From 27f10d52d05fa8b2e350a1e31f7db346e8fb67a8 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 1 Mar 2019 22:42:37 +0100
Subject: [PATCH] mol-plugin: StructureElement.Loci.getBoundary
---
src/mol-model/loci.ts | 20 +-----------
src/mol-model/structure/structure/element.ts | 32 +++++++++++++++++++
.../dynamic/volume-streaming/behavior.ts | 17 +++++-----
3 files changed, 41 insertions(+), 28 deletions(-)
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 34bb4d4e6..35cad50ed 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -81,25 +81,7 @@ namespace Loci {
if (loci.kind === 'structure-loci') {
return Sphere3D.copy(boundingSphere, loci.structure.boundary.sphere)
} else if (loci.kind === 'element-loci') {
- for (const e of loci.elements) {
- const { indices } = e;
- const pos = e.unit.conformation.position;
- const { elements } = e.unit;
- for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
- pos(elements[OrderedSet.getAt(indices, i)], tempPos);
- sphereHelper.includeStep(tempPos);
- }
- }
- sphereHelper.finishedIncludeStep();
- for (const e of loci.elements) {
- const { indices } = e;
- const pos = e.unit.conformation.position;
- const { elements } = e.unit;
- for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
- pos(elements[OrderedSet.getAt(indices, i)], tempPos);
- sphereHelper.radiusStep(tempPos);
- }
- }
+ return StructureElement.Loci.getBoundary(loci).sphere;
} else if (loci.kind === 'link-loci') {
for (const e of loci.links) {
e.aUnit.conformation.position(e.aUnit.elements[e.aIndex], tempPos);
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 4e5148225..1bd19cde9 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -9,6 +9,9 @@ import Unit from './unit'
import { ElementIndex } from '../model';
import { ResidueIndex, ChainIndex } from '../model/indexing';
import Structure from './structure';
+import { Boundary } from './util/boundary';
+import { BoundaryHelper } from 'mol-math/geometry/boundary-helper';
+import { Vec3 } from 'mol-math/linear-algebra';
interface StructureElement<U = Unit> {
readonly kind: 'element-location',
@@ -208,6 +211,35 @@ namespace StructureElement {
return Loci(loci.structure, elements);
}
+
+ const boundaryHelper = new BoundaryHelper(), tempPos = Vec3.zero();
+ export function getBoundary(loci: Loci): Boundary {
+ boundaryHelper.reset(0);
+
+ for (const e of loci.elements) {
+ const { indices } = e;
+ const pos = e.unit.conformation.position, r = e.unit.conformation.r;
+ const { elements } = e.unit;
+ for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+ const eI = elements[OrderedSet.getAt(indices, i)];
+ pos(eI, tempPos);
+ boundaryHelper.boundaryStep(tempPos, r(eI));
+ }
+ }
+ boundaryHelper.finishBoundaryStep();
+ for (const e of loci.elements) {
+ const { indices } = e;
+ const pos = e.unit.conformation.position, r = e.unit.conformation.r;
+ const { elements } = e.unit;
+ for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
+ const eI = elements[OrderedSet.getAt(indices, i)];
+ pos(eI, tempPos);
+ boundaryHelper.extendStep(tempPos, r(eI));
+ }
+ }
+
+ return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
+ }
}
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index d2ce4aa51..846b9d299 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -19,7 +19,6 @@ import { Box3D } from 'mol-math/geometry';
import { urlCombine } from 'mol-util/url';
import { volumeFromDensityServerData } from 'mol-model-formats/volume/density-server';
import { StructureElement } from 'mol-model/structure';
-import { Loci } from 'mol-model/loci';
import { CreateVolumeStreamingBehavior } from './transformers';
export class VolumeStreaming extends PluginStateObject.CreateBehavior<VolumeStreaming.Behavior>({ name: 'Volume Streaming' }) { }
@@ -150,18 +149,15 @@ export namespace VolumeStreaming {
this.subscribeObservable(this.plugin.events.canvas3d.click, ({ current }) => {
if (this.params.view.name !== 'selection-box') return;
+ // TODO: support link loci as well?
+ // Perhaps structure loci too?
if (!StructureElement.isLoci(current.loci)) return;
// TODO: check if it's the related structure
-
const loci = StructureElement.Loci.extendToWholeResidues(current.loci);
const eR = this.params.view.params.radius;
-
- const sphere = Loci.getBoundingSphere(loci)!;
- const r = Vec3.create(sphere.radius + eR, sphere.radius + eR, sphere.radius + eR);
- const box = Box3D.create(Vec3.sub(Vec3.zero(), sphere.center, r), Vec3.add(Vec3.zero(), sphere.center, r));
-
+ const box = StructureElement.Loci.getBoundary(loci).box;
const update = this.plugin.state.dataState.build().to(ref)
.update(CreateVolumeStreamingBehavior, old => ({
...old,
@@ -188,10 +184,13 @@ export namespace VolumeStreaming {
case 'box':
box = Box3D.create(params.view.params.bottomLeft, params.view.params.topRight);
break;
- case 'selection-box':
- box = Box3D.create(params.view.params.bottomLeft, params.view.params.topRight);
+ case 'selection-box': {
+ box = Box3D.create(Vec3.clone(params.view.params.bottomLeft), Vec3.clone(params.view.params.topRight));
+ const r = params.view.params.radius;
emptyData = Box3D.volume(box) < 0.0001;
+ Box3D.expand(box, box, Vec3.create(r, r, r));
break;
+ }
case 'cell':
box = this.info.kind === 'x-ray'
? this.info.structure.boundary.box
--
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