repr tweaks

src/mol-math/geometry/gaussian-density/cpu.ts

@@ -17,8 +17,8 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
     const { indices, x, y, z } = position
     const n = OrderedSet.size(indices)
 
-    const v = Vec3.zero()
-    const p = Vec3.zero()
+    const v = Vec3()
+    const p = Vec3()
 
     let maxRadius = 0
     for (let i = 0; i < n; ++i) {
@@ -49,7 +49,7 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
 
     const densData = space.create()
 
-    const c = Vec3.zero()
+    const c = Vec3()
 
     const alpha = smoothness
 
@@ -58,8 +58,8 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
     Vec3.mul(_radius2, _radius2, delta)
     const updateChunk = Math.ceil(10000 / (_radius2[0] * _radius2[1] * _radius2[2]))
 
-    const beg = Vec3.zero()
-    const end = Vec3.zero()
+    const beg = Vec3()
+    const end = Vec3()
 
     const gridPad = 1 / Math.max(...delta)
 

src/mol-repr/structure/visual/util/common.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,6 +9,7 @@ import { Mat4 } from 'mol-math/linear-algebra';
 import { TransformData, createTransform } from 'mol-geo/geometry/transform-data';
 import { OrderedSet, SortedArray } from 'mol-data/int';
 import { EmptyLoci, Loci } from 'mol-model/loci';
+import { PhysicalSizeTheme } from 'mol-theme/size/physical';
 
 /** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
 export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
@@ -55,4 +56,68 @@ export function includesUnitKind(unitKinds: UnitKind[], unit: Unit) {
         if (Unit.isGaussians(unit) && unitKinds[i] === 'gaussians') return true
     }
     return false
+}
+
+//
+
+export function getConformation(unit: Unit) {
+    switch (unit.kind) {
+        case Unit.Kind.Atomic: return unit.model.atomicConformation
+        case Unit.Kind.Spheres: return unit.model.coarseConformation.spheres
+        case Unit.Kind.Gaussians: return unit.model.coarseConformation.gaussians
+    }
+}
+
+export function getUnitConformationAndRadius(unit: Unit) {
+    const conformation = getConformation(unit)
+    const { elements } = unit
+    const position = {
+        indices: elements,
+        x: conformation.x,
+        y: conformation.y,
+        z: conformation.z
+    }
+
+    const l = StructureElement.create(unit)
+    const sizeTheme = PhysicalSizeTheme({}, {})
+    const radius = (index: number) => {
+        l.element = index as ElementIndex
+        return sizeTheme.size(l)
+    }
+
+    return { position, radius }
+}
+
+export function getStructureConformationAndRadius(structure: Structure) {
+    const n = structure.elementCount
+
+    const xs = new Float32Array(n)
+    const ys = new Float32Array(n)
+    const zs = new Float32Array(n)
+    const rs = new Float32Array(n)
+
+    const l = StructureElement.create()
+    const sizeTheme = PhysicalSizeTheme({}, {})
+
+    let m = 0
+    for (let i = 0, il = structure.units.length; i < il; ++i) {
+        const unit = structure.units[i]
+        const { elements } = unit
+        const { x, y, z } = unit.conformation
+        l.unit = unit
+        for (let j = 0, jl = elements.length; j < jl; ++j) {
+            const eI = elements[j]
+            xs[m + j] = x(eI)
+            ys[m + j] = y(eI)
+            zs[m + j] = z(eI)
+            l.element = eI
+            rs[m + j] = sizeTheme.size(l)
+        }
+        m += elements.length
+    }
+
+    const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
+    const radius = (index: number) => rs[index]
+
+    return { position, radius }
 }

src/mol-repr/structure/visual/util/gaussian.ts

@@ -4,15 +4,14 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Unit, StructureElement, ElementIndex, Structure } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
 import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
 import { Task } from 'mol-task';
 import { ParamDefinition as PD } from 'mol-util/param-definition';
 import { GaussianDensityTexture, GaussianDensityTexture2d } from 'mol-math/geometry/gaussian-density/gpu';
 import { Texture } from 'mol-gl/webgl/texture';
 import { WebGLContext } from 'mol-gl/webgl/context';
-import { PhysicalSizeTheme } from 'mol-theme/size/physical';
-import { OrderedSet } from 'mol-data/int';
+import { getUnitConformationAndRadius, getStructureConformationAndRadius } from './common';
 
 export const GaussianDensityParams = {
     resolution: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
@@ -33,34 +32,6 @@ export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTexturePr
 
 //
 
-function getConformation(unit: Unit) {
-    switch (unit.kind) {
-        case Unit.Kind.Atomic: return unit.model.atomicConformation
-        case Unit.Kind.Spheres: return unit.model.coarseConformation.spheres
-        case Unit.Kind.Gaussians: return unit.model.coarseConformation.gaussians
-    }
-}
-
-function getUnitConformationAndRadius(unit: Unit) {
-    const conformation = getConformation(unit)
-    const { elements } = unit
-    const position = {
-        indices: elements,
-        x: conformation.x,
-        y: conformation.y,
-        z: conformation.z
-    }
-
-    const l = StructureElement.create(unit)
-    const sizeTheme = PhysicalSizeTheme({}, {})
-    const radius = (index: number) => {
-        l.element = index as ElementIndex
-        return sizeTheme.size(l)
-    }
-
-    return { position, radius }
-}
-
 export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
     const { position, radius } = getUnitConformationAndRadius(unit)
     return Task.create('Gaussian Density', async ctx => {
@@ -84,40 +55,6 @@ export function computeUnitGaussianDensityTexture2d(unit: Unit, props: GaussianD
 
 //
 
-function getStructureConformationAndRadius(structure: Structure) {
-    const n = structure.elementCount
-
-    const xs = new Float32Array(n)
-    const ys = new Float32Array(n)
-    const zs = new Float32Array(n)
-    const rs = new Float32Array(n)
-
-    const l = StructureElement.create()
-    const sizeTheme = PhysicalSizeTheme({}, {})
-
-    let m = 0
-    for (let i = 0, il = structure.units.length; i < il; ++i) {
-        const unit = structure.units[i]
-        const { elements } = unit
-        const { x, y, z } = unit.conformation
-        l.unit = unit
-        for (let j = 0, jl = elements.length; j < jl; ++j) {
-            const eI = elements[j]
-            xs[m + j] = x(eI)
-            ys[m + j] = y(eI)
-            zs[m + j] = z(eI)
-            l.element = eI
-            rs[m + j] = sizeTheme.size(l)
-        }
-        m += elements.length
-    }
-
-    const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
-    const radius = (index: number) => rs[index]
-
-    return { position, radius }
-}
-
 export function computeStructureGaussianDensity(structure: Structure, props: GaussianDensityProps, webgl?: WebGLContext) {
     const { position, radius } = getStructureConformationAndRadius(structure)
     return Task.create('Gaussian Density', async ctx => {