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Commit af338aff authored by Alexander Rose's avatar Alexander Rose
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wip, polymer repr

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src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+ 22
− 91
View file @ af338aff
......@@ -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
......
src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+ 16
− 74
View file @ af338aff
......@@ -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()
......
src/mol-geo/representation/structure/visual/util/polymer.ts
+ 310
− 60
View file @ af338aff
......@@ -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
src/mol-view/stage.ts
+ 20
− 6
View file @ af338aff
......@@ -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) {
......
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