From 456ee97b5fda3913f9ee4f9e95932616ecfcc7df Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 12 Jul 2018 19:25:49 -0700
Subject: [PATCH] polymer iterator cleanup
---
.../visual/polymer-backbone-cylinder.ts | 18 +-
.../structure/visual/polymer-trace-mesh.ts | 6 +-
.../structure/visual/util/polymer.ts | 297 ++++++------------
3 files changed, 106 insertions(+), 215 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
index 21debef67..949d4d9f4 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -23,6 +23,7 @@ import { createMeshValues, updateMeshValues, updateRenderableState, createRender
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
import { getElementLoci, markElement } from './util/element';
+import { Vec3 } from 'mol-math/linear-algebra';
async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
@@ -32,15 +33,22 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
// TODO better vertex count estimates
const builder = MeshBuilder.create(polymerElementCount * 30, polymerElementCount * 30 / 2, mesh)
+ const { elements } = unit
+ const pos = unit.conformation.invariantPosition
+ const pA = Vec3.zero()
+ const pB = Vec3.zero()
+
let i = 0
const polymerBackboneIt = PolymerBackboneIterator(unit)
while (polymerBackboneIt.hasNext) {
- const { indexA, indexB, posA, posB } = polymerBackboneIt.move()
- builder.setId(indexA)
// TODO size theme
- builder.addCylinder(posA, posB, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
- builder.setId(indexB)
- builder.addCylinder(posB, posA, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
+ const { centerA, centerB } = polymerBackboneIt.move()
+ pos(centerA.element, pA)
+ pos(centerB.element, pB)
+ builder.setId(elements[centerA.element])
+ builder.addCylinder(pA, pB, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
+ builder.setId(elements[centerB.element])
+ builder.addCylinder(pB, pA, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
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 027cda9f8..96207c6a3 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -73,7 +73,7 @@ function interpolateNormals(controlPoints: Helpers.NumberArray, tangentVectors:
// console.warn(i, 'flip compared to prev', radToDeg(Math.acos(Vec3.dot(prevNormal, normalVec))))
// }
Vec3.copy(prevNormal, normalVec)
-
+
Vec3.normalize(binormalVec, Vec3.cross(binormalVec, tangentVec, normalVec))
Vec3.toArray(binormalVec, binormalVectors, i * 3)
}
@@ -84,6 +84,8 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
console.log('polymerElementCount', polymerElementCount)
if (!polymerElementCount) return Mesh.createEmpty(mesh)
+ const { elements } = unit
+
// TODO better vertex count estimates
const builder = MeshBuilder.create(polymerElementCount * 30, polymerElementCount * 30 / 2, mesh)
const linearSegments = 12
@@ -108,7 +110,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setId(v.index)
+ builder.setId(elements[v.center.element])
for (let j = 0; j <= linearSegments; ++j) {
const t = j * 1.0 / linearSegments;
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 2a6e5eead..9565bd1c4 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,15 +4,14 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureElement, StructureProperties, Model, ElementIndex } from 'mol-model/structure';
+import { Unit, StructureElement, Model, ElementIndex, ResidueIndex } from 'mol-model/structure';
import { Segmentation, OrderedSet, Interval } from 'mol-data/int';
import { MoleculeType, SecondaryStructureType } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
import { Vec3 } from 'mol-math/linear-algebra';
-import { SymmetryOperator } from 'mol-math/geometry';
import SortedRanges from 'mol-data/int/sorted-ranges';
-export function getPolymerRanges(unit: Unit) {
+export function getPolymerRanges(unit: Unit): SortedRanges<ElementIndex> {
switch (unit.kind) {
case Unit.Kind.Atomic: return unit.model.atomicHierarchy.polymerRanges
case Unit.Kind.Spheres: return unit.model.coarseHierarchy.spheres.polymerRanges
@@ -48,78 +47,49 @@ export function getPolymerElementCount(unit: Unit) {
return count
}
-function getTraceName(l: StructureElement) {
- const compId = StructureProperties.residue.label_comp_id(l)
- const chemCompMap = l.unit.model.properties.chemicalComponentMap
- const cc = chemCompMap.get(compId)
- const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
- let traceName = ''
- if (moleculeType === MoleculeType.protein) {
- traceName = 'CA'
- } else if (moleculeType === MoleculeType.DNA || moleculeType === MoleculeType.RNA) {
- traceName = 'P'
- }
- return traceName
-}
-
-function setTraceElement(l: StructureElement, residueSegment: Segmentation.Segment) {
- const elements = l.unit.elements
- l.element = elements[residueSegment.start]
- const traceName = getTraceName(l)
-
- for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- l.element = elements[j];
- if (StructureProperties.atom.label_atom_id(l) === traceName) return j
+function getResidueTypeAtomId(moleculeType: MoleculeType, atomType: 'trace' | 'direction') {
+ switch (moleculeType) {
+ case MoleculeType.protein:
+ switch (atomType) {
+ case 'trace': return 'CA'
+ case 'direction': return 'O'
+ }
+ break
+ case MoleculeType.RNA:
+ switch (atomType) {
+ case 'trace': return 'C4\''
+ case 'direction': return 'C3\''
+ }
+ break
+ case MoleculeType.DNA:
+ switch (atomType) {
+ case 'trace': return 'C3\''
+ case 'direction': return 'O4\''
+ }
+ break
}
- return residueSegment.end - 1
+ return ''
}
-
-function getTraceName2(model: Model, residueModelIndex: number) {
- const compId = model.atomicHierarchy.residues.label_comp_id.value(residueModelIndex)
+function getMoleculeType(model: Model, residueIndex: number) {
+ const compId = model.atomicHierarchy.residues.label_comp_id.value(residueIndex)
const chemCompMap = model.properties.chemicalComponentMap
const cc = chemCompMap.get(compId)
- const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
- let traceName = ''
- if (moleculeType === MoleculeType.protein) {
- traceName = 'CA'
- } else if (moleculeType === MoleculeType.DNA) {
- // traceName = 'P'
- traceName = 'C3\''
- } else if (moleculeType === MoleculeType.RNA) {
- // traceName = 'P'
- traceName = 'C4\''
- }
- return traceName
+ return cc ? cc.moleculeType : MoleculeType.unknown
}
-// TODO fix type
-function getTraceElement2(model: Model, residueModelSegment: Segmentation.Segment<number>) {
- const traceName = getTraceName2(model, residueModelSegment.index)
-
- for (let j = residueModelSegment.start, _j = residueModelSegment.end; j < _j; j++) {
- if (model.atomicHierarchy.atoms.label_atom_id.value(j) === traceName) return j
+function getElementIndexForAtomId(unit: Unit.Atomic, residueSegment: Segmentation.Segment, atomId: string) {
+ const elements = unit.elements
+ const { label_atom_id } = unit.model.atomicHierarchy.atoms
+ for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+ if (label_atom_id.value(elements[j]) === atomId) return j as ElementIndex
}
- console.log(`trace name element "${traceName}" not found`, { ...residueModelSegment })
- return residueModelSegment.start
+ return residueSegment.end - 1 as ElementIndex
}
-function getDirectionName2(model: Model, residueModelIndex: number) {
- const compId = model.atomicHierarchy.residues.label_comp_id.value(residueModelIndex)
- const chemCompMap = model.properties.chemicalComponentMap
- const cc = chemCompMap.get(compId)
- const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
- let traceName = ''
- if (moleculeType === MoleculeType.protein) {
- traceName = 'O'
- } else if (moleculeType === MoleculeType.DNA) {
- traceName = 'O4\''
- } else if (moleculeType === MoleculeType.RNA) {
- traceName = 'C3\''
- } else {
- console.log('molecule type unknown', Number.isInteger(residueModelIndex) ? compId : residueModelIndex, chemCompMap)
- }
- return traceName
+function getResidueTypeAtomIdElementIndex(unit: Unit.Atomic, residueSegment: Segmentation.Segment, type: 'trace' | 'direction') {
+ const atomId = getResidueTypeAtomId(getMoleculeType(unit.model, residueSegment.index), type)
+ return getElementIndexForAtomId(unit, residueSegment, atomId)
}
// function residueLabel(model: Model, rI: number) {
@@ -130,18 +100,6 @@ function getDirectionName2(model: Model, residueModelIndex: number) {
// return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`
// }
-// TODO fix type
-function getDirectionElement2(model: Model, residueModelSegment: Segmentation.Segment<number>) {
- const traceName = getDirectionName2(model, residueModelSegment.index)
-
- for (let j = residueModelSegment.start, _j = residueModelSegment.end; j < _j; j++) {
- if (model.atomicHierarchy.atoms.label_atom_id.value(j) === traceName) return j
- }
- // console.log('direction name element not found', { ...residueModelSegment })
- return residueModelSegment.start
-}
-
-
/** Iterates over consecutive pairs of residues/coarse elements in polymers */
export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
switch (unit.kind) {
@@ -155,20 +113,12 @@ export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePai
interface PolymerBackbonePair {
centerA: StructureElement
centerB: StructureElement
- indexA: number
- indexB: number
- posA: Vec3
- posB: Vec3
}
function createPolymerBackbonePair (unit: Unit) {
return {
centerA: StructureElement.create(unit),
centerB: StructureElement.create(unit),
- indexA: 0,
- indexB: 0,
- posA: Vec3.zero(),
- posB: Vec3.zero()
}
}
@@ -176,29 +126,19 @@ const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextR
export class AtomicPolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
private value: PolymerBackbonePair
-
private polymerIt: SortedRanges.Iterator<ElementIndex>
- private residueIt: Segmentation.SegmentIterator<number> // TODO specific type
- private polymerSegment: Segmentation.Segment<ElementIndex>
+ private residueIt: Segmentation.SegmentIterator<ResidueIndex>
private state: AtomicPolymerBackboneIteratorState = AtomicPolymerBackboneIteratorState.nextPolymer
- private pos: SymmetryOperator.CoordinateMapper
-
hasNext: boolean = false;
move() {
- const { residueIt, polymerIt, value, pos } = this
-
if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
- while (polymerIt.hasNext) {
- this.polymerSegment = polymerIt.move();
- // console.log('polymerSegment', this.polymerSegment)
- residueIt.setSegment(this.polymerSegment);
-
- const residueSegment = residueIt.move();
- // console.log('first residueSegment', residueSegment, residueIt.hasNext)
- if (residueIt.hasNext) {
- value.indexB = setTraceElement(value.centerB, residueSegment)
- pos(value.centerB.element, value.posB)
+ while (this.polymerIt.hasNext) {
+ const residueSegment = this.polymerIt.move()
+ this.residueIt.setSegment(residueSegment);
+ if (this.residueIt.hasNext) {
+ this.value.centerB.element = getResidueTypeAtomIdElementIndex(this.unit, residueSegment, 'trace')
+ // setTraceElement(this.value.centerB, this.residueIt.move())
this.state = AtomicPolymerBackboneIteratorState.nextResidue
break
}
@@ -206,36 +146,23 @@ export class AtomicPolymerBackboneIterator<T extends number = number> implements
}
if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
- const residueSegment = residueIt.move();
- // console.log('next residueSegment', residueSegment)
- value.centerA.element = value.centerB.element
- value.indexA = value.indexB
- Vec3.copy(value.posA, value.posB)
- value.indexB = setTraceElement(value.centerB, residueSegment)
- pos(value.centerB.element, value.posB)
-
- if (!residueIt.hasNext) {
+ this.value.centerA.element = this.value.centerB.element
+ this.value.centerB.element = getResidueTypeAtomIdElementIndex(this.unit, this.residueIt.move(), 'trace')
+ // setTraceElement(this.value.centerB, this.residueIt.move())
+ if (!this.residueIt.hasNext) {
// TODO need to advance to a polymer that has two or more residues (can't assume it has)
this.state = AtomicPolymerBackboneIteratorState.nextPolymer
}
}
- this.hasNext = residueIt.hasNext || polymerIt.hasNext
-
- // console.log('hasNext', this.hasNext)
- // console.log('value', this.value)
-
+ this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext
return this.value;
}
- constructor(unit: Unit.Atomic) {
- const { residueAtomSegments } = unit.model.atomicHierarchy
- // console.log('unit.elements', OrderedSet.toArray(unit.elements))
+ constructor(private unit: Unit.Atomic) {
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
- this.residueIt = Segmentation.transientSegments(residueAtomSegments, unit.elements)
- this.pos = unit.conformation.invariantPosition
+ this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements)
this.value = createPolymerBackbonePair(unit)
-
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
}
}
@@ -244,29 +171,20 @@ const enum CoarsePolymerBackboneIteratorState { nextPolymer, nextElement }
export class CoarsePolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
private value: PolymerBackbonePair
-
private polymerIt: SortedRanges.Iterator<ElementIndex>
private polymerSegment: Segmentation.Segment<ElementIndex>
private state: CoarsePolymerBackboneIteratorState = CoarsePolymerBackboneIteratorState.nextPolymer
- private pos: SymmetryOperator.CoordinateMapper
private elementIndex: number
-
hasNext: boolean = false;
move() {
- const { polymerIt, value, pos } = this
-
if (this.state === CoarsePolymerBackboneIteratorState.nextPolymer) {
- if (polymerIt.hasNext) {
- this.polymerSegment = polymerIt.move();
- console.log('polymer', this.polymerSegment)
+ if (this.polymerIt.hasNext) {
+ this.polymerSegment = this.polymerIt.move();
this.elementIndex = this.polymerSegment.start
- this.elementIndex += 1
+ // this.elementIndex += 1
if (this.elementIndex + 1 < this.polymerSegment.end) {
- value.centerB.element = value.centerB.unit.elements[this.elementIndex]
- value.indexB = this.elementIndex
- pos(value.centerB.element, value.posB)
-
+ this.value.centerB.element = this.value.centerB.unit.elements[this.elementIndex]
this.state = CoarsePolymerBackboneIteratorState.nextElement
} else {
this.state = CoarsePolymerBackboneIteratorState.nextPolymer
@@ -276,31 +194,20 @@ export class CoarsePolymerBackboneIterator<T extends number = number> implements
if (this.state === CoarsePolymerBackboneIteratorState.nextElement) {
this.elementIndex += 1
- value.centerA.element = value.centerB.element
- value.indexA = value.indexB
- Vec3.copy(value.posA, value.posB)
-
- value.centerB.element = value.centerB.unit.elements[this.elementIndex]
- value.indexB = this.elementIndex
- pos(value.centerB.element, value.posB)
-
+ this.value.centerA.element = this.value.centerB.element
+ this.value.centerB.element = this.value.centerB.unit.elements[this.elementIndex]
if (this.elementIndex + 1 >= this.polymerSegment.end) {
this.state = CoarsePolymerBackboneIteratorState.nextPolymer
}
}
- this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || polymerIt.hasNext
+ this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || this.polymerIt.hasNext
return this.value;
}
constructor(unit: Unit.Spheres | Unit.Gaussians) {
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
-
- this.pos = unit.conformation.invariantPosition
this.value = createPolymerBackbonePair(unit)
-
- console.log('CoarsePolymerBackboneIterator', this.polymerIt.hasNext)
-
this.hasNext = this.polymerIt.hasNext
}
}
@@ -323,37 +230,19 @@ export function PolymerTraceIterator(unit: Unit): Iterator<PolymerTraceElement>
interface PolymerTraceElement {
center: StructureElement
- index: number
- first: boolean
- last: boolean
+ first: boolean, last: boolean
secStrucType: SecondaryStructureType
-
- t0: Vec3
- t1: Vec3
- t2: Vec3
- t3: Vec3
- t4: Vec3
-
- d12: Vec3
- d23: Vec3
+ t0: Vec3, t1: Vec3, t2: Vec3, t3: Vec3, t4: Vec3
+ d12: Vec3, d23: Vec3
}
function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
return {
center: StructureElement.create(unit),
- index: 0,
- first: false,
- last: false,
+ first: false, last: false,
secStrucType: SecondaryStructureType.create(SecondaryStructureType.Flag.NA),
-
- t0: Vec3.zero(),
- t1: Vec3.zero(),
- t2: Vec3.zero(),
- t3: Vec3.zero(),
- t4: Vec3.zero(),
-
- d12: Vec3.zero(),
- d23: Vec3.zero(),
+ t0: Vec3.zero(), t1: Vec3.zero(), t2: Vec3.zero(), t3: Vec3.zero(), t4: Vec3.zero(),
+ d12: Vec3.zero(), d23: Vec3.zero(),
}
}
@@ -372,17 +261,13 @@ function setSegment (outSegment: Segmentation.Segment<number>, index: number, se
export class AtomicPolymerTraceIterator<T extends number = number> implements Iterator<PolymerTraceElement> {
private value: PolymerTraceElement
-
private polymerIt: SortedRanges.Iterator<ElementIndex>
- private residueIt: Segmentation.SegmentIterator<number> // TODO specialize type
- private residueSegmentMin: number
- private residueSegmentMax: number
+ private residueIt: Segmentation.SegmentIterator<ResidueIndex>
+ private residueAtomSegmentMin: number
+ private residueAtomSegmentMax: number
private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
- private residueSegments: Segmentation<ElementIndex>
-
- private tmpSegment: Segmentation.Segment<number>
-
- private unit: Unit.Atomic
+ private residueAtomSegments: Segmentation<ElementIndex, ResidueIndex>
+ private tmpSegment: Segmentation.Segment<ResidueIndex>
hasNext: boolean = false;
@@ -396,8 +281,8 @@ export class AtomicPolymerTraceIterator<T extends number = number> implements It
const { polymerRanges, residueAtomSegments } = this.unit.model.atomicHierarchy
const sMin = polymerRanges[polymerSegment.index * 2]
const sMax = polymerRanges[polymerSegment.index * 2 + 1]
- this.residueSegmentMin = residueAtomSegments.index[sMin]
- this.residueSegmentMax = residueAtomSegments.index[sMax]
+ this.residueAtomSegmentMin = residueAtomSegments.index[sMin]
+ this.residueAtomSegmentMax = residueAtomSegments.index[sMax]
}
move() {
@@ -417,32 +302,32 @@ export class AtomicPolymerTraceIterator<T extends number = number> implements It
}
if (this.state === AtomicPolymerTraceIteratorState.nextResidue) {
- const { tmpSegment, residueSegments, residueSegmentMin, residueSegmentMax } = this
+ const { tmpSegment, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax } = this
const residueSegment = residueIt.move();
const resSegIdx = residueSegment.index
// console.log(residueLabel(this.unit.model, resSegIdx), resSegIdx, this.unit.model.properties.secondaryStructure.type[resSegIdx])
- value.index = setTraceElement(value.center, residueSegment)
+ value.center.element = getResidueTypeAtomIdElementIndex(this.unit, residueSegment, 'trace')
- setSegment(tmpSegment, resSegIdx - 2, residueSegments, residueSegmentMin, residueSegmentMax)
- this.pos(value.t0, getTraceElement2(this.unit.model, tmpSegment))
+ setSegment(tmpSegment, resSegIdx - 2, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax)
+ this.pos(value.t0, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'trace'))
- setSegment(tmpSegment, resSegIdx - 1, residueSegments, residueSegmentMin, residueSegmentMax)
- this.pos(value.t1, getTraceElement2(this.unit.model, tmpSegment))
- this.pos(value.d12, getDirectionElement2(this.unit.model, tmpSegment))
+ setSegment(tmpSegment, resSegIdx - 1, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax)
+ this.pos(value.t1, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'trace'))
+ this.pos(value.d12, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'direction'))
- setSegment(tmpSegment, resSegIdx, residueSegments, residueSegmentMin, residueSegmentMax)
+ setSegment(tmpSegment, resSegIdx, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax)
value.secStrucType = this.unit.model.properties.secondaryStructure.type[resSegIdx]
- this.pos(value.t2, getTraceElement2(this.unit.model, tmpSegment))
- this.pos(value.d23, getDirectionElement2(this.unit.model, tmpSegment))
+ this.pos(value.t2, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'trace'))
+ this.pos(value.d23, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'direction'))
- setSegment(tmpSegment, resSegIdx + 1, residueSegments, residueSegmentMin, residueSegmentMax)
- this.pos(value.t3, getTraceElement2(this.unit.model, tmpSegment))
+ setSegment(tmpSegment, resSegIdx + 1, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax)
+ this.pos(value.t3, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'trace'))
- setSegment(tmpSegment, resSegIdx + 2, residueSegments, residueSegmentMin, residueSegmentMax)
- this.pos(value.t4, getTraceElement2(this.unit.model, tmpSegment))
+ setSegment(tmpSegment, resSegIdx + 2, residueAtomSegments, residueAtomSegmentMin, residueAtomSegmentMax)
+ this.pos(value.t4, getResidueTypeAtomIdElementIndex(this.unit, tmpSegment, 'trace'))
- value.first = resSegIdx === residueSegmentMin
- value.last = resSegIdx === residueSegmentMax
+ value.first = resSegIdx === residueAtomSegmentMin
+ value.last = resSegIdx === residueAtomSegmentMax
if (!residueIt.hasNext) {
this.state = AtomicPolymerTraceIteratorState.nextPolymer
@@ -454,17 +339,13 @@ export class AtomicPolymerTraceIterator<T extends number = number> implements It
return this.value;
}
- constructor(unit: Unit.Atomic) {
- const { residueAtomSegments } = unit.model.atomicHierarchy
+ constructor(private unit: Unit.Atomic) {
+ this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments
this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements)
- this.residueIt = Segmentation.transientSegments(residueAtomSegments, unit.elements);
- this.residueSegments = residueAtomSegments
+ this.residueIt = Segmentation.transientSegments(this.residueAtomSegments, unit.elements);
this.value = createPolymerTraceElement(unit)
+ this.tmpSegment = { index: 0 as ResidueIndex, start: 0 as ElementIndex, end: 0 as ElementIndex }
this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
-
- this.tmpSegment = { index: 0, start: 0 as ElementIndex, end: 0 as ElementIndex }
-
- this.unit = unit
}
}
--
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