From e7a0ba8db09187703507bfc69b10d34011e501fb Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 29 Aug 2018 18:10:36 -0700
Subject: [PATCH] wip, better boundary calculation, making use of
transformations
---
src/apps/canvas/structure-view.ts | 64 ++++++++--
.../structure/structure/util/boundary.ts | 110 +++++++++++++++++-
2 files changed, 159 insertions(+), 15 deletions(-)
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index 13f8b3f16..912f0090b 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -12,6 +12,13 @@ import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
import { ShapeRepresentation, ShapeProps } from 'mol-geo/representation/shape';
import { getAxesShape } from './assembly-symmetry';
import Viewer from 'mol-view/viewer';
+import { CarbohydrateRepresentation } from 'mol-geo/representation/structure/representation/carbohydrate';
+import { MeshBuilder } from 'mol-geo/mesh/mesh-builder';
+import { addSphere } from 'mol-geo/mesh/builder/sphere';
+import { Shape } from 'mol-model/shape';
+import { Color } from 'mol-util/color';
+import { computeUnitBoundary } from 'mol-model/structure/structure/util/boundary';
+import { addBoundingBox } from 'mol-geo/mesh/builder/bounding-box';
export interface StructureView {
readonly label: string
@@ -21,7 +28,8 @@ export interface StructureView {
readonly cartoon: CartoonRepresentation
readonly ballAndStick: BallAndStickRepresentation
- readonly axes: ShapeRepresentation<ShapeProps>
+ readonly carbohydrate: CarbohydrateRepresentation
+ readonly symmetryAxes: ShapeRepresentation<ShapeProps>
readonly modelId: number
readonly assemblyId: string
@@ -45,7 +53,9 @@ interface StructureViewProps {
export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>, props: StructureViewProps = {}): Promise<StructureView> {
const cartoon = CartoonRepresentation()
const ballAndStick = BallAndStickRepresentation()
- const axes = ShapeRepresentation()
+ const carbohydrate = CarbohydrateRepresentation()
+ const symmetryAxes = ShapeRepresentation()
+ const polymerSphere = ShapeRepresentation()
let label: string
let model: Model | undefined
@@ -156,14 +166,46 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
useFog: false // TODO fog not working properly
}, structure).run()
+ await carbohydrate.createOrUpdate({
+ colorTheme: { name: 'carbohydrate-symbol' },
+ sizeTheme: { name: 'uniform', value: 1, factor: 1 },
+ useFog: false // TODO fog not working properly
+ }, structure).run()
+
viewer.center(structure.boundary.sphere.center)
+
+ const mb = MeshBuilder.create()
+ mb.setGroup(0)
+ addSphere(mb, structure.boundary.sphere.center, structure.boundary.sphere.radius, 3)
+ addBoundingBox(mb, structure.boundary.box, 1, 2, 8)
+ for (let i = 0, il = structure.units.length; i < il; ++i) {
+ mb.setGroup(1)
+ const u = structure.units[i]
+ const ci = u.model.atomicHierarchy.chainAtomSegments.index[u.elements[0]]
+ const ek = u.model.atomicHierarchy.getEntityKey(ci)
+ if (u.model.entities.data.type.value(ek) === 'water') continue
+ const boundary = computeUnitBoundary(u)
+ addSphere(mb, boundary.sphere.center, boundary.sphere.radius, 3)
+ addBoundingBox(mb, boundary.box, 0.5, 2, 8)
+ }
+ const shape = Shape.create('boundary', mb.getMesh(), [Color(0xCC6633), Color(0x3366CC)], ['sphere boundary'])
+ await polymerSphere.createOrUpdate({
+ alpha: 0.5,
+ doubleSided: false,
+ depthMask: false,
+ useFog: false // TODO fog not working properly
+ }, shape).run()
} else {
cartoon.destroy()
ballAndStick.destroy()
+ carbohydrate.destroy()
+ polymerSphere.destroy()
}
viewer.add(cartoon)
viewer.add(ballAndStick)
+ viewer.add(carbohydrate)
+ viewer.add(polymerSphere)
}
async function createSymmetryRepr() {
@@ -173,21 +215,21 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const axesShape = getAxesShape(symmetryFeatureId, assemblySymmetry)
if (axesShape) {
// getClusterColorTheme(symmetryFeatureId, assemblySymmetry)
- await axes.createOrUpdate({
+ await symmetryAxes.createOrUpdate({
colorTheme: { name: 'shape-group' },
// colorTheme: { name: 'uniform', value: Color(0xFFCC22) },
useFog: false // TODO fog not working properly
}, axesShape).run()
} else {
- axes.destroy()
+ symmetryAxes.destroy()
}
} else {
- axes.destroy()
+ symmetryAxes.destroy()
}
} else {
- axes.destroy()
+ symmetryAxes.destroy()
}
- viewer.add(axes)
+ viewer.add(symmetryAxes)
viewer.requestDraw()
}
@@ -201,7 +243,8 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
cartoon,
ballAndStick,
- axes,
+ carbohydrate,
+ symmetryAxes,
get modelId() { return modelId },
get assemblyId() { return assemblyId },
@@ -217,12 +260,13 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
destroy: () => {
viewer.remove(cartoon)
viewer.remove(ballAndStick)
- viewer.remove(axes)
+ viewer.remove(carbohydrate)
+ viewer.remove(symmetryAxes)
viewer.requestDraw()
cartoon.destroy()
ballAndStick.destroy()
- axes.destroy()
+ symmetryAxes.destroy()
}
}
}
diff --git a/src/mol-model/structure/structure/util/boundary.ts b/src/mol-model/structure/structure/util/boundary.ts
index 2a595f8cd..ec3821263 100644
--- a/src/mol-model/structure/structure/util/boundary.ts
+++ b/src/mol-model/structure/structure/util/boundary.ts
@@ -2,13 +2,115 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import Structure from '../structure'
-import { Box3D, Sphere3D } from 'mol-math/geometry';
+import Unit from '../unit';
+import { Box3D, Sphere3D, SymmetryOperator } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
+import { SortedArray } from 'mol-data/int';
+import { ElementIndex } from '../../model/indexing';
-function computeStructureBoundary(s: Structure): { box: Box3D, sphere: Sphere3D } {
+export type Boundary = { box: Box3D, sphere: Sphere3D }
+
+function computeElementsPositionBoundary(elements: SortedArray<ElementIndex>, position: SymmetryOperator.CoordinateMapper): Boundary {
+ const min = Vec3.create(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE)
+ const max = Vec3.create(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE)
+ const center = Vec3.zero()
+
+ let radiusSq = 0
+ let size = 0
+
+ const p = Vec3.zero()
+
+ size += elements.length
+ for (let j = 0, _j = elements.length; j < _j; j++) {
+ position(elements[j], p)
+ Vec3.min(min, min, p)
+ Vec3.max(max, max, p)
+ Vec3.add(center, center, p)
+ }
+
+ if (size > 0) Vec3.scale(center, center, 1/size)
+
+ for (let j = 0, _j = elements.length; j < _j; j++) {
+ position(elements[j], p)
+ const d = Vec3.squaredDistance(p, center)
+ if (d > radiusSq) radiusSq = d;
+ }
+
+ return {
+ box: { min, max },
+ sphere: { center, radius: Math.sqrt(radiusSq) }
+ };
+}
+
+function computeInvariantUnitBoundary(u: Unit): Boundary {
+ return computeElementsPositionBoundary(u.elements, u.conformation.invariantPosition)
+}
+
+export function computeUnitBoundary(u: Unit): Boundary {
+ return computeElementsPositionBoundary(u.elements, u.conformation.position)
+}
+
+const tmpBox = Box3D.empty()
+const tmpSphere = Sphere3D.zero()
+
+export function computeStructureBoundary(s: Structure): Boundary {
+ const min = Vec3.create(Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE)
+ const max = Vec3.create(-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE)
+ const center = Vec3.zero()
+
+ const { units } = s;
+
+ const boundaryMap: Map<number, Boundary> = new Map()
+ function getInvariantBoundary(u: Unit) {
+ let boundary: Boundary
+ if (boundaryMap.has(u.invariantId)) {
+ boundary = boundaryMap.get(u.invariantId)!
+ } else {
+ boundary = computeInvariantUnitBoundary(u)
+ boundaryMap.set(u.invariantId, boundary)
+ }
+ return boundary
+ }
+
+ let radiusSq = 0;
+ let size = 0;
+
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ size += 1
+ const u = units[i]
+ const invariantBoundary = getInvariantBoundary(u)
+ const m = u.conformation.operator.matrix
+ Box3D.transform(tmpBox, invariantBoundary.box, m)
+ Vec3.min(min, min, tmpBox.min)
+ Vec3.max(max, max, tmpBox.max)
+ Sphere3D.transform(tmpSphere, invariantBoundary.sphere, m)
+ Vec3.add(center, center, tmpSphere.center)
+ }
+
+ if (size > 0) Vec3.scale(center, center, 1/size)
+
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ const u = units[i]
+ const invariantBoundary = getInvariantBoundary(u)
+ const m = u.conformation.operator.matrix
+ Sphere3D.transform(tmpSphere, invariantBoundary.sphere, m)
+ const d = Vec3.squaredDistance(tmpSphere.center, center) + (tmpSphere.radius * tmpSphere.radius) * 4
+ if (d > radiusSq) radiusSq = d
+ }
+
+ const b = {
+ box: { min, max },
+ sphere: { center, radius: Math.sqrt(radiusSq) }
+ };
+ console.log(b, computeStructureBoundary2(s))
+ return b
+}
+
+export function computeStructureBoundary2(s: Structure): Boundary {
const min = [Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE];
const max = [-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE];
@@ -62,6 +164,4 @@ function computeStructureBoundary(s: Structure): { box: Box3D, sphere: Sphere3D
box: { min: Vec3.ofArray(min), max: Vec3.ofArray(max) },
sphere: { center: Vec3.create(cx, cy, cz), radius: Math.sqrt(radiusSq) }
};
-}
-
-export { computeStructureBoundary }
\ No newline at end of file
+}
\ No newline at end of file
--
GitLab