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 68ce664400f7cc82f57173ec336244781f63c714..1882c8ea49ec73a401ce75267193936723a52339 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -22,20 +22,75 @@ import { createMeshValues, updateMeshValues, updateRenderableState, createRender
import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { createUniformColor } from '../../../util/color-data';
+import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
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 pd = Vec3.zero()
+ const p1 = Vec3.zero()
+ const p2 = Vec3.zero()
const carbohydrates = structure.carbohydrates
- const linkParams = { radiusTop: 0.2, radiusBottom: 0.2 }
+ 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 coneParams = { radiusTop: radius, radiusBottom: 0.0, topCap: true }
+
+ const linkParams = { radiusTop: 0.4, radiusBottom: 0.4 }
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 })
+ const shapeType = getSaccharideShape(c.component.type)
+ switch (shapeType) {
+ case SaccharideShapes.FilledSphere:
+ builder.addIcosahedron(c.center, radius, 1)
+ break;
+ case SaccharideShapes.FilledCube:
+ centerAlign(c.center, c.normal, c.direction)
+ builder.addBox(t, { width: side, height: side, depth: side })
+ break;
+ case SaccharideShapes.CrossedCube:
+ // TODO split
+ centerAlign(c.center, c.normal, c.direction)
+ builder.addBox(t, { width: side, height: side, depth: side })
+ break;
+ case SaccharideShapes.FilledCone:
+ Vec3.scaleAndAdd(p1, c.center, c.normal, radius)
+ Vec3.scaleAndSub(p2, c.center, c.normal, radius)
+ builder.addCylinder(p1, p2, 1, coneParams)
+ break
+ case SaccharideShapes.DevidedCone:
+ // TODO split
+ Vec3.scaleAndAdd(p1, c.center, c.normal, radius)
+ Vec3.scaleAndSub(p2, c.center, c.normal, radius)
+ builder.addCylinder(p1, p2, 1, coneParams)
+ break
+ case SaccharideShapes.FlatBox:
+ centerAlign(c.center, c.normal, c.direction)
+ builder.addBox(t, { width: side, height: side / 2, depth: side })
+ break
+ case SaccharideShapes.FilledDiamond:
+ case SaccharideShapes.DividedDiamond:
+ case SaccharideShapes.FilledStar:
+ case SaccharideShapes.FlatDiamond:
+ case SaccharideShapes.Pentagon:
+ centerAlign(c.center, c.normal, c.direction)
+ builder.addBox(t, { width: side, height: 0.5, depth: side })
+ break
+ case SaccharideShapes.FlatHexagon:
+ default:
+ centerAlign(c.center, c.normal, c.direction)
+ builder.addBox(t, { width: side, height: 0.1, depth: side })
+ break
+ }
}
for (let i = 0, il = carbohydrates.links.length; i < il; ++i) {
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index 659e35acc0c005e151f43ace20d3e0ffc5c13e01..0dddd92f0886f9eeaabd174d1258465862d32eab 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -132,6 +132,14 @@ namespace Vec3 {
return out;
}
+ /** Scales b, then subtracts b from a */
+ export function scaleAndSub(out: Vec3, a: Vec3, b: Vec3, scale: number) {
+ out[0] = a[0] - (b[0] * scale);
+ out[1] = a[1] - (b[1] * scale);
+ out[2] = a[2] - (b[2] * scale);
+ return out;
+ }
+
/**
* Math.round the components of a Vec3
*/
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 94705c6ede10279b8e84df4f2554f28e7aa1c483..2d560f6eee2aea13fb084b3998dcdc3668f533cc 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -11,11 +11,12 @@ import Structure from '../structure';
import { Carbohydrates, CarbohydrateLink, CarbohydrateTerminalLink, CarbohydrateElement } from './data';
import { SaccharideNameMap, UnknownSaccharideComponent } from './constants';
import { Vec3 } from 'mol-math/linear-algebra';
-import { getCenterAndRadius, getMoleculeType } from '../../util';
-import { MoleculeType } from '../../model/types';
+import { getMoleculeType, getPositionMatrix } from '../../util';
+import { MoleculeType, ElementSymbol } from '../../model/types';
import { areConnected } from 'mol-math/graph';
import { combinations } from 'mol-data/util/combination';
import { fillSerial } from 'mol-util/array';
+import PrincipalAxes from 'mol-math/linear-algebra/matrix/principal-axes';
function getResidueIndex(elementIndex: number, unit: Unit.Atomic) {
return unit.model.atomicHierarchy.residueAtomSegments.index[unit.elements[elementIndex]]
@@ -40,6 +41,32 @@ function getRingIndices(unit: Unit.Atomic, rI: ResidueIndex) {
return sugarRings
}
+const C = ElementSymbol('C')
+function getDirection(direction: Vec3, unit: Unit.Atomic, indices: ReadonlyArray<number>, center: Vec3) {
+ let indexC1 = -1, indexC1X = -1, indexC = -1
+ const { elements } = unit
+ const { position } = unit.conformation
+ const { label_atom_id, type_symbol } = unit.model.atomicHierarchy.atoms
+ for (let i = 0, il = indices.length; i < il; ++i) {
+ const ei = elements[indices[i]]
+ const atomId = label_atom_id.value(ei)
+ if (atomId === 'C1') {
+ indexC1 = ei
+ break
+ } else if (indexC1X === -1 && atomId.startsWith('C1')) {
+ indexC1X = ei
+ } else if (indexC === -1 && type_symbol.value(ei) === C) {
+ indexC = ei
+ }
+ }
+ const index = indexC1 !== -1 ? indexC1
+ : indexC1X !== -1 ? indexC1X
+ : indexC !== -1 ? indexC
+ : elements[indices[0]]
+ Vec3.normalize(direction, Vec3.sub(direction, center, position(index, direction)))
+ return direction
+}
+
export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = []
@@ -76,15 +103,15 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const sugarRings = getRingIndices(unit, residueIndex)
const ringElements: number[] = []
- console.log('sugarRings', sugarRings)
for (let j = 0, jl = sugarRings.length; j < jl; ++j) {
- const center = Vec3.zero()
- const normal = Vec3.zero()
- const direction = Vec3.zero()
- const elementIndex = elements.length
- getCenterAndRadius(center, unit, sugarRings[j])
+ const pa = new PrincipalAxes(getPositionMatrix(unit, sugarRings[j]))
+ const center = Vec3.copy(Vec3.zero(), pa.center)
+ const normal = Vec3.copy(Vec3.zero(), pa.normVecC)
+ const direction = getDirection(Vec3.zero(), unit, sugarRings[j], center)
+ Vec3.orthogonalize(direction, normal, direction)
+ const elementIndex = elements.length
ringElements.push(elementIndex)
elementsMap.set(elementKey(residueIndex, unit.id), elementIndex)
elements.push({ center, normal, direction, unit, residueIndex, component: saccharideComp })
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index b5b617a2ea17d41aabc321f8cf84e82e10566c6a..eddb98e1bf3ec18746c73b21ca48533756cac274 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -175,7 +175,11 @@ const Monosaccharides: SaccharideComponent[] = [
const CommonSaccharideNames: { [k: string]: string[] } = {
// Hexose
- Glc: ['GLC', 'BGC'],
+ Glc: [
+ 'GLC', 'BGC',
+ 'BOG', // via GlyFinder
+ 'TRE', // via GlyFinder, disaccharide but homomer
+ ],
Man: ['MAN', 'BMA'],
Gal: ['GAL', 'GLA'],
Gul: ['GUP', 'GL0'],
@@ -192,7 +196,10 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
TalNAc: [],
IdoNAc: ['HSQ'],
// Hexosamine
- GlcN: ['GCS', 'PA1'],
+ GlcN: [
+ 'GCS', 'PA1',
+ 'IDU', 'SGN', 'SUS', // via GlyFinder
+ ],
ManN: ['95Z'],
GalN: ['X6X', '1GN'],
GulN: [],
@@ -208,7 +215,10 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
AltA: [],
AllA: [],
TalA: ['X0X', 'X1X'],
- IdoA: ['IDR'],
+ IdoA: [
+ 'IDR',
+ 'IDS', // via GlyFinder
+ ],
// Deoxyhexose
Qui: ['G6D'],
Rha: ['RAM', 'RM4'],
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index bac2778ca445ea5ed1d17fb7103cc17c5748f9a2..a20abb42e47bf97df10a7d7feb76d9dc01794407 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -8,6 +8,7 @@ import { Model, ResidueIndex, ElementIndex } from './model';
import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId } from './model/types';
import { Vec3 } from 'mol-math/linear-algebra';
import { Unit } from './structure';
+import Matrix from 'mol-math/linear-algebra/matrix/matrix';
export function getMoleculeType(model: Model, rI: ResidueIndex) {
const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
@@ -60,4 +61,16 @@ export function getCenterAndRadius(centroid: Vec3, unit: Unit, indices: ArrayLik
}
Vec3.scale(centroid, centroid, 1/indices.length)
return Vec3.distance(centerMin, centroid)
+}
+
+const matrixPos = Vec3.zero()
+export function getPositionMatrix(unit: Unit, indices: ArrayLike<number>) {
+ const pos = unit.conformation.position
+ const mat = Matrix.create(3, indices.length)
+ const { elements } = unit
+ for (let i = 0, il = indices.length; i < il; ++i) {
+ pos(elements[indices[i]], matrixPos)
+ Vec3.toArray(matrixPos, mat.data, i * 3)
+ }
+ return mat
}
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 78d1ef9d6247c1b4af0419ef086501e0ee90f184..96a24b36b5b657dc82b6e1435c343f77ae0b554a 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -96,14 +96,20 @@ export class Stage {
// this.loadPdbid('1gfl') // GFP, flourophore has carbonyl oxygen removed
// this.loadPdbid('1sfi') // contains cyclic peptid
// this.loadPdbid('3sn6') // discontinuous chains
- // this.loadPdbid('2zex') // small, contains carbohydrate polymer
+ // this.loadPdbid('2zex') // contains carbohydrate polymer
+ // this.loadPdbid('3sgj') // contains carbohydrate polymer
+ // this.loadPdbid('3ina') // contains GlcN and IdoA
+ this.loadPdbid('1umz') // contains Xyl (Xyloglucan)
+ // this.loadPdbid('1mfb') // contains Abe
// this.loadPdbid('2gdu') // contains sucrose
// this.loadPdbid('2fnc') // contains maltotriose
- this.loadPdbid('4zs9') // contains raffinose
+ // this.loadPdbid('4zs9') // contains raffinose
+ // this.loadPdbid('2yft') // contains kestose
// this.loadPdbid('2b5t') // contains large carbohydrate polymer
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)
// this.loadMmcifUrl(`../../examples/1crn.cif`)
+ // this.loadPdbid('1zag') // temp
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok
// this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`) // ok