27. package/fonts/Rubik/static/Rubik-MediumItalic.ttf +0 -0
  28. package/fonts/Rubik/static/Rubik-Regular.ttf +0 -0
  29. package/fonts/Rubik/static/Rubik-SemiBold.ttf +0 -0
  30. package/fonts/Rubik/static/Rubik-SemiBoldItalic.ttf +0 -0
  31. package/index.html +25 -0
  32. package/index.js +11 -0
  33. package/jsconf.json +14 -0
  34. package/lib/assets/fonts/Rubik-Medium.fnt +297 -0
  35. package/lib/assets/fonts/Rubik-Medium.png +0 -0
  36. package/lib/assets/fonts/bmpfonts.in.js +16 -0
  37. package/lib/assets/fonts/bmpfonts.js +9 -0
  38. package/lib/assets/fonts/font.js +82 -0
  39. package/lib/assets/fonts/index.js +14 -0
  40. package/lib/assets/fonts/threebmfont.js +28 -0
  41. package/lib/data.js +125 -0
  42. package/lib/formats/cell.js +114 -0
  43. package/lib/formats/cif.js +22 -0
  44. package/lib/formats/magres.js +337 -0
  45. package/lib/formats/xyz.js +124 -0
  46. package/lib/loader.js +87 -0
  47. package/lib/model.js +2076 -0
  48. package/lib/modelview.js +382 -0
  49. package/lib/nmrdata.js +2898 -0
  50. package/lib/orbit.js +1233 -0
  51. package/lib/primitives/atoms.js +261 -0
  52. package/lib/primitives/cell.js +160 -0
  53. package/lib/primitives/dither.js +156 -0
  54. package/lib/primitives/ellipsoid.js +183 -0
  55. package/lib/primitives/geometries.js +20 -0
  56. package/lib/primitives/index.js +48 -0
  57. package/lib/primitives/isosurface.js +171 -0
  58. package/lib/primitives/shapes.js +100 -0
  59. package/lib/primitives/sprites.js +172 -0
  60. package/lib/query.js +158 -0
  61. package/lib/render.js +440 -0
  62. package/lib/selbox.js +361 -0
  63. package/lib/shaders/aura.frag +26 -0
  64. package/lib/shaders/aura.vert +37 -0
  65. package/lib/shaders/dither.frag +42 -0
  66. package/lib/shaders/dither.vert +8 -0
  67. package/lib/shaders/index.in.js +17 -0
  68. package/lib/shaders/index.js +25 -0
  69. package/lib/shaders/msdf300.frag +25 -0
  70. package/lib/shaders/msdf300.vert +45 -0
  71. package/lib/tensor.js +227 -0
  72. package/lib/utils.js +168 -0
  73. package/lib/visualizer.js +480 -0
  74. package/package.json +106 -0
  75. package/scripts/build-bundle.js +17 -0
  76. package/scripts/build-fonts.js +43 -0
  77. package/scripts/build-resources.js +46 -0
  78. package/scripts/plugins-shim.js +10 -0
  79. package/test/chemdata.js +69 -0
  80. package/test/data/CHA.cif +74 -0
  81. package/test/data/H2O.xyz +8 -0
  82. package/test/data/H2_bound.xyz +4 -0
  83. package/test/data/ethanol.cell +25 -0
  84. package/test/data/ethanol.magres +238 -0
  85. package/test/data/example_single.cif +789 -0
  86. package/test/data/frac.cell +8 -0
  87. package/test/data/org.cif +427 -0
  88. package/test/data/pyridine.xyz +13 -0
  89. package/test/data/si8.xyz +10 -0
  90. package/test/loader.js +107 -0
  91. package/test/model.js +368 -0
  92. package/test/query.js +135 -0
  93. package/test/tensor.js +133 -0
  94. package/test/test-html/examples.js +1485 -0
  95. package/test/test-html/index.html +33 -0
  96. package/test/test-html/index.js +279 -0
  97. package/tools/compile_colors.py +120 -0
  98. package/tools/compile_periodic.py +96 -0
  99. package/tools/ptable.json +497 -0
  100. package/tools/test +5844 -0
package/test/test-html/index.html ADDED
@@ -0,0 +1,33 @@
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+ <!doctype html>
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+ <html>
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+ <head>
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+ <meta charset="utf-8">
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+ <meta http-equiv="x-ua-compatible" content="ie=edge">
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+ <title>CrystVis.js test</title>
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+ <meta name="description" content="">
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+ <meta name="viewport" content="width=device-width, initial-scale=1">
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+
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+ <link rel="stylesheet" href="/node_modules/mocha/mocha.css">
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+
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+ <style type="text/css">
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+ #main-app {
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+ padding: 20px;
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+ background-color: #ececec;
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+ min-height: 500px;
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+ }
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+ </style>
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+
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+ </head>
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+ <body>
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+
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+ <div id="main-app"></div>
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+ <div id="mocha"></div>
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+ <script src="/node_modules/mocha/mocha.js"></script>
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+ <script src="/node_modules/chai/chai.js"></script>
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+ <script>mocha.setup('bdd')</script>
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+
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+ <script type="text/javascript" src="/test/test-html/testbuild.js"></script>
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+
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+ <script type="text/javascript">mocha.run()</script>
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+ </body>
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+ </html>
package/test/test-html/index.js ADDED
@@ -0,0 +1,279 @@
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+ 'use strict';
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+
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+ import _ from 'lodash';
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+ import $ from 'jquery';
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+ import * as THREE from 'three';
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+ import chroma from 'chroma-js';
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+
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+ import chai from 'chai';
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+ import {
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+ Renderer
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+ } from '../../lib/render.js';
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+ import {
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+ Model
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+ } from '../../lib/model.js';
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+ import {
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+ CrystVis
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+ } from '../../lib/visualizer.js';
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+ import * as Primitives from '../../lib/primitives';
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+ import {
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+ RubikMedium
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+ } from '../../lib/assets/fonts';
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+
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+ import {
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+ exampleFiles
25
+ } from './examples.js';
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+
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+ var renderer;
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+ var visualizer;
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+
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+ describe('Font tests', function() {
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+
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+ it('should successfully create a BitmapFont', function() {
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+ chai.expect(RubikMedium.ready).to.equal(true);
34
+ });
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+
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+ it('should successfully create a geometry from said font', function() {
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+
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+ var geo = RubikMedium.getTextGeometry('Hello world');
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+ });
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+ });
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+
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+ describe('Renderer tests', function() {
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+ it('should successfully load a Renderer', function() {
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+ renderer = new Renderer('#main-app', 640, 480);
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+ });
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+ it('should successfully create an atom', function() {
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+ var a = new Primitives.AtomMesh([0, 0, 0], 0.5, 0xff0000);
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+ renderer.add(a, 'model');
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+ chai.expect(renderer._groups.model.children).to.include(a);
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+ renderer.remove(a, 'model');
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+ });
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+ it('should successfully create a unit cell', function() {
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+ var latt = new THREE.Matrix3();
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+ latt.set(10, 0, 0, 1, 8, 0, 0, 0, 9).transpose();
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+
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+ var box = new Primitives.BoxMesh(latt);
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+ var ax = new Primitives.AxesMesh(latt);
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+
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+ renderer.add(box, 'model');
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+ renderer.add(ax, 'model');
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+
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+ chai.expect(renderer._groups.model.children).to.include.members([box, ax]);
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+
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+ renderer.remove(box, 'model');
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+ renderer.remove(ax, 'model');
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+ });
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+ it('should successfully create a bond', function() {
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+ var b = new Primitives.BondMesh([0, 0, 0], [1, 0, 0]);
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+
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+ renderer.add(b, 'model');
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+
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+ chai.expect(renderer._groups.model.children).to.include(b);
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+
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+ renderer.remove(b, 'model');
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+ });
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+ it('should successfully render sprites', function() {
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+ var ts = new Primitives.TextSprite('Hello world');
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+ renderer.add(ts, 'primitives');
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+
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+ chai.expect(renderer._groups.primitives.children).to.include.members([ts]);
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+
82
+ renderer.remove(ts);
83
+ });
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+ it('should successfully clear a scene', function() {
85
+
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+ var a = new Primitives.AtomMesh([0, 0, 0], 0.5, 0xff0000);
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+ renderer.add(a);
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+
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+ renderer.clear();
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+
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+ });
92
+
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+ after(function() {
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+ // Destroy the renderer
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+ renderer = null;
96
+ $('#main-app').empty();
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+ });
98
+ });
99
+
100
+ describe('Visualizer tests', function() {
101
+ it('should successfully load a CrystVis visualizer', function() {
102
+ visualizer = new CrystVis('#main-app', 640, 480);
103
+ });
104
+
105
+ it('should load new models in the visualizer', function() {
106
+
107
+ var m1 = visualizer.loadModels(exampleFiles['H2O.xyz'], 'xyz', 'xyz', {
108
+ supercell: [3, 3, 3]
109
+ });
110
+ var m2 = visualizer.loadModels(exampleFiles['org.cif']);
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+ var m3 = visualizer.loadModels(exampleFiles['si8.xyz'], 'xyz');
112
+ var m4 = visualizer.loadModels(exampleFiles['example_single.cif']);
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+ var m5 = visualizer.loadModels(exampleFiles['ethanol.magres'], 'magres');
114
+
115
+ chai.expect(visualizer.modelList.sort()).to.deep.equal(['cif_1501936', 'cif_I', 'magres', 'xyz', 'xyz_1']);
116
+ });
117
+
118
+ it('should correctly visualize a model', function() {
119
+
120
+ visualizer.displayModel('cif_I');
121
+
122
+ });
123
+
124
+ it('should correctly apply changes in properties to the displayed atoms', function() {
125
+
126
+ visualizer.displayed.setProperty('color', 0xff0000);
127
+ visualizer.displayed.setProperty('color');
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+
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+ visualizer.displayed.setProperty('opacity', 0.4);
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+ visualizer.displayed.setProperty('opacity');
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+
132
+ visualizer.displayed.addLabels();
133
+ visualizer.displayed.addLabels(function(a, i) {
134
+ return a.radius;
135
+ }, 'radius', {
136
+ shift: [0.1, -0.03, 0],
137
+ color: 0xff0000
138
+ });
139
+
140
+ });
141
+
142
+ it('should correctly add/remove ellipsoids to the displayed atoms', function() {
143
+
144
+ var data = {
145
+ eigenvalues: [1, 2, 4],
146
+ eigenvectors: [
147
+ [1, 1, 0],
148
+ [1, -1, 0],
149
+ [0, 0, 1]
150
+ ]
151
+ };
152
+
153
+ visualizer.displayed.atoms[0].addEllipsoid(data, 'test');
154
+ visualizer.displayed.atoms[1].addEllipsoid(data, 'test2', {
155
+ color: 0x00ee88
156
+ });
157
+ visualizer.displayed.atoms[0].removeEllipsoid('test');
158
+
159
+ // Set their properties
160
+ visualizer.displayed.atoms[1].ellipsoidProperty('test2', 'color', 0x8800ee);
161
+
162
+ });
163
+
164
+ it('should correctly draw simple primitives', function() {
165
+
166
+ var a1 = visualizer.displayed.atoms[0];
167
+ var a2 = visualizer.displayed.atoms[1];
168
+ var a3 = visualizer.displayed.atoms[2];
169
+ var line1 = new Primitives.LineMesh(a1, a2);
170
+ var line2 = new Primitives.LineMesh(a2, a3, {
171
+ color: 0xff9900,
172
+ dashed: true,
173
+ });
174
+
175
+ visualizer.addPrimitive(line1);
176
+ visualizer.addPrimitive(line2);
177
+ visualizer.removePrimitive(line1);
178
+
179
+ });
180
+
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+ });
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+
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+
184
+ // Bootstrap the whole thing!
185
+ $(document).ready(function() {
186
+
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+
188
+ // var Atoms = require('crystcif-parse').Atoms;
189
+
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+ // var a = new Atoms(['C'], [[0, 0, 1]], [[2, 0, 0], [0, 2, 0], [0, 1, 2]]);
191
+
192
+ // var m = new Model(a);
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+
194
+ // console.log(m);
195
+ // r = new Renderer('.main-app-content', 640, 480);
196
+
197
+ // var O = new THREE.Vector3(0, 0, 1);
198
+ // var H1 = new THREE.Vector3(0.9, 0, -0.2);
199
+ // var H2 = new THREE.Vector3(-0.9, 0, -0.2);
200
+
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+
202
+ // r._addAtom(O, 0.5, 0xff0000);
203
+ // r._addAtom(H1, 0.35, 0xeeeeee);
204
+ // r._addAtom(H2, 0.35, 0xeeeeee);
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+
206
+ // r._addBond(O, H1, 0.2, 0xff0000, 0xeeeeee);
207
+ // r._addBond(O, H2, 0.2, 0xff0000, 0xeeeeee);
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+
209
+ // var latt = new THREE.Matrix3();
210
+ // latt.set(10, 0, 0, 1, 8, 0, 0, 0, 9).transpose();
211
+
212
+ // var ba = r._addLattice(latt);
213
+ // box = ba[0];
214
+ // arrows = ba[1];
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+
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+ // r._addBillBoard(O.clone().add(new THREE.Vector3(0.6, 0.6, 0)), 'Hello world');
217
+
218
+ // ellipsoids = [];
219
+ // ellipsoids.push(r._addEllipsoid(O, new THREE.Vector3(1, -1, 0),
220
+ // new THREE.Vector3(2, 2, 0), new THREE.Vector3(0, 0, 3),
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+ // 0xde3300, 0.3, Renderer.DITHERNET));
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+ // ellipsoids.push(r._addEllipsoid(H1, new THREE.Vector3(1, 0, 0),
223
+ // new THREE.Vector3(0, 0.8, 0), new THREE.Vector3(0, 0, 1.2),
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+ // 0x0033de, 0.3, Renderer.DITHER));
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+
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+ // // Vector field test
227
+ // var points = [];
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+ // var vectors = [];
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+
230
+ // for (var x = 0; x <= 3; x += 0.5) {
231
+ // for (var y = 0; y <= 3; y += 0.5) {
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+ // for (var z = 0; z <= 2; z += 0.5) {
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+ // points.push(new THREE.Vector3(x, y, z));
234
+ // vectors.push(new THREE.Vector3(Math.cos(3*x)*0.2, Math.sin(3*y)*0.2, 0));
235
+ // }
236
+ // }
237
+ // }
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+
239
+ // var bez = chroma.bezier(['red', 'blue']);
240
+ // // r._addVectorField(points, vectors, function(p, v, i) {
241
+ // // return bez(p.length()/6.0).hex();
242
+ // // });
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+
244
+ // // Testing the isosurface
245
+
246
+ // var N = 20;
247
+ // var sfield = [];
248
+ // for (var x = 0; x < N; x++) {
249
+ // sfield.push([]);
250
+ // for (var y = 0; y < N; y++) {
251
+ // sfield[x].push([]);
252
+ // for (var z = 0; z < N; z++) {
253
+ // var f = Math.abs(x-N/2.0)*Math.abs(y-N/2.0)*Math.abs(z-N/2.0);
254
+ // f = Math.cos(x)+Math.cos(y)+Math.cos(z);
255
+ // sfield[x][y].push(f);
256
+ // }
257
+ // }
258
+ // }
259
+
260
+ // r._addIsosurface(sfield, 0.5, latt, 0x00ffff, 0.3, Renderer.PHONG, Renderer.ISO_SURFACE_NETS);
261
+
262
+ // r._addSprite(H1, 'circle.png', 1, 0xffffff);
263
+ //
264
+
265
+ // var vs = new CrystVis('.main-app-content', {'width': 640, 'height': 480});
266
+
267
+ });
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+
269
+ // window.hide_arrows = function() {
270
+ // arrows.visible = !arrows.visible;
271
+ // }
272
+
273
+ // window.rescale_ellipsoids = function(e) {
274
+ // var s = parseFloat(e.target.value);
275
+
276
+ // _.forEach(ellipsoids, function(el) {
277
+ // el._rescale(s);
278
+ // });
279
+ // }
package/tools/compile_colors.py ADDED
@@ -0,0 +1,120 @@
1
+ colortable = """1 H [255,255,255] FFFFFF FFFFFF
2
+ 2 He [217,255,255] D9FFFF FFC0CB
3
+ 3 Li [204,128,255] CC80FF B22222 B22121
4
+ 4 Be [194,255,0] C2FF00 FF1493
5
+ 5 B [255,181,181] FFB5B5 00FF00
6
+ 6 C [144,144,144] 909090 C8C8C8 D3D3D3
7
+ 7 N [48,80,248] 3050F8 8F8FFF 87CEE6
8
+ 8 O [255,13,13] FF0D0D F00000 FF0000
9
+ 9 F [144,224,80] 90E050 DAA520
10
+ 10 Ne [179,227,245] B3E3F5 FF1493
11
+ 11 Na [171,92,242] AB5CF2 0000FF
12
+ 12 Mg [138,255,0] 8AFF00 228B22
13
+ 13 Al [191,166,166] BFA6A6 808090 696969
14
+ 14 Si [240,200,160] F0C8A0 DAA520
15
+ 15 P [255,128,0] FF8000 FFA500 FFAA00
16
+ 16 S [255,255,48] FFFF30 FFC832 FFFF00
17
+ 17 Cl [31,240,31] 1FF01F 00FF00
18
+ 18 Ar [128,209,227] 80D1E3 FF1493
19
+ 19 K [143,64,212] 8F40D4 FF1493
20
+ 20 Ca [61,255,0] 3DFF00 808090 696969
21
+ 21 Sc [230,230,230] E6E6E6 FF1493
22
+ 22 Ti [191,194,199] BFC2C7 808090 696969
23
+ 23 V [166,166,171] A6A6AB FF1493
24
+ 24 Cr [138,153,199] 8A99C7 808090 696969
25
+ 25 Mn [156,122,199] 9C7AC7 808090 696969
26
+ 26 Fe [224,102,51] E06633 FFA500 FFAA00
27
+ 27 Co [240,144,160] F090A0 FF1493
28
+ 28 Ni [80,208,80] 50D050 A52A2A 802828
29
+ 29 Cu [200,128,51] C88033 A52A2A 802828
30
+ 30 Zn [125,128,176] 7D80B0 A52A2A 802828
31
+ 31 Ga [194,143,143] C28F8F FF1493
32
+ 32 Ge [102,143,143] 668F8F FF1493
33
+ 33 As [189,128,227] BD80E3 FF1493
34
+ 34 Se [255,161,0] FFA100 FF1493
35
+ 35 Br [166,41,41] A62929 A52A2A 802828
36
+ 36 Kr [92,184,209] 5CB8D1 FF1493
37
+ 37 Rb [112,46,176] 702EB0 FF1493
38
+ 38 Sr [0,255,0] 00FF00 FF1493
39
+ 39 Y [148,255,255] 94FFFF FF1493
40
+ 40 Zr [148,224,224] 94E0E0 FF1493
41
+ 41 Nb [115,194,201] 73C2C9 FF1493
42
+ 42 Mo [84,181,181] 54B5B5 FF1493
43
+ 43 Tc [59,158,158] 3B9E9E FF1493
44
+ 44 Ru [36,143,143] 248F8F FF1493
45
+ 45 Rh [10,125,140] 0A7D8C FF1493
46
+ 46 Pd [0,105,133] 006985 FF1493
47
+ 47 Ag [192,192,192] C0C0C0 808090 696969
48
+ 48 Cd [255,217,143] FFD98F FF1493
49
+ 49 In [166,117,115] A67573 FF1493
50
+ 50 Sn [102,128,128] 668080 FF1493
51
+ 51 Sb [158,99,181] 9E63B5 FF1493
52
+ 52 Te [212,122,0] D47A00 FF1493
53
+ 53 I [148,0,148] 940094 A020F0
54
+ 54 Xe [66,158,176] 429EB0 FF1493
55
+ 55 Cs [87,23,143] 57178F FF1493
56
+ 56 Ba [0,201,0] 00C900 FFA500 FFAA00
57
+ 57 La [112,212,255] 70D4FF FF1493
58
+ 58 Ce [255,255,199] FFFFC7 FF1493
59
+ 59 Pr [217,255,199] D9FFC7 FF1493
60
+ 60 Nd [199,255,199] C7FFC7 FF1493
61
+ 61 Pm [163,255,199] A3FFC7 FF1493
62
+ 62 Sm [143,255,199] 8FFFC7 FF1493
63
+ 63 Eu [97,255,199] 61FFC7 FF1493
64
+ 64 Gd [69,255,199] 45FFC7 FF1493
65
+ 65 Tb [48,255,199] 30FFC7 FF1493
66
+ 66 Dy [31,255,199] 1FFFC7 FF1493
67
+ 67 Ho [0,255,156] 00FF9C FF1493
68
+ 68 Er [0,230,117] 00E675 FF1493
69
+ 69 Tm [0,212,82] 00D452 FF1493
70
+ 70 Yb [0,191,56] 00BF38 FF1493
71
+ 71 Lu [0,171,36] 00AB24 FF1493
72
+ 72 Hf [77,194,255] 4DC2FF FF1493
73
+ 73 Ta [77,166,255] 4DA6FF FF1493
74
+ 74 W [33,148,214] 2194D6 FF1493
75
+ 75 Re [38,125,171] 267DAB FF1493
76
+ 76 Os [38,102,150] 266696 FF1493
77
+ 77 Ir [23,84,135] 175487 FF1493
78
+ 78 Pt [208,208,224] D0D0E0 FF1493
79
+ 79 Au [255,209,35] FFD123 DAA520
80
+ 80 Hg [184,184,208] B8B8D0 FF1493
81
+ 81 Tl [166,84,77] A6544D FF1493
82
+ 82 Pb [87,89,97] 575961 FF1493
83
+ 83 Bi [158,79,181] 9E4FB5 FF1493
84
+ 84 Po [171,92,0] AB5C00 FF1493
85
+ 85 At [117,79,69] 754F45 FF1493
86
+ 86 Rn [66,130,150] 428296 FF1493
87
+ 87 Fr [66,0,102] 420066 FF1493
88
+ 88 Ra [0,125,0] 007D00 FF1493
89
+ 89 Ac [112,171,250] 70ABFA FF1493
90
+ 90 Th [0,186,255] 00BAFF FF1493
91
+ 91 Pa [0,161,255] 00A1FF FF1493
92
+ 92 U [0,143,255] 008FFF FF1493
93
+ 93 Np [0,128,255] 0080FF FF1493
94
+ 94 Pu [0,107,255] 006BFF FF1493
95
+ 95 Am [84,92,242] 545CF2 FF1493
96
+ 96 Cm [120,92,227] 785CE3 FF1493
97
+ 97 Bk [138,79,227] 8A4FE3 FF1493
98
+ 98 Cf [161,54,212] A136D4 FF1493
99
+ 99 Es [179,31,212] B31FD4 FF1493
100
+ 100 Fm [179,31,186] B31FBA FF1493
101
+ 101 Md [179,13,166] B30DA6 FF1493
102
+ 102 No [189,13,135] BD0D87 FF1493
103
+ 103 Lr [199,0,102] C70066 FF1493
104
+ 104 Rf [204,0,89] CC0059 FF1493
105
+ 105 Db [209,0,79] D1004F FF1493
106
+ 106 Sg [217,0,69] D90045 FF1493
107
+ 107 Bh [224,0,56] E00038 FF1493
108
+ 108 Hs [230,0,46] E6002E FF1493
109
+ 109 Mt [235,0,38] EB0026 FF1493 """
110
+
111
+ lines = colortable.split('\n')
112
+ colors = ['0xff1493']*110
113
+
114
+ for l in lines:
115
+ l = l.strip().split()
116
+ Z = int(l[0])
117
+ c = l[3]
118
+ colors[Z] = '0x'+c.lower()
119
+
120
+ print('[' + ', '.join(colors) + ']')
package/tools/compile_periodic.py ADDED
@@ -0,0 +1,96 @@
1
+ import json
2
+ from periodictable import elements
3
+ from soprano.data.nmr import _nmr_data
4
+
5
+ element_data = {};
6
+
7
+ for el in elements:
8
+ sym = el.symbol
9
+ Z = el.number
10
+
11
+ if sym == 'n':
12
+ # No use for neutrons; instead we use Muonium
13
+ sym = 'Mu'
14
+
15
+ data = {
16
+ 'symbol': sym,
17
+ 'Z': Z,
18
+ 'isotopes': {}
19
+ }
20
+
21
+ # Most abundant isotopes?
22
+ most_iso = None
23
+ most_iso_ab = 0
24
+
25
+ most_NMR_iso = None
26
+ most_NMR_iso_ab = 0
27
+
28
+ most_Q_iso = None
29
+ most_Q_iso_ab = 0
30
+
31
+ nmr = _nmr_data.get(sym, {})
32
+
33
+ for iso in el:
34
+
35
+ mass = iso.mass
36
+ if sym == 'Mu':
37
+ mass = 0.113428913072988
38
+ A = iso.isotope
39
+ ab = iso.abundance
40
+
41
+ if ab == 0: # Does not exist in nature, irrelevant
42
+ continue
43
+
44
+ iso_nmr = nmr.get(str(A), {})
45
+ spin = iso_nmr.get('I', None)
46
+ gamma = iso_nmr.get('gamma', None)
47
+ Q = iso_nmr.get('Q', None)
48
+
49
+ # We completely skip including anything that has no spin data, and
50
+ # is LESS abundant than any NMR-active isotope
51
+
52
+ if spin is None:
53
+ if ab < min(most_NMR_iso_ab, most_Q_iso_ab):
54
+ continue
55
+ else:
56
+ spin = 0 # A safe assumption
57
+
58
+ if ab > most_iso_ab:
59
+ most_iso = A
60
+ most_iso_ab = ab
61
+
62
+ if ab > most_NMR_iso_ab and spin:
63
+ most_NMR_iso = A
64
+ most_NMR_iso_ab = ab
65
+
66
+ if ab > most_Q_iso_ab and Q:
67
+ most_Q_iso = A
68
+ most_Q_iso_ab = ab
69
+
70
+ data['isotopes'][A] = {
71
+ 'A': A,
72
+ 'mass': mass,
73
+ 'abundance': ab,
74
+ 'spin': spin,
75
+ 'gamma': gamma,
76
+ 'Q': Q
77
+ }
78
+
79
+ if most_iso is None:
80
+ # No useful information...
81
+ continue
82
+
83
+ data['maxiso'] = str(most_iso) if most_iso else None
84
+ data['maxiso_NMR'] = str(most_NMR_iso) if most_NMR_iso else None
85
+ data['maxiso_Q'] = str(most_Q_iso) if most_Q_iso else None
86
+
87
+ element_data[sym] = data
88
+
89
+ jsonstr = json.dumps(element_data, indent=2)
90
+
91
+ template = """const nmrData = {0};
92
+
93
+ export default nmrData;
94
+ """
95
+
96
+ print(template.format(jsonstr))