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Commit 9208dbd6 authored by Alexander Rose's avatar Alexander Rose
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wip, carbohydrate themes

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src/mol-geo/representation/structure/cartoon.ts
+ 22
− 9
View file @ 9208dbd6
...@@ -15,6 +15,7 @@ import { PolymerGapVisual, DefaultPolymerGapProps } from './visual/polymer-gap-c ...@@ -15,6 +15,7 @@ import { PolymerGapVisual, DefaultPolymerGapProps } from './visual/polymer-gap-c
import { NucleotideBlockVisual, DefaultNucleotideBlockProps } from './visual/nucleotide-block-mesh'; import { NucleotideBlockVisual, DefaultNucleotideBlockProps } from './visual/nucleotide-block-mesh';
import { PolymerDirectionVisual, DefaultPolymerDirectionProps } from './visual/polymer-direction-wedge'; import { PolymerDirectionVisual, DefaultPolymerDirectionProps } from './visual/polymer-direction-wedge';
import { CarbohydrateSymbolVisual } from './visual/carbohydrate-symbol-mesh'; import { CarbohydrateSymbolVisual } from './visual/carbohydrate-symbol-mesh';
import { CarbohydrateLinkVisual } from './visual/carbohydrate-link-cylinder';
export const DefaultCartoonProps = { export const DefaultCartoonProps = {
...DefaultPolymerTraceProps, ...DefaultPolymerTraceProps,
...@@ -29,14 +30,20 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> { ...@@ -29,14 +30,20 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const gapRepr = StructureUnitsRepresentation(PolymerGapVisual) const gapRepr = StructureUnitsRepresentation(PolymerGapVisual)
const blockRepr = StructureUnitsRepresentation(NucleotideBlockVisual) const blockRepr = StructureUnitsRepresentation(NucleotideBlockVisual)
const directionRepr = StructureUnitsRepresentation(PolymerDirectionVisual) const directionRepr = StructureUnitsRepresentation(PolymerDirectionVisual)
const carbohydrateRepr = StructureRepresentation(CarbohydrateSymbolVisual)
// TODO move to own repr
const carbohydrateSymbolRepr = StructureRepresentation(CarbohydrateSymbolVisual)
const carbohydrateLinkRepr = StructureRepresentation(CarbohydrateLinkVisual)
return { return {
get renderObjects() { get renderObjects() {
return [ ...traceRepr.renderObjects, ...gapRepr.renderObjects, ...blockRepr.renderObjects, ...directionRepr.renderObjects, ...carbohydrateRepr.renderObjects ] return [ ...traceRepr.renderObjects, ...gapRepr.renderObjects,
...blockRepr.renderObjects, ...directionRepr.renderObjects,
...carbohydrateSymbolRepr.renderObjects, ...carbohydrateLinkRepr.renderObjects ]
}, },
get props() { get props() {
return { ...traceRepr.props, ...gapRepr.props, ...blockRepr.props, ...carbohydrateRepr.props } return { ...traceRepr.props, ...gapRepr.props, ...blockRepr.props,
...carbohydrateSymbolRepr.props, ...carbohydrateLinkRepr.props }
}, },
create: (structure: Structure, props: CartoonProps = {} as CartoonProps) => { create: (structure: Structure, props: CartoonProps = {} as CartoonProps) => {
const p = Object.assign({}, DefaultCartoonProps, props) const p = Object.assign({}, DefaultCartoonProps, props)
...@@ -45,7 +52,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> { ...@@ -45,7 +52,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
await gapRepr.create(structure, p).runInContext(ctx) await gapRepr.create(structure, p).runInContext(ctx)
await blockRepr.create(structure, p).runInContext(ctx) await blockRepr.create(structure, p).runInContext(ctx)
await directionRepr.create(structure, p).runInContext(ctx) await directionRepr.create(structure, p).runInContext(ctx)
await carbohydrateRepr.create(structure, p).runInContext(ctx) await carbohydrateSymbolRepr.create(structure, p).runInContext(ctx)
await carbohydrateLinkRepr.create(structure, p).runInContext(ctx)
}) })
}, },
update: (props: CartoonProps) => { update: (props: CartoonProps) => {
...@@ -55,7 +63,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> { ...@@ -55,7 +63,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
await gapRepr.update(p).runInContext(ctx) await gapRepr.update(p).runInContext(ctx)
await blockRepr.update(p).runInContext(ctx) await blockRepr.update(p).runInContext(ctx)
await directionRepr.update(p).runInContext(ctx) await directionRepr.update(p).runInContext(ctx)
await carbohydrateRepr.update(p).runInContext(ctx) await carbohydrateSymbolRepr.update(p).runInContext(ctx)
await carbohydrateLinkRepr.update(p).runInContext(ctx)
}) })
}, },
getLoci: (pickingId: PickingId) => { getLoci: (pickingId: PickingId) => {
...@@ -63,26 +72,30 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> { ...@@ -63,26 +72,30 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const gapLoci = gapRepr.getLoci(pickingId) const gapLoci = gapRepr.getLoci(pickingId)
const blockLoci = blockRepr.getLoci(pickingId) const blockLoci = blockRepr.getLoci(pickingId)
const directionLoci = directionRepr.getLoci(pickingId) const directionLoci = directionRepr.getLoci(pickingId)
const carbohydrateRepr = directionRepr.getLoci(pickingId) const carbohydrateSymbolLoci = carbohydrateSymbolRepr.getLoci(pickingId)
const carbohydrateLinkLoci = carbohydrateLinkRepr.getLoci(pickingId)
return !isEmptyLoci(traceLoci) ? traceLoci return !isEmptyLoci(traceLoci) ? traceLoci
: !isEmptyLoci(gapLoci) ? gapLoci : !isEmptyLoci(gapLoci) ? gapLoci
: !isEmptyLoci(blockLoci) ? blockLoci : !isEmptyLoci(blockLoci) ? blockLoci
: !isEmptyLoci(directionLoci) ? directionLoci : !isEmptyLoci(directionLoci) ? directionLoci
: carbohydrateRepr : !isEmptyLoci(carbohydrateSymbolLoci) ? carbohydrateSymbolLoci
: carbohydrateLinkLoci
}, },
mark: (loci: Loci, action: MarkerAction) => { mark: (loci: Loci, action: MarkerAction) => {
traceRepr.mark(loci, action) traceRepr.mark(loci, action)
gapRepr.mark(loci, action) gapRepr.mark(loci, action)
blockRepr.mark(loci, action) blockRepr.mark(loci, action)
directionRepr.mark(loci, action) directionRepr.mark(loci, action)
carbohydrateRepr.mark(loci, action) carbohydrateSymbolRepr.mark(loci, action)
carbohydrateLinkRepr.mark(loci, action)
}, },
destroy() { destroy() {
traceRepr.destroy() traceRepr.destroy()
gapRepr.destroy() gapRepr.destroy()
blockRepr.destroy() blockRepr.destroy()
directionRepr.destroy() directionRepr.destroy()
carbohydrateRepr.destroy() carbohydrateSymbolRepr.destroy()
carbohydrateLinkRepr.destroy()
} }
} }
} }
\ No newline at end of file
src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts 0 → 100644
+ 189
− 0
View file @ 9208dbd6
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
import { Unit, Structure, Link, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, StructureVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { createIdentityTransform, createColors } from './util/common';
import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { createMarkers, MarkerAction, MarkerData } from '../../../util/marker-data';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { Vec3 } from 'mol-math/linear-algebra';
import { deepEqual } from 'mol-util';
import { LocationIterator } from './util/location-iterator';
import { createValueColor } from '../../../util/color-data';
import { createLinkCylinderMesh, DefaultLinkCylinderProps, LinkCylinderProps } from './util/link';
import { OrderedSet } from 'mol-data/int';
// TODO create seperate visual
// for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
// const tl = carbohydrates.terminalLinks[i]
// const center = carbohydrates.elements[tl.carbohydrateIndex].geometry.center
// tl.elementUnit.conformation.position(tl.elementUnit.elements[tl.elementIndex], p)
// if (tl.fromCarbohydrate) {
// builder.addCylinder(center, p, 0.5, linkParams)
// } else {
// builder.addCylinder(p, center, 0.5, linkParams)
// }
// }
async function createCarbohydrateLinkCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
const { links, elements } = structure.carbohydrates
const builderProps = {
linkCount: links.length,
referencePosition: (edgeIndex: number) => null,
position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
const l = links[edgeIndex]
Vec3.copy(posA, elements[l.carbohydrateIndexA].geometry.center)
Vec3.copy(posB, elements[l.carbohydrateIndexB].geometry.center)
},
order: (edgeIndex: number) => 1,
flags: (edgeIndex: number) => 0
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
}
export const DefaultCarbohydrateLinkProps = {
...DefaultMeshProps,
...DefaultStructureProps,
...DefaultLinkCylinderProps,
sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
detail: 0,
unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
}
export type CarbohydrateLinkProps = Partial<typeof DefaultCarbohydrateLinkProps>
export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps> {
let renderObject: MeshRenderObject
let currentProps: typeof DefaultCarbohydrateLinkProps
let mesh: Mesh
let currentStructure: Structure
return {
get renderObject () { return renderObject },
async create(ctx: RuntimeContext, structure: Structure, props: CarbohydrateLinkProps = {}) {
currentProps = Object.assign({}, DefaultCarbohydrateLinkProps, props)
currentStructure = structure
const { colorTheme } = { ...DefaultCarbohydrateLinkProps, ...props }
const instanceCount = 1
const elementCount = currentStructure.elementCount
mesh = await createCarbohydrateLinkCylinderMesh(ctx, currentStructure, currentProps, mesh)
// console.log(mesh)
const transforms = createIdentityTransform()
const color = createValueColor(0x119911)//createColors(colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
const values: MeshValues = {
...getMeshData(mesh),
...color,
...marker,
aTransform: transforms,
elements: mesh.indexBuffer,
...createMeshValues(currentProps, counts),
aColor: ValueCell.create(new Float32Array(mesh.vertexCount * 3))
}
const state = createRenderableState(currentProps)
renderObject = createMeshRenderObject(values, state)
},
async update(ctx: RuntimeContext, props: CarbohydrateLinkProps) {
const newProps = Object.assign({}, currentProps, props)
if (!renderObject) return false
let updateColor = false
// if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
// updateColor = true
// }
// if (updateColor) {
// createColors(LinkIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
// }
updateMeshValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
currentProps = newProps
return false
},
getLoci(pickingId: PickingId) {
return getLinkLoci(pickingId, currentStructure, renderObject.id)
},
mark(loci: Loci, action: MarkerAction) {
// TODO
// markLink(loci, action, currentStructure, renderObject.values)
},
destroy() {
// TODO
}
}
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, elementId } = pickingId
if (id === objectId) {
const { links, elements } = structure.carbohydrates
const l = links[elementId]
const carbA = elements[l.carbohydrateIndexA]
const carbB = elements[l.carbohydrateIndexB]
const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
const indexB = OrderedSet.findPredecessorIndex(carbB.unit.elements, carbB.anomericCarbon)
return Link.Loci([
Link.Location(
carbA.unit, indexA as StructureElement.UnitIndex,
carbB.unit, indexB as StructureElement.UnitIndex
)
])
}
return EmptyLoci
}
// TODO
// function markLink(loci: Loci, action: MarkerAction, structure: Structure, values: MarkerData) {
// const tMarker = values.tMarker
// const links = structure.links
// const elementCount = links.bondCount
// const instanceCount = 1
// let changed = false
// const array = tMarker.ref.value.array
// if (isEveryLoci(loci)) {
// applyMarkerAction(array, 0, elementCount * instanceCount, action)
// changed = true
// } else if (Link.isLoci(loci)) {
// for (const b of loci.links) {
// const _idx = structure.links.getBondIndex(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
// if (_idx !== -1) {
// const idx = _idx
// if (applyMarkerAction(array, idx, idx + 1, action) && !changed) {
// changed = true
// }
// }
// }
// } else {
// return
// }
// if (changed) {
// ValueCell.update(tMarker, tMarker.ref.value)
// }
// }
\ No newline at end of file
src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+ 87
− 51
View file @ 9208dbd6
...@@ -7,26 +7,27 @@ ...@@ -7,26 +7,27 @@
import { ValueCell } from 'mol-util/value-cell' import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object' import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
import { Unit, Structure } from 'mol-model/structure'; import { Unit, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, StructureVisual } from '..'; import { DefaultStructureProps, StructureVisual } from '..';
import { RuntimeContext } from 'mol-task' import { RuntimeContext } from 'mol-task'
import { createIdentityTransform } from './util/common'; import { createIdentityTransform, createColors } from './util/common';
import { MeshValues } from 'mol-gl/renderable'; import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../util/mesh-data'; import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh'; import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking'; import { PickingId } from '../../../util/picking';
import { createMarkers, MarkerAction } from '../../../util/marker-data'; import { createMarkers, MarkerAction, MarkerData, applyMarkerAction } from '../../../util/marker-data';
import { Loci, EmptyLoci } from 'mol-model/loci'; import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme'; import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util'; import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder'; import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra'; import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { createValueColor } from '../../../util/color-data';
import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants'; import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
import { deepEqual } from 'mol-util';
import { LocationIterator } from './util/location-iterator';
import { OrderedSet } from 'mol-data/int';
const t = Mat4.identity() const t = Mat4.identity()
const sVec = Vec3.zero() const sVec = Vec3.zero()
const p = Vec3.zero()
const pd = Vec3.zero() const pd = Vec3.zero()
async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, mesh?: Mesh) { async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, mesh?: Mesh) {
...@@ -34,89 +35,74 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru ...@@ -34,89 +35,74 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
const carbohydrates = structure.carbohydrates const carbohydrates = structure.carbohydrates
function centerAlign(center: Vec3, normal: Vec3, direction: Vec3) {
Vec3.add(pd, center, direction)
Mat4.targetTo(t, center, pd, normal)
Mat4.setTranslation(t, center)
}
const side = 1.75 * 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4) const side = 1.75 * 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
const radius = 1.75 const radius = 1.75
const linkParams = { radiusTop: 0.4, radiusBottom: 0.4 }
for (let i = 0, il = carbohydrates.elements.length; i < il; ++i) { for (let i = 0, il = carbohydrates.elements.length; i < il; ++i) {
const c = carbohydrates.elements[i]; const c = carbohydrates.elements[i];
if (!c.hasRing) continue;
const cGeo = c.geometry!
const shapeType = getSaccharideShape(c.component.type) const shapeType = getSaccharideShape(c.component.type)
const { center, normal, direction } = c.geometry
Vec3.add(pd, center, direction)
Mat4.targetTo(t, center, pd, normal)
Mat4.setTranslation(t, center)
builder.setId(i)
switch (shapeType) { switch (shapeType) {
case SaccharideShapes.FilledSphere: case SaccharideShapes.FilledSphere:
builder.addSphere(cGeo.center, radius, 2) builder.addSphere(center, radius, 2)
break; break;
case SaccharideShapes.FilledCube: case SaccharideShapes.FilledCube:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side) Mat4.scaleUniformly(t, t, side)
builder.addBox(t) builder.addBox(t)
break; break;
case SaccharideShapes.CrossedCube: case SaccharideShapes.CrossedCube:
// TODO split // TODO split
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side) Mat4.scaleUniformly(t, t, side)
builder.addBox(t) builder.addBox(t)
break; break;
case SaccharideShapes.FilledCone: case SaccharideShapes.FilledCone:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side * 1.2) Mat4.scaleUniformly(t, t, side * 1.2)
builder.addOctagonalPyramid(t) builder.addOctagonalPyramid(t)
break break
case SaccharideShapes.DevidedCone: case SaccharideShapes.DevidedCone:
// TODO split // TODO split
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side * 1.2) Mat4.scaleUniformly(t, t, side * 1.2)
builder.addOctagonalPyramid(t) builder.addOctagonalPyramid(t)
break break
case SaccharideShapes.FlatBox: case SaccharideShapes.FlatBox:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2)) Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addBox(t) builder.addBox(t)
break break
case SaccharideShapes.FilledStar: case SaccharideShapes.FilledStar:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
builder.addStar(t, { outerRadius: side, innerRadius: side / 2, thickness: side / 2, pointCount: 5 }) builder.addStar(t, { outerRadius: side, innerRadius: side / 2, thickness: side / 2, pointCount: 5 })
break break
case SaccharideShapes.FilledDiamond: case SaccharideShapes.FilledDiamond:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4)) Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t) builder.addOctahedron(t)
break break
case SaccharideShapes.DividedDiamond: case SaccharideShapes.DividedDiamond:
// TODO split // TODO split
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4)) Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t) builder.addOctahedron(t)
break break
case SaccharideShapes.FlatDiamond: case SaccharideShapes.FlatDiamond:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2)) Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2))
builder.addDiamondPrism(t) builder.addDiamondPrism(t)
break break
case SaccharideShapes.Pentagon: case SaccharideShapes.Pentagon:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90) Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2)) Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addPentagonalPrism(t) builder.addPentagonalPrism(t)
break break
case SaccharideShapes.FlatHexagon: case SaccharideShapes.FlatHexagon:
default: default:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZYZ90) Mat4.mul(t, t, Mat4.rotZYZ90)
Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side , side / 2)) Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side , side / 2))
builder.addHexagonalPrism(t) builder.addHexagonalPrism(t)
...@@ -124,24 +110,6 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru ...@@ -124,24 +110,6 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
} }
} }
for (let i = 0, il = carbohydrates.links.length; i < il; ++i) {
const l = carbohydrates.links[i]
const centerA = carbohydrates.elements[l.carbohydrateIndexA].geometry!.center
const centerB = carbohydrates.elements[l.carbohydrateIndexB].geometry!.center
builder.addCylinder(centerA, centerB, 0.5, linkParams)
}
for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
const tl = carbohydrates.terminalLinks[i]
const center = carbohydrates.elements[tl.carbohydrateIndex].geometry!.center
tl.elementUnit.conformation.position(tl.elementUnit.elements[tl.elementIndex], p)
if (tl.fromCarbohydrate) {
builder.addCylinder(center, p, 0.5, linkParams)
} else {
builder.addCylinder(p, center, 0.5, linkParams)
}
}
return builder.getMesh() return builder.getMesh()
} }
...@@ -166,14 +134,14 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr ...@@ -166,14 +134,14 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
currentProps = Object.assign({}, DefaultCarbohydrateSymbolProps, props) currentProps = Object.assign({}, DefaultCarbohydrateSymbolProps, props)
currentStructure = structure currentStructure = structure
const { colorTheme } = { ...DefaultCarbohydrateSymbolProps, ...props }
const instanceCount = 1 const instanceCount = 1
const elementCount = currentStructure.elementCount const elementCount = currentStructure.elementCount
mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh) mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
// console.log(mesh)
const transforms = createIdentityTransform() const transforms = createIdentityTransform()
const color = createValueColor(0x999911) // TODO const color = createColors(createCarbohydrateIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount) const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount } const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
...@@ -196,19 +164,87 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr ...@@ -196,19 +164,87 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
if (!renderObject) return false if (!renderObject) return false
let updateColor = false
if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
updateColor = true
}
if (updateColor) {
createColors(createCarbohydrateIterator(currentStructure), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps) updateMeshValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps) updateRenderableState(renderObject.state, newProps)
currentProps = newProps
return false return false
}, },
getLoci(pickingId: PickingId) { getLoci(pickingId: PickingId) {
return EmptyLoci return getCarbohydrateLoci(pickingId, currentStructure, renderObject.id)
}, },
mark(loci: Loci, action: MarkerAction) { mark(loci: Loci, action: MarkerAction) {
// TODO markCarbohydrate(loci, action, currentStructure, renderObject.values)
}, },
destroy() { destroy() {
// TODO // TODO
} }
} }
} }
function createCarbohydrateIterator(structure: Structure): LocationIterator {
const carbs = structure.carbohydrates.elements
const elementCount = carbs.length
const instanceCount = 1
const location = StructureElement.create()
const getLocation = (elementIndex: number, instanceIndex: number) => {
const carb = carbs[elementIndex]
location.unit = carb.unit
location.element = carb.anomericCarbon
return location
}
return LocationIterator(elementCount, instanceCount, getLocation)
}
function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, elementId } = pickingId
if (id === objectId) {
const carb = structure.carbohydrates.elements[elementId]
const { unit } = carb
const index = OrderedSet.findPredecessorIndex(unit.elements, carb.anomericCarbon)
const indices = OrderedSet.ofSingleton(index as StructureElement.UnitIndex)
return StructureElement.Loci([{ unit, indices }])
}
return EmptyLoci
}
function markCarbohydrate(loci: Loci, action: MarkerAction, structure: Structure, values: MarkerData) {
const tMarker = values.tMarker
const { byUnitAndElement } = structure.carbohydrates
const elementCount = structure.carbohydrates.elements.length
let changed = false
const array = tMarker.ref.value.array
if (isEveryLoci(loci)) {
if (applyMarkerAction(array, 0, elementCount, action)) {
changed = true
}
} else if (StructureElement.isLoci(loci)) {
for (const e of loci.elements) {
OrderedSet.forEach(e.indices, index => {
const idx = byUnitAndElement(e.unit, e.unit.elements[index])
if (idx !== undefined) {
if (applyMarkerAction(array, idx, idx + 1, action) && !changed) {
changed = true
}
}
})
}
} else {
return
}
if (changed) {
ValueCell.update(tMarker, tMarker.ref.value)
}
}
\ No newline at end of file
src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+ 1
− 1
View file @ 9208dbd6
...@@ -105,7 +105,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?: ...@@ -105,7 +105,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
} }
if (i % 10000 === 0 && ctx.shouldUpdate) { if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Gap mesh', current: i }); await ctx.update({ message: 'Nucleotide block mesh', current: i });
} }
++i ++i
} }
......
src/mol-geo/representation/structure/visual/util/common.ts
+ 3
− 0
View file @ 9208dbd6
...@@ -16,6 +16,7 @@ import { ColorTheme, SizeTheme } from '../../../../theme'; ...@@ -16,6 +16,7 @@ import { ColorTheme, SizeTheme } from '../../../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../../../theme/structure/color'; import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../../../theme/structure/color';
import { ValueCell, defaults } from 'mol-util'; import { ValueCell, defaults } from 'mol-util';
import { LocationIterator } from './location-iterator'; import { LocationIterator } from './location-iterator';
import { carbohydrateSymbolColorData } from '../../../../theme/structure/color/carbohydrate-symbol';
export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) { export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) {
const unitCount = units.length const unitCount = units.length
...@@ -37,6 +38,8 @@ export function createColors(locationIt: LocationIterator, props: ColorTheme, co ...@@ -37,6 +38,8 @@ export function createColors(locationIt: LocationIterator, props: ColorTheme, co
switch (props.name) { switch (props.name) {
case 'atom-index': case 'atom-index':
return elementIndexColorData(locationIt, colorData) return elementIndexColorData(locationIt, colorData)
case 'carbohydrate-symbol':
return carbohydrateSymbolColorData(locationIt, colorData)
case 'chain-id': case 'chain-id':
return chainIdColorData(locationIt, colorData) return chainIdColorData(locationIt, colorData)
case 'element-symbol': case 'element-symbol':
......
src/mol-geo/theme/index.ts
+ 5
− 19
View file @ 9208dbd6
...@@ -5,8 +5,6 @@ ...@@ -5,8 +5,6 @@
*/ */
import { Color } from 'mol-util/color'; import { Color } from 'mol-util/color';
// import { Loci } from 'mol-model/loci';
// import { Structure } from 'mol-model/structure';
export interface UniformColorTheme { export interface UniformColorTheme {
name: 'uniform' name: 'uniform'
...@@ -14,27 +12,15 @@ export interface UniformColorTheme { ...@@ -14,27 +12,15 @@ export interface UniformColorTheme {
} }
export interface ScaleColorTheme { export interface ScaleColorTheme {
name: 'atom-index' | 'chain-id' | 'element-symbol' | 'instance-index' name: 'atom-index' | 'chain-id'| 'instance-index'
domain?: [number, number] domain?: [number, number]
} }
// interface StructureColorProvider { export interface TableColorTheme {
// uniform(): Color name: 'carbohydrate-symbol' | 'element-symbol'
// instance(instanceIdx: number): Color }
// element(elementIdx: number): Color
// elementInstance(elementIdx: number, instanceIdx: number): Color
// lociColor(loci: Loci): Color
// }
// export namespace ColorProvider {
// export function fromLociColor(lociColor: (loci: Loci) => Color) {
// return
// }
// }
export type ColorTheme = UniformColorTheme | ScaleColorTheme export type ColorTheme = UniformColorTheme | ScaleColorTheme | TableColorTheme
export interface UniformSizeTheme { export interface UniformSizeTheme {
name: 'uniform', name: 'uniform',
......
src/mol-geo/theme/structure/color/carbohydrate-symbol.ts 0 → 100644
+ 45
− 0
View file @ 9208dbd6
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
import { ColorData, createElementColor } from '../../../util/color-data';
import { ColorScale, Color } from 'mol-util/color';
import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
function getAsymId(unit: Unit): StructureElement.Property<string> {
switch (unit.kind) {
case Unit.Kind.Atomic:
return StructureProperties.chain.label_asym_id
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
return StructureProperties.coarse.asym_id
}
}
export function carbohydrateSymbolColorData(locationIt: LocationIterator, colorData?: ColorData) {
const l = StructureElement.create()
function colorFn(locationValue: LocationValue): Color {
const { location } = locationValue
if (StructureElement.isLocation(location)) {
const map = location.unit.model.properties.asymIdSerialMap
const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
const asym_id = getAsymId(location.unit)
return scale.color(map.get(asym_id(location)) || 0)
} else if (Link.isLocation(location)) {
const map = location.aUnit.model.properties.asymIdSerialMap
const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
const asym_id = getAsymId(location.aUnit)
l.unit = location.aUnit
l.element = location.aUnit.elements[location.aIndex]
return scale.color(map.get(asym_id(l)) || 0)
}
return 0
}
return createElementColor(locationIt, colorFn, colorData)
}
\ No newline at end of file
src/mol-model/structure/structure/carbohydrates/compute.ts
+ 22
− 9
View file @ 9208dbd6
...@@ -18,7 +18,7 @@ import StructureElement from '../element'; ...@@ -18,7 +18,7 @@ import StructureElement from '../element';
import Structure from '../structure'; import Structure from '../structure';
import Unit from '../unit'; import Unit from '../unit';
import { SaccharideNameMap, UnknownSaccharideComponent } from './constants'; import { SaccharideNameMap, UnknownSaccharideComponent } from './constants';
import { CarbohydrateElement, CarbohydrateLink, Carbohydrates, CarbohydrateTerminalLink } from './data'; import { CarbohydrateElement, CarbohydrateLink, Carbohydrates, CarbohydrateTerminalLink, PartialCarbohydrateElement } from './data';
import { UnitRings, UnitRing } from '../unit/rings'; import { UnitRings, UnitRing } from '../unit/rings';
import { ElementIndex } from '../../model/indexing'; import { ElementIndex } from '../../model/indexing';
...@@ -49,7 +49,7 @@ function getAnomericCarbon(unit: Unit.Atomic, ringAtoms: ArrayLike<StructureElem ...@@ -49,7 +49,7 @@ function getAnomericCarbon(unit: Unit.Atomic, ringAtoms: ArrayLike<StructureElem
// possibly an anomeric carbon if this is a mono-saccharide without a glycosidic bond // possibly an anomeric carbon if this is a mono-saccharide without a glycosidic bond
indexHasOxygenAndCarbon = ei indexHasOxygenAndCarbon = ei
} else if (label_atom_id.value(ei).startsWith('C1')) { } else if (label_atom_id.value(ei).startsWith('C1')) {
// likely the anomeric carbon as it is name C1 by convention // likely the anomeric carbon as it is named C1 by convention
indexHasC1Name = ei indexHasC1Name = ei
} else { } else {
// use any carbon as a fallback // use any carbon as a fallback
...@@ -122,6 +122,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates { ...@@ -122,6 +122,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = [] const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = [] const terminalLinks: CarbohydrateTerminalLink[] = []
const elements: CarbohydrateElement[] = [] const elements: CarbohydrateElement[] = []
const partialElements: PartialCarbohydrateElement[] = []
const elementsWithRingMap = new Map<string, number>() const elementsWithRingMap = new Map<string, number>()
...@@ -173,10 +174,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates { ...@@ -173,10 +174,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const sugarRings = filterFusedRings(unit.rings, sugarResidueMap.get(residueIndex)); const sugarRings = filterFusedRings(unit.rings, sugarResidueMap.get(residueIndex));
if (!sugarRings || !sugarRings.length) { if (!sugarRings || !sugarRings.length) {
elements.push({ partialElements.push({ unit, residueIndex, component: saccharideComp })
hasRing: false,
unit, residueIndex, component: saccharideComp
})
continue; continue;
} }
...@@ -199,8 +197,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates { ...@@ -199,8 +197,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
elementsWithRingMap.set(elementKey(residueIndex, unit.id, altId), elementIndex) elementsWithRingMap.set(elementKey(residueIndex, unit.id, altId), elementIndex)
elements.push({ elements.push({
geometry: { center, normal, direction }, geometry: { center, normal, direction },
hasRing: true, component: saccharideComp,
unit, residueIndex, component: saccharideComp unit, residueIndex, anomericCarbon
}) })
} }
...@@ -279,5 +277,20 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates { ...@@ -279,5 +277,20 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}) })
} }
return { links, terminalLinks, elements } // build lookup map
const map = new Map<string, number>()
for (let i = 0, il = elements.length; i < il; ++i) {
const { unit, anomericCarbon } = elements[i]
map.set(key(unit, anomericCarbon), i)
}
function key(unit: Unit, anomericCarbon: ElementIndex) {
return `${unit.id}|${anomericCarbon}`
}
function byUnitAndElement(unit: Unit, anomericCarbon: ElementIndex) {
return map.get(key(unit, anomericCarbon))
}
return { links, terminalLinks, elements, partialElements, byUnitAndElement }
} }
\ No newline at end of file
src/mol-model/structure/structure/carbohydrates/data.ts
+ 13
− 5
View file @ 9208dbd6
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
import Unit from '../unit'; import Unit from '../unit';
import { Vec3 } from 'mol-math/linear-algebra'; import { Vec3 } from 'mol-math/linear-algebra';
import { ResidueIndex } from '../../model'; import { ResidueIndex, ElementIndex } from '../../model';
import { SaccharideComponent } from './constants'; import { SaccharideComponent } from './constants';
export interface CarbohydrateLink { export interface CarbohydrateLink {
...@@ -23,16 +23,24 @@ export interface CarbohydrateTerminalLink { ...@@ -23,16 +23,24 @@ export interface CarbohydrateTerminalLink {
} }
export interface CarbohydrateElement { export interface CarbohydrateElement {
// geometry is only defined if at least one ring is present. readonly geometry: { readonly center: Vec3, readonly normal: Vec3, readonly direction: Vec3 },
readonly geometry?: { readonly center: Vec3, readonly normal: Vec3, readonly direction: Vec3 }, readonly anomericCarbon: ElementIndex,
readonly hasRing: boolean,
readonly unit: Unit.Atomic, readonly unit: Unit.Atomic,
readonly residueIndex: ResidueIndex, readonly residueIndex: ResidueIndex,
readonly component: SaccharideComponent readonly component: SaccharideComponent,
}
// partial carbohydrate with no ring present
export interface PartialCarbohydrateElement {
readonly unit: Unit.Atomic,
readonly residueIndex: ResidueIndex,
readonly component: SaccharideComponent,
} }
export interface Carbohydrates { export interface Carbohydrates {
links: ReadonlyArray<CarbohydrateLink> links: ReadonlyArray<CarbohydrateLink>
terminalLinks: ReadonlyArray<CarbohydrateTerminalLink> terminalLinks: ReadonlyArray<CarbohydrateTerminalLink>
elements: ReadonlyArray<CarbohydrateElement> elements: ReadonlyArray<CarbohydrateElement>
partialElements: ReadonlyArray<PartialCarbohydrateElement>
byUnitAndElement: (unit: Unit, element: ElementIndex) => number | undefined
} }
\ No newline at end of file
src/mol-view/stage.ts
+ 4
− 3
View file @ 9208dbd6
...@@ -110,7 +110,8 @@ export class Stage { ...@@ -110,7 +110,8 @@ export class Stage {
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`) // this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`) // this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)
// this.loadMmcifUrl(`../../examples/1crn.cif`) // this.loadMmcifUrl(`../../examples/1crn.cif`)
// this.loadPdbid('1zag') // temp // this.loadPdbid('5u0q') // mixed dna/rna in same polymer
// this.loadPdbid('5u0q') // temp
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`) // ok // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`) // ok
...@@ -154,8 +155,8 @@ export class Stage { ...@@ -154,8 +155,8 @@ export class Stage {
} }
loadPdbid (pdbid: string) { loadPdbid (pdbid: string) {
return this.loadMmcifUrl(`http://www.ebi.ac.uk/pdbe/static/entry/${pdbid}_updated.cif`) // return this.loadMmcifUrl(`http://www.ebi.ac.uk/pdbe/static/entry/${pdbid}_updated.cif`)
// return this.loadMmcifUrl(`https://files.rcsb.org/download/${pdbid}.cif`) return this.loadMmcifUrl(`https://files.rcsb.org/download/${pdbid}.cif`)
} }
dispose () { dispose () {
......
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