From e04a80880a1c41809dca7034026d2ab30601e7e6 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 19 Sep 2018 17:46:26 -0700
Subject: [PATCH] tweaks to carbohydrate handling for remediated structures
(and fixes)
---
.../structure/carbohydrates/compute.ts | 64 +++++++++++++------
.../structure/structure/carbohydrates/data.ts | 1 +
2 files changed, 47 insertions(+), 18 deletions(-)
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 68dae32ba..1c0a7f7ea 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -131,13 +131,13 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}
function fixLinkDirection(iA: number, iB: number) {
- Vec3.sub(elements[iA].geometry!.direction, elements[iB].geometry!.center, elements[iA].geometry!.center)
- Vec3.normalize(elements[iA].geometry!.direction, elements[iA].geometry!.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, geo = elements[iA].geometry!;
+ 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)
}
@@ -191,36 +191,35 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const direction = getDirection(Vec3.zero(), unit, anomericCarbon, center)
Vec3.orthogonalize(direction, normal, direction)
- const altId = getRingAltId(unit, ringAtoms)
+ const ringAltId = getRingAltId(unit, ringAtoms)
const elementIndex = elements.length
ringElements.push(elementIndex)
- elementsWithRingMap.set(ringElementKey(residueIndex, unit.id, altId), elementIndex)
+ elementsWithRingMap.set(ringElementKey(residueIndex, unit.id, ringAltId), elementIndex)
elements.push({
geometry: { center, normal, direction },
component: saccharideComp,
- unit, residueIndex, anomericCarbon
+ unit, residueIndex, anomericCarbon, ringAltId
})
}
// add carbohydrate links induced by intra-residue bonds
+ // (e.g. for structures from the PDB archive __before__ carbohydrate remediation)
const ringCombinations = combinations(fillSerial(new Array(sugarRings.length) as number[]), 2)
for (let j = 0, jl = ringCombinations.length; j < jl; ++j) {
const rc = ringCombinations[j];
const r0 = rings.all[sugarRings[rc[0]]], r1 = rings.all[sugarRings[rc[1]]];
// 1,6 glycosidic links are distance 3 and 1,4 glycosidic links are distance 2
if (IntAdjacencyGraph.areVertexSetsConnected(unit.links, r0, r1, 3)) {
- // TODO handle better, for now fix both directions as it is unclear where the C1 atom is
- // would need to know the path connecting the two rings
- fixLinkDirection(ringElements[rc[0]], ringElements[rc[1]])
- fixLinkDirection(ringElements[rc[1]], ringElements[rc[0]])
- links.push({
- carbohydrateIndexA: ringElements[rc[0]],
- carbohydrateIndexB: ringElements[rc[1]]
- })
- links.push({
- carbohydrateIndexA: ringElements[rc[1]],
- carbohydrateIndexB: ringElements[rc[0]]
- })
+ const re0 = ringElements[rc[0]]
+ const re1 = ringElements[rc[1]]
+ if (elements[re0].ringAltId === elements[re1].ringAltId) {
+ // TODO handle better, for now fix both directions as it is unclear where the C1 atom is
+ // would need to know the path connecting the two rings
+ fixLinkDirection(re0, re1)
+ fixLinkDirection(re1, re0)
+ links.push({ carbohydrateIndexA: re0, carbohydrateIndexB: re1 })
+ links.push({ carbohydrateIndexA: re1, carbohydrateIndexB: re0 })
+ }
}
}
}
@@ -231,7 +230,36 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
return elementsWithRingMap.get(ringElementKey(unit.getResidueIndex(index), unit.id, getAltId(unit, index)))
}
+ // add carbohydrate links induced by intra-unit bonds
+ // (e.g. for structures from the PDB archive __after__ carbohydrate remediation)
+ for (let i = 0, il = elements.length; i < il; ++i) {
+ const carbohydrate = elements[i]
+ const { unit, residueIndex, anomericCarbon } = carbohydrate
+ const { offset, b } = unit.links
+ const ac = SortedArray.indexOf(unit.elements, anomericCarbon) as StructureElement.UnitIndex
+
+ for (let j = offset[ac], jl = offset[ac + 1]; j < jl; ++j) {
+ const bj = b[j] as StructureElement.UnitIndex
+ if (residueIndex !== unit.getResidueIndex(bj)) {
+ const ringElementIndex = getRingElementIndex(unit, bj)
+ if (ringElementIndex !== undefined && ringElementIndex !== i) {
+ fixLinkDirection(i, ringElementIndex)
+ links.push({
+ carbohydrateIndexA: i,
+ carbohydrateIndexB: ringElementIndex
+ })
+ links.push({
+ carbohydrateIndexA: ringElementIndex,
+ carbohydrateIndexB: i
+ })
+ }
+ }
+ }
+
+ }
+
// get carbohydrate links induced by inter-unit bonds
+ // (e.g. for structures from the PDB archive __before__ carbohydrate remediation)
for (let i = 0, il = structure.units.length; i < il; ++i) {
const unit = structure.units[i]
if (!Unit.isAtomic(unit)) continue
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index 4afcf03e4..0a8d38375 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -28,6 +28,7 @@ export interface CarbohydrateElement {
readonly unit: Unit.Atomic,
readonly residueIndex: ResidueIndex,
readonly component: SaccharideComponent,
+ readonly ringAltId: string,
}
// partial carbohydrate with no ring present
--
GitLab