From 3d9c485cf1b23d1836e20903a3b0b58c500012f3 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Tue, 26 Feb 2019 22:52:10 -0800
Subject: [PATCH] improved coarse backbone trace, e.g. 1jgq
---
.../structure/visual/polymer-trace-mesh.ts | 2 +-
.../visual/util/polymer/trace-iterator.ts | 18 ++++++++++++++++--
2 files changed, 17 insertions(+), 3 deletions(-)
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 11ef2c8a6..c30503dc1 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -89,7 +89,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
h2 = w2
}
interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift)
- addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, v.secStrucFirst, v.secStrucLast)
+ addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, v.secStrucFirst || v.coarseBackboneFirst, v.secStrucLast || v.coarseBackboneLast)
}
++i
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 9099462cd..6216c5307 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -36,6 +36,7 @@ interface PolymerTraceElement {
secStrucType: SecondaryStructureType
moleculeType: MoleculeType
isCoarseBackbone: boolean
+ coarseBackboneFirst: boolean, coarseBackboneLast: boolean
p0: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, p4: Vec3
d12: Vec3, d23: Vec3
@@ -52,6 +53,7 @@ function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
secStrucFirst: false, secStrucLast: false,
secStrucType: SecStrucTypeNA,
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),
@@ -72,6 +74,9 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
private prevSecStrucType: SecondaryStructureType
private currSecStrucType: SecondaryStructureType
private nextSecStrucType: SecondaryStructureType
+ private prevCoarseBackbone: boolean
+ private currCoarseBackbone: boolean
+ private nextCoarseBackbone: boolean
private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
private residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>
private traceElementIndex: ArrayLike<ElementIndex>
@@ -148,6 +153,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.state = AtomicPolymerTraceIteratorState.nextResidue
this.currSecStrucType = SecStrucTypeNA
this.nextSecStrucType = this.secondaryStructureType[this.residueSegmentMin]
+ this.currCoarseBackbone = false
+ this.nextCoarseBackbone = this.directionElementIndex[this.residueSegmentMin] === -1
break
}
}
@@ -159,11 +166,18 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.currSecStrucType = this.nextSecStrucType
this.nextSecStrucType = residueIt.hasNext ? this.secondaryStructureType[residueIndex + 1] : SecStrucTypeNA
+ this.prevCoarseBackbone = this.currCoarseBackbone
+ this.currCoarseBackbone = this.nextCoarseBackbone
+ this.nextCoarseBackbone = residueIt.hasNext ? this.directionElementIndex[residueIndex + 1] === -1 : false
+
value.secStrucType = this.currSecStrucType
- value.first = residueIndex === this.residueSegmentMin
- value.last = residueIndex === this.residueSegmentMax
value.secStrucFirst = this.prevSecStrucType !== this.currSecStrucType
value.secStrucLast = this.currSecStrucType !== this.nextSecStrucType
+ value.isCoarseBackbone = this.currCoarseBackbone
+ value.coarseBackboneFirst = this.prevCoarseBackbone !== this.currCoarseBackbone
+ value.coarseBackboneLast = this.currCoarseBackbone !== this.nextCoarseBackbone
+ value.first = residueIndex === this.residueSegmentMin
+ value.last = residueIndex === this.residueSegmentMax
value.moleculeType = this.moleculeType[residueIndex]
const residueIndexPrev3 = this.getResidueIndex(residueIndex - 3)
--
GitLab