From da738d87e6797080647bf5bc047a9410dcd30d0f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 29 Aug 2018 11:13:46 -0700
Subject: [PATCH] better handling of missing atoms in trace, block, backbone
visuals
---
.../structure/visual/nucleotide-block-mesh.ts | 23 ++++++++------
.../visual/util/polymer/backbone-iterator.ts | 13 ++++++--
.../visual/util/polymer/trace-iterator.ts | 31 ++++++++++---------
src/mol-model/structure/util.ts | 4 +--
4 files changed, 41 insertions(+), 30 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index 0ace3c526..03a2eeb94 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -82,18 +82,21 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props:
idx6 = getElementIndexForAtomRole(model, residueIndex, 'trace')
}
- if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1 && idx5 !== -1 && idx6 !== -1) {
- pos(idx1, p1); pos(idx2, p2); pos(idx3, p3); pos(idx4, p4); pos(idx5, p5); pos(idx6, p6)
- Vec3.normalize(v12, Vec3.sub(v12, p2, p1))
- Vec3.normalize(v34, Vec3.sub(v34, p4, p3))
- Vec3.normalize(vC, Vec3.cross(vC, v12, v34))
- Mat4.targetTo(t, p1, p2, vC)
- Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2)
- Mat4.scale(t, t, Vec3.set(sVec, width, depth, height))
- Mat4.setTranslation(t, center)
+ if (idx5 !== -1 && idx6 !== -1) {
+ pos(idx5, p5); pos(idx6, p6)
builder.setGroup(SortedArray.findPredecessorIndex(elements, idx6))
- builder.add(t, box)
addCylinder(builder, p5, p6, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
+ if (idx1 !== -1 && idx2 !== -1 && idx3 !== -1 && idx4 !== -1) {
+ pos(idx1, p1); pos(idx2, p2); pos(idx3, p3); pos(idx4, p4);
+ Vec3.normalize(v12, Vec3.sub(v12, p2, p1))
+ Vec3.normalize(v34, Vec3.sub(v34, p4, p3))
+ Vec3.normalize(vC, Vec3.cross(vC, v12, v34))
+ Mat4.targetTo(t, p1, p2, vC)
+ Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2)
+ Mat4.scale(t, t, Vec3.set(sVec, width, depth, height))
+ Mat4.setTranslation(t, center)
+ builder.add(t, box)
+ }
}
}
diff --git a/src/mol-geo/representation/structure/visual/util/polymer/backbone-iterator.ts b/src/mol-geo/representation/structure/visual/util/polymer/backbone-iterator.ts
index eaa3c029c..31170313f 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer/backbone-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer/backbone-iterator.ts
@@ -10,6 +10,7 @@ import Iterator from 'mol-data/iterator';
import SortedRanges from 'mol-data/int/sorted-ranges';
import { getElementIndexForAtomRole } from 'mol-model/structure/util';
import { getPolymerRanges } from '../polymer';
+import { AtomRole } from 'mol-model/structure/model/types';
/** Iterates over consecutive pairs of residues/coarse elements in polymers */
export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
@@ -43,13 +44,19 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
private residueSegment: Segmentation.Segment<ResidueIndex>
hasNext: boolean = false;
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const { atomicHierarchy } = this.unit.model
+ const elementIndex = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
+ return elementIndex === -1 ? atomicHierarchy.residueAtomSegments.offsets[residueIndex] : elementIndex
+ }
+
move() {
if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
while (this.polymerIt.hasNext) {
this.residueIt.setSegment(this.polymerIt.move());
if (this.residueIt.hasNext) {
this.residueSegment = this.residueIt.move()
- this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, this.residueSegment.index, 'trace')
+ this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
this.state = AtomicPolymerBackboneIteratorState.nextResidue
break
}
@@ -59,7 +66,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
this.residueSegment = this.residueIt.move()
this.value.centerA.element = this.value.centerB.element
- this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, this.residueSegment.index, 'trace')
+ this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
if (!this.residueIt.hasNext) {
if (this.unit.model.atomicHierarchy.cyclicPolymerMap.has(this.residueSegment.index)) {
this.state = AtomicPolymerBackboneIteratorState.cycle
@@ -71,7 +78,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
} else if (this.state === AtomicPolymerBackboneIteratorState.cycle) {
const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
this.value.centerA.element = this.value.centerB.element
- this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, cyclicPolymerMap.get(this.residueSegment.index)!, 'trace')
+ this.value.centerB.element = this.getElementIndex(cyclicPolymerMap.get(this.residueSegment.index)!, 'trace')
// TODO need to advance to a polymer that has two or more residues (can't assume it has)
this.state = AtomicPolymerBackboneIteratorState.nextPolymer
}
diff --git a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
index df4cfabc5..e4b98c009 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
@@ -89,24 +89,25 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.residueSegmentMax = index[this.unit.elements[polymerSegment.end - 1]]
}
- private getAtomIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
- const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
+ private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
+ const { atomicHierarchy } = this.unit.model
if (residueIndex < this.residueSegmentMin) {
- const cyclicIndex = cyclicPolymerMap.get(this.residueSegmentMin)
+ const cyclicIndex = atomicHierarchy.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 = cyclicPolymerMap.get(this.residueSegmentMax)
+ const cyclicIndex = atomicHierarchy.cyclicPolymerMap.get(this.residueSegmentMax)
if (cyclicIndex !== undefined) {
residueIndex = cyclicIndex + (residueIndex - this.residueSegmentMax - 1) as ResidueIndex
} else {
residueIndex = this.residueSegmentMax
}
}
- return getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
+ const elementIndex = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
+ return elementIndex === -1 ? atomicHierarchy.residueAtomSegments.offsets[residueIndex] : elementIndex
}
private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
@@ -135,19 +136,19 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (this.state === AtomicPolymerTraceIteratorState.nextResidue) {
const { index: residueIndex } = residueIt.move();
- value.center.element = this.getAtomIndex(residueIndex, 'trace')
+ value.center.element = this.getElementIndex(residueIndex, 'trace')
- this.pos(this.p0, this.getAtomIndex(residueIndex - 3 as ResidueIndex, 'trace'))
- this.pos(this.p1, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'trace'))
- this.pos(this.p2, this.getAtomIndex(residueIndex - 1 as ResidueIndex, 'trace'))
- this.pos(this.p3, this.getAtomIndex(residueIndex, 'trace'))
- this.pos(this.p4, this.getAtomIndex(residueIndex + 1 as ResidueIndex, 'trace'))
- this.pos(this.p5, this.getAtomIndex(residueIndex + 2 as ResidueIndex, 'trace'))
- this.pos(this.p6, this.getAtomIndex(residueIndex + 3 as ResidueIndex, 'trace'))
+ 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'))
// this.pos(this.v01, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'direction'))
- this.pos(this.v12, this.getAtomIndex(residueIndex - 1 as ResidueIndex, 'direction'))
- this.pos(this.v23, this.getAtomIndex(residueIndex, 'direction'))
+ this.pos(this.v12, this.getElementIndex(residueIndex - 1 as ResidueIndex, 'direction'))
+ this.pos(this.v23, this.getElementIndex(residueIndex, 'direction'))
// this.pos(this.v34, this.getAtomIndex(residueIndex + 1 as ResidueIndex, 'direction'))
this.value.secStrucType = this.unit.model.properties.secondaryStructure.type[residueIndex]
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index a20abb42e..ba416db93 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -26,13 +26,13 @@ export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomR
return ''
}
-export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId: string): ElementIndex {
+export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId: string): ElementIndex | -1 {
const { offsets } = model.atomicHierarchy.residueAtomSegments
const { label_atom_id } = model.atomicHierarchy.atoms
for (let j = offsets[rI], _j = offsets[rI + 1]; j < _j; j++) {
if (label_atom_id.value(j) === atomId) return j as ElementIndex
}
- return offsets[rI] as ElementIndex
+ return -1
}
export function getElementIndexForAtomRole(model: Model, rI: ResidueIndex, atomRole: AtomRole) {
--
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