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 1237923f8ff594a22a1b66ef17dfd7fabaae3e4e..4ab1548d5fdda9a642b40eefc8d23c49e9d2693d 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, Element, StructureProperties } from 'mol-model/structure';
+import { Unit } from 'mol-model/structure';
import { DefaultStructureProps, UnitsVisual } from '../index';
import { RuntimeContext } from 'mol-task'
import { createTransforms, createColors } from './util/common';
@@ -16,101 +16,36 @@ import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
-import { Segmentation } from 'mol-data/int';
import { createMarkers, MarkerAction } from '../../../util/marker-data';
-import { Loci, EmptyLoci } from 'mol-model/loci';
+import { Loci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
-import { Vec3 } from 'mol-math/linear-algebra';
-import { getPolymerElementCount } from './util/polymer';
-import { MoleculeType } from 'mol-model/structure/model/types';
+import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
+import { getElementLoci, markElement } from './util/element';
async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
+ console.log('polymerElementCount backbone', polymerElementCount)
if (!polymerElementCount) return Mesh.createEmpty(mesh)
// TODO better vertex count estimates
const builder = MeshBuilder.create(polymerElementCount * 30, polymerElementCount * 30 / 2, mesh)
- const chemCompMap = unit.model.properties.chemicalComponentMap
- const { elements } = unit
- const curV = Vec3.zero()
- const prevV = Vec3.zero()
- const pos = unit.conformation.invariantPosition
- const l = Element.Location(unit)
-
- if (Unit.isAtomic(unit)) {
- const { polymerSegments, residueSegments } = unit.model.atomicHierarchy
- const polymerIt = Segmentation.transientSegments(polymerSegments, elements);
- const residuesIt = Segmentation.transientSegments(residueSegments, elements);
-
- let i = 0
- let first = true
-
- while (polymerIt.hasNext) {
- const polymerSegment = polymerIt.move();
- residuesIt.setSegment(polymerSegment);
- first = true
- while (residuesIt.hasNext) {
- const residueSegment = residuesIt.move();
- l.element = elements[residueSegment.start];
-
- const compId = StructureProperties.residue.label_comp_id(l)
- 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'
- }
-
- for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- l.element = elements[j];
- if (StructureProperties.atom.label_atom_id(l) === traceName) break
- }
- pos(l.element, curV)
-
- if (!first) {
- builder.setId(residueSegment.start)
- builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
- } else {
- first = false
- }
-
- Vec3.copy(prevV, curV)
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
- }
- ++i
- }
- }
- } else if (Unit.isSpheres(unit)) {
- let prevSeqIdEnd = -1
- for (let i = 0, il = elements.length; i < il; ++i) {
- l.element = elements[i]
- if (StructureProperties.entity.type(l) !== 'polymer') continue;
-
- pos(elements[i], curV)
- const seqIdBegin = StructureProperties.coarse.seq_id_begin(l)
- const seqIdEnd = StructureProperties.coarse.seq_id_end(l)
-
- pos(elements[i], curV)
-
- if (seqIdBegin - 1 === prevSeqIdEnd) {
- builder.setId(i)
- builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
- }
-
- Vec3.copy(prevV, curV)
- prevSeqIdEnd = seqIdEnd
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
- }
+ let i = 0
+ const polymerTraceIt = PolymerBackboneIterator(unit)
+ while (polymerTraceIt.hasNext) {
+ const { indexA, indexB, posA, posB } = polymerTraceIt.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 })
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
}
+ ++i
}
return builder.getMesh()
@@ -145,14 +80,10 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
mesh = unitKinds.includes(unit.kind)
? await createPolymerBackboneCylinderMesh(ctx, unit, mesh)
: Mesh.createEmpty(mesh)
+ console.log(mesh)
- if (ctx.shouldUpdate) await ctx.update('Computing trace transforms');
const transforms = createTransforms(group)
-
- if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
const color = createColors(group, elementCount, colorTheme)
-
- if (ctx.shouldUpdate) await ctx.update('Computing trace marks');
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -164,6 +95,7 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
aTransform: transforms,
elements: mesh.indexBuffer,
...createMeshValues(currentProps, counts),
+ aColor: ValueCell.create(new Float32Array(mesh.vertexCount * 3))
}
const state = createRenderableState(currentProps)
@@ -200,11 +132,10 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
return true
},
getLoci(pickingId: PickingId) {
- // TODO
- return EmptyLoci
+ return getElementLoci(renderObject.id, currentGroup, pickingId)
},
mark(loci: Loci, action: MarkerAction) {
- // TODO
+ markElement(renderObject.values.tMarker, currentGroup, loci, action)
},
destroy() {
// TODO
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 c5fa69d17e8b9c52f4416e2e8762d4dac700b755..75cccb7ab0beb27269f970193c61f32af954975a 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, Element, StructureProperties } from 'mol-model/structure';
+import { Unit, Element } from 'mol-model/structure';
import { DefaultStructureProps, UnitsVisual } from '../index';
import { RuntimeContext } from 'mol-task'
import { createTransforms, createColors } from './util/common';
@@ -17,14 +17,13 @@ import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
-import { OrderedSet, Segmentation } from 'mol-data/int';
+import { OrderedSet } from 'mol-data/int';
import { createMarkers, MarkerAction } from '../../../util/marker-data';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
-import { Vec3 } from 'mol-math/linear-algebra';
-import { getPolymerElementCount } from './util/polymer';
+import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
@@ -34,77 +33,20 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
// TODO better vertex count estimates
const builder = MeshBuilder.create(polymerElementCount * 30, polymerElementCount * 30 / 2, mesh)
- const { elements } = unit
- const curV = Vec3.zero()
- const prevV = Vec3.zero()
- const pos = unit.conformation.invariantPosition
- const l = Element.Location(unit)
-
- if (Unit.isAtomic(unit)) {
- const { chainSegments, residueSegments } = unit.model.atomicHierarchy
- const chainsIt = Segmentation.transientSegments(chainSegments, elements);
- const residuesIt = Segmentation.transientSegments(residueSegments, elements);
-
- let i = 0
- let prevSeqId = -1
-
- while (chainsIt.hasNext) {
- const chainSegment = chainsIt.move();
- residuesIt.setSegment(chainSegment);
- while (residuesIt.hasNext) {
- const residueSegment = residuesIt.move();
- l.element = elements[residueSegment.start];
- if (StructureProperties.entity.type(l) !== 'polymer') continue;
-
- const seqId = StructureProperties.residue.label_seq_id(l)
-
- // for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
- // l.element = elements[j];
- // }
- // TODO get proper trace element
- pos(l.element, curV)
-
- if (seqId - 1 === prevSeqId) {
- // TODO draw trace
- builder.setId(residueSegment.start)
- builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
- }
-
- Vec3.copy(prevV, curV)
- prevSeqId = seqId
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Cartoon mesh', current: i, max: polymerElementCount });
- }
- ++i
- }
- }
- } else if (Unit.isSpheres(unit)) {
- let prevSeqIdEnd = -1
- for (let i = 0, il = elements.length; i < il; ++i) {
- l.element = elements[i]
- if (StructureProperties.entity.type(l) !== 'polymer') continue;
- // console.log(elementLabel(l), StructureProperties.entity.type(l))
-
- pos(elements[i], curV)
- const seqIdBegin = StructureProperties.coarse.seq_id_begin(l)
- const seqIdEnd = StructureProperties.coarse.seq_id_end(l)
-
- pos(elements[i], curV)
-
- if (seqIdBegin - 1 === prevSeqIdEnd) {
- // TODO draw trace
- builder.setId(i)
- builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
- }
-
- Vec3.copy(prevV, curV)
- prevSeqIdEnd = seqIdEnd
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
- }
+ let i = 0
+ const polymerTraceIt = PolymerBackboneIterator(unit)
+ while (polymerTraceIt.hasNext) {
+ const v = polymerTraceIt.move()
+ builder.setId(v.indexA)
+ // TODO size theme
+ builder.addCylinder(v.posA, v.posB, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
+ builder.setId(v.indexB)
+ builder.addCylinder(v.posB, v.posA, 0.5, { radiusTop: 0.2, radiusBottom: 0.2 })
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
}
+ ++i
}
return builder.getMesh()
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 3f8c7bf3f9ff5dfa156f9de0ff57b38bdd6bac1d..b663fc5a08ffbbeeb0e0ba988ed94b9cc7f51bb0 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -6,7 +6,11 @@
import { Unit, Element, StructureProperties } from 'mol-model/structure';
import { Segmentation } from 'mol-data/int';
-// import Iterator from 'mol-data/iterator';
+import { MoleculeType } from 'mol-model/structure/model/types';
+import Iterator from 'mol-data/iterator';
+import { SegmentIterator } from 'mol-data/int/impl/segmentation';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { SymmetryOperator } from 'mol-math/geometry';
export function getPolymerElementCount(unit: Unit) {
let count = 0
@@ -32,62 +36,308 @@ export function getPolymerElementCount(unit: Unit) {
return count
}
-// interface PolymerTrace {
-// center: Element
-// direction: Element
-// }
-
-// export class PolymerTraceIterator<T extends number = number> implements Iterator<PolymerTrace> {
-// private segmentMin = 0;
-// private segmentMax = 0;
-// private setRange = Interval.Empty;
-// private value: TraceSegment = { index: 0, start: 0 as T, end: 0 as T };
-
-// hasNext: boolean = false;
-
-// move() {
-// while (this.hasNext) {
-// if (this.updateValue()) {
-// this.value.index = this.segmentMin++;
-// this.hasNext = this.segmentMax >= this.segmentMin && Interval.size(this.setRange) > 0;
-// break;
-// } else {
-// this.updateSegmentRange();
-// }
-// }
-// return this.value;
-// }
-
-// private updateValue() {
-// const segmentEnd = this.segments[this.segmentMin + 1];
-// // TODO: add optimized version for interval and array?
-// const setEnd = OrderedSet.findPredecessorIndexInInterval(this.set, segmentEnd, this.setRange);
-// this.value.start = Interval.start(this.setRange) as T;
-// this.value.end = setEnd as T;
-// this.setRange = Interval.ofBounds(setEnd, Interval.end(this.setRange));
-// return setEnd > this.value.start;
-// }
-
-// private updateSegmentRange() {
-// const sMin = Interval.min(this.setRange), sMax = Interval.max(this.setRange);
-// if (sMax < sMin) {
-// this.hasNext = false;
-// return;
-// }
-
-// this.segmentMin = this.segmentMap[OrderedSet.getAt(this.set, sMin)];
-// this.segmentMax = this.segmentMap[OrderedSet.getAt(this.set, sMax)];
-
-// this.hasNext = this.segmentMax >= this.segmentMin;
-// }
-
-// setSegment(segment: Segs.Segment<T>) {
-// this.setRange = Interval.ofBounds(segment.start, segment.end);
-// this.updateSegmentRange();
-// }
-
-// constructor(private segments: SortedArray, private segmentMap: Int32Array, private set: OrderedSet, inputRange: Interval) {
-// this.setRange = inputRange;
-// this.updateSegmentRange();
-// }
-// }
\ No newline at end of file
+function getTraceName(l: Element.Location) {
+ 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: Element.Location, residueSegment: Segmentation.Segment<Element>) {
+ 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
+ }
+ return residueSegment.end - 1
+}
+
+/** Iterates over consecutive pairs of residues/coarse elements in polymers */
+export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
+ switch (unit.kind) {
+ case Unit.Kind.Atomic: return new AtomicPolymerBackboneIterator(unit)
+ case Unit.Kind.Spheres:
+ case Unit.Kind.Gaussians:
+ return new CoarsePolymerBackboneIterator(unit)
+ }
+}
+
+interface PolymerBackbonePair {
+ centerA: Element.Location
+ centerB: Element.Location
+ indexA: number
+ indexB: number
+ posA: Vec3
+ posB: Vec3
+}
+
+function createPolymerBackbonePair (unit: Unit) {
+ return {
+ centerA: Element.Location(unit),
+ centerB: Element.Location(unit),
+ indexA: 0,
+ indexB: 0,
+ posA: Vec3.zero(),
+ posB: Vec3.zero()
+ }
+}
+
+const enum AtomicPolymerBackboneIteratorState { nextPolymer, firstResidue, nextResidue }
+
+export class AtomicPolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
+ private value: PolymerBackbonePair
+
+ private polymerIt: SegmentIterator<Element>
+ private residueIt: SegmentIterator<Element>
+ private polymerSegment: Segmentation.Segment<Element>
+ private state: AtomicPolymerBackboneIteratorState = AtomicPolymerBackboneIteratorState.nextPolymer
+ private pos: SymmetryOperator.CoordinateMapper
+
+ hasNext: boolean = false;
+
+ move() {
+ const { residueIt, polymerIt, value, pos } = this
+
+ if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
+ if (polymerIt.hasNext) {
+ this.polymerSegment = polymerIt.move();
+ residueIt.setSegment(this.polymerSegment);
+ this.state = AtomicPolymerBackboneIteratorState.firstResidue
+ }
+ }
+
+ if (this.state === AtomicPolymerBackboneIteratorState.firstResidue) {
+ const residueSegment = residueIt.move();
+ if (residueIt.hasNext) {
+ value.indexB = setTraceElement(value.centerB, residueSegment)
+ pos(value.centerB.element, value.posB)
+ this.state = AtomicPolymerBackboneIteratorState.nextResidue
+ } else {
+ this.state = AtomicPolymerBackboneIteratorState.nextPolymer
+ }
+
+ }
+
+ if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
+ const residueSegment = residueIt.move();
+ 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.state = AtomicPolymerBackboneIteratorState.nextPolymer
+ }
+ }
+
+ this.hasNext = residueIt.hasNext || polymerIt.hasNext
+
+ return this.value;
+ }
+
+ constructor(unit: Unit.Atomic) {
+ const { polymerSegments, residueSegments } = unit.model.atomicHierarchy
+ this.polymerIt = Segmentation.transientSegments(polymerSegments, unit.elements);
+ this.residueIt = Segmentation.transientSegments(residueSegments, unit.elements);
+ this.pos = unit.conformation.invariantPosition
+ this.value = createPolymerBackbonePair(unit)
+ this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext
+ }
+}
+
+const enum CoarsePolymerBackboneIteratorState { nextPolymer, firstElement, nextElement }
+
+export class CoarsePolymerBackboneIterator<T extends number = number> implements Iterator<PolymerBackbonePair> {
+ private value: PolymerBackbonePair
+
+ private polymerIt: SegmentIterator<Element>
+ private polymerSegment: Segmentation.Segment<Element>
+ 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();
+ this.elementIndex = this.polymerSegment.start
+ this.state = CoarsePolymerBackboneIteratorState.firstElement
+ }
+ }
+
+ if (this.state === CoarsePolymerBackboneIteratorState.firstElement) {
+ 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.state = CoarsePolymerBackboneIteratorState.nextElement
+ } else {
+ this.state = CoarsePolymerBackboneIteratorState.nextPolymer
+ }
+
+ }
+
+ 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)
+
+ if (this.elementIndex + 1 >= this.polymerSegment.end) {
+ this.state = CoarsePolymerBackboneIteratorState.nextPolymer
+ }
+ }
+
+ this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || polymerIt.hasNext
+
+ return this.value;
+ }
+
+ constructor(unit: Unit.Spheres | Unit.Gaussians) {
+ const { polymerSegments } = Unit.isSpheres(unit)
+ ? unit.model.coarseHierarchy.spheres
+ : unit.model.coarseHierarchy.gaussians
+ this.polymerIt = Segmentation.transientSegments(polymerSegments, unit.elements);
+
+ this.pos = unit.conformation.invariantPosition
+ this.value = createPolymerBackbonePair(unit)
+
+ this.hasNext = this.polymerIt.hasNext
+ }
+}
+
+
+
+
+/**
+ * Iterates over individual residues/coarse elements in polymers while providing information
+ * about the neighbourhood in the underlying model for drawing splines
+ */
+export function PolymerTraceIterator(unit: Unit): Iterator<PolymerTraceElement> {
+ switch (unit.kind) {
+ case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit)
+ case Unit.Kind.Spheres:
+ case Unit.Kind.Gaussians:
+ return new CoarsePolymerTraceIterator(unit)
+ }
+}
+
+interface PolymerTraceElement {
+ center: Element.Location
+ index: number
+ pos: Vec3
+ posPrev: Vec3
+ posNext: Vec3
+ posNextNext: Vec3
+}
+
+function createPolymerTraceElement (unit: Unit) {
+ return {
+ center: Element.Location(unit),
+ index: 0,
+ pos: Vec3.zero(),
+ posPrev: Vec3.zero(),
+ posNext: Vec3.zero(),
+ posNextNext: Vec3.zero()
+ }
+}
+
+// const enum AtomicPolymerTraceIteratorState { nextPolymer, firstResidue, nextResidue }
+
+export class AtomicPolymerTraceIterator<T extends number = number> implements Iterator<PolymerTraceElement> {
+ private value: PolymerTraceElement
+
+ private polymerIt: SegmentIterator<Element>
+ private residueIt: SegmentIterator<Element>
+ // private polymerSegment: Segmentation.Segment<Element>
+ // private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
+ // private pos: SymmetryOperator.CoordinateMapper
+
+ hasNext: boolean = false;
+
+ move() {
+ // const { residueIt, polymerIt, value, pos } = this
+
+ // if (this.state === AtomicPolymerTraceIteratorState.nextPolymer) {
+ // if (polymerIt.hasNext) {
+ // this.polymerSegment = polymerIt.move();
+ // residueIt.setSegment(this.polymerSegment);
+ // this.state = AtomicPolymerTraceIteratorState.firstResidue
+ // }
+ // }
+
+ // if (this.state === AtomicPolymerTraceIteratorState.firstResidue) {
+ // const residueSegment = residueIt.move();
+ // if (residueIt.hasNext) {
+ // value.indexB = setTraceElement(value.centerB, residueSegment)
+ // pos(value.centerB.element, value.posB)
+ // this.state = AtomicPolymerTraceIteratorState.nextResidue
+ // } else {
+ // this.state = AtomicPolymerTraceIteratorState.nextPolymer
+ // }
+
+ // }
+
+ // if (this.state === AtomicPolymerTraceIteratorState.nextResidue) {
+ // const residueSegment = residueIt.move();
+ // 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.state = AtomicPolymerTraceIteratorState.nextPolymer
+ // }
+ // }
+
+ // this.hasNext = residueIt.hasNext || polymerIt.hasNext
+
+ return this.value;
+ }
+
+ constructor(unit: Unit.Atomic) {
+ const { polymerSegments, residueSegments } = unit.model.atomicHierarchy
+ this.polymerIt = Segmentation.transientSegments(polymerSegments, unit.elements);
+ this.residueIt = Segmentation.transientSegments(residueSegments, unit.elements);
+ // this.pos = unit.conformation.invariantPosition
+ this.value = createPolymerTraceElement(unit)
+ this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext
+ }
+}
+
+export class CoarsePolymerTraceIterator<T extends number = number> implements Iterator<PolymerTraceElement> {
+ private value: PolymerTraceElement
+
+ hasNext: boolean = false;
+
+ move() {
+ return this.value;
+ }
+
+ constructor(unit: Unit.Spheres | Unit.Gaussians) {
+ this.value = createPolymerTraceElement(unit)
+ this.hasNext = false
+ }
+}
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 3809a7271bfb22e64a7a5ddcfdbc536f66da6b24..923423527eb39b00c3c9754983484dafb215fb1a 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import Viewer from 'mol-view/viewer'
+import Viewer from './viewer'
import { StateContext } from './state/context';
import { Progress } from 'mol-task';
import { MmcifUrlToModel, ModelToStructure, StructureToSpacefill, StructureToBallAndStick, StructureToDistanceRestraint, StructureToCartoon, StructureToBackbone } from './state/transform';
@@ -15,6 +15,7 @@ import { BallAndStickProps } from 'mol-geo/representation/structure/ball-and-sti
import { CartoonProps } from 'mol-geo/representation/structure/cartoon';
import { DistanceRestraintProps } from 'mol-geo/representation/structure/distance-restraint';
import { BackboneProps } from 'mol-geo/representation/structure/backbone';
+import { Queries as Q, StructureProperties as SP, Query, Selection } from 'mol-model/structure';
const spacefillProps: SpacefillProps = {
doubleSided: true,
@@ -26,7 +27,8 @@ const spacefillProps: SpacefillProps = {
const ballAndStickProps: BallAndStickProps = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
- sizeTheme: { name: 'uniform', value: 0.25 },
+ sizeTheme: { name: 'uniform', value: 0.05 },
+ linkRadius: 0.05,
quality: 'auto',
useFog: false
}
@@ -68,16 +70,20 @@ export class Stage {
// this.loadPdbid('1jj2')
// this.loadPdbid('4umt') // ligand has bond with order 3
- // this.loadPdbid('1crn') // small
+ this.loadPdbid('1crn') // small
// this.loadPdbid('1rb8') // virus
// this.loadPdbid('1blu') // metal coordination
// this.loadPdbid('3pqr') // inter unit bonds
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
- this.loadPdbid('3sn6') // ...
+ // this.loadPdbid('3sn6') // discontinuous chains
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`)
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000003.cif`)
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000004.cif`)
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000005.cif`)
}
async loadMmcifUrl (url: string) {
@@ -85,13 +91,21 @@ export class Stage {
const modelEntity = await MmcifUrlToModel.apply(this.ctx, urlEntity)
const structureEntity = await ModelToStructure.apply(this.ctx, modelEntity)
+ StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: true })
StructureToSpacefill.apply(this.ctx, structureEntity, { ...spacefillProps, visible: false })
- StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: false })
StructureToDistanceRestraint.apply(this.ctx, structureEntity, { ...distanceRestraintProps, visible: false })
- StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: true })
+ // StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: true })
StructureToCartoon.apply(this.ctx, structureEntity, { ...cartoonProps, visible: false })
this.globalContext.components.sequenceView.setState({ structure: structureEntity.value });
+
+ const structureEntity2 = await ModelToStructure.apply(this.ctx, modelEntity)
+ const q1 = Q.generators.atoms({
+ residueTest: l => SP.residue.label_seq_id(l) > 30
+ });
+ structureEntity2.value = Selection.unionStructure(await Query(q1)(structureEntity2.value).run());
+ StructureToBackbone.apply(this.ctx, structureEntity2, { ...backboneProps, visible: true })
+ StructureToCartoon.apply(this.ctx, structureEntity2, { ...cartoonProps, visible: true })
}
loadPdbid (pdbid: string) {