New shape: Icosahedron

src/buffer/icosahedron-buffer.ts

@@ -0,0 +1,68 @@
+/**
+ * @file Icosahedron Buffer
+ * @private
+ */
+
+import { IcosahedronGeometry, Vector3, Matrix4 } from 'three'
+
+import { BufferRegistry } from '../globals'
+import GeometryBuffer from './geometry-buffer'
+import { BufferData, BufferParameters } from './buffer'
+
+const scale = new Vector3()
+const target = new Vector3()
+const up = new Vector3()
+const eye = new Vector3(0, 0, 0)
+
+export interface IcosahedronBufferData extends BufferData {
+  heightAxis: Float32Array
+  depthAxis: Float32Array
+  size: Float32Array
+}
+
+/**
+ * Icosahedron buffer. Draws Icosahedrons.
+ *
+ * @example
+ * var icosahedronBuffer = new IcosahedronBuffer({
+ *   position: new Float32Array([ 0, 3, 0, -2, 0, 0 ]),
+ *   color: new Float32Array([ 1, 0, 1, 0, 1, 0 ]),
+ *   size: new Float32Array([ 2, 1.5 ]),
+ *   heightAxis: new Float32Array([ 0, 1, 1, 0, 2, 0 ]),
+ *   depthAxis: new Float32Array([ 1, 0, 1, 0, 0, 2 ])
+ * })
+ */
+class IcosahedronBuffer extends GeometryBuffer {
+  updateNormals = true
+
+  _heightAxis: Float32Array
+  _depthAxis: Float32Array
+  _size: Float32Array
+
+  constructor (data: IcosahedronBufferData, params: Partial<BufferParameters> = {}) {
+    super(data, params, new IcosahedronGeometry(1, 0))
+
+    this.setAttributes(data, true)
+  }
+
+  applyPositionTransform (matrix: Matrix4, i: number, i3: number) {
+    target.fromArray(this._heightAxis as any, i3)
+    up.fromArray(this._depthAxis as any, i3)
+    matrix.lookAt(eye, target, up)
+
+    scale.set(this._size[ i ], up.length(), target.length())
+    matrix.scale(scale)
+  }
+
+  setAttributes (data: Partial<IcosahedronBufferData> = {}, initNormals?: boolean) {
+    if (data.size) this._size = data.size
+    if (data.heightAxis) this._heightAxis = data.heightAxis
+    if (data.depthAxis) this._depthAxis = data.depthAxis
+
+    super.setAttributes(data, initNormals)
+  }
+}
+
+BufferRegistry.add('icosahedron', IcosahedronBuffer)
+
+export default IcosahedronBuffer

src/controls/picking-proxy.ts

@@ -248,6 +248,10 @@ class PickingProxy {
    * @type {Object}
    */
   get ellipsoid () { return this._objectIfType('ellipsoid') as ShapePrimitive }
+  /**
+   * @type {Object}
+   */
+  get icosahedron () { return this._objectIfType('icosahedron') as ShapePrimitive }
   /**
    * @type {Object}
    */
@@ -326,6 +330,8 @@ class PickingProxy {
       msg = `distance: ${this.distance.atom1.qualifiedName()} - ${this.distance.atom2.qualifiedName()} (${this.distance.structure.name})`
     } else if (this.ellipsoid) {
       msg = this.ellipsoid.name
+    } else if (this.icosahedron) {
+      msg = this.icosahedron.name
     } else if (this.octahedron) {
       msg = this.octahedron.name
     } else if (this.point) {

src/geometry/primitive.ts

@@ -181,6 +181,13 @@ export class TetrahedronPrimitive extends BoxPrimitive {
   static type = 'tetrahedron'
 }
 
+/**
+ * Icosahedron geometry primitive
+ */
+export class IcosahedronPrimitive extends BoxPrimitive {
+  static type = 'icosahedron'
+}
+
 /**
  * Cylinder geometry primitive
  */

src/geometry/shape.ts

@@ -11,7 +11,7 @@ import { createParams, ensureFloat32Array, getUintArray } from '../utils'
 import {
   ArrowPrimitive, BoxPrimitive, ConePrimitive, CylinderPrimitive, EllipsoidPrimitive,
   OctahedronPrimitive, SpherePrimitive, TetrahedronPrimitive, TextPrimitive,
-  TorusPrimitive, PointPrimitive, WidelinePrimitive
+  TorusPrimitive, PointPrimitive, WidelinePrimitive, IcosahedronPrimitive
 } from './primitive'
 import { MeshPicker } from '../utils/picker'
 import Buffer from '../buffer/buffer'
@@ -23,7 +23,7 @@ const tmpBox = new Box3()
 const Primitives = [
   ArrowPrimitive, BoxPrimitive, ConePrimitive, CylinderPrimitive,
   EllipsoidPrimitive, OctahedronPrimitive, SpherePrimitive, TetrahedronPrimitive,
-  TextPrimitive, TorusPrimitive, PointPrimitive, WidelinePrimitive
+  TextPrimitive, TorusPrimitive, PointPrimitive, WidelinePrimitive, IcosahedronPrimitive
 ]
 
 export const ShapeDefaultParameters = {
@@ -329,6 +329,26 @@ class Shape {
     return this
   }
 
+  /**
+   * Add an icosahedron
+   * @example
+   * shape.addIcosahedron([ 0, 3, 0 ], [ 1, 0, 1 ], 2, [ 0, 1, 1 ], [ 1, 0, 1 ]);
+   *
+   * @param {Vector3|Array} position - position vector or array
+   * @param {Color|Array} color - color object or array
+   * @param {Float} size - size value
+   * @param {Vector3|Array} heightAxis - height axis vector or array
+   * @param {Vector3|Array} depthAxis - depth axis vector or array
+   * @param {String} [name] - text
+   * @return {Shape} this object
+   */
+  addIcosahedron (position: Vector3|[number, number, number], color: Color|[number, number, number], size: number, heightAxis: Vector3|[number, number, number], depthAxis: Vector3|[number, number, number], name: string) {
+    IcosahedronPrimitive.objectToShape(
+      this, { position, color, size, heightAxis, depthAxis, name }
+    )
+    return this
+  }
+
   /**
    * Add text
    * @example

src/ngl.ts

@@ -117,6 +117,7 @@ import BoxBuffer from './buffer/box-buffer'
 import ConeBuffer from './buffer/cone-buffer'
 import CylinderBuffer from './buffer/cylinder-buffer'
 import EllipsoidBuffer from './buffer/ellipsoid-buffer'
+import IcosahedronBuffer from './buffer/icosahedron-buffer'
 import MeshBuffer from './buffer/mesh-buffer'
 import OctahedronBuffer from './buffer/octahedron-buffer'
 import PointBuffer from './buffer/point-buffer'
@@ -298,6 +299,7 @@ export {
   ConeBuffer,
   CylinderBuffer,
   EllipsoidBuffer,
+  IcosahedronBuffer,
   MeshBuffer,
   OctahedronBuffer,
   PointBuffer,

src/utils/picker.ts

@@ -12,7 +12,8 @@ import Selection from '../selection/selection'
 import {
   ArrowPrimitive, BoxPrimitive, ConePrimitive, CylinderPrimitive,
   EllipsoidPrimitive, OctahedronPrimitive, SpherePrimitive,
-  TetrahedronPrimitive, TorusPrimitive, PointPrimitive, WidelinePrimitive
+  TetrahedronPrimitive, TorusPrimitive, PointPrimitive, WidelinePrimitive,
+  IcosahedronPrimitive
 } from '../geometry/primitive'
 import { contactTypeName, Contacts } from '../chemistry/interactions/contact'
 import { TypedArray } from '../types';
@@ -283,6 +284,10 @@ class EllipsoidPicker extends ShapePicker {
   get primitive () { return EllipsoidPrimitive }
 }
 
+class IcosahedronPicker extends ShapePicker {
+  get primitive () { return IcosahedronPrimitive }
+}
+
 class OctahedronPicker extends ShapePicker {
   get primitive () { return OctahedronPrimitive }
 }
@@ -442,6 +447,7 @@ PickerRegistry.add('box', BoxPicker)
 PickerRegistry.add('cone', ConePicker)
 PickerRegistry.add('cylinder', CylinderPicker)
 PickerRegistry.add('ellipsoid', EllipsoidPicker)
+PickerRegistry.add('icosahedron', IcosahedronPicker)
 PickerRegistry.add('octahedron', OctahedronPicker)
 PickerRegistry.add('sphere', SpherePicker)
 PickerRegistry.add('tetrahedron', TetrahedronPicker)
@@ -463,6 +469,7 @@ export {
   ClashPicker,
   DistancePicker,
   EllipsoidPicker,
+  IcosahedronPicker,
   IgnorePicker,
   OctahedronPicker,
   MeshPicker,