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 22916064d52e50d22a7aad9364bbc5df710d364f..ad9c384dabeefb3071fa5fbb4ada91bb9d7621cf 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -47,50 +47,53 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
const linkParams = { radiusTop: 0.4, radiusBottom: 0.4 }
for (let i = 0, il = carbohydrates.elements.length; i < il; ++i) {
- const c = carbohydrates.elements[i]
+ const c = carbohydrates.elements[i];
+ if (!c.hasRing) continue;
+
+ const cGeo = c.geometry!
const shapeType = getSaccharideShape(c.component.type)
switch (shapeType) {
case SaccharideShapes.FilledSphere:
- builder.addIcosahedron(c.center, radius, 2)
+ builder.addIcosahedron(cGeo.center, radius, 2)
break;
case SaccharideShapes.FilledCube:
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addBox(t, { width: side, height: side, depth: side })
break;
case SaccharideShapes.CrossedCube:
// TODO split
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addBox(t, { width: side, height: side, depth: side })
break;
case SaccharideShapes.FilledCone:
- Vec3.scaleAndAdd(p1, c.center, c.direction, radius)
- Vec3.scaleAndSub(p2, c.center, c.direction, radius)
+ Vec3.scaleAndAdd(p1, cGeo.center, cGeo.direction, radius)
+ Vec3.scaleAndSub(p2, cGeo.center, cGeo.direction, radius)
builder.addCylinder(p1, p2, 1, coneParams)
break
case SaccharideShapes.DevidedCone:
// TODO split
- Vec3.scaleAndAdd(p1, c.center, c.direction, radius)
- Vec3.scaleAndSub(p2, c.center, c.direction, radius)
+ Vec3.scaleAndAdd(p1, cGeo.center, cGeo.direction, radius)
+ Vec3.scaleAndSub(p2, cGeo.center, cGeo.direction, radius)
builder.addCylinder(p1, p2, 1, coneParams)
break
case SaccharideShapes.FlatBox:
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addBox(t, { width: side, height: side / 2, depth: side })
break
case SaccharideShapes.FilledStar:
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addStar(t, { outerRadius: side, innerRadius: side / 2, thickness: side / 2, pointCount: 5 })
break
case SaccharideShapes.FilledDiamond:
case SaccharideShapes.DividedDiamond:
case SaccharideShapes.FlatDiamond:
case SaccharideShapes.Pentagon:
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addBox(t, { width: side, height: side, depth: 0.5 })
break
case SaccharideShapes.FlatHexagon:
default:
- centerAlign(c.center, c.normal, c.direction)
+ centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
builder.addBox(t, { width: side, height: side, depth: 0.1 })
break
}
@@ -98,14 +101,14 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
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
+ const centerA = carbohydrates.elements[l.carbohydrateIndexA].geometry!.center
+ const centerB = carbohydrates.elements[l.carbohydrateIndexB].geometry!.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
+ 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)
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 5014945536e7048333054e912d3e8201ef410d66..eb441c0d1cce720a116ddeee1b79d0ce797ce86e 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -90,22 +90,22 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const terminalLinks: CarbohydrateTerminalLink[] = []
const elements: CarbohydrateElement[] = []
- const elementsMap = new Map<string, number>()
+ const elementsWithRingMap = new Map<string, number>()
function elementKey(residueIndex: number, unitId: number) {
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)
+ Vec3.sub(elements[iA].geometry!.direction, elements[iB].geometry!.center, elements[iA].geometry!.center)
+ Vec3.normalize(elements[iA].geometry!.direction, elements[iA].geometry!.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)
+ const pos = unitB.conformation.position, geo = elements[iA].geometry!;
+ Vec3.sub(geo.direction, pos(unitB.elements[indexB], tmpV), geo.center)
+ Vec3.normalize(geo.direction, geo.direction)
}
// get carbohydrate elements and carbohydrate links induced by intra-residue bonds
@@ -140,7 +140,10 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const sugarRings = sugarResidueMap.get(residueIndex);
if (!sugarRings || !sugarRings.length) {
- console.warn(`No ring found for carbohydrate on residue with index ${residueIndex}, unit ${unit.id}. Residue skipped.`);
+ elements.push({
+ hasRing: false,
+ unit, residueIndex, component: saccharideComp
+ })
continue;
}
@@ -158,8 +161,12 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const elementIndex = elements.length
ringElements.push(elementIndex)
- elementsMap.set(elementKey(residueIndex, unit.id), elementIndex)
- elements.push({ center, normal, direction, unit, residueIndex, component: saccharideComp })
+ elementsWithRingMap.set(elementKey(residueIndex, unit.id), elementIndex)
+ elements.push({
+ geometry: { center, normal, direction, },
+ hasRing: true,
+ unit, residueIndex, component: saccharideComp
+ })
}
// add carbohydrate links induced by intra-residue bonds
@@ -195,8 +202,8 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
pairBonds.getBonds(indexA).forEach(bondInfo => {
const { unitA, unitB } = pairBonds
const indexB = bondInfo.indexB
- const elementIndexA = elementsMap.get(elementKey(getResidueIndex(indexA, unitA), unitA.id))
- const elementIndexB = elementsMap.get(elementKey(getResidueIndex(indexB, unitB), unitB.id))
+ const elementIndexA = elementsWithRingMap.get(elementKey(getResidueIndex(indexA, unitA), unitA.id))
+ const elementIndexB = elementsWithRingMap.get(elementKey(getResidueIndex(indexB, unitB), unitB.id))
if (elementIndexA !== undefined && elementIndexB !== undefined) {
if (getAtomId(unitA, indexA).startsWith('C1')) {
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index c8f22a1fe31c26c5155a26071c1002a52cc39dd8..0c9361042df84c5d713888b20be4424cb96f66b3 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -23,11 +23,11 @@ export interface CarbohydrateTerminalLink {
}
export interface CarbohydrateElement {
- readonly center: Vec3,
- readonly normal: Vec3,
- readonly direction: Vec3,
- readonly unit: Unit.Atomic
- readonly residueIndex: ResidueIndex
+ // geometry is only defined if at least one ring is present.
+ readonly geometry?: { readonly center: Vec3, readonly normal: Vec3, readonly direction: Vec3 },
+ readonly hasRing: boolean,
+ readonly unit: Unit.Atomic,
+ readonly residueIndex: ResidueIndex,
readonly component: SaccharideComponent
}