From d549b1c4c319c6d226f94dfc66c2191df6f6c669 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Thu, 7 Jun 2018 12:51:47 +0200
Subject: [PATCH] bond picking
---
src/mol-geo/representation/structure/bond.ts | 125 +++++++++++-------
src/mol-geo/representation/structure/point.ts | 7 +-
.../representation/structure/spacefill.ts | 12 +-
src/mol-geo/representation/structure/utils.ts | 4 +-
src/mol-geo/util/flag-data.ts | 6 +-
src/mol-math/graph/int/graph.ts | 2 +-
src/mol-model/structure/structure/element.ts | 6 +-
.../structure/structure/unit/bonds.ts | 20 +--
src/mol-view/label.ts | 12 +-
src/mol-view/stage.ts | 9 +-
10 files changed, 122 insertions(+), 81 deletions(-)
diff --git a/src/mol-geo/representation/structure/bond.ts b/src/mol-geo/representation/structure/bond.ts
index 1495ab1c0..afb2cf89c 100644
--- a/src/mol-geo/representation/structure/bond.ts
+++ b/src/mol-geo/representation/structure/bond.ts
@@ -8,7 +8,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, Element } from 'mol-model/structure';
+import { Unit, Element, Bond } from 'mol-model/structure';
import { UnitsRepresentation, DefaultStructureProps } from './index';
import { Task } from 'mol-task'
import { createTransforms } from './utils';
@@ -21,20 +21,21 @@ import { MeshBuilder } from '../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { createUniformColor } from '../../util/color-data';
import { defaults } from 'mol-util';
-import { Loci } from 'mol-model/loci';
-import { FlagAction, createEmptyFlags } from '../../util/flag-data';
+import { Loci, isEveryLoci } from 'mol-model/loci';
+import { FlagAction, applyFlagAction, createFlags } from '../../util/flag-data';
function createBondMesh(unit: Unit, mesh?: Mesh) {
return Task.create('Cylinder mesh', async ctx => {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const elements = unit.elements;
- const { count, offset, neighbor } = unit.bonds;
-
- if (!count) return Mesh.createEmpty(mesh)
+ const bonds = unit.bonds
+ const { edgeCount, a, b } = bonds
+
+ if (!edgeCount) return Mesh.createEmpty(mesh)
// TODO calculate vertextCount properly
- const vertexCount = 32 * count
+ const vertexCount = 32 * edgeCount
const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
const va = Vec3.zero()
@@ -46,34 +47,23 @@ function createBondMesh(unit: Unit, mesh?: Mesh) {
const l = Element.Location()
l.unit = unit
- for (let j = 0; j < offset.length - 1; ++j) {
- const start = offset[j]
- const end = offset[j + 1]
-
- if (end <= start) continue
-
- const aI = elements[j]
- va[0] = x(aI)
- va[1] = y(aI)
- va[2] = z(aI)
- for (let _bI = start; _bI < end; ++_bI) {
- const bI = elements[neighbor[_bI]]
- if (bI > aI) continue
-
- vb[0] = x(bI)
- vb[1] = y(bI)
- vb[2] = z(bI)
-
- Vec3.scale(vt, Vec3.add(vt, va, vb), 0.5)
- Vec3.makeRotation(m, Vec3.create(0, 1, 0), Vec3.sub(vb, vb, va))
- Mat4.setTranslation(m, vt)
-
- meshBuilder.setId(j)
- meshBuilder.addCylinder(m, { radiusTop: 0.2, radiusBottom: 0.2 })
- }
-
- if (j % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Cylinder mesh', current: j, max: count });
+ for (let edgeIndex = 0, _eI = edgeCount * 2; edgeIndex < _eI; ++edgeIndex) {
+ const aI = elements[a[edgeIndex]], bI = elements[b[edgeIndex]];
+ // each edge is included twice because of the "adjacency list" structure
+ // keep only the 1st occurence.
+ if (aI >= bI) continue;
+ va[0] = x(aI); va[1] = y(aI); va[2] = z(aI)
+ vb[0] = x(bI); vb[1] = y(bI); vb[2] = z(bI)
+
+ Vec3.scale(vt, Vec3.add(vt, va, vb), 0.5)
+ Vec3.makeRotation(m, Vec3.create(0, 1, 0), Vec3.sub(vb, vb, va))
+ Mat4.setTranslation(m, vt)
+
+ meshBuilder.setId(edgeIndex)
+ meshBuilder.addCylinder(m, { radiusTop: 0.2, radiusBottom: 0.2 })
+
+ if (edgeIndex % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Cylinder mesh', current: edgeIndex, max: edgeCount });
}
}
@@ -88,7 +78,7 @@ export const DefaultBondProps = {
}
export type BondProps = Partial<typeof DefaultBondProps>
-export default function Bond(): UnitsRepresentation<BondProps> {
+export default function BondUnitsRepresentation(): UnitsRepresentation<BondProps> {
const renderObjects: RenderObject[] = []
let cylinders: MeshRenderObject
let currentProps: typeof DefaultBondProps
@@ -105,7 +95,12 @@ export default function Bond(): UnitsRepresentation<BondProps> {
renderObjects.length = 0 // clear
currentGroup = group
- mesh = await createBondMesh(group.units[0]).runAsChild(ctx, 'Computing bond mesh')
+ const unit = group.units[0]
+ const elementCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0
+ const instanceCount = group.units.length
+
+ mesh = await createBondMesh(unit).runAsChild(ctx, 'Computing bond mesh')
+
// console.log(mesh)
// vertexMap = VertexMap.fromMesh(mesh)
@@ -116,9 +111,7 @@ export default function Bond(): UnitsRepresentation<BondProps> {
const color = createUniformColor({ value: 0xFF0000 })
await ctx.update('Computing bond flags');
- const flag = createEmptyFlags()
-
- const instanceCount = group.units.length
+ const flag = createFlags(instanceCount * elementCount)
const values: MeshValues = {
...getMeshData(mesh),
@@ -129,7 +122,7 @@ export default function Bond(): UnitsRepresentation<BondProps> {
uAlpha: ValueCell.create(defaults(props.alpha, 1.0)),
uInstanceCount: ValueCell.create(instanceCount),
- uElementCount: ValueCell.create(group.elements.length),
+ uElementCount: ValueCell.create(elementCount),
elements: mesh.indexBuffer,
@@ -168,17 +161,51 @@ export default function Bond(): UnitsRepresentation<BondProps> {
})
},
getLoci(pickingId: PickingId) {
- // const { objectId, instanceId, elementId } = pickingId
- // if (cylinders.id === objectId) {
- // const unit = currentGroup.units[instanceId]
- // const elements = SortedArray.ofSingleton(currentGroup.elements[elementId])
- // return Element.Loci([{ unit, elements }])
- // }
+ const { objectId, instanceId, elementId } = pickingId
+ const unit = currentGroup.units[instanceId]
+ if (cylinders.id === objectId && Unit.isAtomic(unit)) {
+ return Bond.Loci([{
+ aUnit: unit,
+ aIndex: unit.bonds.a[elementId],
+ bUnit: unit,
+ bIndex: unit.bonds.b[elementId]
+ }])
+ }
return null
},
applyFlags(loci: Loci, action: FlagAction) {
- currentGroup
- // TODO
+ const group = currentGroup
+ const tFlag = cylinders.values.tFlag
+ const unit = group.units[0]
+ if (!Unit.isAtomic(unit)) return
+
+ const elementCount = unit.bonds.edgeCount * 2
+ const instanceCount = group.units.length
+
+ let changed = false
+ const array = tFlag.ref.value.array
+ if (isEveryLoci(loci)) {
+ applyFlagAction(array, 0, elementCount * instanceCount, action)
+ changed = true
+ } else if (Bond.isLoci(loci)) {
+ for (const b of loci.bonds) {
+ const unitIdx = Unit.findUnitById(b.aUnit.id, group.units)
+ if (unitIdx !== -1) {
+ const _idx = unit.bonds.getEdgeIndex(b.aIndex, b.bIndex)
+ if (_idx !== -1) {
+ const idx = _idx
+ if (applyFlagAction(array, idx, idx + 1, action) && !changed) {
+ changed = true
+ }
+ }
+ }
+ }
+ } else {
+ return
+ }
+ if (changed) {
+ ValueCell.update(tFlag, tFlag.ref.value)
+ }
}
}
}
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index a45facb64..2daed89a6 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -47,7 +47,7 @@ export function createPointVertices(unit: Unit) {
return vertices
}
-export default function Point(): UnitsRepresentation<PointProps> {
+export default function PointUnitsRepresentation(): UnitsRepresentation<PointProps> {
const renderObjects: RenderObject[] = []
let points: PointRenderObject
let currentProps = DefaultPointProps
@@ -70,6 +70,7 @@ export default function Point(): UnitsRepresentation<PointProps> {
const { colorTheme, sizeTheme } = currentProps
const elementCount = _elements.length
+ const instanceCount = group.units.length
const vertexMap = VertexMap.create(
elementCount,
@@ -91,9 +92,7 @@ export default function Point(): UnitsRepresentation<PointProps> {
const size = createSizes(group, vertexMap, sizeTheme)
await ctx.update('Computing spacefill flags');
- const flag = createFlags(group)
-
- const instanceCount = group.units.length
+ const flag = createFlags(instanceCount * elementCount)
const values: PointValues = {
aPosition: ValueCell.create(vertices),
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index d1056a033..573c18547 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -33,7 +33,7 @@ function createSpacefillMesh(unit: Unit, detail: number, mesh?: Mesh) {
console.warn('Unsupported unit type')
return Task.constant('Empty mesh', Mesh.createEmpty(mesh))
}
- return createSphereMesh(unit, (l) => radius(l) * 1.0, detail, mesh)
+ return createSphereMesh(unit, (l) => radius(l) * 0.3, detail, mesh)
}
export const DefaultSpacefillProps = {
@@ -44,7 +44,7 @@ export const DefaultSpacefillProps = {
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
-export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
+export default function SpacefillUnitsRepresentation(): UnitsRepresentation<SpacefillProps> {
const renderObjects: RenderObject[] = []
let spheres: MeshRenderObject
let currentProps: typeof DefaultSpacefillProps
@@ -62,6 +62,8 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
currentGroup = group
const { detail, colorTheme } = { ...DefaultSpacefillProps, ...props }
+ const instanceCount = group.units.length
+ const elementCount = group.elements.length
mesh = await createSpacefillMesh(group.units[0], detail).runAsChild(ctx, 'Computing spacefill mesh')
// console.log(mesh)
@@ -74,9 +76,7 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
const color = createColors(group, vertexMap, colorTheme)
await ctx.update('Computing spacefill flags');
- const flag = createFlags(group)
-
- const instanceCount = group.units.length
+ const flag = createFlags(instanceCount * elementCount)
const values: MeshValues = {
...getMeshData(mesh),
@@ -87,7 +87,7 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
uAlpha: ValueCell.create(defaults(props.alpha, 1.0)),
uInstanceCount: ValueCell.create(instanceCount),
- uElementCount: ValueCell.create(group.elements.length),
+ uElementCount: ValueCell.create(elementCount),
elements: mesh.indexBuffer,
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index a0a17964c..e6719eaa7 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -73,9 +73,7 @@ export function createSphereMesh(unit: Unit, radius: Element.Property<number>, d
for (let i = 0; i < elementCount; i++) {
l.element = elements[i]
- v[0] = x(l.element)
- v[1] = y(l.element)
- v[2] = z(l.element)
+ v[0] = x(l.element); v[1] = y(l.element); v[2] = z(l.element)
Mat4.setTranslation(m, v)
meshBuilder.setId(i)
diff --git a/src/mol-geo/util/flag-data.ts b/src/mol-geo/util/flag-data.ts
index 206f1aeae..e8049a53e 100644
--- a/src/mol-geo/util/flag-data.ts
+++ b/src/mol-geo/util/flag-data.ts
@@ -4,7 +4,6 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure'
import { ValueCell } from 'mol-util/value-cell'
import { Vec2 } from 'mol-math/linear-algebra'
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
@@ -72,10 +71,7 @@ export function applyFlagAction(array: Uint8Array, start: number, end: number, a
return changed
}
-export function createFlags(group: Unit.SymmetryGroup, flagData?: FlagData): FlagData {
- const instanceCount = group.units.length
- const elementCount = group.elements.length
- const count = instanceCount * elementCount
+export function createFlags(count: number, flagData?: FlagData): FlagData {
const flags = flagData && flagData.tFlag.ref.value.array.length >= count
? flagData.tFlag.ref.value
: createTextureImage(count, 1)
diff --git a/src/mol-math/graph/int/graph.ts b/src/mol-math/graph/int/graph.ts
index fb50ee13f..bc2666a2c 100644
--- a/src/mol-math/graph/int/graph.ts
+++ b/src/mol-math/graph/int/graph.ts
@@ -86,7 +86,7 @@ namespace IntGraph {
* builder.addNextEdge();
* builder.assignProperty(property, srcProp[i]);
* }
- * return builder.createGraph({ property });
+ * return builder.createGraph({ property });
*/
addNextEdge() {
const a = this.xs[this.current], b = this.ys[this.current];
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index c9645caa8..af6a4cdb2 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -23,7 +23,11 @@ namespace Element {
export function createEmptyArray(n: number): Element[] { return new Float64Array(n) as any; }
/** All the information required to access element properties */
- export interface Location { unit: Unit, element: number }
+ export interface Location {
+ unit: Unit,
+ /** Index into element (atomic/coarse) properties of unit.model */
+ element: number
+ }
export function Location(unit?: Unit, element?: number): Location { return { unit: unit as any, element: element || 0 }; }
export interface Property<T> { (location: Location): T }
export interface Predicate extends Property<boolean> { }
diff --git a/src/mol-model/structure/structure/unit/bonds.ts b/src/mol-model/structure/structure/unit/bonds.ts
index 73b6ff8d6..d72687428 100644
--- a/src/mol-model/structure/structure/unit/bonds.ts
+++ b/src/mol-model/structure/structure/unit/bonds.ts
@@ -4,23 +4,27 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Element } from '../../structure'
+import { Unit } from '../../structure'
export * from './bonds/intra-data'
export * from './bonds/intra-compute'
-interface Bond {
- readonly a: Readonly<Element.Location>,
- readonly b: Readonly<Element.Location>
-}
-
namespace Bond {
+ export interface Location {
+ readonly aUnit: Unit,
+ /** Index into aUnit.elements */
+ readonly aIndex: number,
+ readonly bUnit: Unit,
+ /** Index into bUnit.elements */
+ readonly bIndex: number,
+ }
+
export interface Loci {
readonly kind: 'bond-loci',
- readonly bonds: ReadonlyArray<Bond>
+ readonly bonds: ReadonlyArray<Location>
}
- export function Loci(bonds: ArrayLike<Bond>): Loci {
+ export function Loci(bonds: ArrayLike<Location>): Loci {
return { kind: 'bond-loci', bonds: bonds as Loci['bonds'] };
}
diff --git a/src/mol-view/label.ts b/src/mol-view/label.ts
index 311abab26..578a4a7a5 100644
--- a/src/mol-view/label.ts
+++ b/src/mol-view/label.ts
@@ -9,6 +9,14 @@ import { Unit, Element, Queries } from 'mol-model/structure';
import { Bond } from 'mol-model/structure/structure/unit/bonds';
import { Loci } from 'mol-model/loci';
+const elementLocA = Element.Location()
+const elementLocB = Element.Location()
+
+function setElementLocation(loc: Element.Location, unit: Unit, index: number) {
+ loc.unit = unit
+ loc.element = unit.elements[index]
+}
+
export function labelFirst(loci: Loci) {
if(Element.isLoci(loci)) {
const e = loci.elements[0]
@@ -18,7 +26,9 @@ export function labelFirst(loci: Loci) {
} else if (Bond.isLoci(loci)) {
const bond = loci.bonds[0]
if (bond) {
- return `${elementLabel(bond.a)} - ${elementLabel(bond.b)}`
+ setElementLocation(elementLocA, bond.aUnit, bond.aIndex)
+ setElementLocation(elementLocB, bond.bUnit, bond.bIndex)
+ return `${elementLabel(elementLocA)} - ${elementLabel(elementLocB)}`
}
}
return ''
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 1992d98de..af44bda4b 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -7,7 +7,7 @@
import Viewer from 'mol-view/viewer'
import { StateContext } from './state/context';
import { Progress } from 'mol-task';
-import { MmcifUrlToSpacefill } from './state/transform';
+import { MmcifUrlToModel, ModelToStructure, StructureToSpacefill, StructureToBond } from './state/transform';
import { UrlEntity } from './state/entity';
import { SpacefillProps } from 'mol-geo/representation/structure/spacefill';
@@ -42,9 +42,12 @@ export class Stage {
this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
}
- loadMmcifUrl (url: string) {
+ async loadMmcifUrl (url: string) {
const urlEntity = UrlEntity.ofUrl(this.ctx, url)
- MmcifUrlToSpacefill.apply(this.ctx, urlEntity, spacefillProps)
+ const modelEntity = await MmcifUrlToModel.apply(this.ctx, urlEntity)
+ const structureEntity = await ModelToStructure.apply(this.ctx, modelEntity)
+ StructureToSpacefill.apply(this.ctx, structureEntity, spacefillProps)
+ StructureToBond.apply(this.ctx, structureEntity, spacefillProps) // TODO props
}
loadPdbid (pdbid: string) {
--
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