From 5c0fd3df3d394e081ff8dbf38c19381e80a793f5 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 13 Jul 2018 15:49:56 -0700
Subject: [PATCH] support for smoothing control points and direction vectors
---
.../structure/visual/polymer-trace-mesh.ts | 14 +++--
.../structure/visual/util/polymer.ts | 58 ++++++++++++++++---
src/mol-geo/shape/mesh-builder.ts | 13 +----
3 files changed, 63 insertions(+), 22 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index 45be0c382..048ab13b4 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -160,7 +160,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
// Vec3.fromArray(normalVec, normalVectors, j * 3)
// Vec3.fromArray(binormalVec, binormalVectors, j * 3)
// Vec3.fromArray(tangentVec, tangentVectors, j * 3)
- // builder.addIcosahedron(controlPoint, 0.1, 1)
+ // builder.addIcosahedron(controlPoint, 0.25, 1)
// builder.addCylinder(
// controlPoint,
// Vec3.add(tmp, controlPoint, normalVec),
@@ -181,18 +181,24 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
// )
// }
+ // builder.addIcosahedron(v.t0, 0.25, 1)
+ // builder.addIcosahedron(v.t1, 0.25, 1)
+ // builder.addIcosahedron(v.t2, 0.25, 1)
+ // builder.addIcosahedron(v.t3, 0.25, 1)
+ // builder.addIcosahedron(v.t4, 0.25, 1)
+
let width = 0.2
let height = 0.2
if (
SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta) ||
SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)
) {
- width = 0.2
- height = 0.6
+ width = 0.1
+ height = 0.8
}
// TODO size theme
- builder.addTube(controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, width, height)
+ builder.addTube(controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, width, height, 1)
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Polymer trace mesh', current: i, max: polymerElementCount });
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 9e369770c..ccf98a9fa 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -265,6 +265,19 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
private residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>
+ private p0 = Vec3.zero();
+ private p1 = Vec3.zero();
+ private p2 = Vec3.zero();
+ private p3 = Vec3.zero();
+ private p4 = Vec3.zero();
+ private p5 = Vec3.zero();
+ private p6 = Vec3.zero();
+
+ private v01 = Vec3.zero();
+ private v12 = Vec3.zero();
+ private v23 = Vec3.zero();
+ private v34 = Vec3.zero();
+
hasNext: boolean = false;
private pos(target: Vec3, index: number) {
@@ -294,6 +307,24 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
return elementIndex === -1 ? 0 as ElementIndex : elementIndex
}
+ setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: number) {
+ const ss = this.unit.model.properties.secondaryStructure.type[residueIndex]
+ if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
+ Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p3, Vec3.add(out, p2, p2))), 1/4)
+ } else {
+ Vec3.copy(out, p2)
+ }
+ }
+
+ setDirectionVector(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: number) {
+ const ss = this.unit.model.properties.secondaryStructure.type[residueIndex]
+ if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
+ Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p2, p3)), 1/3)
+ } else {
+ Vec3.copy(out, p2)
+ }
+ }
+
move() {
const { residueIt, polymerIt, value } = this
@@ -313,17 +344,30 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
const { index: residueIndex } = residueIt.move();
value.center.element = this.getElementIndex(residueIndex, 'trace')
- this.pos(value.t0, this.getAtomIndex(residueIndex - 2, 'trace'))
- this.pos(value.t1, this.getAtomIndex(residueIndex - 1, 'trace'))
- this.pos(value.t2, this.getAtomIndex(residueIndex, 'trace'))
- this.pos(value.t3, this.getAtomIndex(residueIndex + 1, 'trace'))
- this.pos(value.t4, this.getAtomIndex(residueIndex + 2, 'trace'))
+ this.pos(this.p0, this.getAtomIndex(residueIndex - 3, 'trace'))
+ this.pos(this.p1, this.getAtomIndex(residueIndex - 2, 'trace'))
+ this.pos(this.p2, this.getAtomIndex(residueIndex - 1, 'trace'))
+ this.pos(this.p3, this.getAtomIndex(residueIndex, 'trace'))
+ this.pos(this.p4, this.getAtomIndex(residueIndex + 1, 'trace'))
+ this.pos(this.p5, this.getAtomIndex(residueIndex + 2, 'trace'))
+ this.pos(this.p6, this.getAtomIndex(residueIndex + 3, 'trace'))
- this.pos(value.d12, this.getAtomIndex(residueIndex - 1, 'direction'))
- this.pos(value.d23, this.getAtomIndex(residueIndex, 'direction'))
+ this.pos(this.v01, this.getAtomIndex(residueIndex - 2, 'direction'))
+ this.pos(this.v12, this.getAtomIndex(residueIndex - 1, 'direction'))
+ this.pos(this.v23, this.getAtomIndex(residueIndex, 'direction'))
+ this.pos(this.v34, this.getAtomIndex(residueIndex + 1, 'direction'))
this.value.secStrucType = this.unit.model.properties.secondaryStructure.type[residueIndex]
+ this.setControlPoint(value.t0, this.p0, this.p1, this.p2, residueIndex - 2)
+ this.setControlPoint(value.t1, this.p1, this.p2, this.p3, residueIndex - 1)
+ this.setControlPoint(value.t2, this.p2, this.p3, this.p4, residueIndex)
+ this.setControlPoint(value.t3, this.p3, this.p4, this.p5, residueIndex + 1)
+ this.setControlPoint(value.t4, this.p4, this.p5, this.p6, residueIndex + 2)
+
+ this.setDirectionVector(value.d12, this.v01, this.v12, this.v23, residueIndex)
+ this.setDirectionVector(value.d23, this.v12, this.v23, this.v34, residueIndex + 1)
+
value.first = residueIndex === this.polymerSegment.start
value.last = residueIndex === this.polymerSegment.end - 1
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index 94d8a3cd6..8b5ff31e0 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -27,7 +27,7 @@ export interface MeshBuilder {
addDoubleCylinder(start: Vec3, end: Vec3, lengthScale: number, shift: Vec3, props: CylinderProps): void
addFixedCountDashedCylinder(start: Vec3, end: Vec3, lengthScale: number, segmentCount: number, props: CylinderProps): void
addIcosahedron(center: Vec3, radius: number, detail: number): void
- addTube(controlPoints: Helpers.NumberArray, torsionVectors: Helpers.NumberArray, normalVectors: Helpers.NumberArray, linearSegments: number, radialSegments: number, width: number, height: number): void
+ addTube(controlPoints: Helpers.NumberArray, torsionVectors: Helpers.NumberArray, normalVectors: Helpers.NumberArray, linearSegments: number, radialSegments: number, width: number, height: number, waveFactor: number): void
setId(id: number): void
getMesh(): Mesh
}
@@ -176,11 +176,7 @@ export namespace MeshBuilder {
setIcosahedronMat(tmpIcosahedronMat, center)
add(tmpIcosahedronMat, vertices, normals, indices)
},
- addTube: (controlPoints: Helpers.NumberArray, normalVectors: Helpers.NumberArray, binormalVectors: Helpers.NumberArray, linearSegments: number, radialSegments: number, width: number, height: number) => {
- // console.log(controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments)
-
- // const ico = getIcosahedron({ radius: 0.1, detail: 1 })
-
+ addTube: (controlPoints: Helpers.NumberArray, normalVectors: Helpers.NumberArray, binormalVectors: Helpers.NumberArray, linearSegments: number, radialSegments: number, width: number, height: number, waveFactor: number) => {
const normalVector = Vec3.zero()
const binormalVector = Vec3.zero()
const tempPos = Vec3.zero()
@@ -189,8 +185,6 @@ export namespace MeshBuilder {
const u = Vec3.zero()
const v = Vec3.zero()
- const waveFactor = 1
-
const vertexCount = vertices.elementCount
const di = 1 / linearSegments
@@ -229,9 +223,6 @@ export namespace MeshBuilder {
ChunkedArray.add3(vertices, tempPos[0], tempPos[1], tempPos[2]);
ChunkedArray.add3(normals, normalVector[0], normalVector[1], normalVector[2]);
ChunkedArray.add(ids, currentId);
-
- // setIcosahedronMat(tmpIcosahedronMat, tempPos)
- // add(tmpIcosahedronMat, ico.vertices, ico.normals, ico.indices)
}
}
--
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