diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
index 83be8d6a34304e4b244bfc558222fc7e9a1ca4c1..49676477f3217edfaf6f8897a03f80e2927481a0 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -15,14 +15,13 @@ 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 { 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 { 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';
@@ -86,7 +85,7 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
// console.log(mesh)
const transforms = createIdentityTransform()
- const color = createValueColor(0x119911)//createColors(colorTheme)
+ const color = createColors(createCarbohydrateLinkIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -97,8 +96,7 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
...marker,
aTransform: transforms,
elements: mesh.indexBuffer,
- ...createMeshValues(currentProps, counts),
- aColor: ValueCell.create(new Float32Array(mesh.vertexCount * 3))
+ ...createMeshValues(currentProps, counts)
}
const state = createRenderableState(currentProps)
@@ -111,13 +109,13 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
let updateColor = false
- // if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- // updateColor = true
- // }
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
+ updateColor = true
+ }
- // if (updateColor) {
- // createColors(LinkIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- // }
+ if (updateColor) {
+ createColors(createCarbohydrateLinkIterator(currentStructure), newProps.colorTheme, renderObject.values)
+ }
updateMeshValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
@@ -129,8 +127,7 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
return getLinkLoci(pickingId, currentStructure, renderObject.id)
},
mark(loci: Loci, action: MarkerAction) {
- // TODO
- // markLink(loci, action, currentStructure, renderObject.values)
+ markLink(loci, action, currentStructure, renderObject.values)
},
destroy() {
// TODO
@@ -138,6 +135,26 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
}
}
+function createCarbohydrateLinkIterator(structure: Structure): LocationIterator {
+ const { elements, links } = structure.carbohydrates
+ const elementCount = links.length
+ const instanceCount = 1
+ const location = Link.Location()
+ const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const link = links[elementIndex]
+ const carbA = elements[link.carbohydrateIndexA]
+ const carbB = elements[link.carbohydrateIndexB]
+ const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
+ const indexB = OrderedSet.findPredecessorIndex(carbB.unit.elements, carbB.anomericCarbon)
+ location.aUnit = carbA.unit
+ location.aIndex = indexA as StructureElement.UnitIndex
+ location.bUnit = carbB.unit
+ location.bIndex = indexB as StructureElement.UnitIndex
+ return location
+ }
+ return LocationIterator(elementCount, instanceCount, getLocation)
+}
+
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, elementId } = pickingId
if (id === objectId) {
@@ -157,33 +174,31 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
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
+function markLink(loci: Loci, action: MarkerAction, structure: Structure, values: MarkerData) {
+ const tMarker = values.tMarker
+
+ const { getLinkIndex } = 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 (Link.isLoci(loci)) {
+ for (const l of loci.links) {
+ const idx = getLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
+ 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/carbohydrate-symbol-mesh.ts b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
index b0352d0b4986b46413924663351f65f1b5c38807..e51b2049c9b18dfa6a1c4092f0a8a40dc08e1850 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -141,7 +141,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
const transforms = createIdentityTransform()
- const color = createColors(createCarbohydrateIterator(structure), colorTheme)
+ const color = createColors(createCarbohydrateElementIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -152,8 +152,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
...marker,
aTransform: transforms,
elements: mesh.indexBuffer,
- ...createMeshValues(currentProps, counts),
- aColor: ValueCell.create(new Float32Array(mesh.vertexCount * 3))
+ ...createMeshValues(currentProps, counts)
}
const state = createRenderableState(currentProps)
@@ -171,7 +170,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
}
if (updateColor) {
- createColors(createCarbohydrateIterator(currentStructure), newProps.colorTheme, renderObject.values)
+ createColors(createCarbohydrateElementIterator(currentStructure), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
@@ -192,13 +191,13 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
}
}
-function createCarbohydrateIterator(structure: Structure): LocationIterator {
- const carbs = structure.carbohydrates.elements
- const elementCount = carbs.length
+function createCarbohydrateElementIterator(structure: Structure): LocationIterator {
+ const carbElements = structure.carbohydrates.elements
+ const elementCount = carbElements.length
const instanceCount = 1
const location = StructureElement.create()
const getLocation = (elementIndex: number, instanceIndex: number) => {
- const carb = carbs[elementIndex]
+ const carb = carbElements[elementIndex]
location.unit = carb.unit
location.element = carb.anomericCarbon
return location
@@ -221,7 +220,7 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
function markCarbohydrate(loci: Loci, action: MarkerAction, structure: Structure, values: MarkerData) {
const tMarker = values.tMarker
- const { byUnitAndElement } = structure.carbohydrates
+ const { getElementIndex } = structure.carbohydrates
const elementCount = structure.carbohydrates.elements.length
let changed = false
@@ -233,7 +232,7 @@ function markCarbohydrate(loci: Loci, action: MarkerAction, structure: Structure
} 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])
+ const idx = getElementIndex(e.unit, e.unit.elements[index])
if (idx !== undefined) {
if (applyMarkerAction(array, idx, idx + 1, action) && !changed) {
changed = true
diff --git a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
index 585fd7c9979348967fd913ebb9b0dc76f92f07a6..1282c57a0f6b53220379af3bfa7786afaaeddb97 100644
--- a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
@@ -144,13 +144,13 @@ function markLink(loci: Loci, action: MarkerAction, structure: Structure, values
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
+ if (applyMarkerAction(array, 0, elementCount, 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)
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index cb1f9a33aa945d78624476e51a55b601038a90ac..ebf52e14c8dee07e214c32fa59b26fe8d5a1481a 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -126,7 +126,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const elementsWithRingMap = new Map<string, number>()
- function elementKey(residueIndex: number, unitId: number, altId: string) {
+ function ringElementKey(residueIndex: number, unitId: number, altId: string) {
return `${residueIndex}|${unitId}|${altId}`
}
@@ -194,7 +194,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const altId = getRingAltId(unit, ringAtoms)
const elementIndex = elements.length
ringElements.push(elementIndex)
- elementsWithRingMap.set(elementKey(residueIndex, unit.id, altId), elementIndex)
+ elementsWithRingMap.set(ringElementKey(residueIndex, unit.id, altId), elementIndex)
elements.push({
geometry: { center, normal, direction },
component: saccharideComp,
@@ -227,8 +227,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}
}
- function getElementIndex(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
- return elementsWithRingMap.get(elementKey(unit.getResidueIndex(index), unit.id, getAltId(unit, index)))
+ function getRingElementIndex(unit: Unit.Atomic, index: StructureElement.UnitIndex) {
+ return elementsWithRingMap.get(ringElementKey(unit.getResidueIndex(index), unit.id, getAltId(unit, index)))
}
// get carbohydrate links induced by inter-unit bonds
@@ -241,32 +241,32 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
pairBonds.getBonds(indexA).forEach(bondInfo => {
const { unitA, unitB } = pairBonds
const indexB = bondInfo.indexB
- const elementIndexA = getElementIndex(unitA, indexA)
- const elementIndexB = getElementIndex(unitB, indexB)
+ const ringElementIndexA = getRingElementIndex(unitA, indexA)
+ const ringElementIndexB = getRingElementIndex(unitB, indexB)
- if (elementIndexA !== undefined && elementIndexB !== undefined) {
+ if (ringElementIndexA !== undefined && ringElementIndexB !== undefined) {
const atomIdA = getAtomId(unitA, indexA)
if (atomIdA.startsWith('O1') || atomIdA.startsWith('C1')) {
- fixLinkDirection(elementIndexA, elementIndexB)
+ fixLinkDirection(ringElementIndexA, ringElementIndexB)
}
links.push({
- carbohydrateIndexA: elementIndexA,
- carbohydrateIndexB: elementIndexB
+ carbohydrateIndexA: ringElementIndexA,
+ carbohydrateIndexB: ringElementIndexB
})
- } else if (elementIndexA !== undefined) {
+ } else if (ringElementIndexA !== undefined) {
const atomIdA = getAtomId(unitA, indexA)
if (atomIdA.startsWith('O1') || atomIdA.startsWith('C1')) {
- fixTerminalLinkDirection(elementIndexA, indexB, unitB)
+ fixTerminalLinkDirection(ringElementIndexA, indexB, unitB)
}
terminalLinks.push({
- carbohydrateIndex: elementIndexA,
+ carbohydrateIndex: ringElementIndexA,
elementIndex: indexB,
elementUnit: unitB,
fromCarbohydrate: true
})
- } else if (elementIndexB !== undefined) {
+ } else if (ringElementIndexB !== undefined) {
terminalLinks.push({
- carbohydrateIndex: elementIndexB,
+ carbohydrateIndex: ringElementIndexB,
elementIndex: indexA,
elementUnit: unitA,
fromCarbohydrate: false
@@ -277,20 +277,43 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
})
}
- // build lookup map
- const map = new Map<string, number>()
+ return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links) }
+}
+
+function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[]) {
+ // element lookup
+
+ function elementKey(unit: Unit, anomericCarbon: ElementIndex) {
+ return `${unit.id}|${anomericCarbon}`
+ }
+
+ const elementMap = new Map<string, number>()
for (let i = 0, il = elements.length; i < il; ++i) {
const { unit, anomericCarbon } = elements[i]
- map.set(key(unit, anomericCarbon), i)
+ elementMap.set(elementKey(unit, anomericCarbon), i)
}
- function key(unit: Unit, anomericCarbon: ElementIndex) {
- return `${unit.id}|${anomericCarbon}`
+ function getElementIndex(unit: Unit, anomericCarbon: ElementIndex) {
+ return elementMap.get(elementKey(unit, anomericCarbon))
+ }
+
+ // link lookup
+
+ function linkKey(unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) {
+ return `${unitA.id}|${anomericCarbonA}|${unitB.id}|${anomericCarbonB}`
+ }
+
+ const linkMap = new Map<string, number>()
+ for (let i = 0, il = links.length; i < il; ++i) {
+ const l = links[i]
+ const { unit: unitA, anomericCarbon: anomericCarbonA } = elements[l.carbohydrateIndexA]
+ const { unit: unitB, anomericCarbon: anomericCarbonB } = elements[l.carbohydrateIndexB]
+ linkMap.set(linkKey(unitA, anomericCarbonA, unitB, anomericCarbonB), i)
}
- function byUnitAndElement(unit: Unit, anomericCarbon: ElementIndex) {
- return map.get(key(unit, anomericCarbon))
+ function getLinkIndex(unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) {
+ return linkMap.get(linkKey(unitA, anomericCarbonA, unitB, anomericCarbonB))
}
- return { links, terminalLinks, elements, partialElements, byUnitAndElement }
+ return { getElementIndex, getLinkIndex }
}
\ 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 046748f921acd5d5efc31d5e6d42166d7797d1a4..c69bde439533cd91c36936588394870fde68c83f 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -42,5 +42,6 @@ export interface Carbohydrates {
terminalLinks: ReadonlyArray<CarbohydrateTerminalLink>
elements: ReadonlyArray<CarbohydrateElement>
partialElements: ReadonlyArray<PartialCarbohydrateElement>
- byUnitAndElement: (unit: Unit, element: ElementIndex) => number | undefined
+ getElementIndex: (unit: Unit, anomericCarbon: ElementIndex) => number | undefined
+ getLinkIndex: (unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) => number | undefined
}
\ No newline at end of file