From 48d3c6151f99e41e82d407d39f5576ca53deef68 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 24 Nov 2018 19:03:08 -0800
Subject: [PATCH] wip, trace iterator opt
---
.../visual/util/polymer/trace-iterator.ts | 44 ++++++++++++-------
1 file changed, 29 insertions(+), 15 deletions(-)
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 d29292d89..d64b49076 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -60,6 +60,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private polymerIt: SortedRanges.Iterator<ElementIndex, ResidueIndex>
private residueIt: Segmentation.SegmentIterator<ResidueIndex>
private polymerSegment: Segmentation.Segment<ResidueIndex>
+ private cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
private secondaryStructureType: ArrayLike<SecondaryStructureType>
private residueSegmentMin: ResidueIndex
private residueSegmentMax: ResidueIndex
@@ -97,25 +98,28 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.residueSegmentMax = index[this.unit.elements[polymerSegment.end - 1]]
}
- private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
- const { atomicHierarchy } = this.unit.model
+ private getResidueIndex(residueIndex: ResidueIndex) {
if (residueIndex < this.residueSegmentMin) {
- const cyclicIndex = atomicHierarchy.cyclicPolymerMap.get(this.residueSegmentMin)
+ const cyclicIndex = this.cyclicPolymerMap.get(this.residueSegmentMin)
if (cyclicIndex !== undefined) {
residueIndex = cyclicIndex - (this.residueSegmentMin - residueIndex - 1) as ResidueIndex
} else {
residueIndex = this.residueSegmentMin
}
} else if (residueIndex > this.residueSegmentMax) {
- const cyclicIndex = atomicHierarchy.cyclicPolymerMap.get(this.residueSegmentMax)
+ const cyclicIndex = this.cyclicPolymerMap.get(this.residueSegmentMax)
if (cyclicIndex !== undefined) {
residueIndex = cyclicIndex + (residueIndex - this.residueSegmentMax - 1) as ResidueIndex
} else {
residueIndex = this.residueSegmentMax
}
}
+ return residueIndex
+ }
+
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
const elementIndex = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
- return elementIndex === -1 ? atomicHierarchy.residueAtomSegments.offsets[residueIndex] : elementIndex
+ return elementIndex === -1 ? this.residueAtomSegments.offsets[residueIndex] : elementIndex
}
private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
@@ -158,18 +162,27 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
value.secStrucLast = this.currSecStrucType !== this.nextSecStrucType
value.moleculeType = getAtomicMoleculeType(this.unit.model, residueIndex)
- this.pos(this.p0, this.getElementIndex(residueIndex - 3 as ResidueIndex, 'trace'))
- this.pos(this.p1, this.getElementIndex(residueIndex - 2 as ResidueIndex, 'trace'))
- this.pos(this.p2, this.getElementIndex(residueIndex - 1 as ResidueIndex, 'trace'))
- this.pos(this.p3, this.getElementIndex(residueIndex, 'trace'))
- this.pos(this.p4, this.getElementIndex(residueIndex + 1 as ResidueIndex, 'trace'))
- this.pos(this.p5, this.getElementIndex(residueIndex + 2 as ResidueIndex, 'trace'))
- this.pos(this.p6, this.getElementIndex(residueIndex + 3 as ResidueIndex, 'trace'))
+ if (value.first) {
+ this.pos(this.p0, this.getElementIndex(this.getResidueIndex(residueIndex - 3 as ResidueIndex), 'trace'))
+ this.pos(this.p1, this.getElementIndex(this.getResidueIndex(residueIndex - 2 as ResidueIndex), 'trace'))
+ this.pos(this.p2, this.getElementIndex(this.getResidueIndex(residueIndex - 1 as ResidueIndex), 'trace'))
+ this.pos(this.p3, value.center.element)
+ this.pos(this.p4, this.getElementIndex(this.getResidueIndex(residueIndex + 1 as ResidueIndex), 'trace'))
+ this.pos(this.p5, this.getElementIndex(this.getResidueIndex(residueIndex + 2 as ResidueIndex), 'trace'))
- // this.pos(this.v01, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'direction'))
- this.pos(this.v12, this.getElementIndex(residueIndex - 1 as ResidueIndex, 'direction'))
+ this.pos(this.v12, this.getElementIndex(residueIndex - 1 as ResidueIndex, 'direction'))
+ } else {
+ Vec3.copy(this.p0, this.p1)
+ Vec3.copy(this.p1, this.p2)
+ Vec3.copy(this.p2, this.p3)
+ Vec3.copy(this.p3, this.p4)
+ Vec3.copy(this.p4, this.p5)
+ Vec3.copy(this.p5, this.p6)
+
+ Vec3.copy(this.v12, this.v23)
+ }
+ this.pos(this.p6, this.getElementIndex(this.getResidueIndex(residueIndex + 3 as ResidueIndex), 'trace'))
this.pos(this.v23, this.getElementIndex(residueIndex, 'direction'))
- // this.pos(this.v34, this.getAtomIndex(residueIndex + 1 as ResidueIndex, 'direction'))
this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndex - 2 as ResidueIndex)
this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndex - 1 as ResidueIndex)
@@ -193,6 +206,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
constructor(private unit: Unit.Atomic) {
this.atomicConformation = unit.model.atomicConformation
this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
+ this.cyclicPolymerMap = unit.model.atomicHierarchy.cyclicPolymerMap
this.secondaryStructureType = unit.model.properties.secondaryStructure.type
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
--
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