diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index c2616d4970b52d6ac0dbe104494fa3072915b4b1..1682f2ed840c6543a2cf094dc2a737509d339d4e 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -17,10 +17,10 @@ import Spacefill, { SpacefillProps } from 'mol-geo/representation/structure/spac
import Point, { PointProps } from 'mol-geo/representation/structure/point'
import { Run } from 'mol-task'
-import { Symmetry, Structure } from 'mol-model/structure'
+import { Symmetry, Structure, Model } from 'mol-model/structure'
// import mcubes from './utils/mcubes'
-import { getStructuresFromPdbId, getStructuresFromFile, log } from './utils'
+import { getModelFromPdbId, getModelFromFile, log } from './utils'
import { StructureRepresentation } from 'mol-geo/representation/structure';
import { Color } from 'mol-util/color';
// import Cylinder from 'mol-geo/primitive/cylinder';
@@ -87,18 +87,24 @@ export default class State {
this.viewer.animate()
}
- async initStructure (structure: Structure) {
+ async initStructure (model: Model) {
const { viewer, loading } = this
viewer.clear()
- const struct = await Run(Symmetry.buildAssembly(structure, '1'), log, 100)
+ let structure: Structure
+ const assemblies = model.symmetry.assemblies
+ if (assemblies.length) {
+ structure = await Run(Symmetry.buildAssembly(Structure.ofModel(model), '1'), log, 100)
+ } else {
+ structure = Structure.ofModel(model)
+ }
this.pointRepr = StructureRepresentation(Point)
- await Run(this.pointRepr.create(struct, this.getPointProps()), log, 100)
+ await Run(this.pointRepr.create(structure, this.getPointProps()), log, 100)
viewer.add(this.pointRepr)
this.spacefillRepr = StructureRepresentation(Spacefill)
- await Run(this.spacefillRepr.create(struct, this.getSpacefillProps()), log, 100)
+ await Run(this.spacefillRepr.create(structure, this.getSpacefillProps()), log, 100)
viewer.add(this.spacefillRepr)
this.updateVisibility()
@@ -112,7 +118,7 @@ export default class State {
this.viewer.clear()
this.loading.next(true)
- const structures = await getStructuresFromFile(file)
+ const structures = await getModelFromFile(file)
this.initStructure(structures[0])
}
@@ -121,7 +127,7 @@ export default class State {
if (this.pdbId.length !== 4) return
this.loading.next(true)
- const structures = await getStructuresFromPdbId(this.pdbId)
+ const structures = await getModelFromPdbId(this.pdbId)
this.initStructure(structures[0])
}
@@ -154,87 +160,4 @@ export default class State {
}
this.viewer.requestDraw()
}
-}
-
-
-
-// async foo () {
-// const p1 = Vec3.create(0, 4, 0)
-// const p2 = Vec3.create(-3, 0, 0)
-
-// // const position = ValueCell.create(new Float32Array([0, -1, 0, -1, 0, 0, 1, 1, 0]))
-// // const normal = ValueCell.create(new Float32Array([0, 0, 0, 0, 0, 0, 0, 0, 0]))
-
-// const transformArray1 = ValueCell.create(new Float32Array(16))
-// const transformArray2 = ValueCell.create(new Float32Array(16 * 3))
-// const m4 = Mat4.identity()
-// Mat4.toArray(m4, transformArray1.ref.value, 0)
-// Mat4.toArray(m4, transformArray2.ref.value, 0)
-// Mat4.setTranslation(m4, p1)
-// Mat4.toArray(m4, transformArray2.ref.value, 16)
-// Mat4.setTranslation(m4, p2)
-// Mat4.toArray(m4, transformArray2.ref.value, 32)
-
-// const color = ValueCell.create(createColorTexture(3))
-// color.ref.value.set([
-// 0, 0, 255,
-// 0, 255, 0,
-// 255, 0, 0
-// ])
-
-// // const points = createRenderObject('point', {
-// // position,
-// // transform: transformArray1
-// // })
-// // // renderer.add(points)
-
-// // const mesh = createRenderObject('mesh', {
-// // position,
-// // normal,
-// // color,
-// // transform: transformArray2
-// // })
-// // renderer.add(mesh)
-
-// // const cylinder = Cylinder({ height: 3, radiusBottom: 0.5, radiusTop: 0.5 })
-// // console.log(cylinder)
-// // const cylinderMesh = createRenderObject('mesh', {
-// // position: ValueCell.create(cylinder.vertices),
-// // normal: ValueCell.create(cylinder.normals),
-// // color,
-// // transform: transformArray2
-// // }, cylinder.indices)
-// // renderer.add(cylinderMesh)
-
-// // const sphere = Icosahedron()
-// // console.log(sphere)
-
-// // const box = Box()
-// // console.log(box)
-
-// // const points2 = createRenderObject('point', {
-// // position: ValueCell.create(new Float32Array(box.vertices)),
-// // transform: transformArray1
-// // })
-// // renderer.add(points2)
-
-// // let rr = 0.7;
-// // function cubesF(x: number, y: number, z: number) {
-// // return x * x + y * y + z * z - rr * rr;
-// // }
-// // let cubes = await mcubes(cubesF);
-
-// // const makeCubesMesh = () => createRenderObject('mesh', {
-// // position: cubes.surface.vertexBuffer,
-// // normal: cubes.surface.normalBuffer,
-// // color,
-// // transform: transformArray2,
-// // elements: cubes.surface.indexBuffer,
-
-// // instanceCount: transformArray2.ref.value.length / 16,
-// // elementCount: cubes.surface.triangleCount,
-// // positionCount: cubes.surface.vertexCount
-// // }, {});
-// // const mesh2 = makeCubesMesh();
-// // renderer.add(mesh2)
-// }
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/apps/render-test/utils/index.ts b/src/apps/render-test/utils/index.ts
index 738bd7851a542c6522ccd07cb869a73e11ee6891..3225ea529bb68181355139fea35389f62fce238d 100644
--- a/src/apps/render-test/utils/index.ts
+++ b/src/apps/render-test/utils/index.ts
@@ -6,7 +6,7 @@
import CIF from 'mol-io/reader/cif'
import { Run, Progress } from 'mol-task'
-import { Structure } from 'mol-model/structure'
+import { Model } from 'mol-model/structure'
export function log(progress: Progress) {
const p = progress.root.progress
@@ -20,10 +20,10 @@ export async function parseCif(data: string|Uint8Array) {
return parsed
}
-export async function getStructuresFromPdbId(pdbid: string) {
+export async function getModelFromPdbId(pdbid: string) {
const data = await fetch(`https://files.rcsb.org/download/${pdbid}.cif`)
const parsed = await parseCif(await data.text())
- return Structure.ofData({ kind: 'mmCIF', data: CIF.schema.mmCIF(parsed.result.blocks[0]) })
+ return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(parsed.result.blocks[0]) })
}
const readFileAsText = (file: File) => {
@@ -38,7 +38,7 @@ const readFileAsText = (file: File) => {
})
}
-export async function getStructuresFromFile(file: File) {
+export async function getModelFromFile(file: File) {
const parsed = await parseCif(await readFileAsText(file))
- return Structure.ofData({ kind: 'mmCIF', data: CIF.schema.mmCIF(parsed.result.blocks[0]) })
+ return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(parsed.result.blocks[0]) })
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 6f994adee431d2f060fd375b62031bf9d47a67b0..4e2f9168361a547201b789eb28fdbddc9b66309b 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -18,6 +18,7 @@ import { VdwRadius } from 'mol-model/structure/model/properties/atomic';
import { createTransforms, createColors } from './utils';
import { ColorTheme } from '../../theme';
import VertexMap from '../../shape/vertex-map';
+import CoarseGrained from 'mol-model/structure/model/properties/coarse-grained';
export const DefaultSpacefillProps = {
detail: 0,
@@ -25,9 +26,9 @@ export const DefaultSpacefillProps = {
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
-function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: number) {
- return Task.create('Spacefill', async ctx => {
- const meshBuilder = MeshBuilder.create()
+function buildAtomSpheres(meshBuilder: MeshBuilder, unit: Unit, elementGroup: ElementGroup, detail: number) {
+ return Task.create('Atom spheres', async ctx => {
+ if (!Unit.isAtomic(unit)) return
const v = Vec3.zero()
const m = Mat4.identity()
@@ -43,15 +44,54 @@ function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: num
Mat4.setTranslation(m, v)
meshBuilder.setId(i)
- meshBuilder.addIcosahedron(m, {
- radius: VdwRadius(type_symbol.value(e)),
- detail
- })
+ meshBuilder.addIcosahedron(m, { radius: VdwRadius(type_symbol.value(e)), detail })
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Atom spheres', current: i, max: elementCount });
+ }
+ }
+ })
+}
+
+function buildCoarseSpheres(meshBuilder: MeshBuilder, unit: Unit, elementGroup: ElementGroup, detail: number) {
+ return Task.create('Coarse spheres', async ctx => {
+ if (!Unit.isCoarse(unit) || unit.elementType !== CoarseGrained.ElementType.Sphere) return
+
+ const v = Vec3.zero()
+ const m = Mat4.identity()
+
+ const { x, y, z, radius } = unit.model.coarseGrained.spheres
+ const elementCount = OrderedSet.size(elementGroup.elements)
+ console.log('building coarse spheres', elementCount)
+ for (let i = 0; i < elementCount; i++) {
+ const e = OrderedSet.getAt(elementGroup.elements, i)
+ v[0] = x[e]
+ v[1] = y[e]
+ v[2] = z[e]
+ Mat4.setTranslation(m, v)
+
+ meshBuilder.setId(i)
+ meshBuilder.addIcosahedron(m, { radius: radius.value(e), detail })
if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Spacefill', current: i, max: elementCount });
+ await ctx.update({ message: 'Coarse spheres', current: i, max: elementCount });
}
}
+ })
+}
+
+function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: number) {
+ return Task.create('Spacefill', async ctx => {
+ const meshBuilder = MeshBuilder.create()
+
+ if (Unit.isAtomic(unit)) {
+ await ctx.runChild(buildAtomSpheres(meshBuilder, unit, elementGroup, detail))
+ }
+
+ if (Unit.isCoarse(unit) && unit.elementType === CoarseGrained.ElementType.Sphere) {
+ console.log('building coarse spheres')
+ await ctx.runChild(buildCoarseSpheres(meshBuilder, unit, elementGroup, detail))
+ }
return meshBuilder.getMesh()
})
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index a7a1d158781faa97ca8f3100319e74b4b2a05c0b..65f7b35962d4b6eb769b8d34de2d4ff3ece77f59 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -12,7 +12,7 @@ import { createUniformSize } from '../../util/size-data';
import { vdwSizeData } from '../../theme/structure/size/vdw';
import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
-import { atomIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
+import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
export function createTransforms(units: ReadonlyArray<Unit>) {
const unitCount = units.length
@@ -26,7 +26,7 @@ export function createTransforms(units: ReadonlyArray<Unit>) {
export function createColors(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, vertexMap: VertexMap, props: ColorTheme) {
switch (props.name) {
case 'atom-index':
- return atomIndexColorData({ units, elementGroup, vertexMap })
+ return elementIndexColorData({ units, elementGroup, vertexMap })
case 'chain-id':
return chainIdColorData({ units, elementGroup, vertexMap })
case 'element-symbol':
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index a6bd36b1aad179b0f1ac8269c47fcaa357994a53..43dfc0db654e236eaf9af30e8ed49b16d033d5be 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -4,21 +4,32 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementGroup, Model } from 'mol-model/structure';
+import { ElementGroup, Unit, Queries, Element } from 'mol-model/structure';
import { StructureColorDataProps } from '.';
import { createAttributeOrElementColor } from '../../../util/color-data';
import { ColorScale } from 'mol-util/color';
+import { Column } from 'mol-data/db';
-function createChainIdMap(model: Model) {
- const { chains } = model.hierarchy
- const { label_asym_id } = chains
-
+function createChainIdMap(unit: Unit) {
const map = new Map<string, number>()
let index = 0
- for (let i = 0, il = chains._rowCount; i < il; ++i) {
- const chainId = label_asym_id.value(i)
+ let count: number
+ let asym_id: Column<string>
+ if (Unit.isAtomic(unit)) {
+ asym_id = unit.hierarchy.chains.label_asym_id
+ count = unit.hierarchy.chains._rowCount
+ } else if (Unit.isCoarse(unit)) {
+ asym_id = unit.siteBases.asym_id
+ count = unit.siteBases.count
+ } else {
+ console.warn('Unknown unit type')
+ return { map, count: index }
+ }
+
+ for (let i = 0; i < count; ++i) {
+ const chainId = asym_id.value(i)
if (map.get(chainId) === undefined) {
map.set(chainId, index)
index += 1
@@ -31,20 +42,25 @@ export function chainIdColorData(props: StructureColorDataProps) {
const { units, elementGroup, vertexMap } = props
const unit = units[0]
- const { chains, chainSegments } = unit.model.hierarchy
- const { label_asym_id } = chains
- const { map, count } = createChainIdMap(unit.model)
+ const { map, count } = createChainIdMap(unit)
const domain = [ 0, count - 1 ]
const scale = ColorScale.create({ domain })
+ let asym_id: Element.Property<string>
+ if (Unit.isAtomic(unit)) {
+ asym_id = Queries.props.chain.label_asym_id
+ } else if (Unit.isCoarse(unit)) {
+ asym_id = Queries.props.coarse_grained.asym_id
+ }
+
+ const l = Element.Location()
+ l.unit = unit
+
return createAttributeOrElementColor(vertexMap, {
colorFn: (elementIdx: number) => {
- const aI = ElementGroup.getAt(elementGroup, elementIdx);
- const cI = chainSegments.segmentMap[aI]
- const chainId = label_asym_id.value(cI)
-
- return scale.color(map.get(chainId) || 0)
+ l.element = ElementGroup.getAt(elementGroup, elementIdx)
+ return scale.color(map.get(asym_id(l)) || 0)
},
vertexMap
})
diff --git a/src/mol-geo/theme/structure/color/atom-index.ts b/src/mol-geo/theme/structure/color/element-index.ts
similarity index 91%
rename from src/mol-geo/theme/structure/color/atom-index.ts
rename to src/mol-geo/theme/structure/color/element-index.ts
index 1bd61c99a132c2a85b027b3cbcb7c1fdb189be2b..b205043d46ffb5a1fee65485dc9f026644f7a2c6 100644
--- a/src/mol-geo/theme/structure/color/atom-index.ts
+++ b/src/mol-geo/theme/structure/color/element-index.ts
@@ -9,7 +9,7 @@ import { StructureColorDataProps } from '.';
import { OrderedSet } from 'mol-data/int';
import { createElementInstanceColor } from '../../../util/color-data';
-export function atomIndexColorData(props: StructureColorDataProps) {
+export function elementIndexColorData(props: StructureColorDataProps) {
const { units, elementGroup, vertexMap } = props
const instanceCount = units.length
const elementCount = OrderedSet.size(elementGroup.elements)
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 435874109499156465610b627b86287d4f2d6b6c..82d5b22a6c6535744d2c1000f5d0948bdace8311 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -13,7 +13,7 @@ export interface StructureColorDataProps {
vertexMap: VertexMap
}
-export { atomIndexColorData } from './atom-index'
+export { elementIndexColorData } from './element-index'
export { chainIdColorData } from './chain-id'
export { elementSymbolColorData } from './element-symbol'
export { instanceIndexColorData } from './instance-index'
\ No newline at end of file
diff --git a/src/mol-view/viewer.ts b/src/mol-view/viewer.ts
index 0a0f42a580bf9e2b7774b8fc251b2db4b8d49a91..7fef68f8545115e60d9cc8c39910d5050426c9f7 100644
--- a/src/mol-view/viewer.ts
+++ b/src/mol-view/viewer.ts
@@ -55,7 +55,7 @@ namespace Viewer {
input.resize.subscribe(handleResize)
const camera = PerspectiveCamera.create({
- near: 0.01,
+ near: 0.1,
far: 10000,
position: Vec3.create(0, 0, 50)
})