diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 729e7bb56c1b38207f8297e19a457212eec0cd27..d86ed125b4f6d796b02453c432a0017ebb9a89fc 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -262,8 +262,9 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}
- // get carbohydrate links induced by inter-unit bonds
- // (e.g. for structures from the PDB archive __before__ carbohydrate remediation)
+ // get carbohydrate links induced by inter-unit bonds, that is
+ // terminal links plus inter monosaccharide links for structures from the
+ // PDB archive __before__ carbohydrate remediation
for (let i = 0, il = structure.units.length; i < il; ++i) {
const unit = structure.units[i]
if (!Unit.isAtomic(unit)) continue
@@ -309,10 +310,10 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
})
}
- return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links) }
+ return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links, terminalLinks) }
}
-function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[]) {
+function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[], terminalLinks: CarbohydrateTerminalLink[]) {
// element lookup
function elementKey(unit: Unit, anomericCarbon: ElementIndex) {
@@ -347,6 +348,27 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return linkMap.get(linkKey(unitA, anomericCarbonA, unitB, anomericCarbonB))
}
+ // terminal link lookup
+
+ function terminalLinkKey(unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) {
+ return `${unitA.id}|${elementA}|${unitB.id}|${elementB}`
+ }
+
+ const terminalLinkMap = new Map<string, number>()
+ for (let i = 0, il = terminalLinks.length; i < il; ++i) {
+ const { fromCarbohydrate, carbohydrateIndex, elementUnit, elementIndex } = terminalLinks[i]
+ const { unit, anomericCarbon } = elements[carbohydrateIndex]
+ if (fromCarbohydrate) {
+ terminalLinkMap.set(terminalLinkKey(unit, anomericCarbon, elementUnit, elementUnit.elements[elementIndex]), i)
+ } else {
+ terminalLinkMap.set(terminalLinkKey(elementUnit, elementUnit.elements[elementIndex], unit, anomericCarbon), i)
+ }
+ }
+
+ function getTerminalLinkIndex(unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) {
+ return terminalLinkMap.get(terminalLinkKey(unitA, elementA, unitB, elementB))
+ }
+
// anomeric carbon lookup
function anomericCarbonKey(unit: Unit, residueIndex: ResidueIndex) {
@@ -364,5 +386,5 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return anomericCarbonMap.get(anomericCarbonKey(unit, residueIndex))
}
- return { getElementIndex, getLinkIndex, getAnomericCarbon }
+ return { getElementIndex, getLinkIndex, getTerminalLinkIndex, getAnomericCarbon }
}
\ 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 0a8d383755bac79c9ffde4be7de61a4b8f331cf0..7743bd0ba2ab580cd9a5226c07bd0678253953af 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -8,6 +8,7 @@ import Unit from '../unit';
import { Vec3 } from 'mol-math/linear-algebra';
import { ResidueIndex, ElementIndex } from '../../model';
import { SaccharideComponent } from './constants';
+import StructureElement from '../element';
export interface CarbohydrateLink {
readonly carbohydrateIndexA: number
@@ -16,7 +17,7 @@ export interface CarbohydrateLink {
export interface CarbohydrateTerminalLink {
readonly carbohydrateIndex: number
- readonly elementIndex: number
+ readonly elementIndex: StructureElement.UnitIndex
readonly elementUnit: Unit
/** specifies direction of the link */
readonly fromCarbohydrate: boolean
@@ -31,7 +32,7 @@ export interface CarbohydrateElement {
readonly ringAltId: string,
}
-// partial carbohydrate with no ring present
+/** partial carbohydrate with no ring present */
export interface PartialCarbohydrateElement {
readonly unit: Unit.Atomic,
readonly residueIndex: ResidueIndex,
@@ -45,5 +46,6 @@ export interface Carbohydrates {
partialElements: ReadonlyArray<PartialCarbohydrateElement>
getElementIndex: (unit: Unit, anomericCarbon: ElementIndex) => number | undefined
getLinkIndex: (unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) => number | undefined
+ getTerminalLinkIndex: (unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) => number | undefined
getAnomericCarbon: (unit: Unit, residueIndex: ResidueIndex) => ElementIndex | undefined
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/representation/carbohydrate.ts b/src/mol-repr/structure/representation/carbohydrate.ts
index 82660da3fb1f0eba58ad787a8843cca7684450bb..ac2e0d87bd53066ddf807ea3b39c2c2f73c3cc2f 100644
--- a/src/mol-repr/structure/representation/carbohydrate.ts
+++ b/src/mol-repr/structure/representation/carbohydrate.ts
@@ -6,6 +6,7 @@
import { CarbohydrateSymbolVisual, CarbohydrateSymbolParams } from '../visual/carbohydrate-symbol-mesh';
import { CarbohydrateLinkVisual, CarbohydrateLinkParams } from '../visual/carbohydrate-link-cylinder';
+import { CarbohydrateTerminalLinkParams, CarbohydrateTerminalLinkVisual } from '../visual/carbohydrate-terminal-link-cylinder';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ComplexRepresentation } from '../complex-representation';
import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
@@ -17,6 +18,7 @@ import { BuiltInColorThemeOptions, getBuiltInColorThemeParams } from 'mol-theme/
const CarbohydrateVisuals = {
'carbohydrate-symbol': (getParams: RepresentationParamsGetter<Structure, CarbohydrateSymbolParams>) => ComplexRepresentation('Carbohydrate symbol mesh', getParams, CarbohydrateSymbolVisual),
'carbohydrate-link': (getParams: RepresentationParamsGetter<Structure, CarbohydrateLinkParams>) => ComplexRepresentation('Carbohydrate link cylinder', getParams, CarbohydrateLinkVisual),
+ 'carbohydrate-terminal-link': (getParams: RepresentationParamsGetter<Structure, CarbohydrateTerminalLinkParams>) => ComplexRepresentation('Carbohydrate terminal link cylinder', getParams, CarbohydrateTerminalLinkVisual),
}
type CarbohydrateVisualName = keyof typeof CarbohydrateVisuals
const CarbohydrateVisualOptions = Object.keys(CarbohydrateVisuals).map(name => [name, name] as [CarbohydrateVisualName, string])
@@ -24,8 +26,9 @@ const CarbohydrateVisualOptions = Object.keys(CarbohydrateVisuals).map(name => [
export const CarbohydrateParams = {
...CarbohydrateSymbolParams,
...CarbohydrateLinkParams,
+ ...CarbohydrateTerminalLinkParams,
colorTheme: PD.Mapped('carbohydrate-symbol', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
- visuals: PD.MultiSelect<CarbohydrateVisualName>(['carbohydrate-symbol', 'carbohydrate-link'], CarbohydrateVisualOptions),
+ visuals: PD.MultiSelect<CarbohydrateVisualName>(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], CarbohydrateVisualOptions),
}
PD.getDefaultValues(CarbohydrateParams).colorTheme.name
export type CarbohydrateParams = typeof CarbohydrateParams
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index e58322f57d5b6f1eb90db7832db26dbe61007433..05d5a04b0d66afd2c4bf649fb66826835538fe13 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -7,7 +7,7 @@
import { Structure, Link, StructureElement } from 'mol-model/structure';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { Vec3 } from 'mol-math/linear-algebra';
-import { createLinkCylinderMesh, LinkCylinderProps, LinkCylinderParams } from './util/link';
+import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
import { OrderedSet, Interval } from 'mol-data/int';
import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';
import { LinkType } from 'mol-model/structure/model/types';
@@ -21,22 +21,10 @@ import { VisualUpdateState } from '../../util';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-// 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)
-// }
-// }
-
-const radiusFactor = 0.3
-
-async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: LinkCylinderProps, mesh?: Mesh) {
+async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateLinkParams>, mesh?: Mesh) {
const { links, elements } = structure.carbohydrates
+ const { linkSizeFactor } = props
+
const location = StructureElement.create()
const builderProps = {
@@ -53,7 +41,7 @@ async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure:
const l = links[edgeIndex]
location.unit = elements[l.carbohydrateIndexA].unit
location.element = elements[l.carbohydrateIndexA].anomericCarbon
- return theme.size.size(location) * radiusFactor
+ return theme.size.size(location) * linkSizeFactor
}
}
@@ -64,6 +52,7 @@ export const CarbohydrateLinkParams = {
...UnitsMeshParams,
...LinkCylinderParams,
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
}
export type CarbohydrateLinkParams = typeof CarbohydrateLinkParams
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index 440d6e834e948a8b2ae6de8cdf85855686316368..7a5acbf598fc3d6b1241632712d95c97ee30358e 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -30,8 +30,7 @@ const t = Mat4.identity()
const sVec = Vec3.zero()
const pd = Vec3.zero()
-const sideFactor = 1.75 * 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
-const radiusFactor = 1.75
+const SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
const box = Box()
const perforatedBox = PerforatedBox()
@@ -47,7 +46,7 @@ const hexagonalPrism = HexagonalPrism()
async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateSymbolParams>, mesh?: Mesh) {
const builder = MeshBuilder.create(256, 128, mesh)
- const { detail } = props
+ const { detail, sizeFactor } = props
const carbohydrates = structure.carbohydrates
const n = carbohydrates.elements.length
@@ -60,8 +59,8 @@ async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Struc
l.unit = c.unit
l.element = c.unit.elements[c.anomericCarbon]
const size = theme.size.size(l)
- const radius = size * radiusFactor
- const side = size * sideFactor
+ const radius = size * sizeFactor
+ const side = size * sizeFactor * SideFactor
const { center, normal, direction } = c.geometry
Vec3.add(pd, center, direction)
@@ -148,6 +147,7 @@ async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Struc
export const CarbohydrateSymbolParams = {
...ComplexMeshParams,
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ sizeFactor: PD.Numeric(1.75, { min: 0, max: 10, step: 0.01 }),
}
export type CarbohydrateSymbolParams = typeof CarbohydrateSymbolParams
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7d594fd788a192d1fa5fb1df4e2ec6f2bff9ca65
--- /dev/null
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -0,0 +1,147 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Structure, Link, StructureElement } from 'mol-model/structure';
+import { Loci, EmptyLoci } from 'mol-model/loci';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
+import { OrderedSet, Interval } from 'mol-data/int';
+import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';
+import { LinkType } from 'mol-model/structure/model/types';
+import { BitFlags } from 'mol-util';
+import { UnitsMeshParams } from '../units-visual';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+import { LocationIterator } from 'mol-geo/util/location-iterator';
+import { PickingId } from 'mol-geo/geometry/picking';
+import { VisualUpdateState } from '../../util';
+import { VisualContext } from 'mol-repr/representation';
+import { Theme } from 'mol-theme/theme';
+
+async function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateTerminalLinkParams>, mesh?: Mesh) {
+ const { terminalLinks, elements } = structure.carbohydrates
+ const { linkSizeFactor } = props
+
+ const location = StructureElement.create()
+
+ const builderProps = {
+ linkCount: terminalLinks.length,
+ referencePosition: (edgeIndex: number) => null,
+ position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+ const l = terminalLinks[edgeIndex]
+ if (l.fromCarbohydrate) {
+ Vec3.copy(posA, elements[l.carbohydrateIndex].geometry.center)
+ l.elementUnit.conformation.position(l.elementIndex, posB)
+ } else {
+ l.elementUnit.conformation.position(l.elementIndex, posA)
+ Vec3.copy(posB, elements[l.carbohydrateIndex].geometry.center)
+ }
+ },
+ order: (edgeIndex: number) => 1,
+ flags: (edgeIndex: number) => BitFlags.create(LinkType.Flag.None),
+ radius: (edgeIndex: number) => {
+ const l = terminalLinks[edgeIndex]
+ if (l.fromCarbohydrate) {
+ location.unit = elements[l.carbohydrateIndex].unit
+ location.element = elements[l.carbohydrateIndex].anomericCarbon
+ } else {
+ location.unit = l.elementUnit
+ location.element = l.elementUnit.elements[l.elementIndex]
+ }
+ return theme.size.size(location) * linkSizeFactor
+ }
+ }
+
+ return createLinkCylinderMesh(ctx, builderProps, props, mesh)
+}
+
+export const CarbohydrateTerminalLinkParams = {
+ ...UnitsMeshParams,
+ ...LinkCylinderParams,
+ detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
+}
+export type CarbohydrateTerminalLinkParams = typeof CarbohydrateTerminalLinkParams
+
+export function CarbohydrateTerminalLinkVisual(): ComplexVisual<CarbohydrateTerminalLinkParams> {
+ return ComplexMeshVisual<CarbohydrateTerminalLinkParams>({
+ defaultProps: PD.getDefaultValues(CarbohydrateTerminalLinkParams),
+ createGeometry: createCarbohydrateTerminalLinkCylinderMesh,
+ createLocationIterator: CarbohydrateTerminalLinkIterator,
+ getLoci: getTerminalLinkLoci,
+ mark: markTerminalLink,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateTerminalLinkParams>, currentProps: PD.Values<CarbohydrateTerminalLinkParams>) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
+ }
+ })
+}
+
+function CarbohydrateTerminalLinkIterator(structure: Structure): LocationIterator {
+ const { elements, terminalLinks } = structure.carbohydrates
+ const groupCount = terminalLinks.length
+ const instanceCount = 1
+ const location = Link.Location()
+ const getLocation = (groupIndex: number) => {
+ const terminalLink = terminalLinks[groupIndex]
+ const carb = elements[terminalLink.carbohydrateIndex]
+ const indexCarb = OrderedSet.indexOf(carb.unit.elements, carb.anomericCarbon)
+ if (terminalLink.fromCarbohydrate) {
+ location.aUnit = carb.unit
+ location.aIndex = indexCarb as StructureElement.UnitIndex
+ location.bUnit = terminalLink.elementUnit
+ location.bIndex = terminalLink.elementIndex
+ } else {
+ location.aUnit = terminalLink.elementUnit
+ location.aIndex = terminalLink.elementIndex
+ location.bUnit = carb.unit
+ location.bIndex = indexCarb as StructureElement.UnitIndex
+ }
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation, true)
+}
+
+function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
+ const { objectId, groupId } = pickingId
+ if (id === objectId) {
+ const { terminalLinks, elements } = structure.carbohydrates
+ const l = terminalLinks[groupId]
+ const carb = elements[l.carbohydrateIndex]
+ const carbIndex = OrderedSet.indexOf(carb.unit.elements, carb.anomericCarbon)
+
+ if (l.fromCarbohydrate) {
+ return Link.Loci(structure, [
+ Link.Location(
+ carb.unit, carbIndex as StructureElement.UnitIndex,
+ l.elementUnit, l.elementIndex
+ )
+ ])
+ } else {
+ return Link.Loci(structure, [
+ Link.Location(
+ l.elementUnit, l.elementIndex,
+ carb.unit, carbIndex as StructureElement.UnitIndex
+ )
+ ])
+ }
+ }
+ return EmptyLoci
+}
+
+function markTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+ const { getTerminalLinkIndex } = structure.carbohydrates
+
+ let changed = false
+ if (Link.isLoci(loci)) {
+ for (const l of loci.links) {
+ const idx = getTerminalLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
+ if (idx !== undefined) {
+ if (apply(Interval.ofSingleton(idx))) changed = true
+ }
+ }
+ }
+ return changed
+}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index 31e82c69c78b9f1e5bad8b5022b02b3a2f7e7e8c..f85233d3541260ded2037f1c37c814e17e00be24 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -7,7 +7,7 @@
import { Link, Structure, StructureElement } from 'mol-model/structure';
import { ComplexVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { LinkCylinderProps, createLinkCylinderMesh, LinkIterator, LinkCylinderParams } from './util/link';
+import { createLinkCylinderMesh, LinkIterator, LinkCylinderParams } from './util/link';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { ComplexMeshVisual, ComplexMeshParams } from '../complex-visual';
@@ -19,9 +19,10 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: LinkCylinderProps, mesh?: Mesh) {
+async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitLinkParams>, mesh?: Mesh) {
const links = structure.links
const { bondCount, bonds } = links
+ const { sizeFactor } = props
if (!bondCount) return Mesh.createEmpty(mesh)
@@ -42,7 +43,7 @@ async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: St
const b = bonds[edgeIndex]
location.unit = b.unitA
location.element = b.unitA.elements[b.indexA]
- return theme.size.size(location)
+ return theme.size.size(location) * sizeFactor
}
}
@@ -52,6 +53,7 @@ async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: St
export const InterUnitLinkParams = {
...ComplexMeshParams,
...LinkCylinderParams,
+ sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
}
export type InterUnitLinkParams = typeof InterUnitLinkParams