From e0c6ebd2194619b6ab39ae1c181071734de74ece Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 5 Apr 2019 17:11:20 -0700
Subject: [PATCH] repr tweaks
---
src/mol-math/geometry/gaussian-density/cpu.ts | 10 +--
src/mol-repr/structure/visual/util/common.ts | 67 ++++++++++++++++++-
.../structure/visual/util/gaussian.ts | 67 +------------------
3 files changed, 73 insertions(+), 71 deletions(-)
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index a52619139..b4c65cd53 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/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)
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index cd0e2271a..f2f8faa6d 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/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 }
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/gaussian.ts b/src/mol-repr/structure/visual/util/gaussian.ts
index d50d95c8f..cf5c77264 100644
--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/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 => {
--
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