From a476c2a16740c495ba2bc7a06ba2590bbcb0f2be Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 9 Dec 2019 17:02:32 -0800
Subject: [PATCH] rename Structure.links to .interUnitBonds
---
src/apps/structure-info/model.ts | 2 +-
src/mol-model/structure/query/queries/filters.ts | 2 +-
src/mol-model/structure/query/queries/generators.ts | 2 +-
src/mol-model/structure/query/queries/modifiers.ts | 2 +-
.../structure/structure/carbohydrates/compute.ts | 2 +-
src/mol-model/structure/structure/structure.ts | 10 +++++-----
src/mol-model/structure/structure/unit/links.ts | 4 ++--
src/mol-repr/structure/visual/util/link.ts | 4 ++--
src/perf-tests/structure.ts | 2 +-
9 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 77e0263c2..da5d663a8 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -87,7 +87,7 @@ export function printLinks(structure: Structure, showIntra: boolean, showInter:
if (showInter) {
console.log('\nInter Unit Links\n=============');
- const links = structure.links;
+ const links = structure.interUnitBonds;
for (const unit of structure.units) {
if (!Unit.isAtomic(unit)) continue;
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index ad053fa6c..9194feeb9 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -238,7 +238,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
const { queryCtx, input, target, disjunct } = ctx;
const atomicLink = queryCtx.atomicLink;
- const interLinks = input.links;
+ const interLinks = input.interUnitBonds;
for (const unit of structure.units) {
if (!Unit.isAtomic(unit)) continue;
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index 74fe040c9..7aaba0ab3 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -280,7 +280,7 @@ export function linkedAtomicPairs(linkTest?: QueryPredicate): StructureQuery {
return function query_linkedAtomicPairs(ctx) {
const structure = ctx.inputStructure;
- const interLinks = structure.links;
+ const interLinks = structure.interUnitBonds;
// Note: each link is called twice, that's why we need the unique builder.
const ret = StructureSelection.UniqueBuilder(ctx.inputStructure);
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index 553a92ee9..38b862ae2 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -332,7 +332,7 @@ function includeConnectedStep(ctx: QueryContext, wholeResidues: boolean, structu
function expandConnected(ctx: QueryContext, structure: Structure) {
const inputStructure = ctx.inputStructure;
- const interLinks = inputStructure.links;
+ const interLinks = inputStructure.interUnitBonds;
const builder = new StructureUniqueSubsetBuilder(inputStructure);
// Note: each link is visited twice so that link.atom-a and link.atom-b both get the "swapped values"
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index edf106ffd..e2adb4004 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -276,7 +276,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const unit = structure.units[i]
if (!Unit.isAtomic(unit)) continue
- structure.links.getLinkedUnits(unit).forEach(pairBonds => {
+ structure.interUnitBonds.getLinkedUnits(unit).forEach(pairBonds => {
pairBonds.linkedElementIndices.forEach(indexA => {
pairBonds.getBonds(indexA).forEach(bondInfo => {
const { unitA, unitB } = pairBonds
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index b024cc88c..68425c7eb 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -40,7 +40,7 @@ class Structure {
private _props: {
parent?: Structure,
lookup3d?: StructureLookup3D,
- links?: InterUnitBonds,
+ interUnitBonds?: InterUnitBonds,
crossLinkRestraints?: PairRestraints<CrossLinkRestraint>,
unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
unitSymmetryGroupsIndexMap?: IntMap<number>,
@@ -200,10 +200,10 @@ class Structure {
return this._props.lookup3d;
}
- get links() {
- if (this._props.links) return this._props.links;
- this._props.links = computeInterUnitBonds(this);
- return this._props.links;
+ get interUnitBonds() {
+ if (this._props.interUnitBonds) return this._props.interUnitBonds;
+ this._props.interUnitBonds = computeInterUnitBonds(this);
+ return this._props.interUnitBonds;
}
get crossLinkRestraints() {
diff --git a/src/mol-model/structure/structure/unit/links.ts b/src/mol-model/structure/structure/unit/links.ts
index 12e2830c1..bd12a1376 100644
--- a/src/mol-model/structure/structure/unit/links.ts
+++ b/src/mol-model/structure/structure/unit/links.ts
@@ -123,7 +123,7 @@ namespace Link {
if (idx < 0) return LinkType.create(LinkType.Flag.None);
return LinkType.create(links.edgeProps.flags[idx]);
} else {
- const bond = structure.links.getBondFromLocation(link);
+ const bond = structure.interUnitBonds.getBondFromLocation(link);
if (bond) return LinkType.create(bond.flag);
return LinkType.create(LinkType.Flag.None);
}
@@ -136,7 +136,7 @@ namespace Link {
if (idx < 0) return 0;
return links.edgeProps.order[idx];
} else {
- const bond = structure.links.getBondFromLocation(link);
+ const bond = structure.interUnitBonds.getBondFromLocation(link);
if (bond) return bond.order;
return 0;
}
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index bcd3b7a56..5bed0a7e0 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -142,11 +142,11 @@ export namespace LinkIterator {
}
export function fromStructure(structure: Structure): LocationIterator {
- const groupCount = structure.links.bondCount
+ const groupCount = structure.interUnitBonds.bondCount
const instanceCount = 1
const location = Link.Location()
const getLocation = (groupIndex: number) => {
- const bond = structure.links.bonds[groupIndex]
+ const bond = structure.interUnitBonds.bonds[groupIndex]
location.aUnit = bond.unitA
location.aIndex = bond.indexA as StructureElement.UnitIndex
location.bUnit = bond.unitB
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 1b619cced..fce146290 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -375,7 +375,7 @@ export namespace PropertyAccess {
export async function runLinks() {
const { structures } = await readCIF('e:/test/quick/3j3q_full.bcif');
console.time('links');
- structures[0].links
+ structures[0].interUnitBonds
console.timeEnd('links');
}
--
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