From 2013ed921fe08c3221ae1169c89f660a9a22d05e Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 1 Mar 2019 22:18:55 +0100
Subject: [PATCH] mol-plugin: StructureElement.Loci.extendToWholeResidues
---
src/mol-math/linear-algebra/3d/vec3.ts | 5 ++-
src/mol-model/structure/structure/element.ts | 32 +++++++++++++++++++
.../dynamic/volume-streaming/behavior.ts | 4 ++-
3 files changed, 37 insertions(+), 4 deletions(-)
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index c0437fd57..3e8fd5d5e 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -452,14 +452,13 @@ namespace Vec3 {
}
const rotTemp = zero();
- const flipMatrix = Mat4.fromScaling(Mat4.zero(), create(-1, -1, -1))
+ const flipScaling = create(-1, -1, -1);
export function makeRotation(mat: Mat4, a: Vec3, b: Vec3): Mat4 {
const by = angle(a, b);
if (Math.abs(by) < 0.0001) return Mat4.setIdentity(mat);
if (Math.abs(by - Math.PI) < EPSILON.Value) {
// here, axis can be [0,0,0] but the rotation is a simple flip
- Mat4.copy(mat, flipMatrix);
- return mat;
+ return Mat4.fromScaling(mat, flipScaling);
}
const axis = cross(rotTemp, a, b);
return Mat4.fromRotation(mat, by, axis);
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 8b39d2215..4e5148225 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -176,6 +176,38 @@ namespace StructureElement {
return false;
}
+
+ export function extendToWholeResidues(loci: Loci): Loci {
+ const elements: Loci['elements'][0][] = [];
+
+ for (const lociElement of loci.elements) {
+ if (lociElement.unit.kind !== Unit.Kind.Atomic) elements[elements.length] = lociElement;
+
+ const unitElements = lociElement.unit.elements;
+ const h = lociElement.unit.model.atomicHierarchy;
+
+ const { index: residueIndex, offsets: residueOffsets } = h.residueAtomSegments;
+
+ const newIndices: UnitIndex[] = [];
+ const indices = lociElement.indices, len = OrderedSet.size(indices);
+ let i = 0;
+ while (i < len) {
+ const rI = residueIndex[unitElements[OrderedSet.getAt(indices, i)]];
+ while (i < len && residueIndex[unitElements[OrderedSet.getAt(indices, i)]] === rI) {
+ i++;
+ }
+
+ for (let j = residueOffsets[rI], _j = residueOffsets[rI + 1]; j < _j; j++) {
+ const idx = OrderedSet.indexOf(unitElements, j);
+ if (idx >= 0) newIndices[newIndices.length] = idx as UnitIndex;
+ }
+ }
+
+ elements[elements.length] = { unit: lociElement.unit, indices: SortedArray.ofSortedArray(newIndices) };
+ }
+
+ return Loci(loci.structure, elements);
+ }
}
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
index 7990e753d..d2ce4aa51 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/behavior.ts
@@ -154,9 +154,11 @@ export namespace VolumeStreaming {
// 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(current.loci)!;
+ 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));
--
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