@@ -6,111 +6,112 @@ import { ATOM_GROUP_NAME } from "../enums";
66 * Mixin containing the logic for dealing with atoms.
77 * Draws atoms as spheres and handles actions performed on them.
88 */
9- export const AtomsMixin = ( superclass ) => class extends superclass {
10- constructor ( config ) {
11- super ( config ) ;
9+ export const AtomsMixin = ( superclass ) =>
10+ class extends superclass {
11+ constructor ( config ) {
12+ super ( config ) ;
1213
13- // to draw atoms as spheres
14- this . initSphereParameters ( ) ;
14+ // to draw atoms as spheres
15+ this . initSphereParameters ( ) ;
1516
16- this . drawAtomsAsSpheres = this . drawAtomsAsSpheres . bind ( this ) ;
17- this . getAtomColorByElement = this . getAtomColorByElement . bind ( this ) ;
17+ this . drawAtomsAsSpheres = this . drawAtomsAsSpheres . bind ( this ) ;
18+ this . getAtomColorByElement = this . getAtomColorByElement . bind ( this ) ;
1819
19- this . setStructure ( this . _structure ) ;
20- }
20+ this . setStructure ( this . _structure ) ;
21+ }
2122
22- get structure ( ) {
23- return this . _structure ;
24- }
23+ get structure ( ) {
24+ return this . _structure ;
25+ }
2526
26- /**
27+ /**
2728 * Helper function to set the structural information.
2829 * @param {Made.Material } s - Structural information as Made.Material.
2930 */
30- setStructure ( s ) {
31- this . _structure = s . clone ( ) ; // clone original structure to assert that any updates are propagated to parents
32- this . _basis = s . Basis ;
33- this . _basis . originalUnits = this . _basis . units ;
34- this . _basis . toCartesian ( ) ;
35- }
36-
37- get basis ( ) {
38- return this . _basis ;
39- }
40-
41- initSphereParameters ( ) {
42- // radius, segment, ring
43- const sphereGeometry = new THREE . SphereGeometry (
44- 1 ,
45- this . settings . sphereQuality ,
46- this . settings . sphereQuality ,
47- ) ;
48- const sphereMaterial = new THREE . MeshLambertMaterial ( ) ;
49- this . sphereMesh = new THREE . Mesh ( sphereGeometry , sphereMaterial ) ;
50- }
51-
52- /**
31+ setStructure ( s ) {
32+ this . _structure = s . clone ( ) ; // clone original structure to assert that any updates are propagated to parents
33+ this . _basis = s . Basis ;
34+ this . _basis . originalUnits = this . _basis . units ;
35+ this . _basis . toCartesian ( ) ;
36+ }
37+
38+ get basis ( ) {
39+ return this . _basis ;
40+ }
41+
42+ initSphereParameters ( ) {
43+ // radius, segment, ring
44+ const sphereGeometry = new THREE . SphereGeometry (
45+ 1 ,
46+ this . settings . sphereQuality ,
47+ this . settings . sphereQuality ,
48+ ) ;
49+ const sphereMaterial = new THREE . MeshLambertMaterial ( ) ;
50+ this . sphereMesh = new THREE . Mesh ( sphereGeometry , sphereMaterial ) ;
51+ }
52+
53+ /**
5354 * Prepares a sphere mesh object
5455 * @param {String } color
5556 * @param {Number } radius
5657 * @param {Array } coordinate
5758 * @return {THREE.Object3D }
5859 */
59- getSphereMeshObject ( {
60- color = this . settings . defaultColor ,
61- radius = this . settings . sphereRadius ,
62- coordinate = [ ] ,
63- } ) {
64- // clone original mesh to optimize the speed
65- const sphereMesh = this . sphereMesh . clone ( ) ;
66- // set material color after cloning to optimize the speed and avoid re-creating material object
67- sphereMesh . material = sphereMesh . material . clone ( ) ;
68- sphereMesh . material . setValues ( { color } ) ;
69-
70- // eslint-disable-next-line no-multi-assign
71- sphereMesh . scale . x = sphereMesh . scale . y = sphereMesh . scale . z = radius ;
72- sphereMesh . position . set ( ...coordinate ) ;
73-
74- return sphereMesh ;
75- }
76-
77- _getDefaultSettingsForElement (
78- element = this . settings . defaultElement ,
79- scale = this . settings . atomRadiiScale ,
80- ) {
81- return {
82- color : this . getAtomColorByElement ( element ) ,
83- radius : this . getAtomRadiusByElement ( element , scale ) ,
84- } ;
85- }
86-
87- createAtomsGroup ( basis , atomRadiiScale ) {
88- const atomsGroup = new THREE . Group ( ) ;
89- atomsGroup . name = ATOM_GROUP_NAME ;
90- basis . coordinates . forEach ( ( atomicCoordinate , atomicIndex ) => {
91- const element = basis . getElementByIndex ( atomicIndex ) ;
92- const sphereMesh = this . getSphereMeshObject ( {
93- ...this . _getDefaultSettingsForElement ( element , atomRadiiScale ) ,
94- coordinate : atomicCoordinate . value ,
60+ getSphereMeshObject ( {
61+ color = this . settings . defaultColor ,
62+ radius = this . settings . sphereRadius ,
63+ coordinate = [ ] ,
64+ } ) {
65+ // clone original mesh to optimize the speed
66+ const sphereMesh = this . sphereMesh . clone ( ) ;
67+ // set material color after cloning to optimize the speed and avoid re-creating material object
68+ sphereMesh . material = sphereMesh . material . clone ( ) ;
69+ sphereMesh . material . setValues ( { color } ) ;
70+
71+ // eslint-disable-next-line no-multi-assign
72+ sphereMesh . scale . x = sphereMesh . scale . y = sphereMesh . scale . z = radius ;
73+ sphereMesh . position . set ( ...coordinate ) ;
74+
75+ return sphereMesh ;
76+ }
77+
78+ _getDefaultSettingsForElement (
79+ element = this . settings . defaultElement ,
80+ scale = this . settings . atomRadiiScale ,
81+ ) {
82+ return {
83+ color : this . getAtomColorByElement ( element ) ,
84+ radius : this . getAtomRadiusByElement ( element , scale ) ,
85+ } ;
86+ }
87+
88+ createAtomsGroup ( basis , atomRadiiScale ) {
89+ const atomsGroup = new THREE . Group ( ) ;
90+ atomsGroup . name = ATOM_GROUP_NAME ;
91+ basis . coordinates . forEach ( ( atomicCoordinate , atomicIndex ) => {
92+ const element = basis . getElementByIndex ( atomicIndex ) ;
93+ const sphereMesh = this . getSphereMeshObject ( {
94+ ...this . _getDefaultSettingsForElement ( element , atomRadiiScale ) ,
95+ coordinate : atomicCoordinate . value ,
96+ } ) ;
97+ sphereMesh . name = `${ element } ${ atomicIndex } ;
98+ atomsGroup . add ( sphereMesh ) ;
9599 } ) ;
96- sphereMesh . name = `${ element } ${ atomicIndex } ;
97- atomsGroup . add ( sphereMesh ) ;
98- } ) ;
99- return atomsGroup ;
100- }
101-
102- drawAtomsAsSpheres ( atomRadiiScale ) {
103- const basis = this . areNonPeriodicBoundariesPresent
104- ? this . basisWithElementsInsideNonPeriodicBoundaries
105- : this . basis ;
106- this . repeatAtomsAtRepetitionCoordinates ( this . createAtomsGroup ( basis , atomRadiiScale ) ) ;
107- }
108-
109- getAtomColorByElement ( element , pallette = this . settings . elementColors ) {
110- return pallette [ element ] || this . settings . defaultColor ;
111- }
112-
113- getAtomRadiusByElement ( element , scale = 1.0 , radiimap = this . settings . vdwRadii ) {
114- return ( radiimap [ element ] || this . settings . sphereRadius ) * scale ;
115- }
116- } ;
100+ return atomsGroup ;
101+ }
102+
103+ drawAtomsAsSpheres ( atomRadiiScale ) {
104+ const basis = this . areNonPeriodicBoundariesPresent
105+ ? this . basisWithElementsInsideNonPeriodicBoundaries
106+ : this . basis ;
107+ this . repeatAtomsAtRepetitionCoordinates ( this . createAtomsGroup ( basis , atomRadiiScale ) ) ;
108+ }
109+
110+ getAtomColorByElement ( element , pallette = this . settings . elementColors ) {
111+ return pallette [ element ] || this . settings . defaultColor ;
112+ }
113+
114+ getAtomRadiusByElement ( element , scale = 1.0 , radiimap = this . settings . vdwRadii ) {
115+ return ( radiimap [ element ] || this . settings . sphereRadius ) * scale ;
116+ }
117+ } ;
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