From 0f0185e18cfb937a2d3dc89c9116b0f17fc3304d Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 5 Feb 2023 13:34:33 -0800
Subject: [PATCH] add fast boundary helper and unit trait
---
CHANGELOG.md | 4 +++-
src/mol-math/geometry/boundary.ts | 10 +++++++---
src/mol-model/structure/structure/unit.ts | 13 +++++++++----
3 files changed, 19 insertions(+), 8 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index fa13409da..dd69f369d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,10 +11,12 @@ Note that since we don't clearly distinguish between a public and private interf
- The average position of the residues of the first chain should be in the first quadrant if there is more than one chain
- Add `HeadlessPluginContext` and `HeadlessScreenshotHelper` to be used in Node.js
- Add example `image-renderer`
-- Fix wrong offset when rendering text with orthographic projection
+- Fix wrong offset when rendering text with orthographic projectio
+n
- Update camera/handle helper when `devicePixelRatio` changes
- Add various options to customize the axes camera-helper
- Fix issue with texture-mesh color smoothing when changing themes
+- Add fast boundary helper and corresponding unit trait
## [v3.30.0] - 2023-01-29
diff --git a/src/mol-math/geometry/boundary.ts b/src/mol-math/geometry/boundary.ts
index 52e1cb198..888e5b36d 100644
--- a/src/mol-math/geometry/boundary.ts
+++ b/src/mol-math/geometry/boundary.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 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>
@@ -22,6 +22,11 @@ function getBoundaryHelper(count: number) {
return count > 10_000 ? boundaryHelperCoarse : boundaryHelperFine;
}
+export function getFastBoundary(data: PositionData): Boundary {
+ const box = Box3D.computeBounding(data);
+ return { box, sphere: Sphere3D.fromBox3D(Sphere3D(), box) };
+}
+
const p = Vec3();
export function getBoundary(data: PositionData): Boundary {
@@ -29,8 +34,7 @@ export function getBoundary(data: PositionData): Boundary {
const n = OrderedSet.size(indices);
if (n > 250_000) {
- const box = Box3D.computeBounding(data);
- return { box, sphere: Sphere3D.fromBox3D(Sphere3D(), box) };
+ return getFastBoundary(data);
}
const boundaryHelper = getBoundaryHelper(n);
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 6f6d1a814..65d407684 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -20,7 +20,7 @@ import { getAtomicPolymerElements, getCoarsePolymerElements, getAtomicGapElement
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
import { getPrincipalAxes } from './util/principal-axes';
-import { Boundary, getBoundary } from '../../../mol-math/geometry/boundary';
+import { Boundary, getBoundary, getFastBoundary } from '../../../mol-math/geometry/boundary';
import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-cache';
@@ -128,7 +128,8 @@ namespace Unit {
export enum Trait {
None = 0x0,
MultiChain = 0x1,
- Partitioned = 0x2
+ Partitioned = 0x2,
+ FastBoundary = 0x4,
}
export namespace Traits {
export const is: (t: Traits, f: Trait) => boolean = BitFlags.has;
@@ -255,7 +256,9 @@ namespace Unit {
get boundary() {
if (this.props.boundary) return this.props.boundary;
const { x, y, z } = this.model.atomicConformation;
- this.props.boundary = getBoundary({ x, y, z, indices: this.elements });
+ this.props.boundary = Traits.is(this.traits, Trait.FastBoundary)
+ ? getFastBoundary({ x, y, z, indices: this.elements })
+ : getBoundary({ x, y, z, indices: this.elements });
return this.props.boundary;
}
@@ -417,7 +420,9 @@ namespace Unit {
if (this.props.boundary) return this.props.boundary;
// TODO: support sphere radius?
const { x, y, z } = this.getCoarseConformation();
- this.props.boundary = getBoundary({ x, y, z, indices: this.elements });
+ this.props.boundary = Traits.is(this.traits, Trait.FastBoundary)
+ ? getFastBoundary({ x, y, z, indices: this.elements })
+ : getBoundary({ x, y, z, indices: this.elements });
return this.props.boundary;
}
--
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