diff --git a/src/mol-geo/primitive/prism.ts b/src/mol-geo/primitive/prism.ts
index 22f12872e9490c7b792a3c0c5efd80e77765d755..f019a5bef2e63f29618b125229bd2213282f321e 100644
--- a/src/mol-geo/primitive/prism.ts
+++ b/src/mol-geo/primitive/prism.ts
@@ -78,10 +78,22 @@ export function PentagonalPrism() {
let hexagonalPrism: Primitive
export function HexagonalPrism() {
- if (!hexagonalPrism) hexagonalPrism = Prism(polygon(6, true))
+ if (!hexagonalPrism) hexagonalPrism = Prism(polygon(6, false))
return hexagonalPrism
}
+let shiftedHexagonalPrism: Primitive
+export function ShiftedHexagonalPrism() {
+ if (!shiftedHexagonalPrism) shiftedHexagonalPrism = Prism(polygon(6, true))
+ return shiftedHexagonalPrism
+}
+
+let heptagonalPrism: Primitive
+export function HeptagonalPrism() {
+ if (!heptagonalPrism) heptagonalPrism = Prism(polygon(7, false))
+ return heptagonalPrism
+}
+
//
/**
@@ -133,6 +145,6 @@ export function PentagonalPrismCage() {
let hexagonalPrismCage: Cage
export function HexagonalPrismCage() {
- if (!hexagonalPrismCage) hexagonalPrismCage = PrismCage(polygon(6, true))
+ if (!hexagonalPrismCage) hexagonalPrismCage = PrismCage(polygon(6, false))
return hexagonalPrismCage
}
\ 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 183bd430ebdd655d02a432085fc5516aa64852ea..70bd7eb4f0bd5ad1a026c099f61ced0139156c72 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 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>
@@ -203,7 +203,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
elements.push({
geometry: { center, normal, direction },
component: saccharideComp,
- unit, residueIndex, anomericCarbon, ringAltId
+ unit, residueIndex, anomericCarbon, ringAltId,
+ ringMemberCount: ringAtoms.length
})
}
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index 7dcb8b51ad3d98cf012da8b64d85098817915ec3..a3ba451b47cb6e2483e2b1d52a5a3164d15bf8b2 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 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>
@@ -9,9 +9,13 @@ import { Color, ColorMap } from '../../../../mol-util/color';
// follows community standard from https://www.ncbi.nlm.nih.gov/glycans/snfg.html
-export const enum SaccharideShapes {
+export const enum SaccharideShape {
+ // standard shapes
FilledSphere, FilledCube, CrossedCube, DividedDiamond, FilledCone, DevidedCone,
- FlatBox, FilledStar, FilledDiamond, FlatDiamond, FlatHexagon, Pentagon
+ FlatBox, FilledStar, FilledDiamond, FlatDiamond, FlatHexagon, Pentagon,
+
+ // generic shapes for rings with 4, 5, 6, or 7 members
+ DiamondPrism, PentagonalPrism, HexagonalPrism, HeptagonalPrism
}
export const SaccharideColors = ColorMap({
@@ -53,22 +57,30 @@ export function getSaccharideName(type: SaccharideType) {
}
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,
+ [SaccharideType.Hexose]: SaccharideShape.FilledSphere,
+ [SaccharideType.HexNAc]: SaccharideShape.FilledCube,
+ [SaccharideType.Hexosamine]: SaccharideShape.CrossedCube,
+ [SaccharideType.Hexuronate]: SaccharideShape.DividedDiamond,
+ [SaccharideType.Deoxyhexose]: SaccharideShape.FilledCone,
+ [SaccharideType.DeoxyhexNAc]: SaccharideShape.DevidedCone,
+ [SaccharideType.DiDeoxyhexose]: SaccharideShape.FlatBox,
+ [SaccharideType.Pentose]: SaccharideShape.FilledStar,
+ [SaccharideType.Deoxynonulosonate]: SaccharideShape.FilledDiamond,
+ [SaccharideType.DiDeoxynonulosonate]: SaccharideShape.FlatDiamond,
+ [SaccharideType.Unknown]: SaccharideShape.FlatHexagon,
+ [SaccharideType.Assigned]: SaccharideShape.Pentagon,
}
-export function getSaccharideShape(type: SaccharideType) {
- return SaccharideTypeShapeMap[type]
+export function getSaccharideShape(type: SaccharideType, ringMemberCount: number): SaccharideShape {
+ if (type === SaccharideType.Unknown) {
+ if (ringMemberCount === 4) return SaccharideShape.DiamondPrism
+ else if (ringMemberCount === 5) return SaccharideShape.PentagonalPrism
+ else if (ringMemberCount === 6) return SaccharideShape.HexagonalPrism
+ else if (ringMemberCount === 7) return SaccharideShape.HeptagonalPrism
+ else return SaccharideShape.FlatHexagon
+ } else {
+ return SaccharideTypeShapeMap[type]
+ }
}
export type SaccharideComponent = {
@@ -172,19 +184,6 @@ const Monosaccharides: SaccharideComponent[] = [
{ 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 },
-
- { abbr: 'Hexose', name: 'Hexose', color: SaccharideColors.Secondary, type: SaccharideType.Hexose },
- { abbr: 'HexNAc', name: 'HexNAc', color: SaccharideColors.Secondary, type: SaccharideType.HexNAc },
- { abbr: 'Hexosamine', name: 'Hexosamine', color: SaccharideColors.Secondary, type: SaccharideType.Hexosamine },
- { abbr: 'Hexuronate', name: 'Hexuronate', color: SaccharideColors.Secondary, type: SaccharideType.Hexuronate },
- { abbr: 'Deoxyhexose', name: 'Deoxyhexose', color: SaccharideColors.Secondary, type: SaccharideType.Deoxyhexose },
- { abbr: 'DeoxyhexNAc', name: 'DeoxyhexNAc', color: SaccharideColors.Secondary, type: SaccharideType.DeoxyhexNAc },
- { abbr: 'Di-deoxyhexose', name: 'Di-deoxyhexose', color: SaccharideColors.Secondary, type: SaccharideType.DiDeoxyhexose },
- { abbr: 'Pentose', name: 'Pentose', color: SaccharideColors.Secondary, type: SaccharideType.Pentose },
- { abbr: 'Deoxynonulosonate', name: 'Deoxynonulosonate', color: SaccharideColors.Secondary, type: SaccharideType.Deoxynonulosonate },
- { abbr: 'Di-deoxynonulosonate', name: 'Di-deoxynonulosonate', color: SaccharideColors.Secondary, type: SaccharideType.DiDeoxynonulosonate },
- { abbr: 'Unknown', name: 'Unknown', color: SaccharideColors.Secondary, type: SaccharideType.Unknown },
- { abbr: 'Assigned', name: 'Assigned', color: SaccharideColors.Secondary, type: SaccharideType.Assigned },
]
export const SaccharidesSnfgMap = (function () {
@@ -301,24 +300,13 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
Tag: ['T6T'],
Sor: ['SOE'],
Psi: ['PSV'],
- // Generic
- Hexose: [],
- HexNAc: [],
- Hexosamine: [],
- Hexuronate: [],
- Deoxyhexose: [],
- DeoxyhexNAc: [],
- 'Di-deoxyhexose': [],
- Pentose: [],
- Deoxynonulosonate: [],
- 'Di-deoxynonulosonate': [],
- Unknown: [],
- Assigned: ['PUF'],
}
const UnknownSaccharideNames = [
'NGZ', // via CCD
'LAT', // BETA-LACTOSE, Gal-Glc di-saccharide via GlyFinder
+
+ 'PUF', 'GDA', '9WJ', // via updated CCD
]
export const SaccharideCompIdMap = (function () {
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index de873ca3c434d12b347602244709c846ce023db7..01aafab225a1396efe624f034c42bf580f9348d3 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -30,6 +30,7 @@ export interface CarbohydrateElement {
readonly residueIndex: ResidueIndex,
readonly component: SaccharideComponent,
readonly ringAltId: string,
+ readonly ringMemberCount: number,
}
/** partial carbohydrate with no ring present */
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index 93665ab844f151c4cf563ccaaac47ab17d1d4136..14e4299bc671589f449f9188e6124bf5b4a9a2eb 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -9,11 +9,11 @@ import { Box, PerforatedBox } from '../../../mol-geo/primitive/box';
import { OctagonalPyramid, PerforatedOctagonalPyramid } from '../../../mol-geo/primitive/pyramid';
import { Star } from '../../../mol-geo/primitive/star';
import { Octahedron, PerforatedOctahedron } from '../../../mol-geo/primitive/octahedron';
-import { DiamondPrism, PentagonalPrism, HexagonalPrism } from '../../../mol-geo/primitive/prism';
+import { DiamondPrism, PentagonalPrism, ShiftedHexagonalPrism, HexagonalPrism, HeptagonalPrism } from '../../../mol-geo/primitive/prism';
import { Structure, StructureElement } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { getSaccharideShape, SaccharideShapes } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { getSaccharideShape, SaccharideShape } from '../../../mol-model/structure/structure/carbohydrates/constants';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { ComplexMeshParams, ComplexMeshVisual } from '../complex-visual';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -43,6 +43,8 @@ const perforatedOctahedron = PerforatedOctahedron()
const diamondPrism = DiamondPrism()
const pentagonalPrism = PentagonalPrism()
const hexagonalPrism = HexagonalPrism()
+const shiftedHexagonalPrism = ShiftedHexagonalPrism()
+const heptagonalPrism = HeptagonalPrism()
function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateSymbolParams>, mesh?: Mesh) {
const builderState = MeshBuilder.createState(256, 128, mesh)
@@ -55,7 +57,7 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
for (let i = 0; i < n; ++i) {
const c = carbohydrates.elements[i];
- const shapeType = getSaccharideShape(c.component.type)
+ const shapeType = getSaccharideShape(c.component.type, c.ringMemberCount)
l.unit = c.unit
l.element = c.unit.elements[c.anomericCarbon]
@@ -71,47 +73,47 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
builderState.currentGroup = i * 2
switch (shapeType) {
- case SaccharideShapes.FilledSphere:
+ case SaccharideShape.FilledSphere:
addSphere(builderState, center, radius, detail)
break;
- case SaccharideShapes.FilledCube:
+ case SaccharideShape.FilledCube:
Mat4.scaleUniformly(t, t, side)
MeshBuilder.addPrimitive(builderState, t, box)
break;
- case SaccharideShapes.CrossedCube:
+ case SaccharideShape.CrossedCube:
Mat4.scaleUniformly(t, t, side)
MeshBuilder.addPrimitive(builderState, t, perforatedBox)
Mat4.mul(t, t, Mat4.rotZ90X180)
builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedBox)
break;
- case SaccharideShapes.FilledCone:
+ case SaccharideShape.FilledCone:
Mat4.scaleUniformly(t, t, side * 1.2)
MeshBuilder.addPrimitive(builderState, t, octagonalPyramid)
break
- case SaccharideShapes.DevidedCone:
+ case SaccharideShape.DevidedCone:
Mat4.scaleUniformly(t, t, side * 1.2)
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid)
Mat4.mul(t, t, Mat4.rotZ90)
builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid)
break
- case SaccharideShapes.FlatBox:
+ case SaccharideShape.FlatBox:
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
MeshBuilder.addPrimitive(builderState, t, box)
break
- case SaccharideShapes.FilledStar:
+ case SaccharideShape.FilledStar:
Mat4.scaleUniformly(t, t, side)
Mat4.mul(t, t, Mat4.rotZY90)
MeshBuilder.addPrimitive(builderState, t, star)
break
- case SaccharideShapes.FilledDiamond:
+ case SaccharideShape.FilledDiamond:
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
MeshBuilder.addPrimitive(builderState, t, octahedron)
break
- case SaccharideShapes.DividedDiamond:
+ case SaccharideShape.DividedDiamond:
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron)
@@ -119,21 +121,37 @@ function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure,
builderState.currentGroup += 1
MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron)
break
- case SaccharideShapes.FlatDiamond:
+ case SaccharideShape.FlatDiamond:
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2))
MeshBuilder.addPrimitive(builderState, t, diamondPrism)
break
- case SaccharideShapes.Pentagon:
+ case SaccharideShape.DiamondPrism:
+ Mat4.mul(t, t, Mat4.rotZY90)
+ Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
+ MeshBuilder.addPrimitive(builderState, t, diamondPrism)
+ break
+ case SaccharideShape.PentagonalPrism:
+ case SaccharideShape.Pentagon:
Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
MeshBuilder.addPrimitive(builderState, t, pentagonalPrism)
break
- case SaccharideShapes.FlatHexagon:
+ case SaccharideShape.HexagonalPrism:
+ Mat4.mul(t, t, Mat4.rotZY90)
+ Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
+ MeshBuilder.addPrimitive(builderState, t, hexagonalPrism)
+ break
+ case SaccharideShape.HeptagonalPrism:
+ Mat4.mul(t, t, Mat4.rotZY90)
+ Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
+ MeshBuilder.addPrimitive(builderState, t, heptagonalPrism)
+ break
+ case SaccharideShape.FlatHexagon:
default:
Mat4.mul(t, t, Mat4.rotZYZ90)
Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side , side / 2))
- MeshBuilder.addPrimitive(builderState, t, hexagonalPrism)
+ MeshBuilder.addPrimitive(builderState, t, shiftedHexagonalPrism)
break
}
}