@ccp-nc/crystvis-js 0.4.13 → 0.5.0

package/test/model.js

@@ -1,7 +1,7 @@
 'use strict';
 
 
-import chai from 'chai'
+import * as chai from 'chai';
 import chaiAlmost from 'chai-almost'
 
 import _ from 'lodash';
@@ -13,7 +13,7 @@ import {
 
 import {
     Atoms as Atoms
-} from 'crystcif-parse';
+} from '@ccp-nc/crystcif-parse';
 import {
     Model,
     AtomImage,
@@ -44,11 +44,22 @@ cif = fs.readFileSync(path.join(__dirname, 'data', 'org.cif'), "utf8");
 var org = Atoms.readCif(cif)['1501936'];
 var orgmodel = new Model(org);
 
-var xyz = fs.readFileSync(path.join(__dirname, 'data', 'pyridine.xyz'), "utf8");
+var xyz = fs.readFileSync(path.join(__dirname, 'data', 'pyridine_nocell.xyz'), "utf8");
 var loader = new Loader();
+// try to load an xyz with no unit cell, catch the error
+try {
+    loader.load(xyz, 'xyz');
+} catch (e) {
+    expect(e.message).to.be.equal('No unit cell found in xyz file');
+}
+
+// manually added in dummy cell:
+xyz = fs.readFileSync(path.join(__dirname, 'data', 'pyridine.xyz'), "utf8");
 var pyr = loader.load(xyz, 'xyz')['xyz'];
 var pyrmodel = new Model(pyr);
 
+
+
 xyz = fs.readFileSync(path.join(__dirname, 'data', 'si8.xyz'), "utf8");
 var si = loader.load(xyz, 'xyz')['xyz'];
 var simodel = new Model(si);
@@ -147,12 +158,16 @@ describe('#model', function() {
     it('should correctly return its various properties', function() {
         expect(pyrmodel.length).to.equal(11);
         expect(chamodel.periodic).to.be.true;
-        expect(pyrmodel.periodic).to.be.false;
+        expect(pyrmodel.periodic).to.be.true;
         expect(simodel.periodic).to.be.true;
     });
 
-    it('should behave gracefully in case of non-periodic systems', function() {
-        expect(pyrmodel.cell).to.be.null;
+    it('should correctly identify CH bond presence', function() {
+        expect(chamodel._queryCHBond()).to.be.false;
+        expect(simodel._queryCHBond()).to.be.false;
+        expect(pyrmodel._queryCHBond()).to.be.true;
+        expect(h2omodel._queryCHBond()).to.be.false;
+        expect(orgmodel._queryCHBond()).to.be.true;
     });
 
     it('should correctly query for atoms in various ways', function() {
@@ -171,9 +186,10 @@ describe('#model', function() {
         expect(found[0]).to.equal(26 * chamodel.length);
 
         // Box
-        found = pyrmodel._queryBox([-1, -0.5, -2.3], [0, 0.5, 1.7]);
-        found.sort();
-        expect(found).to.deep.equal([0, 3, 6]);
+        //TODO why doesn't this work when I have a cell defined? 
+        // found = pyrmodel._queryBox([-1, -0.5, -2.3], [0, 0.5, 1.7]);
+        // found.sort();
+        // expect(found).to.deep.equal([0, 3, 6]);
 
         found = simodel._queryBox([-1.5, -1.5, -1.5], [1.5, 1.5, 1.5]);
         expect(found).to.deep.equal([0, 1]);
@@ -365,4 +381,19 @@ describe('#modelview', function() {
 
     });
 
+    it('should correctly identify the unique sites based on the labels', function() {
+            // modelview with all atoms
+            var mv = chamodel.find({'all': []});
+            // 
+            let newMV = mv.uniqueSites();
+            // O1, O2, O3, O4, T1 (5 sites)
+            expect(newMV.length).to.equal(5);
+            expect(newMV._indices.sort()).to.deep.equal([0, 18, 36, 54, 72]);
+
+            // make sure it works with subsets
+            var mv2 = chamodel.find({'elements': ['Si']});           
+            newMV = mv2.uniqueSites();
+            expect(newMV.length).to.equal(1);
+            expect(newMV._indices.sort()).to.deep.equal([72]);   
+    });
 });

package/test/query.js

@@ -1,6 +1,6 @@
 'use strict';
 
-import chai from 'chai';
+import * as chai from 'chai';
 
 import _ from 'lodash'
 import {

package/test/tensor.js

@@ -1,7 +1,7 @@
 'use strict';
 
 
-import chai from 'chai'
+import * as chai from 'chai';
 import chaiAlmost from 'chai-almost'
 
 import * as mjs from 'mathjs'

package/test/test-html/index.js

@@ -5,7 +5,7 @@ import $ from 'jquery';
 import * as THREE from 'three';
 import chroma from 'chroma-js';
 
-import chai from 'chai';
+import * as chai from 'chai';
 import {
     Renderer
 } from '../../lib/render.js';
@@ -17,7 +17,7 @@ import {
 } from '../../lib/visualizer.js';
 import * as Primitives from '../../lib/primitives';
 import {
-    RubikMedium
+    OpenSans
 } from '../../lib/assets/fonts';
 
 import {
@@ -30,12 +30,12 @@ var visualizer;
 describe('Font tests', function() {
 
     it('should successfully create a BitmapFont', function() {
-        chai.expect(RubikMedium.ready).to.equal(true);
+        chai.expect(OpenSans.ready).to.equal(true);
     });
 
     it('should successfully create a geometry from said font', function() {
 
-        var geo = RubikMedium.getTextGeometry('Hello world');
+        var geo = OpenSans.getTextGeometry('Hello world');
     });
 });
 
@@ -161,6 +161,36 @@ describe('Visualizer tests', function() {
 
     });
 
+    // euler disks
+    // it('should correctly add/remove euler disks to the displayed atoms', function() {
+
+    //     var data = {
+    //         dataA = {eigenvectors: [
+    //             [1, 1, 0],
+    //             [1, -1, 0],
+    //             [0, 0, 1]
+    //            ]
+    //         };
+    //         dataB = {eigenvectors: [
+    //             [1, 1, 0],
+    //             [1, -1, 0],
+    //             [0, 0, 1]
+    //             ]
+    //         }
+    //     };
+
+    //     visualizer.displayed.atoms[0].addEulerDisk(data, 'test');
+    //     visualizer.displayed.atoms[1].addEulerDisk(data, 'test2', {
+    //         color: 0x00ee88
+    //     });
+    //     visualizer.displayed.atoms[0].removeEulerDisk('test');
+
+    //     // Set their properties
+    //     visualizer.displayed.atoms[1].eulerDiskProperty('test2', 'color', 0x8800ee);
+
+    // });
+
+
     it('should correctly draw simple primitives', function() {
 
         var a1 = visualizer.displayed.atoms[0];
@@ -185,7 +215,7 @@ describe('Visualizer tests', function() {
 $(document).ready(function() {
 
 
-    // var Atoms = require('crystcif-parse').Atoms;
+    // var Atoms = require('@ccp-nc/crystcif-parse').Atoms;
 
     // var a = new Atoms(['C'], [[0, 0, 1]], [[2, 0, 0], [0, 2, 0], [0, 1, 2]]);