diff --git a/src/mol-geo/representation/structure/cartoon.ts b/src/mol-geo/representation/structure/cartoon.ts
index 3e56c507a491bc014221ef1811db9b94e7d00aa1..6296fce4978ef5d1795770ebb30baae35f74a9af 100644
--- a/src/mol-geo/representation/structure/cartoon.ts
+++ b/src/mol-geo/representation/structure/cartoon.ts
@@ -14,6 +14,7 @@ import { PolymerTraceVisual, DefaultPolymerTraceProps } from './visual/polymer-t
import { PolymerGapVisual, DefaultPolymerGapProps } from './visual/polymer-gap-cylinder';
import { NucleotideBlockVisual, DefaultNucleotideBlockProps } from './visual/nucleotide-block-mesh';
import { PolymerDirectionVisual, DefaultPolymerDirectionProps } from './visual/polymer-direction-wedge';
+import { CarbohydrateSymbolVisual } from './visual/carbohydrate-symbol-mesh';
export const DefaultCartoonProps = {
...DefaultPolymerTraceProps,
@@ -28,13 +29,14 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const gapRepr = StructureUnitsRepresentation(PolymerGapVisual)
const blockRepr = StructureUnitsRepresentation(NucleotideBlockVisual)
const directionRepr = StructureUnitsRepresentation(PolymerDirectionVisual)
+ const carbohydrateRepr = StructureRepresentation(CarbohydrateSymbolVisual)
return {
get renderObjects() {
- return [ ...traceRepr.renderObjects, ...gapRepr.renderObjects, ...blockRepr.renderObjects, ...directionRepr.renderObjects ]
+ return [ ...traceRepr.renderObjects, ...gapRepr.renderObjects, ...blockRepr.renderObjects, ...directionRepr.renderObjects, ...carbohydrateRepr.renderObjects ]
},
get props() {
- return { ...traceRepr.props, ...gapRepr.props, ...blockRepr.props, ...directionRepr.props }
+ return { ...traceRepr.props, ...gapRepr.props, ...blockRepr.props, ...carbohydrateRepr.props }
},
create: (structure: Structure, props: CartoonProps = {} as CartoonProps) => {
const p = Object.assign({}, DefaultCartoonProps, props)
@@ -43,6 +45,7 @@ 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)
})
},
update: (props: CartoonProps) => {
@@ -52,6 +55,7 @@ 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)
})
},
getLoci: (pickingId: PickingId) => {
@@ -59,22 +63,26 @@ 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)
return !isEmptyLoci(traceLoci) ? traceLoci
: !isEmptyLoci(gapLoci) ? gapLoci
: !isEmptyLoci(blockLoci) ? blockLoci
- : directionLoci
+ : !isEmptyLoci(directionLoci) ? directionLoci
+ : carbohydrateRepr
},
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)
},
destroy() {
traceRepr.destroy()
gapRepr.destroy()
blockRepr.destroy()
directionRepr.destroy()
+ carbohydrateRepr.destroy()
}
}
}
\ 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
new file mode 100644
index 0000000000000000000000000000000000000000..6ff36dd809382fb496132b8a7e5b9c2e6cf81b71
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -0,0 +1,128 @@
+/**
+ * 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 } from 'mol-model/structure';
+import { DefaultStructureProps, StructureVisual } from '..';
+import { RuntimeContext } from 'mol-task'
+import { createIdentityTransform } 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 { 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 { createUniformColor } from '../../../util/color-data';
+
+async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, mesh?: Mesh) {
+ const builder = MeshBuilder.create(256, 128, mesh)
+
+ const t = Mat4.identity()
+ const p = Vec3.zero()
+ const { carbohydrates } = structure
+
+ const linkParams = { radiusTop: 0.2, radiusBottom: 0.2 }
+
+ for (let i = 0, il = carbohydrates.elements.length; i < il; ++i) {
+ const c = carbohydrates.elements[i]
+ Mat4.setTranslation(t, c.center)
+ builder.addBox(t, { width: 2, height: 2, depth: 2 })
+ }
+
+ for (let i = 0, il = carbohydrates.links.length; i < il; ++i) {
+ const l = carbohydrates.links[i]
+ const centerA = carbohydrates.elements[l.carbohydrateIndexA].center
+ const centerB = carbohydrates.elements[l.carbohydrateIndexB].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].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()
+}
+
+export const DefaultCarbohydrateSymbolProps = {
+ ...DefaultMeshProps,
+ ...DefaultStructureProps,
+ sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
+ detail: 0,
+ unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+}
+export type CarbohydrateSymbolProps = Partial<typeof DefaultCarbohydrateSymbolProps>
+
+export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolProps> {
+ let renderObject: MeshRenderObject
+ let currentProps: typeof DefaultCarbohydrateSymbolProps
+ let mesh: Mesh
+ let currentStructure: Structure
+
+ return {
+ get renderObject () { return renderObject },
+ async create(ctx: RuntimeContext, structure: Structure, props: CarbohydrateSymbolProps = {}) {
+ currentProps = Object.assign({}, DefaultCarbohydrateSymbolProps, props)
+ currentStructure = structure
+
+ const instanceCount = 1
+ const elementCount = currentStructure.elementCount
+
+ mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
+ // console.log(mesh)
+
+ const transforms = createIdentityTransform()
+ const color = createUniformColor({ value: 0x999911 }) // TODO
+ 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: CarbohydrateSymbolProps) {
+ const newProps = Object.assign({}, currentProps, props)
+
+ if (!renderObject) return false
+
+ updateMeshValues(renderObject.values, newProps)
+ updateRenderableState(renderObject.state, newProps)
+
+ return false
+ },
+ getLoci(pickingId: PickingId) {
+ return EmptyLoci
+ },
+ mark(loci: Loci, action: MarkerAction) {
+ // TODO
+ },
+ destroy() {
+ // TODO
+ }
+ }
+}
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 69fe8db7a0e47b3d9847764f367b94df952a2557..cbb68b1d1ba0e2ff36dad1260e4f466e540d3576 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -33,8 +33,8 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
const builder = MeshBuilder.create(256, 128, mesh)
const { elements, model } = unit
- const { chemicalComponentMap, modifiedResidues } = unit.model.properties
- const { chainAtomSegments, residueAtomSegments, residues } = unit.model.atomicHierarchy
+ const { chemicalComponentMap, modifiedResidues } = model.properties
+ const { chainAtomSegments, residueAtomSegments, residues } = model.atomicHierarchy
const { label_comp_id } = residues
const pos = unit.conformation.invariantPosition
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 4b8efbb13edcadf19dbb83b5fc1838fc79c713d6..659e35acc0c005e151f43ace20d3e0ffc5c13e01 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -162,6 +162,26 @@ namespace Vec3 {
return out;
}
+ /**
+ * Returns the minimum of two Vec3's
+ */
+ export function min(out: Vec3, a: Vec3, b: Vec3) {
+ out[0] = Math.min(a[0], b[0]);
+ out[1] = Math.min(a[1], b[1]);
+ out[2] = Math.min(a[2], b[2]);
+ return out;
+ }
+
+ /**
+ * Returns the maximum of two Vec3's
+ */
+ export function max(out: Vec3, a: Vec3, b: Vec3) {
+ out[0] = Math.max(a[0], b[0]);
+ out[1] = Math.max(a[1], b[1]);
+ out[2] = Math.max(a[2], b[2]);
+ return out;
+ }
+
export function distance(a: Vec3, b: Vec3) {
const x = b[0] - a[0],
y = b[1] - a[1],
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1b9ad695d50117af9442eaade7cda6396d7cb0bc
--- /dev/null
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -0,0 +1,127 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import Unit from '../unit';
+import { ResidueIndex } from '../../model';
+import { Interval, Segmentation } from 'mol-data/int';
+import Structure from '../structure';
+import { Carbohydrates, CarbohydrateLink, CarbohydrateTerminalLink, CarbohydrateElement } from './data';
+import { SaccharideNameMap } from './constants';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { getCenterAndRadius } from '../../util';
+
+function getResidueIndex(elementIndex: number, unit: Unit.Atomic) {
+ return unit.model.atomicHierarchy.residueAtomSegments.index[unit.elements[elementIndex]]
+}
+
+function getRingIndices(unit: Unit.Atomic, rI: ResidueIndex) {
+ const { offsets } = unit.model.atomicHierarchy.residueAtomSegments
+ const { elements } = unit
+ const interval = Interval.ofBounds(offsets[rI], offsets[rI + 1])
+ const rings = unit.rings.byFingerprint.get('C-C-C-C-C-O') || unit.rings.byFingerprint.get('C-C-C-C-O')
+ if (rings) {
+ for (let i = 0, il = rings.length; i < il; ++i) {
+ let withinIntervalCount = 0
+ const ring = unit.rings.all[rings[i]]
+ for (let j = 0, jl = ring.length; j < jl; ++j) {
+ if (Interval.has(interval, elements[ring[j]])) ++withinIntervalCount
+ }
+ if (withinIntervalCount === ring.length) return ring
+ }
+ }
+}
+
+export function computeCarbohydrates(structure: Structure): Carbohydrates {
+ const links: CarbohydrateLink[] = []
+ const terminalLinks: CarbohydrateTerminalLink[] = []
+ const elements: CarbohydrateElement[] = []
+
+ const elementsMap = new Map<string, number>()
+
+ function elementKey(residueIndex: number, unitId: number) {
+ return `${residueIndex}|${unitId}`
+ }
+
+ for (let i = 0, il = structure.units.length; i < il; ++i) {
+ const unit = structure.units[i]
+ if (!Unit.isAtomic(unit)) continue
+
+ const { model } = unit
+ const { chainAtomSegments, residueAtomSegments, residues } = model.atomicHierarchy
+ const { label_comp_id } = residues
+
+ const chainIt = Segmentation.transientSegments(chainAtomSegments, unit.elements)
+ const residueIt = Segmentation.transientSegments(residueAtomSegments, unit.elements)
+
+ while (chainIt.hasNext) {
+ residueIt.setSegment(chainIt.move());
+
+ while (residueIt.hasNext) {
+ const { index: residueIndex } = residueIt.move();
+
+ const saccharideComp = SaccharideNameMap.get(label_comp_id.value(residueIndex))
+ if (!saccharideComp) continue
+
+ const ringIndices = getRingIndices(unit, residueIndex)
+ if (ringIndices) {
+ const center = Vec3.zero()
+ const normal = Vec3.zero()
+ const direction = Vec3.zero()
+ const ringRadius = getCenterAndRadius(center, unit, ringIndices)
+ console.log(ringRadius, center)
+
+ elementsMap.set(elementKey(residueIndex, unit.id), elements.length)
+ elements.push({ center, normal, direction, unit, residueIndex, component: saccharideComp })
+ } else {
+ console.warn('No ring found for carbohydrate')
+ }
+ }
+ }
+ }
+
+ elementsMap.forEach((elementIndex, key) => {
+ const unit = elements[elementIndex].unit
+ structure.links.getLinkedUnits(unit).forEach(pairBonds => {
+ pairBonds.linkedElementIndices.forEach(indexA => {
+ pairBonds.getBonds(indexA).forEach(bondInfo => {
+ let { unitA, unitB } = pairBonds
+ let indexB = bondInfo.indexB
+ let residueIndexA = getResidueIndex(indexA, unitA)
+ let residueIndexB = getResidueIndex(indexB, unitB)
+ let keyA = elementKey(residueIndexA, unitA.id)
+ let keyB = elementKey(residueIndexB, unitB.id)
+ if (key === keyB) {
+ [keyB, keyA] = [keyA, keyB];
+ [indexB, indexA] = [indexA, indexB];
+ [unitB, unitA] = [unitA, unitB];
+ }
+ const elementIndexB = elementsMap.get(keyB)
+ if (elementIndexB !== undefined) {
+ links.push({
+ carbohydrateIndexA: elementIndex,
+ carbohydrateIndexB: elementIndexB
+ })
+ } else {
+ terminalLinks.push({
+ carbohydrateIndex: elementIndex,
+ elementIndex: indexB,
+ elementUnit: unitB,
+ fromCarbohydrate: true
+ })
+ terminalLinks.push({
+ carbohydrateIndex: elementIndex,
+ elementIndex: indexB,
+ elementUnit: unitB,
+ fromCarbohydrate: false
+ })
+ }
+ })
+ })
+ })
+ })
+
+ return { links, terminalLinks, elements }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8c71acb0f1333ff4d14904b24e9fd288e0f04ed4
--- /dev/null
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -0,0 +1,270 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// https://www.ncbi.nlm.nih.gov/glycans/snfg.html
+
+export const enum SaccharideShapes {
+ FilledSphere, FilledCube, CrossedCube, DividedDiamond, FilledCone, DevidedCone,
+ FlatBox, FilledStar, FilledDiamond, FlatDiamond, FlatHexagon, Pentagon
+}
+
+// TODO move to theme
+const enum SaccharideColors {
+ Blue = 0x0090bc,
+ Green = 0x00a651,
+ Yellow = 0xffd400,
+ Orange = 0xf47920,
+ Pink = 0xf69ea1,
+ Purple = 0xa54399,
+ LightBlue = 0x8fcce9,
+ Brown = 0xa17a4d,
+ Red = 0xed1c24,
+
+ Secondary = 0xf1ece1
+}
+
+export const enum SaccharideType {
+ Hexose, HexNAc, Hexosamine, Hexuronate, Deoxyhexose, DeoxyhexNAc, DiDeoxyhexose,
+ Pentose, Deoxynonulosonate, DiDeoxynonulosonate, Unknown, Assigned
+}
+
+const SaccharideTypeNameMap = {
+ [SaccharideType.Hexose]: 'Hexose',
+ [SaccharideType.HexNAc]: 'HexNAc',
+ [SaccharideType.Hexosamine]: 'Hexosamine',
+ [SaccharideType.Hexuronate]: 'Hexuronate',
+ [SaccharideType.Deoxyhexose]: 'Deoxyhexose',
+ [SaccharideType.DeoxyhexNAc]: 'DeoxyhexNAc',
+ [SaccharideType.DiDeoxyhexose]: 'Di-deoxyhexose',
+ [SaccharideType.Pentose]: 'Pentose',
+ [SaccharideType.Deoxynonulosonate]: 'Deoxynonulosonate',
+ [SaccharideType.DiDeoxynonulosonate]: 'Di-deoxynonulosonate',
+ [SaccharideType.Unknown]: 'Unknown',
+ [SaccharideType.Assigned]: 'Assigned',
+}
+
+export function getSaccharideName(type: SaccharideType) {
+ return SaccharideTypeNameMap[type]
+}
+
+const SaccharideTypeShapeMap = {
+ [SaccharideType.Hexose]: SaccharideShapes.FilledSphere,
+ [SaccharideType.HexNAc]: SaccharideShapes.FilledCube,
+ [SaccharideType.Hexosamine]: SaccharideShapes.CrossedCube,
+ [SaccharideType.Hexuronate]: SaccharideShapes.DividedDiamond,
+ [SaccharideType.Deoxyhexose]: SaccharideShapes.FilledCone,
+ [SaccharideType.DeoxyhexNAc]: SaccharideShapes.DevidedCone,
+ [SaccharideType.DiDeoxyhexose]: SaccharideShapes.FlatBox,
+ [SaccharideType.Pentose]: SaccharideShapes.FilledStar,
+ [SaccharideType.Deoxynonulosonate]: SaccharideShapes.FilledDiamond,
+ [SaccharideType.DiDeoxynonulosonate]: SaccharideShapes.FlatDiamond,
+ [SaccharideType.Unknown]: SaccharideShapes.FlatHexagon,
+ [SaccharideType.Assigned]: SaccharideShapes.Pentagon,
+}
+
+export function getSaccharideShape(type: SaccharideType) {
+ return SaccharideTypeShapeMap[type]
+}
+
+export type SaccharideComponent = {
+ abbr: string
+ name: string
+ color: SaccharideColors
+ type: SaccharideType
+}
+
+const Monosaccharides: SaccharideComponent[] = [
+ { abbr: 'Glc', name: 'Glucose', color: SaccharideColors.Blue, type: SaccharideType.Hexose },
+ { abbr: 'Man', name: 'Mannose', color: SaccharideColors.Green, type: SaccharideType.Hexose },
+ { abbr: 'Gal', name: 'Galactose', color: SaccharideColors.Yellow, type: SaccharideType.Hexose },
+ { abbr: 'Gul', name: 'Gulose', color: SaccharideColors.Orange, type: SaccharideType.Hexose },
+ { abbr: 'Alt', name: 'Altrose', color: SaccharideColors.Pink, type: SaccharideType.Hexose },
+ { abbr: 'All', name: 'Allose', color: SaccharideColors.Purple, type: SaccharideType.Hexose },
+ { abbr: 'Tal', name: 'Talose', color: SaccharideColors.LightBlue, type: SaccharideType.Hexose },
+ { abbr: 'Ido', name: 'Idose', color: SaccharideColors.Brown, type: SaccharideType.Hexose },
+
+ { abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: SaccharideColors.Blue, type: SaccharideType.HexNAc },
+ { abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: SaccharideColors.Green, type: SaccharideType.HexNAc },
+ { abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: SaccharideColors.Yellow, type: SaccharideType.HexNAc },
+ { abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: SaccharideColors.Orange, type: SaccharideType.HexNAc },
+ { abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: SaccharideColors.Pink, type: SaccharideType.HexNAc },
+ { abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: SaccharideColors.Purple, type: SaccharideType.HexNAc },
+ { abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: SaccharideColors.LightBlue, type: SaccharideType.HexNAc },
+ { abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: SaccharideColors.Brown, type: SaccharideType.HexNAc },
+
+ { abbr: 'GlcN', name: 'Glucosamine', color: SaccharideColors.Blue, type: SaccharideType.Hexosamine },
+ { abbr: 'ManN', name: 'Mannosamine', color: SaccharideColors.Green, type: SaccharideType.Hexosamine },
+ { abbr: 'GalN', name: 'Galactosamine', color: SaccharideColors.Yellow, type: SaccharideType.Hexosamine },
+ { abbr: 'GulN', name: 'Gulosamine', color: SaccharideColors.Orange, type: SaccharideType.Hexosamine },
+ { abbr: 'AltN', name: 'Altrosamine', color: SaccharideColors.Pink, type: SaccharideType.Hexosamine },
+ { abbr: 'AllN', name: 'Allosamine', color: SaccharideColors.Purple, type: SaccharideType.Hexosamine },
+ { abbr: 'TalN', name: 'Talosamine', color: SaccharideColors.LightBlue, type: SaccharideType.Hexosamine },
+ { abbr: 'IdoN', name: 'Idosamine', color: SaccharideColors.Brown, type: SaccharideType.Hexosamine },
+
+ { abbr: 'GlcA', name: 'Glucuronic Acid', color: SaccharideColors.Blue, type: SaccharideType.Hexuronate },
+ { abbr: 'ManA', name: 'Mannuronic Acid', color: SaccharideColors.Green, type: SaccharideType.Hexuronate },
+ { abbr: 'GalA', name: 'Galacturonic Acid', color: SaccharideColors.Yellow, type: SaccharideType.Hexuronate },
+ { abbr: 'GulA', name: 'Guluronic Acid', color: SaccharideColors.Orange, type: SaccharideType.Hexuronate },
+ { abbr: 'AltA', name: 'Altruronic Acid', color: SaccharideColors.Pink, type: SaccharideType.Hexuronate },
+ { abbr: 'AllA', name: 'Alluronic Acid', color: SaccharideColors.Purple, type: SaccharideType.Hexuronate },
+ { abbr: 'TalA', name: 'Taluronic Acid', color: SaccharideColors.LightBlue, type: SaccharideType.Hexuronate },
+ { abbr: 'IdoA', name: 'Iduronic Acid', color: SaccharideColors.Brown, type: SaccharideType.Hexuronate },
+
+ { abbr: 'Qui', name: 'Quinovose', color: SaccharideColors.Blue, type: SaccharideType.Deoxyhexose },
+ { abbr: 'Rha', name: 'Rhamnose', color: SaccharideColors.Green, type: SaccharideType.Deoxyhexose },
+ { abbr: '6dGul', name: '6-Deoxy Gulose', color: SaccharideColors.Orange, type: SaccharideType.Deoxyhexose },
+ { abbr: '6dAlt', name: '6-Deoxy Altrose', color: SaccharideColors.Pink, type: SaccharideType.Deoxyhexose },
+ { abbr: '6dTal', name: '6-Deoxy Talose', color: SaccharideColors.LightBlue, type: SaccharideType.Deoxyhexose },
+ { abbr: 'Fuc', name: 'Fucose', color: SaccharideColors.Red, type: SaccharideType.Deoxyhexose },
+
+ { abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: SaccharideColors.Blue, type: SaccharideType.DeoxyhexNAc },
+ { abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: SaccharideColors.Green, type: SaccharideType.DeoxyhexNAc },
+ { abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: SaccharideColors.Pink, type: SaccharideType.DeoxyhexNAc },
+ { abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: SaccharideColors.LightBlue, type: SaccharideType.DeoxyhexNAc },
+ { abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: SaccharideColors.Red, type: SaccharideType.DeoxyhexNAc },
+
+ { abbr: 'Oli', name: 'Olivose', color: SaccharideColors.Blue, type: SaccharideType.DiDeoxyhexose },
+ { abbr: 'Tyv', name: 'Tyvelose', color: SaccharideColors.Green, type: SaccharideType.DiDeoxyhexose },
+ { abbr: 'Abe', name: 'Abequose', color: SaccharideColors.Orange, type: SaccharideType.DiDeoxyhexose },
+ { abbr: 'Par', name: 'Paratose', color: SaccharideColors.Pink, type: SaccharideType.DiDeoxyhexose },
+ { abbr: 'Dig', name: 'Digitoxose', color: SaccharideColors.Purple, type: SaccharideType.DiDeoxyhexose },
+ { abbr: 'Col', name: 'Colitose', color: SaccharideColors.LightBlue, type: SaccharideType.DiDeoxyhexose },
+
+ { abbr: 'Ara', name: 'Arabinose', color: SaccharideColors.Green, type: SaccharideType.Pentose },
+ { abbr: 'Lyx', name: 'Lyxose', color: SaccharideColors.Yellow, type: SaccharideType.Pentose },
+ { abbr: 'Xyl', name: 'Xylose', color: SaccharideColors.Orange, type: SaccharideType.Pentose },
+ { abbr: 'Rib', name: 'Ribose', color: SaccharideColors.Pink, type: SaccharideType.Pentose },
+
+ { abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: SaccharideColors.Green, type: SaccharideType.Deoxynonulosonate },
+ { abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: SaccharideColors.Purple, type: SaccharideType.Deoxynonulosonate },
+ { abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: SaccharideColors.LightBlue, type: SaccharideType.Deoxynonulosonate },
+ { abbr: 'Neu', name: 'Neuraminic Acid', color: SaccharideColors.Brown, type: SaccharideType.Deoxynonulosonate },
+ { abbr: 'Sia', name: 'Sialic acid', color: SaccharideColors.Red, type: SaccharideType.Deoxynonulosonate },
+
+ { abbr: 'Pse', name: 'Pseudaminic Acid', color: SaccharideColors.Green, type: SaccharideType.DiDeoxynonulosonate },
+ { abbr: 'Leg', name: 'Legionaminic Acid', color: SaccharideColors.Yellow, type: SaccharideType.DiDeoxynonulosonate },
+ { abbr: 'Aci', name: 'Acinetaminic Acid', color: SaccharideColors.Pink, type: SaccharideType.DiDeoxynonulosonate },
+ { abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: SaccharideColors.LightBlue, type: SaccharideType.DiDeoxynonulosonate },
+
+ { abbr: 'Bac', name: 'Bacillosamine', color: SaccharideColors.Blue, type: SaccharideType.Unknown },
+ { abbr: 'LDManHep', name: 'L-Glycero-D-Manno Heptose', color: SaccharideColors.Green, type: SaccharideType.Unknown },
+ { abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: SaccharideColors.Yellow, type: SaccharideType.Unknown },
+ { abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: SaccharideColors.Orange, type: SaccharideType.Unknown },
+ { abbr: 'DDManHep', name: 'D-Glycero-D-Manno-Heptose', color: SaccharideColors.Pink, type: SaccharideType.Unknown },
+ { abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: SaccharideColors.Purple, type: SaccharideType.Unknown },
+ { abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: SaccharideColors.LightBlue, type: SaccharideType.Unknown },
+ { abbr: 'Mur', name: 'Muramic Acid', color: SaccharideColors.Brown, type: SaccharideType.Unknown },
+
+ { abbr: 'Api', name: 'Apicose', color: SaccharideColors.Green, type: SaccharideType.Assigned },
+ { abbr: 'Fru', name: 'Fructose', color: SaccharideColors.Green, type: SaccharideType.Assigned },
+ { abbr: 'Tag', name: 'Tagatose', color: SaccharideColors.Yellow, type: SaccharideType.Assigned },
+ { abbr: 'Sor', name: 'Sorbose', color: SaccharideColors.Orange, type: SaccharideType.Assigned },
+ { abbr: 'Psi', name: 'Psicose', color: SaccharideColors.Pink, type: SaccharideType.Assigned },
+]
+
+const CommonSaccharideNames: { [k: string]: string[] } = {
+ // Hexose
+ Glc: ['GLC', 'BGC'],
+ Man: ['MAN', 'BMA'],
+ Gal: ['GAL', 'GLA'],
+ Gul: ['GUP', 'GL0'],
+ Alt: ['ALT'],
+ All: ['ALL', 'AFD'],
+ Tal: ['TAL'],
+ Ido: ['4N2'],
+ // HexNAc
+ GlcNAc: ['NAG', 'NDG'],
+ ManNAc: ['NGA', 'A2G'],
+ GulNAc: [],
+ AltNAc: [],
+ AllNAc: ['NAA'],
+ TalNAc: [],
+ IdoNAc: ['HSQ'],
+ // Hexosamine
+ GlcN: ['GCS', 'PA1'],
+ ManN: ['95Z'],
+ GalN: ['X6X', '1GN'],
+ GulN: [],
+ AltN: [],
+ AllN: [],
+ TalN: [],
+ IdoN: [],
+ // Hexuronate
+ GlcA: ['GCU', 'BDP'],
+ ManA: ['MAV', 'BEM'],
+ GalA: ['ADA', 'GTR'],
+ GulA: ['LGU'],
+ AltA: [],
+ AllA: [],
+ TalA: ['X0X', 'X1X'],
+ IdoA: ['IDR'],
+ // Deoxyhexose
+ Qui: ['G6D'],
+ Rha: ['RAM', 'RM4'],
+ '6dGul': [],
+ '6dAlt': [],
+ '6dTal': [],
+ Fuc: ['FUC', 'FUL'],
+ // DeoxyhexNAc
+ QuiNAc: [],
+ RhaNAc: [],
+ '6dAltNAc': [],
+ '6dTalNAc': [],
+ FucNAc: [],
+ // Di-deoxyhexose
+ Oli: ['DDA'],
+ Tyv: ['TYV'],
+ Abe: ['ABE'],
+ Par: ['PZU'],
+ Dig: [],
+ Col: [],
+ // Pentose
+ Ara: ['ARA', 'ARB'],
+ Lyx: ['LDY'],
+ Xyl: ['XYS', 'XYP'],
+ Rib: ['RIP', '0MK'],
+ // Deoxynonulosonate
+ Kdn: ['KDN', 'KDM'],
+ Neu5Ac: ['SIA', 'SLB'],
+ Neu5Gc: ['NGC', 'NGE'],
+ Neu: [],
+ Sia: [],
+ // Di-deoxynonulosonate
+ Pse: ['6PZ'],
+ Leg: [],
+ Aci: [],
+ '4eLeg': [],
+ // Unknown
+ Bac: ['B6D'],
+ LDManHep: ['GMH'],
+ Kdo: ['KDO'],
+ Dha: [],
+ DDManHep: [],
+ MurNAc: ['AMU'],
+ MurNGc: [],
+ Mur: ['MUR'],
+ // Assigned
+ Api: ['XXM'],
+ Fru: ['BDF'],
+ Tag: ['T6T'],
+ Sor: ['SOE'],
+ Psi: [],
+}
+
+export const SaccharideNameMap = (function () {
+ const map = new Map<string, SaccharideComponent>()
+ for (let i = 0, il = Monosaccharides.length; i < il; ++i) {
+ const saccharide = Monosaccharides[i]
+ const names = CommonSaccharideNames[saccharide.abbr]
+ if (names) {
+ for (let j = 0, jl = names.length; j < jl; ++j) {
+ map.set(names[j], saccharide)
+ }
+ }
+ }
+ return map
+})()
\ 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
new file mode 100644
index 0000000000000000000000000000000000000000..c8f22a1fe31c26c5155a26071c1002a52cc39dd8
--- /dev/null
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -0,0 +1,38 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import Unit from '../unit';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { ResidueIndex } from '../../model';
+import { SaccharideComponent } from './constants';
+
+export interface CarbohydrateLink {
+ readonly carbohydrateIndexA: number
+ readonly carbohydrateIndexB: number
+}
+
+export interface CarbohydrateTerminalLink {
+ readonly carbohydrateIndex: number
+ readonly elementIndex: number
+ readonly elementUnit: Unit
+ /** specifies direction of the link */
+ readonly fromCarbohydrate: boolean
+}
+
+export interface CarbohydrateElement {
+ readonly center: Vec3,
+ readonly normal: Vec3,
+ readonly direction: Vec3,
+ readonly unit: Unit.Atomic
+ readonly residueIndex: ResidueIndex
+ readonly component: SaccharideComponent
+}
+
+export interface Carbohydrates {
+ links: ReadonlyArray<CarbohydrateLink>
+ terminalLinks: ReadonlyArray<CarbohydrateTerminalLink>
+ elements: ReadonlyArray<CarbohydrateElement>
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 73cd16ee0b9c7cb62fb1fc7bc2ba9e84fe2b2769..348e8a7d9f650ba6bdd88b352fad774087d0d99f 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -19,6 +19,8 @@ import { CrossLinkRestraints, extractCrossLinkRestraints } from './unit/pair-res
import StructureSymmetry from './symmetry';
import StructureProperties from './properties';
import { ResidueIndex } from '../model/indexing';
+import { Carbohydrates } from './carbohydrates/data';
+import { computeCarbohydrates } from './carbohydrates/compute';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -86,6 +88,13 @@ class Structure {
return this._unitSymmetryGroups;
}
+ private _carbohydrates?: Carbohydrates = void 0;
+ get carbohydrates(): Carbohydrates {
+ if (this._carbohydrates) return this._carbohydrates;
+ this._carbohydrates = computeCarbohydrates(this);
+ return this._carbohydrates;
+ }
+
constructor(units: ArrayLike<Unit>) {
const map = IntMap.Mutable<Unit>();
let elementCount = 0;
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index fbe525649c4e876ffe7eb21d39c805d030e33af7..bac2778ca445ea5ed1d17fb7103cc17c5748f9a2 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -6,6 +6,8 @@
import { Model, ResidueIndex, ElementIndex } from './model';
import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId } from './model/types';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { Unit } from './structure';
export function getMoleculeType(model: Model, rI: ResidueIndex) {
const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
@@ -43,4 +45,19 @@ export function residueLabel(model: Model, rI: number) {
const { label_asym_id } = chains
const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]]
return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`
+}
+
+const centerPos = Vec3.zero()
+const centerMin = Vec3.zero()
+export function getCenterAndRadius(centroid: Vec3, unit: Unit, indices: ArrayLike<number>) {
+ const pos = unit.conformation.position
+ const { elements } = unit
+ Vec3.set(centroid, 0, 0, 0)
+ for (let i = 0, il = indices.length; i < il; ++i) {
+ pos(elements[indices[i]], centerPos)
+ Vec3.add(centroid, centroid, centerPos)
+ Vec3.min(centerMin, centerMin, centerPos)
+ }
+ Vec3.scale(centroid, centroid, 1/indices.length)
+ return Vec3.distance(centerMin, centroid)
}
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 1fc6ce73a9455caa7e57163f148da127e53dba7c..a886525f57931616070ec6e17c4c17c03b158604 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -27,8 +27,8 @@ const spacefillProps: SpacefillProps = {
const ballAndStickProps: BallAndStickProps = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
- sizeTheme: { name: 'uniform', value: 0.05 },
- linkRadius: 0.05,
+ sizeTheme: { name: 'uniform', value: 0.15 },
+ linkRadius: 0.15,
quality: 'auto',
useFog: false
}
@@ -78,7 +78,7 @@ export class Stage {
// this.loadPdbid('1hrv') // viral assembly
// this.loadPdbid('1rb8') // virus
// this.loadPdbid('1blu') // metal coordination
- // this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water
+ this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
// this.loadPdbid('2np2') // dna
@@ -92,8 +92,10 @@ export class Stage {
// this.loadPdbid('1xv6') // rna, modified nucleotides
// this.loadPdbid('3bbm') // rna with linker
// this.loadPdbid('1gfl') // GFP, flourophore has carbonyl oxygen removed
- this.loadPdbid('1sfi') // contains cyclic peptid
+ // this.loadPdbid('1sfi') // contains cyclic peptid
// this.loadPdbid('3sn6') // discontinuous chains
+ // this.loadPdbid('2zex') // small, contains carbohydrate polymer
+ // this.loadPdbid('2b5t') // contains large carbohydrate polymer
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)
// this.loadMmcifUrl(`../../examples/1crn.cif`)
@@ -119,10 +121,10 @@ export class Stage {
console.log(modelEntity.value)
const structureEntity = await ModelToStructure.apply(this.ctx, modelEntity)
- StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: false })
+ StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: true })
StructureToSpacefill.apply(this.ctx, structureEntity, { ...spacefillProps, visible: false })
StructureToDistanceRestraint.apply(this.ctx, structureEntity, { ...distanceRestraintProps, visible: false })
- StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: true })
+ StructureToBackbone.apply(this.ctx, structureEntity, { ...backboneProps, visible: false })
StructureToCartoon.apply(this.ctx, structureEntity, { ...cartoonProps, visible: true })
StructureCenter.apply(this.ctx, structureEntity)