diff --git a/src/mol-geo/representation/structure/cartoon.ts b/src/mol-geo/representation/structure/cartoon.ts
index 6296fce4978ef5d1795770ebb30baae35f74a9af..37c540cd6551fd95e93f2e4b5ffec426c4a0ba61 100644
--- a/src/mol-geo/representation/structure/cartoon.ts
+++ b/src/mol-geo/representation/structure/cartoon.ts
@@ -15,6 +15,7 @@ import { PolymerGapVisual, DefaultPolymerGapProps } from './visual/polymer-gap-c
import { NucleotideBlockVisual, DefaultNucleotideBlockProps } from './visual/nucleotide-block-mesh';
import { PolymerDirectionVisual, DefaultPolymerDirectionProps } from './visual/polymer-direction-wedge';
import { CarbohydrateSymbolVisual } from './visual/carbohydrate-symbol-mesh';
+import { CarbohydrateLinkVisual } from './visual/carbohydrate-link-cylinder';
export const DefaultCartoonProps = {
...DefaultPolymerTraceProps,
@@ -29,14 +30,20 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const gapRepr = StructureUnitsRepresentation(PolymerGapVisual)
const blockRepr = StructureUnitsRepresentation(NucleotideBlockVisual)
const directionRepr = StructureUnitsRepresentation(PolymerDirectionVisual)
- const carbohydrateRepr = StructureRepresentation(CarbohydrateSymbolVisual)
+
+ // TODO move to own repr
+ const carbohydrateSymbolRepr = StructureRepresentation(CarbohydrateSymbolVisual)
+ const carbohydrateLinkRepr = StructureRepresentation(CarbohydrateLinkVisual)
return {
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() {
- 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) => {
const p = Object.assign({}, DefaultCartoonProps, props)
@@ -45,7 +52,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
await gapRepr.create(structure, p).runInContext(ctx)
await blockRepr.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) => {
@@ -55,7 +63,8 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
await gapRepr.update(p).runInContext(ctx)
await blockRepr.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) => {
@@ -63,26 +72,30 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const gapLoci = gapRepr.getLoci(pickingId)
const blockLoci = blockRepr.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
: !isEmptyLoci(gapLoci) ? gapLoci
: !isEmptyLoci(blockLoci) ? blockLoci
: !isEmptyLoci(directionLoci) ? directionLoci
- : carbohydrateRepr
+ : !isEmptyLoci(carbohydrateSymbolLoci) ? carbohydrateSymbolLoci
+ : carbohydrateLinkLoci
},
mark: (loci: Loci, action: MarkerAction) => {
traceRepr.mark(loci, action)
gapRepr.mark(loci, action)
blockRepr.mark(loci, action)
directionRepr.mark(loci, action)
- carbohydrateRepr.mark(loci, action)
+ carbohydrateSymbolRepr.mark(loci, action)
+ carbohydrateLinkRepr.mark(loci, action)
},
destroy() {
traceRepr.destroy()
gapRepr.destroy()
blockRepr.destroy()
directionRepr.destroy()
- carbohydrateRepr.destroy()
+ carbohydrateSymbolRepr.destroy()
+ carbohydrateLinkRepr.destroy()
}
}
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
new file mode 100644
index 0000000000000000000000000000000000000000..83be8d6a34304e4b244bfc558222fc7e9a1ca4c1
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -0,0 +1,189 @@
+/**
+ * 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
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
index eb65b9e8ddad298fb886976ea0d811693b3c5009..b0352d0b4986b46413924663351f65f1b5c38807 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -7,26 +7,27 @@
import { ValueCell } from 'mol-util/value-cell'
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 { RuntimeContext } from 'mol-task'
-import { createIdentityTransform } from './util/common';
+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 } from '../../../util/marker-data';
-import { Loci, EmptyLoci } from 'mol-model/loci';
+import { createMarkers, MarkerAction, MarkerData, applyMarkerAction } from '../../../util/marker-data';
+import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
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 { deepEqual } from 'mol-util';
+import { LocationIterator } from './util/location-iterator';
+import { OrderedSet } from 'mol-data/int';
const t = Mat4.identity()
const sVec = Vec3.zero()
-const p = Vec3.zero()
const pd = Vec3.zero()
async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, mesh?: Mesh) {
@@ -34,89 +35,74 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
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 radius = 1.75
- const linkParams = { radiusTop: 0.4, radiusBottom: 0.4 }
-
for (let i = 0, il = carbohydrates.elements.length; i < il; ++i) {
const c = carbohydrates.elements[i];
- if (!c.hasRing) continue;
-
- const cGeo = c.geometry!
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) {
case SaccharideShapes.FilledSphere:
- builder.addSphere(cGeo.center, radius, 2)
+ builder.addSphere(center, radius, 2)
break;
case SaccharideShapes.FilledCube:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side)
builder.addBox(t)
break;
case SaccharideShapes.CrossedCube:
// TODO split
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side)
builder.addBox(t)
break;
case SaccharideShapes.FilledCone:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side * 1.2)
builder.addOctagonalPyramid(t)
break
case SaccharideShapes.DevidedCone:
// TODO split
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.scaleUniformly(t, t, side * 1.2)
builder.addOctagonalPyramid(t)
break
case SaccharideShapes.FlatBox:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addBox(t)
break
case SaccharideShapes.FilledStar:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
builder.addStar(t, { outerRadius: side, innerRadius: side / 2, thickness: side / 2, pointCount: 5 })
break
case SaccharideShapes.FilledDiamond:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t)
break
case SaccharideShapes.DividedDiamond:
// TODO split
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t)
break
case SaccharideShapes.FlatDiamond:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2))
builder.addDiamondPrism(t)
break
case SaccharideShapes.Pentagon:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addPentagonalPrism(t)
break
case SaccharideShapes.FlatHexagon:
default:
- centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
Mat4.mul(t, t, Mat4.rotZYZ90)
Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side , side / 2))
builder.addHexagonalPrism(t)
@@ -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()
}
@@ -166,14 +134,14 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
currentProps = Object.assign({}, DefaultCarbohydrateSymbolProps, props)
currentStructure = structure
+ const { colorTheme } = { ...DefaultCarbohydrateSymbolProps, ...props }
const instanceCount = 1
const elementCount = currentStructure.elementCount
mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
- // console.log(mesh)
const transforms = createIdentityTransform()
- const color = createValueColor(0x999911) // TODO
+ const color = createColors(createCarbohydrateIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -196,19 +164,87 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
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)
updateRenderableState(renderObject.state, newProps)
+ currentProps = newProps
return false
},
getLoci(pickingId: PickingId) {
- return EmptyLoci
+ return getCarbohydrateLoci(pickingId, currentStructure, renderObject.id)
},
mark(loci: Loci, action: MarkerAction) {
- // TODO
+ markCarbohydrate(loci, action, currentStructure, renderObject.values)
},
destroy() {
// 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
diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index bf55d079d25cd346fc2436638986917589fb5e01..9a4ec8d3b7973667448955b35b04bf3808564a3f 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -105,7 +105,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
}
if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Gap mesh', current: i });
+ await ctx.update({ message: 'Nucleotide block mesh', current: i });
}
++i
}
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index e2e43030fd29a438e04924175c920d5541c63d9e..07bc94993cb11eafcf00208fd395fe0aed5175dd 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -16,6 +16,7 @@ import { ColorTheme, SizeTheme } from '../../../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../../../theme/structure/color';
import { ValueCell, defaults } from 'mol-util';
import { LocationIterator } from './location-iterator';
+import { carbohydrateSymbolColorData } from '../../../../theme/structure/color/carbohydrate-symbol';
export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) {
const unitCount = units.length
@@ -37,6 +38,8 @@ export function createColors(locationIt: LocationIterator, props: ColorTheme, co
switch (props.name) {
case 'atom-index':
return elementIndexColorData(locationIt, colorData)
+ case 'carbohydrate-symbol':
+ return carbohydrateSymbolColorData(locationIt, colorData)
case 'chain-id':
return chainIdColorData(locationIt, colorData)
case 'element-symbol':
diff --git a/src/mol-geo/theme/index.ts b/src/mol-geo/theme/index.ts
index a306838fc92e1d7afc1d037d078c14c0b633b4a6..d34cb26a6d101a9ff03d58d9d03b136337ce69d1 100644
--- a/src/mol-geo/theme/index.ts
+++ b/src/mol-geo/theme/index.ts
@@ -5,8 +5,6 @@
*/
import { Color } from 'mol-util/color';
-// import { Loci } from 'mol-model/loci';
-// import { Structure } from 'mol-model/structure';
export interface UniformColorTheme {
name: 'uniform'
@@ -14,27 +12,15 @@ export interface UniformColorTheme {
}
export interface ScaleColorTheme {
- name: 'atom-index' | 'chain-id' | 'element-symbol' | 'instance-index'
+ name: 'atom-index' | 'chain-id'| 'instance-index'
domain?: [number, number]
}
-// interface StructureColorProvider {
-// uniform(): Color
-// 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 interface TableColorTheme {
+ name: 'carbohydrate-symbol' | 'element-symbol'
+}
-export type ColorTheme = UniformColorTheme | ScaleColorTheme
+export type ColorTheme = UniformColorTheme | ScaleColorTheme | TableColorTheme
export interface UniformSizeTheme {
name: 'uniform',
diff --git a/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e6f8065b436ea3260b77f9aea806b1f8dead892a
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
@@ -0,0 +1,45 @@
+/**
+ * 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
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 97034a5c5e856fc6b9ba91326ac0c903a6c949d9..cb1f9a33aa945d78624476e51a55b601038a90ac 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -18,7 +18,7 @@ import StructureElement from '../element';
import Structure from '../structure';
import Unit from '../unit';
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 { ElementIndex } from '../../model/indexing';
@@ -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
indexHasOxygenAndCarbon = ei
} 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
} else {
// use any carbon as a fallback
@@ -122,6 +122,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = []
const elements: CarbohydrateElement[] = []
+ const partialElements: PartialCarbohydrateElement[] = []
const elementsWithRingMap = new Map<string, number>()
@@ -173,10 +174,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const sugarRings = filterFusedRings(unit.rings, sugarResidueMap.get(residueIndex));
if (!sugarRings || !sugarRings.length) {
- elements.push({
- hasRing: false,
- unit, residueIndex, component: saccharideComp
- })
+ partialElements.push({ unit, residueIndex, component: saccharideComp })
continue;
}
@@ -199,8 +197,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
elementsWithRingMap.set(elementKey(residueIndex, unit.id, altId), elementIndex)
elements.push({
geometry: { center, normal, direction },
- hasRing: true,
- unit, residueIndex, component: saccharideComp
+ component: saccharideComp,
+ unit, residueIndex, anomericCarbon
})
}
@@ -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
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index 0c9361042df84c5d713888b20be4424cb96f66b3..046748f921acd5d5efc31d5e6d42166d7797d1a4 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -6,7 +6,7 @@
import Unit from '../unit';
import { Vec3 } from 'mol-math/linear-algebra';
-import { ResidueIndex } from '../../model';
+import { ResidueIndex, ElementIndex } from '../../model';
import { SaccharideComponent } from './constants';
export interface CarbohydrateLink {
@@ -23,16 +23,24 @@ export interface CarbohydrateTerminalLink {
}
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 hasRing: boolean,
+ readonly geometry: { readonly center: Vec3, readonly normal: Vec3, readonly direction: Vec3 },
+ readonly anomericCarbon: ElementIndex,
readonly unit: Unit.Atomic,
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 {
links: ReadonlyArray<CarbohydrateLink>
terminalLinks: ReadonlyArray<CarbohydrateTerminalLink>
elements: ReadonlyArray<CarbohydrateElement>
+ partialElements: ReadonlyArray<PartialCarbohydrateElement>
+ byUnitAndElement: (unit: Unit, element: ElementIndex) => number | undefined
}
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index c88e165ecbd419f523053e38b8743c9fa9bbfdfc..ed5ce1cc1e9c53bb933dab8bc12afa39c5c25e3c 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -110,7 +110,8 @@ export class Stage {
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.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_00000002.cif`) // ok
@@ -154,8 +155,8 @@ export class Stage {
}
loadPdbid (pdbid: string) {
- 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(`http://www.ebi.ac.uk/pdbe/static/entry/${pdbid}_updated.cif`)
+ return this.loadMmcifUrl(`https://files.rcsb.org/download/${pdbid}.cif`)
}
dispose () {