From 1d502cbb54e7fef134d2390300b84f32f361cbc6 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 25 Jul 2019 13:49:04 -0700
Subject: [PATCH] loci remapping
---
src/mol-model/structure/structure/element.ts | 27 ++++++++++++++++---
.../structure/structure/unit/links.ts | 23 ++++++++++++++++
.../visual/carbohydrate-link-cylinder.ts | 2 ++
.../visual/carbohydrate-symbol-mesh.ts | 1 +
.../carbohydrate-terminal-link-cylinder.ts | 2 ++
.../visual/cross-link-restraint-cylinder.ts | 1 +
.../visual/inter-unit-link-cylinder.ts | 2 ++
.../visual/intra-unit-link-cylinder.ts | 2 ++
src/mol-repr/structure/visual/util/element.ts | 1 +
.../structure/visual/util/nucleotide.ts | 1 +
src/mol-repr/structure/visual/util/polymer.ts | 3 +++
11 files changed, 61 insertions(+), 4 deletions(-)
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 6c84a030a..80096d969 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -141,10 +141,29 @@ namespace StructureElement {
export function remap(loci: Loci, structure: Structure): Loci {
if (structure === loci.structure) return loci
- return Loci(structure, loci.elements.map(e => ({
- unit: structure.unitMap.get(e.unit.id)!,
- indices: e.indices
- })));
+ const elements: Loci['elements'][0][] = [];
+ loci.elements.forEach(e => {
+ const unit = structure.unitMap.get(e.unit.id)
+ if (!unit) return
+
+ if (SortedArray.areEqual(e.unit.elements, unit.elements)) {
+ elements.push({ unit, indices: e.indices })
+ } else {
+ // TODO optimize
+ const indices: UnitIndex[] = []
+ OrderedSet.forEach(e.indices, (v) => {
+ const eI = e.unit.elements[v]
+ const uI = SortedArray.indexOf(unit.elements, eI) as UnitIndex | -1
+ if (uI !== -1) indices.push(uI)
+ })
+ elements.push({
+ unit,
+ indices: SortedArray.ofSortedArray(indices)
+ })
+ }
+ });
+
+ return Loci(structure, elements);
}
export function union(xs: Loci, ys: Loci): Loci {
diff --git a/src/mol-model/structure/structure/unit/links.ts b/src/mol-model/structure/structure/unit/links.ts
index 3c115c376..8ea138d4d 100644
--- a/src/mol-model/structure/structure/unit/links.ts
+++ b/src/mol-model/structure/structure/unit/links.ts
@@ -62,6 +62,29 @@ namespace Link {
return true
}
+ export function remapLoci(loci: Loci, structure: Structure): Loci {
+ if (structure === loci.structure) return loci
+
+ const links: Loci['links'][0][] = [];
+ loci.links.forEach(l => {
+ const unitA = structure.unitMap.get(l.aUnit.id)
+ if (!unitA) return
+ const unitB = structure.unitMap.get(l.bUnit.id)
+ if (!unitB) return
+
+ const elementA = l.aUnit.elements[l.aIndex]
+ const indexA = SortedArray.indexOf(unitA.elements, elementA) as StructureElement.UnitIndex | -1
+ if (indexA === -1) return
+ const elementB = l.bUnit.elements[l.bIndex]
+ const indexB = SortedArray.indexOf(unitB.elements, elementB) as StructureElement.UnitIndex | -1
+ if (indexB === -1) return
+
+ links.push(Location(unitA, indexA, unitB, indexB))
+ });
+
+ return Loci(structure, links);
+ }
+
export function toStructureElementLoci(loci: Loci): StructureElement.Loci {
const elements: StructureElement.Loci['elements'][0][] = []
const map = new Map<number, number[]>()
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index 7124442af..711e98eb4 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -120,6 +120,7 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
let changed = false
if (Link.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
const { getLinkIndex } = structure.carbohydrates
for (const l of loci.links) {
const idx = getLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
@@ -129,6 +130,7 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
}
} else if (StructureElement.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
// TODO mark link only when both of the link elements are in a StructureElement.Loci
const { getElementIndex, getLinkIndices, elements } = structure.carbohydrates
for (const e of loci.elements) {
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index 5c35ab721..b5adcfe5c 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -197,6 +197,7 @@ function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: In
let changed = false
if (!StructureElement.isLoci(loci)) return false
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
for (const e of loci.elements) {
// TODO make more efficient by handling/grouping `e.indices` by residue index
// TODO only call apply when the full alt-residue of the unit is part of `e`
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index 30aae0eb7..b540d9d49 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -134,6 +134,7 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
let changed = false
if (Link.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
for (const l of loci.links) {
const idx = getTerminalLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
if (idx !== undefined) {
@@ -142,6 +143,7 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
}
} else if (StructureElement.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
// TODO mark link only when both of the link elements are in a StructureElement.Loci
const { getElementIndex, getTerminalLinkIndices, elements } = structure.carbohydrates
for (const e of loci.elements) {
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
index 155ca3c16..b90daa355 100644
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
@@ -108,6 +108,7 @@ function eachCrossLink(loci: Loci, structure: Structure, apply: (interval: Inter
let changed = false
if (Link.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
for (const b of loci.links) {
const indices = crossLinks.getPairIndices(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
if (indices) {
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index 37f0bb0ba..204015f87 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -98,6 +98,7 @@ function eachLink(loci: Loci, structure: Structure, apply: (interval: Interval)
let changed = false
if (Link.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
for (const b of loci.links) {
const idx = structure.links.getBondIndex(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
if (idx !== -1) {
@@ -106,6 +107,7 @@ function eachLink(loci: Loci, structure: Structure, apply: (interval: Interval)
}
} else if (StructureElement.isLoci(loci)) {
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
// TODO mark link only when both of the link elements are in a StructureElement.Loci
for (const e of loci.elements) {
OrderedSet.forEach(e.indices, v => {
diff --git a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
index af8f091cd..55fe6843a 100644
--- a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
@@ -122,6 +122,7 @@ function eachLink(loci: Loci, structureGroup: StructureGroup, apply: (interval:
if (Link.isLoci(loci)) {
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
const unit = group.units[0]
if (!Unit.isAtomic(unit)) return false
const groupCount = unit.links.edgeCount * 2
@@ -137,6 +138,7 @@ function eachLink(loci: Loci, structureGroup: StructureGroup, apply: (interval:
} else if (StructureElement.isLoci(loci)) {
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
const unit = group.units[0]
if (!Unit.isAtomic(unit)) return false
const groupCount = unit.links.edgeCount * 2
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index ec1a76717..e492772ed 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -73,6 +73,7 @@ export function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
const elementCount = group.elements.length
for (const e of loci.elements) {
const unitIdx = group.unitIndexMap.get(e.unit.id)
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index dd3d32c50..5406facc4 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -46,6 +46,7 @@ export function eachNucleotideElement(loci: Loci, structureGroup: StructureGroup
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
const unit = group.units[0]
if (!Unit.isAtomic(unit)) return false
const { nucleotideElements, model, elements } = unit
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 325e631ca..b185f4883 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -96,6 +96,7 @@ export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, a
if (!StructureElement.isLoci(loci)) return false
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
const { polymerElements, model, elements } = group.units[0]
const { index, offsets } = model.atomicHierarchy.residueAtomSegments
const { traceElementIndex } = model.atomicHierarchy.derived.residue
@@ -157,6 +158,7 @@ export function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup
if (Link.isLoci(loci)) {
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = Link.remapLoci(loci, structure)
const groupCount = group.units[0].gapElements.length
for (const b of loci.links) {
const unitIdx = group.unitIndexMap.get(b.aUnit.id)
@@ -171,6 +173,7 @@ export function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup
} else if (StructureElement.isLoci(loci)) {
const { structure, group } = structureGroup
if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
+ loci = StructureElement.Loci.remap(loci, structure)
const groupCount = group.units[0].gapElements.length
for (const e of loci.elements) {
const unitIdx = group.unitIndexMap.get(e.unit.id)
--
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