From 9b3d2f396efc658b84d50b8aab948cbb51812f4c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Wed, 12 Jun 2019 23:14:05 -0700
Subject: [PATCH] polymer-trace improvements
---
.../structure/visual/polymer-trace-mesh.ts | 2 +-
.../visual/util/polymer/curve-segment.ts | 50 ++++++-------
.../visual/util/polymer/trace-iterator.ts | 71 ++++++++++++-------
3 files changed, 74 insertions(+), 49 deletions(-)
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 16793765b..4c94290bb 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -52,7 +52,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const isNucleicType = isNucleic(v.moleculeType)
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)
- const tension = isNucleicType ? 0.5 : 0.9
+ const tension = isHelix ? 0.9 : 0.5
const shift = isNucleicType ? 0.3 : 0.5
interpolateCurveSegment(state, v, tension, shift)
diff --git a/src/mol-repr/structure/visual/util/polymer/curve-segment.ts b/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
index b096422dc..ebb7aaf3d 100644
--- a/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
+++ b/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -19,6 +19,7 @@ export interface CurveSegmentState {
}
export interface CurveSegmentControls {
+ secStrucFirst: boolean, secStrucLast: boolean
p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, p4: Vec3,
d12: Vec3, d23: Vec3
}
@@ -48,20 +49,25 @@ const curvePoint = Vec3.zero()
export function interpolatePointsAndTangents(state: CurveSegmentState, controls: CurveSegmentControls, tension: number, shift: number) {
const { curvePoints, tangentVectors, linearSegments } = state
- const { p0, p1, p2, p3, p4 } = controls
+ const { p0, p1, p2, p3, p4, secStrucFirst, secStrucLast } = controls
const shift1 = 1 - shift
+ const tensionBeg = secStrucFirst ? 0.5 : tension
+ const tensionEnd = secStrucLast ? 0.5 : tension
+
for (let j = 0; j <= linearSegments; ++j) {
const t = j * 1.0 / linearSegments;
if (t < shift1) {
- Vec3.spline(curvePoint, p0, p1, p2, p3, t + shift, tension)
- Vec3.spline(tanA, p0, p1, p2, p3, t + shift + 0.01, tension)
- Vec3.spline(tanB, p0, p1, p2, p3, t + shift - 0.01, tension)
+ const te = lerp(tensionBeg, tension, t)
+ Vec3.spline(curvePoint, p0, p1, p2, p3, t + shift, te)
+ Vec3.spline(tanA, p0, p1, p2, p3, t + shift + 0.01, tensionBeg)
+ Vec3.spline(tanB, p0, p1, p2, p3, t + shift - 0.01, tensionBeg)
} else {
- Vec3.spline(curvePoint, p1, p2, p3, p4, t - shift1, tension)
- Vec3.spline(tanA, p1, p2, p3, p4, t - shift1 + 0.01, tension)
- Vec3.spline(tanB, p1, p2, p3, p4, t - shift1 - 0.01, tension)
+ const te = lerp(tension, tensionEnd, t)
+ Vec3.spline(curvePoint, p1, p2, p3, p4, t - shift1, te)
+ Vec3.spline(tanA, p1, p2, p3, p4, t - shift1 + 0.01, te)
+ Vec3.spline(tanB, p1, p2, p3, p4, t - shift1 - 0.01, te)
}
Vec3.toArray(curvePoint, curvePoints, j * 3)
Vec3.normalize(tangentVec, Vec3.sub(tangentVec, tanA, tanB))
@@ -69,17 +75,15 @@ export function interpolatePointsAndTangents(state: CurveSegmentState, controls:
}
}
-const tmpNormal = Vec3.zero()
-const tangentVec = Vec3.zero()
-const normalVec = Vec3.zero()
-const binormalVec = Vec3.zero()
-const prevNormal = Vec3.zero()
-const firstControlPoint = Vec3.zero()
-const lastControlPoint = Vec3.zero()
-const firstTangentVec = Vec3.zero()
-const lastTangentVec = Vec3.zero()
-const firstNormalVec = Vec3.zero()
-const lastNormalVec = Vec3.zero()
+const tmpNormal = Vec3()
+const tangentVec = Vec3()
+const normalVec = Vec3()
+const binormalVec = Vec3()
+const prevNormal = Vec3()
+const firstTangentVec = Vec3()
+const lastTangentVec = Vec3()
+const firstNormalVec = Vec3()
+const lastNormalVec = Vec3()
/**
* Populate normalVectors by interpolating from firstDirection to lastDirection with
@@ -91,13 +95,11 @@ export function interpolateNormals(state: CurveSegmentState, controls: CurveSegm
const n = curvePoints.length / 3
- Vec3.fromArray(firstControlPoint, curvePoints, 0)
- Vec3.fromArray(lastControlPoint, curvePoints, (n - 1) * 3)
Vec3.fromArray(firstTangentVec, tangentVectors, 0)
- Vec3.fromArray(lastTangentVec, tangentVectors, (n - 1) * 3)
+ Vec3.fromArray(lastTangentVec, tangentVectors, (n - 1) * 3)
- Vec3.orthogonalize(firstNormalVec, firstTangentVec, Vec3.sub(tmpNormal, firstControlPoint, firstDirection))
- Vec3.orthogonalize(lastNormalVec, lastTangentVec, Vec3.sub(tmpNormal, lastControlPoint, lastDirection))
+ Vec3.orthogonalize(firstNormalVec, firstTangentVec, firstDirection)
+ Vec3.orthogonalize(lastNormalVec, lastTangentVec, lastDirection)
if (Vec3.dot(firstNormalVec, lastNormalVec) < 0) {
Vec3.scale(lastNormalVec, lastNormalVec, -1)
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index c73107161..c510f7c3b 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -57,13 +57,16 @@ function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
moleculeType: MoleculeType.unknown,
coarseBackboneFirst: false, coarseBackboneLast: false,
isCoarseBackbone: false,
- p0: Vec3.zero(), p1: Vec3.zero(), p2: Vec3.zero(), p3: Vec3.zero(), p4: Vec3.zero(),
- d12: Vec3.create(1, 0, 0), d23: Vec3.create(1, 0, 0),
+ p0: Vec3(), p1: Vec3(), p2: Vec3(), p3: Vec3(), p4: Vec3(),
+ d12: Vec3(), d23: Vec3()
}
}
const enum AtomicPolymerTraceIteratorState { nextPolymer, nextResidue }
+const tmpVecA = Vec3()
+const tmpVecB = Vec3()
+
export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement> {
private value: PolymerTraceElement
private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
@@ -83,22 +86,23 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
private residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>
private traceElementIndex: ArrayLike<ElementIndex>
- private directionElementIndex: ArrayLike<ElementIndex | -1>
+ private directionFromElementIndex: ArrayLike<ElementIndex | -1>
+ private directionToElementIndex: ArrayLike<ElementIndex | -1>
private moleculeType: ArrayLike<MoleculeType>
private atomicConformation: AtomicConformation
- 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 p0 = Vec3()
+ private p1 = Vec3()
+ private p2 = Vec3()
+ private p3 = Vec3()
+ private p4 = Vec3()
+ private p5 = Vec3()
+ private p6 = Vec3()
- // private v01 = Vec3.zero();
- private v12 = Vec3.create(1, 0, 0);
- private v23 = Vec3.create(1, 0, 0);
- // private v34 = Vec3.zero();
+ private d01 = Vec3()
+ private d12 = Vec3()
+ private d23 = Vec3()
+ private d34 = Vec3()
hasNext: boolean = false;
@@ -148,6 +152,20 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
}
}
+ private setFromToVector(out: Vec3, residueIndex: ResidueIndex) {
+ this.pos(tmpVecA, this.directionFromElementIndex[residueIndex])
+ this.pos(tmpVecB, this.directionToElementIndex[residueIndex])
+ Vec3.sub(out, tmpVecB, tmpVecA)
+ }
+
+ private setDirection(out: Vec3, v1: Vec3, v2: Vec3, v3: Vec3) {
+ Vec3.copy(tmpVecA, v1)
+ Vec3.copy(tmpVecB, v3)
+ if (Vec3.dot(v2, tmpVecA) < 0) Vec3.scale(tmpVecA, tmpVecA, -1)
+ if (Vec3.dot(v2, tmpVecB) < 0) Vec3.scale(tmpVecB, tmpVecB, -1)
+ Vec3.scale(out, Vec3.add(out, tmpVecA, Vec3.add(out, tmpVecB, Vec3.add(out, v2, v2))), 1/4)
+ }
+
move() {
const { residueIt, polymerIt, value } = this
@@ -161,7 +179,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.currSecStrucType = SecStrucTypeNA
this.nextSecStrucType = this.getSecStruc(this.residueSegmentMin)
this.currCoarseBackbone = false
- this.nextCoarseBackbone = this.directionElementIndex[this.residueSegmentMin] === -1
+ this.nextCoarseBackbone = this.directionFromElementIndex[this.residueSegmentMin] === -1 || this.directionToElementIndex[this.residueSegmentMin] === -1
break
}
}
@@ -175,7 +193,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.prevCoarseBackbone = this.currCoarseBackbone
this.currCoarseBackbone = this.nextCoarseBackbone
- this.nextCoarseBackbone = residueIt.hasNext ? this.directionElementIndex[residueIndex + 1] === -1 : false
+ this.nextCoarseBackbone = residueIt.hasNext ? (this.directionFromElementIndex[residueIndex + 1] === -1 || this.directionToElementIndex[residueIndex + 1] === -1) : false
value.secStrucType = this.currSecStrucType
value.secStrucFirst = this.prevSecStrucType !== this.currSecStrucType
@@ -205,7 +223,9 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.pos(this.p4, this.traceElementIndex[residueIndexNext1])
this.pos(this.p5, this.traceElementIndex[residueIndexNext2])
- this.pos(this.v12, this.directionElementIndex[residueIndexPrev1])
+ this.setFromToVector(this.d01, residueIndexPrev1)
+ this.setFromToVector(this.d12, residueIndex)
+ this.setFromToVector(this.d23, residueIndexNext1)
} else {
value.centerPrev.element = value.center.element
value.center.element = value.centerNext.element
@@ -217,12 +237,14 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
Vec3.copy(this.p4, this.p5)
Vec3.copy(this.p5, this.p6)
- Vec3.copy(this.v12, this.v23)
+ Vec3.copy(this.d01, this.d12)
+ Vec3.copy(this.d12, this.d23)
+ Vec3.copy(this.d23, this.d34)
}
value.centerNext.element = this.traceElementIndex[residueIndexNext1]
- this.pos(this.p6, this.traceElementIndex[residueIndexNext3])
- this.pos(this.v23, this.directionElementIndex[residueIndex])
- value.isCoarseBackbone = this.directionElementIndex[residueIndex] === -1
+ this.pos(this.p6, this.traceElementIndex[residueIndexNext3])
+ this.setFromToVector(this.d34, residueIndexNext2)
+ value.isCoarseBackbone = this.directionFromElementIndex[residueIndex] === -1 || this.directionToElementIndex[residueIndex] === -1
this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndexPrev2)
this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndexPrev1)
@@ -230,8 +252,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.setControlPoint(value.p3, this.p3, this.p4, this.p5, residueIndexNext1)
this.setControlPoint(value.p4, this.p4, this.p5, this.p6, residueIndexNext2)
- Vec3.copy(value.d12, this.v12)
- Vec3.copy(value.d23, this.v23)
+ this.setDirection(value.d12, this.d01, this.d12, this.d23)
+ this.setDirection(value.d23, this.d12, this.d23, this.d34)
if (!residueIt.hasNext) {
this.state = AtomicPolymerTraceIteratorState.nextPolymer
@@ -247,7 +269,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.atomicConformation = unit.model.atomicConformation
this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex as ArrayLike<ElementIndex> // can assume it won't be -1 for polymer residues
- this.directionElementIndex = unit.model.atomicHierarchy.derived.residue.directionElementIndex
+ this.directionFromElementIndex = unit.model.atomicHierarchy.derived.residue.directionFromElementIndex
+ this.directionToElementIndex = unit.model.atomicHierarchy.derived.residue.directionToElementIndex
this.moleculeType = unit.model.atomicHierarchy.derived.residue.moleculeType
this.cyclicPolymerMap = unit.model.atomicHierarchy.cyclicPolymerMap
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
--
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