diff --git a/src/mol-app/ui/entity/tree.tsx b/src/mol-app/ui/entity/tree.tsx
index 8c976f5cb366d9daa0e0d50bb10bce9912926c3e..8c1612cd1a3440f1b05e2eb26b29893fef268960 100644
--- a/src/mol-app/ui/entity/tree.tsx
+++ b/src/mol-app/ui/entity/tree.tsx
@@ -13,13 +13,13 @@ import { View } from '../view';
import { EntityTreeController } from '../../controller/entity/tree';
import { Controller } from '../../controller/controller';
import { AnyEntity, RootEntity } from 'mol-view/state/entity';
-import { AnyTransform, SpacefillUpdate, UrlToData, DataToCif, FileToData, CifToMmcif, MmcifToModel, ModelToStructure, StructureToSpacefill, MmcifFileToSpacefill, StructureCenter, StructureToBallAndStick, DistanceRestraintUpdate, CartoonUpdate, BallAndStickUpdate, BackboneUpdate } from 'mol-view/state/transform';
+import { AnyTransform, SpacefillUpdate, UrlToData, DataToCif, FileToData, CifToMmcif, MmcifToModel, ModelToStructure, StructureToSpacefill, MmcifFileToSpacefill, StructureCenter, StructureToBallAndStick, DistanceRestraintUpdate, CartoonUpdate, BallAndStickUpdate, BackboneUpdate, MmcifUrlToSpacefill } from 'mol-view/state/transform';
function getTransforms(entity: AnyEntity): AnyTransform[] {
const transforms: AnyTransform[] = []
switch (entity.kind) {
case 'root':
- transforms.push(MmcifFileToSpacefill)
+ transforms.push(MmcifFileToSpacefill, MmcifUrlToSpacefill)
break;
case 'url':
transforms.push(UrlToData)
diff --git a/src/mol-app/ui/transform/list.tsx b/src/mol-app/ui/transform/list.tsx
index 349dcffceea6e847407c73d0738c1ad6f80e2593..2c09db8a620a3e347924d93dda2c99da2b645034 100644
--- a/src/mol-app/ui/transform/list.tsx
+++ b/src/mol-app/ui/transform/list.tsx
@@ -22,9 +22,12 @@ import { StructureCenter } from './structure';
import { Cartoon } from './cartoon';
import { DistanceRestraint } from './distance-restraint';
import { Backbone } from './backbone';
+import { UrlLoader } from './url-loader';
function getTransformComponent(controller: TransformListController, entity: AnyEntity, transform: AnyTransform) {
switch (transform.kind) {
+ case 'url-to-spacefill':
+ return <UrlLoader controller={controller} ctx={controller.context.stage.ctx}></UrlLoader>
case 'file-to-spacefill':
return <FileLoader controller={controller} ctx={controller.context.stage.ctx}></FileLoader>
case 'model-to-structure':
diff --git a/src/mol-app/ui/transform/url-loader.tsx b/src/mol-app/ui/transform/url-loader.tsx
new file mode 100644
index 0000000000000000000000000000000000000000..e97eff11f34c68579202f962cca790180349502f
--- /dev/null
+++ b/src/mol-app/ui/transform/url-loader.tsx
@@ -0,0 +1,124 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as React from 'react'
+import { View } from '../view';
+import { TransformListController } from '../../controller/transform/list';
+import { UrlEntity } from 'mol-view/state/entity';
+import { ModelToStructure, StructureToBallAndStick, StructureToSpacefill, StructureToDistanceRestraint, StructureToBackbone, MmcifUrlToModel, StructureToCartoon } from 'mol-view/state/transform';
+import { StateContext } from 'mol-view/state/context';
+import { SpacefillProps } from 'mol-geo/representation/structure/spacefill';
+import { BallAndStickProps } from 'mol-geo/representation/structure/ball-and-stick';
+import { DistanceRestraintProps } from 'mol-geo/representation/structure/distance-restraint';
+import { BackboneProps } from 'mol-geo/representation/structure/backbone';
+import { CartoonProps } from 'mol-geo/representation/structure/cartoon';
+
+const spacefillProps: SpacefillProps = {
+ doubleSided: true,
+ colorTheme: { name: 'chain-id' },
+ quality: 'auto',
+ useFog: false
+}
+
+const ballAndStickProps: BallAndStickProps = {
+ doubleSided: true,
+ colorTheme: { name: 'chain-id' },
+ sizeTheme: { name: 'uniform', value: 0.05 },
+ linkRadius: 0.05,
+ quality: 'auto',
+ useFog: false
+}
+
+const distanceRestraintProps: DistanceRestraintProps = {
+ doubleSided: true,
+ colorTheme: { name: 'chain-id' },
+ linkRadius: 0.5,
+ quality: 'auto',
+ useFog: false
+}
+
+const backboneProps: BackboneProps = {
+ doubleSided: true,
+ colorTheme: { name: 'chain-id' },
+ quality: 'auto',
+ useFog: false
+}
+
+const cartoonProps: CartoonProps = {
+ doubleSided: true,
+ colorTheme: { name: 'chain-id' },
+ quality: 'auto',
+ useFog: false
+}
+
+function getPdbdevUrl(pdbdevId: string) {
+ return `https://pdb-dev.wwpdb.org/static/cif/${pdbdevId}.cif`
+}
+
+const exampleUrls = {
+ PDBDEV_00000001: getPdbdevUrl('PDBDEV_00000001'), // ok
+ PDBDEV_00000002: getPdbdevUrl('PDBDEV_00000002'), // ok
+ PDBDEV_00000003: getPdbdevUrl('PDBDEV_00000003'), // ok
+ PDBDEV_00000004: getPdbdevUrl('PDBDEV_00000004'), // TODO issue with cross-link extraction
+ PDBDEV_00000005: getPdbdevUrl('PDBDEV_00000005'), // ok
+ PDBDEV_00000006: getPdbdevUrl('PDBDEV_00000006'), // TODO only three spacefill atoms rendered
+ PDBDEV_00000007: getPdbdevUrl('PDBDEV_00000007'), // TODO only three spacefill atoms rendered
+ PDBDEV_00000008: getPdbdevUrl('PDBDEV_00000008'), // ok
+ PDBDEV_00000010: getPdbdevUrl('PDBDEV_00000010'), // ok
+ PDBDEV_00000011: getPdbdevUrl('PDBDEV_00000011'), // ok
+ PDBDEV_00000012: getPdbdevUrl('PDBDEV_00000012'), // ok
+ PDBDEV_00000014: getPdbdevUrl('PDBDEV_00000014'), // ok
+ PDBDEV_00000016: getPdbdevUrl('PDBDEV_00000016'),
+}
+
+export class UrlLoader extends View<TransformListController, { }, { ctx: StateContext }> {
+ async load(name: keyof typeof exampleUrls) {
+ console.log(exampleUrls[name])
+ const ctx = this.props.ctx
+ const urlEntity = UrlEntity.ofUrl(ctx, exampleUrls[name])
+ console.log(await urlEntity.value.getData())
+ const modelEntity = await MmcifUrlToModel.apply(ctx, urlEntity)
+ const structureEntity = await ModelToStructure.apply(ctx, modelEntity)
+
+ StructureToBallAndStick.apply(ctx, structureEntity, { ...ballAndStickProps, visible: true })
+ StructureToSpacefill.apply(ctx, structureEntity, { ...spacefillProps, visible: false })
+ StructureToDistanceRestraint.apply(ctx, structureEntity, { ...distanceRestraintProps, visible: false })
+ StructureToBackbone.apply(ctx, structureEntity, { ...backboneProps, visible: true })
+ StructureToCartoon.apply(ctx, structureEntity, { ...cartoonProps, visible: false })
+ }
+
+ render() {
+ const exampleOptions = Object.keys(exampleUrls).map(name => {
+ return <option key={name} value={name}>{name}</option>
+ })
+
+ return <div className='molstar-transformer-wrapper'>
+ <div className='molstar-panel molstar-control molstar-transformer molstar-panel-expanded'>
+ <div className='molstar-panel-body'>
+ <div>
+ <div className='molstar-control-row molstar-options-group'>
+ <span>Examples</span>
+ <div>
+ <select
+ className='molstar-form-control'
+ value=''
+ onChange={(e) => {
+ if (e.target.value) {
+ this.load(e.target.value as keyof typeof exampleUrls)}
+ }
+ }
+ >
+ <option key='' value=''></option>
+ {exampleOptions}
+ </select>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-data/int/impl/segmentation.ts b/src/mol-data/int/impl/segmentation.ts
index a5534e52a2d412e9be7e288fe13b9a39ba51e704..f3e7413f97c11d597eae86d519285c418c28671d 100644
--- a/src/mol-data/int/impl/segmentation.ts
+++ b/src/mol-data/int/impl/segmentation.ts
@@ -41,6 +41,7 @@ export function ofOffsets(offsets: ArrayLike<number>, bounds: Interval): Segment
return create(segments);
}
+/** Get number of segments in a segmentation */
export function count({ count }: Segmentation) { return count; }
export function getSegment({ segmentMap }: Segmentation, value: number) { return segmentMap[value]; }
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 4ab1548d5fdda9a642b40eefc8d23c49e9d2693d..fe819c0bf8b90b5c5086144c5f113f009001e981 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -33,9 +33,9 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
const builder = MeshBuilder.create(polymerElementCount * 30, polymerElementCount * 30 / 2, mesh)
let i = 0
- const polymerTraceIt = PolymerBackboneIterator(unit)
- while (polymerTraceIt.hasNext) {
- const { indexA, indexB, posA, posB } = polymerTraceIt.move()
+ 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 })
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 75cccb7ab0beb27269f970193c61f32af954975a..f0bfe33559d7fbaaca324f441706e32d4e9614c0 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -23,7 +23,20 @@ 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 { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
+import { getPolymerElementCount, PolymerTraceIterator } from './util/polymer';
+import { Vec3 } from 'mol-math/linear-algebra';
+
+// export function spline(target: THREE.Vector3, p1: THREE.Vector3, p2: THREE.Vector3, p3: THREE.Vector3, t: number) {
+// let a = Math.pow(1 - t, 2) / 2;
+// let c = Math.pow(t, 2) / 2;
+// let b = 1 - a - c;
+
+// let x = a * p1.x + b * p2.x + c * p3.x;
+// let y = a * p1.y + b * p2.y + c * p3.y;
+// let z = a * p1.z + b * p2.z + c * p3.z;
+
+// target.set(x, y, z);
+// }
async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
@@ -32,16 +45,31 @@ 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 linearSegmentCount = 10
+
+ const v0 = Vec3.zero()
+ const v1 = Vec3.zero()
let i = 0
- const polymerTraceIt = PolymerBackboneIterator(unit)
+ const polymerTraceIt = PolymerTraceIterator(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 })
+
+ Vec3.spline(v1, v.c0, v.c1, v.c2, v.c3, 0.5, 0.5)
+
+ builder.setId(v.index)
+ for (let j = 1; j <= linearSegmentCount; ++j) {
+ let t = j * 1.0 / linearSegmentCount;
+ Vec3.copy(v0, v1)
+ // if ((v.last && t > 0.5) || (v.first && t < 0.5)) break
+ if (t < 0.5) {
+ Vec3.spline(v1, v.c0, v.c1, v.c2, v.c3, t + 0.5, 0.5)
+ } else {
+ Vec3.spline(v1, v.c1, v.c2, v.c3, v.c4, t - 0.5, 0.5)
+ }
+ // TODO size theme
+ builder.addCylinder(v0, v1, 1.0, { radiusTop: 0.1, radiusBottom: 0.1 })
+ }
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/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index b663fc5a08ffbbeeb0e0ba988ed94b9cc7f51bb0..0381dc63b08bdefc3c028b2be77049423d05cf18 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, Element, StructureProperties } from 'mol-model/structure';
+import { Unit, Element, StructureProperties, Model } from 'mol-model/structure';
import { Segmentation } from 'mol-data/int';
import { MoleculeType } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
@@ -12,6 +12,18 @@ import { SegmentIterator } from 'mol-data/int/impl/segmentation';
import { Vec3 } from 'mol-math/linear-algebra';
import { SymmetryOperator } from 'mol-math/geometry';
+// type TraceMap = Map<number, number>
+
+// interface TraceMaps {
+// atomic: TraceMap
+// spheres: TraceMap
+// gaussians: TraceMap
+// }
+
+// function calculateTraceMaps (model: Model): TraceMaps {
+
+// }
+
export function getPolymerElementCount(unit: Unit) {
let count = 0
const { elements } = unit
@@ -62,6 +74,33 @@ function setTraceElement(l: Element.Location, residueSegment: Segmentation.Segme
return residueSegment.end - 1
}
+
+function getTraceName2(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 = 'CA'
+ } else if (moleculeType === MoleculeType.DNA || moleculeType === MoleculeType.RNA) {
+ traceName = 'P'
+ }
+ return traceName
+}
+
+function getTraceElement2(model: Model, residueModelSegment: Segmentation.Segment<Element>) {
+ 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
+ }
+ console.log('trace 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) {
@@ -125,7 +164,6 @@ export class AtomicPolymerBackboneIterator<T extends number = number> implements
} else {
this.state = AtomicPolymerBackboneIteratorState.nextPolymer
}
-
}
if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
@@ -210,7 +248,6 @@ export class CoarsePolymerBackboneIterator<T extends number = number> implements
}
this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || polymerIt.hasNext
-
return this.value;
}
@@ -246,73 +283,108 @@ export function PolymerTraceIterator(unit: Unit): Iterator<PolymerTraceElement>
interface PolymerTraceElement {
center: Element.Location
index: number
- pos: Vec3
- posPrev: Vec3
- posNext: Vec3
- posNextNext: Vec3
+ first: boolean
+ last: boolean
+ c0: Vec3
+ c1: Vec3
+ c2: Vec3
+ c3: Vec3
+ c4: Vec3
}
function createPolymerTraceElement (unit: Unit) {
return {
center: Element.Location(unit),
index: 0,
- pos: Vec3.zero(),
- posPrev: Vec3.zero(),
- posNext: Vec3.zero(),
- posNextNext: Vec3.zero()
+ first: false,
+ last: false,
+ c0: Vec3.zero(),
+ c1: Vec3.zero(),
+ c2: Vec3.zero(),
+ c3: Vec3.zero(),
+ c4: Vec3.zero()
}
}
-// const enum AtomicPolymerTraceIteratorState { nextPolymer, firstResidue, nextResidue }
+const enum AtomicPolymerTraceIteratorState { nextPolymer, nextResidue }
+
+function setSegment (outSegment: Segmentation.Segment<Element>, index: number, segments: Segmentation<Element>, boundingSegment: Segmentation.Segment<Element>): Segmentation.Segment<Element> {
+ index = Math.min(Math.max(0, index), segments.segments.length - 2)
+ outSegment.index = index
+ outSegment.start = segments.segments[index]
+ outSegment.end = segments.segments[index + 1]
+ return outSegment
+}
+
+// const p0 = Vec3.zero()
+// const p1 = Vec3.zero()
+// const p2 = Vec3.zero()
+// const p3 = Vec3.zero()
+// const p4 = Vec3.zero()
+// const p5 = Vec3.zero()
+// const p6 = Vec3.zero()
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
+ private polymerSegment: Segmentation.Segment<Element>
+ private state: AtomicPolymerTraceIteratorState = AtomicPolymerTraceIteratorState.nextPolymer
+ private residueSegments: Segmentation<Element>
+
+ private tmpSegment: Segmentation.Segment<Element>
+
+ private unit: Unit.Atomic
hasNext: boolean = false;
+ private pos(target: Vec3, index: number) {
+ target[0] = this.unit.model.atomicConformation.x[index]
+ target[1] = this.unit.model.atomicConformation.y[index]
+ target[2] = this.unit.model.atomicConformation.z[index]
+ }
+
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
+ const { residueIt, polymerIt, value } = this
+ value.first = false
+ value.last = false
+
+ if (this.state === AtomicPolymerTraceIteratorState.nextPolymer) {
+ if (polymerIt.hasNext) {
+ this.polymerSegment = polymerIt.move();
+ residueIt.setSegment(this.polymerSegment);
+ this.state = AtomicPolymerTraceIteratorState.nextResidue
+ value.first = true
+ }
+ }
+
+ if (this.state === AtomicPolymerTraceIteratorState.nextResidue) {
+ const residueSegment = residueIt.move();
+ value.index = setTraceElement(value.center, residueSegment)
+
+ setSegment(this.tmpSegment, residueSegment.index - 2, this.residueSegments, this.polymerSegment)
+ this.pos(value.c0, getTraceElement2(this.unit.model, this.tmpSegment))
+
+ setSegment(this.tmpSegment, residueSegment.index - 1, this.residueSegments, this.polymerSegment)
+ this.pos(value.c1, getTraceElement2(this.unit.model, this.tmpSegment))
+
+ setSegment(this.tmpSegment, residueSegment.index, this.residueSegments, this.polymerSegment)
+ this.pos(value.c2, getTraceElement2(this.unit.model, this.tmpSegment))
+
+ setSegment(this.tmpSegment, residueSegment.index + 1, this.residueSegments, this.polymerSegment)
+ this.pos(value.c3, getTraceElement2(this.unit.model, this.tmpSegment))
+
+ setSegment(this.tmpSegment, residueSegment.index + 2, this.residueSegments, this.polymerSegment)
+ this.pos(value.c4, getTraceElement2(this.unit.model, this.tmpSegment))
+
+ if (!residueIt.hasNext) {
+ this.state = AtomicPolymerTraceIteratorState.nextPolymer
+ value.last = true
+ }
+ }
+
+ this.hasNext = residueIt.hasNext || polymerIt.hasNext
return this.value;
}
@@ -321,9 +393,15 @@ export class AtomicPolymerTraceIterator<T extends number = number> implements It
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.residueSegments = residueSegments
this.value = createPolymerTraceElement(unit)
this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext
+
+ this.tmpSegment = { index: 0, start: 0 as Element, end: 0 as Element }
+
+ this.unit = unit
+ console.log('model', unit.model)
+ console.log('unit', unit)
}
}
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 2cbbea1e113d8319baff93a497eb31b8d4324e7d..55c138fe3bbad7e1ef13dad567355e3ea01bd8a5 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -19,6 +19,7 @@
import Mat4 from './mat4';
import { Quat, Mat3 } from '../3d';
+import { spline as _spline } from '../../interpolate'
interface Vec3 extends Array<number> { [d: number]: number, '@type': 'vec3', length: 3 }
@@ -279,6 +280,17 @@ namespace Vec3 {
return out;
}
+ /**
+ * Performs a spline interpolation with two control points and a tension parameter
+ */
+ export function spline(out: Vec3, a: Vec3, b: Vec3, c: Vec3, d: Vec3, t: number, tension: number) {
+ out[0] = _spline(a[0], b[0], c[0], d[0], t, tension);
+ out[1] = _spline(a[1], b[1], c[1], d[1], t, tension);
+ out[2] = _spline(a[2], b[2], c[2], d[2], t, tension);
+
+ return out;
+ }
+
/**
* Generates a random vector with the given scale
*/
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index 736c81fe63d4fcc2a062462e22c8088f7a1dfb9f..e9f69f9e607507b6da761812cc92eb041a0d8008 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -78,7 +78,6 @@ function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
&& Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}
-
export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, previous?: Model) {
const hierarchyOffsets = findHierarchyOffsets(atom_site);
const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
diff --git a/src/mol-model/structure/model/properties/utils/coarse-keys.ts b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
index 8ea3f848ca2a2117f11df7f6f41cbcec68318462..dfc035c16ddc5303fad22752138ca09c3a1e5438 100644
--- a/src/mol-model/structure/model/properties/utils/coarse-keys.ts
+++ b/src/mol-model/structure/model/properties/utils/coarse-keys.ts
@@ -82,8 +82,6 @@ export function getCoarseKeys(data: CoarseElementData, entities: Entities): Coar
}
}
-
-
const { findChainKey, findSequenceKey } = createLookUp(entities, chainMaps, seqMaps);
return { chainKey, entityKey, findSequenceKey, findChainKey };
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index c4eb99cd0da1e542910afb4b63dfebcf2b878c97..34c85ffca360ea256642a3d7cf13d14fdbb4122c 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -44,13 +44,16 @@ const distanceRestraintProps: DistanceRestraintProps = {
const backboneProps: BackboneProps = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
+ // colorTheme: { name: 'uniform', value: 0xFF0000 },
quality: 'auto',
- useFog: false
+ useFog: false,
+ alpha: 0.5
}
const cartoonProps: CartoonProps = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
+ // colorTheme: { name: 'uniform', value: 0x2200CC },
quality: 'auto',
useFog: false
}
@@ -71,20 +74,20 @@ export class Stage {
// this.loadPdbid('1jj2')
// this.loadPdbid('4umt') // ligand has bond with order 3
// this.loadPdbid('1crn') // small
- this.loadPdbid('1hrv') // viral assembly
- // this.loadPdbid('1rb8') // virus TODO funky inter unit bonds rendering
+ // this.loadPdbid('1hrv') // viral assembly
+ // 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') // discontinuous chains
+ this.loadPdbid('3sn6') // discontinuous chains
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000003.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000004.cif`) // TODO issue with cross-link extraction
- // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000005.cif`) // TODO only three spacefill atoms rendered
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000005.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000006.cif`) // TODO only three spacefill atoms rendered
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000007.cif`) // TODO only three spacefill atoms rendered
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000008.cif`) // ok
@@ -100,11 +103,11 @@ 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 })
+ // StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: true })
StructureToSpacefill.apply(this.ctx, structureEntity, { ...spacefillProps, visible: false })
StructureToDistanceRestraint.apply(this.ctx, structureEntity, { ...distanceRestraintProps, visible: false })
// StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: true })
- StructureToCartoon.apply(this.ctx, structureEntity, { ...cartoonProps, visible: false })
+ StructureToCartoon.apply(this.ctx, structureEntity, { ...cartoonProps, visible: true })
this.globalContext.components.sequenceView.setState({ structure: structureEntity.value });
diff --git a/src/mol-view/viewer.ts b/src/mol-view/viewer.ts
index 32684d7f413c0fd6ad575311d7ba2f9aff50e733..a26e8aca284cf10c347306c7fc994af847278d55 100644
--- a/src/mol-view/viewer.ts
+++ b/src/mol-view/viewer.ts
@@ -100,7 +100,8 @@ namespace Viewer {
const scene = Scene.create(ctx)
// const controls = TrackballControls.create(input, scene, {})
const controls = TrackballControls.create(input, camera, {})
- const renderer = Renderer.create(ctx, camera)
+ // const renderer = Renderer.create(ctx, camera, { clearColor: 0xFFFFFF })
+ const renderer = Renderer.create(ctx, camera, { clearColor: 0x000000 })
const pickScale = 1 / 4
const pickWidth = Math.round(canvas.width * pickScale)
@@ -152,12 +153,12 @@ namespace Viewer {
camera.near = Math.max(0.01, Math.min(near, targetDistance - 0.5))
let fogNear = targetDistance - camera.near + 1 * focusRadius - nearPlaneDelta;
- let fogFar = targetDistance - camera.near + 2 * focusRadius - nearPlaneDelta;
-
- //console.log(fogNear, fogFar);
+ let fogFar = targetDistance - camera.near + 2 * focusRadius - nearPlaneDelta;
+
+ //console.log(fogNear, fogFar);
camera.fogNear = Math.max(fogNear, 0.1);
camera.fogFar = Math.max(fogFar, 0.2);
-
+
// console.log(camera.fogNear, camera.fogFar, targetDistance)
switch (variant) {