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 23256b8ed47c8c8fe5107b38b893d5cf85df3519..22916064d52e50d22a7aad9364bbc5df710d364f 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -42,7 +42,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
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 coneParams = { radiusTop: 0.0, radiusBottom: radius, bottomCap: true }
const linkParams = { radiusTop: 0.4, radiusBottom: 0.4 }
@@ -63,15 +63,14 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
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)
- // TODO fix cylinder direction flipping code
+ Vec3.scaleAndAdd(p1, c.center, c.direction, radius)
+ Vec3.scaleAndSub(p2, c.center, c.direction, 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)
+ Vec3.scaleAndAdd(p1, c.center, c.direction, radius)
+ Vec3.scaleAndSub(p2, c.center, c.direction, radius)
builder.addCylinder(p1, p2, 1, coneParams)
break
case SaccharideShapes.FlatBox:
@@ -87,12 +86,12 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
case SaccharideShapes.FlatDiamond:
case SaccharideShapes.Pentagon:
centerAlign(c.center, c.normal, c.direction)
- builder.addBox(t, { width: side, height: 0.5, depth: side })
+ builder.addBox(t, { width: side, height: side, depth: 0.5 })
break
case SaccharideShapes.FlatHexagon:
default:
centerAlign(c.center, c.normal, c.direction)
- builder.addBox(t, { width: side, height: 0.1, depth: side })
+ builder.addBox(t, { width: side, height: side, depth: 0.1 })
break
}
}
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index 1fa344ade16569c9ba5b6a2c37505d9e77f7b41e..f566e1b08e37aa3afc290ef5a027edbf5e1adbe9 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -60,14 +60,16 @@ const tmpCylinderCenter = Vec3.zero()
const tmpCylinderMat = Mat4.zero()
// const tmpCylinderMatTrans = Mat4.zero()
const tmpCylinderStart = Vec3.zero()
+const tmpUp = Vec3.zero()
function setCylinderMat(m: Mat4, start: Vec3, dir: Vec3, length: number) {
Vec3.setMagnitude(tmpCylinderMatDir, dir, length / 2)
Vec3.add(tmpCylinderCenter, start, tmpCylinderMatDir)
- // ensure the direction use to create the rotation is always pointing in the same
+ // ensure the direction used to create the rotation is always pointing in the same
// direction so the triangles of adjacent cylinder will line up
- if (Vec3.dot(tmpCylinderMatDir, up) < 0) Vec3.scale(tmpCylinderMatDir, tmpCylinderMatDir, -1)
- Vec3.makeRotation(m, up, tmpCylinderMatDir)
+ Vec3.copy(tmpUp, up)
+ if (Vec3.dot(tmpCylinderMatDir, tmpUp) < 0) Vec3.scale(tmpUp, tmpUp, -1)
+ Vec3.makeRotation(m, tmpUp, tmpCylinderMatDir)
return Mat4.setTranslation(m, tmpCylinderCenter)
}
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 2d560f6eee2aea13fb084b3998dcdc3668f533cc..2e0ac1168b13766bc0d815a7c850d5496d58fa43 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -67,6 +67,12 @@ function getDirection(direction: Vec3, unit: Unit.Atomic, indices: ReadonlyArray
return direction
}
+function getAtomId(unit: Unit.Atomic, index: number) {
+ const { elements } = unit
+ const { label_atom_id } = unit.model.atomicHierarchy.atoms
+ return label_atom_id.value(elements[index])
+}
+
export function computeCarbohydrates(structure: Structure): Carbohydrates {
const links: CarbohydrateLink[] = []
const terminalLinks: CarbohydrateTerminalLink[] = []
@@ -78,6 +84,18 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
return `${residueIndex}|${unitId}`
}
+ function fixLinkDirection(iA: number, iB: number) {
+ Vec3.sub(elements[iA].direction, elements[iB].center, elements[iA].center)
+ Vec3.normalize(elements[iA].direction, elements[iA].direction)
+ }
+
+ const tmpV = Vec3.zero()
+ function fixTerminalLinkDirection(iA: number, indexB: number, unitB: Unit.Atomic) {
+ const pos = unitB.conformation.position
+ Vec3.sub(elements[iA].direction, pos(unitB.elements[indexB], tmpV), elements[iA].center)
+ Vec3.normalize(elements[iA].direction, elements[iA].direction)
+ }
+
// get carbohydrate elements and carbohydrate links induced by intra-residue bonds
for (let i = 0, il = structure.units.length; i < il; ++i) {
const unit = structure.units[i]
@@ -122,6 +140,9 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
for (let j = 0, jl = ringCombinations.length; j < jl; ++j) {
const rc = ringCombinations[j]
if (areConnected(sugarRings[rc[0]], sugarRings[rc[1]], unit.links, 2)) {
+ // fix both directions as it is unlcear where the C1 atom is
+ fixLinkDirection(ringElements[rc[0]], ringElements[rc[1]])
+ fixLinkDirection(ringElements[rc[1]], ringElements[rc[0]])
links.push({
carbohydrateIndexA: ringElements[rc[0]],
carbohydrateIndexB: ringElements[rc[1]]
@@ -154,11 +175,17 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const elementIndexB = elementsMap.get(elementKey(getResidueIndex(indexB, unitB), unitB.id))
if (elementIndexA !== undefined && elementIndexB !== undefined) {
+ if (getAtomId(unitA, indexA).startsWith('C1')) {
+ fixLinkDirection(elementIndexA, elementIndexB)
+ }
links.push({
carbohydrateIndexA: elementIndexA,
carbohydrateIndexB: elementIndexB
})
} else if (elementIndexA !== undefined) {
+ if (getAtomId(unitA, indexA).startsWith('C1')) {
+ fixTerminalLinkDirection(elementIndexA, indexB, unitB)
+ }
terminalLinks.push({
carbohydrateIndex: elementIndexA,
elementIndex: indexB,
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index eddb98e1bf3ec18746c73b21ca48533756cac274..a6c16844db26d6db7587be46f6ba822d37c3e7e2 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -178,7 +178,8 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
Glc: [
'GLC', 'BGC',
'BOG', // via GlyFinder
- 'TRE', // via GlyFinder, disaccharide but homomer
+ 'TRE', // via GlyFinder, di-saccharide but homomer
+ 'MLR', // via GlyFinder, tri-saccharide but homomer
],
Man: ['MAN', 'BMA'],
Gal: ['GAL', 'GLA'],
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 96a24b36b5b657dc82b6e1435c343f77ae0b554a..1317b4024434b7dc431e6ca1725f3ce24c844846 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -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, carbohydrates linked to protein
+ 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
@@ -99,7 +99,7 @@ export class Stage {
// 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('1umz') // contains Xyl (Xyloglucan)
// this.loadPdbid('1mfb') // contains Abe
// this.loadPdbid('2gdu') // contains sucrose
// this.loadPdbid('2fnc') // contains maltotriose