From f22e9815e476599768dbcf65b69a0f054c3b5917 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 27 Nov 2018 18:50:23 -0800
Subject: [PATCH] added assemblyName to structure
---
.../structure/query/queries/generators.ts | 2 +-
.../structure/query/queries/internal.ts | 8 +++----
src/mol-model/structure/query/selection.ts | 2 +-
.../structure/query/utils/structure-set.ts | 4 ++--
.../structure/structure/structure.ts | 24 ++++++++++++-------
src/mol-model/structure/structure/symmetry.ts | 6 ++---
.../structure/util/subset-builder.ts | 2 +-
.../structure/util/unique-subset-builder.ts | 2 +-
8 files changed, 29 insertions(+), 21 deletions(-)
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index 34ce3fd62..64c4451e1 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -171,7 +171,7 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
function getRingStructure(unit: Unit.Atomic, ring: UnitRing) {
const elements = new Int32Array(ring.length) as any as ElementIndex[];
for (let i = 0, _i = ring.length; i < _i; i++) elements[i] = unit.elements[ring[i]];
- return Structure.create([unit.getChild(SortedArray.ofSortedArray(elements))])
+ return Structure.create([unit.getChild(SortedArray.ofSortedArray(elements))], '')
}
export function rings(fingerprints?: ArrayLike<UnitRing.Fingerprint>): StructureQuery {
diff --git a/src/mol-model/structure/query/queries/internal.ts b/src/mol-model/structure/query/queries/internal.ts
index 8cf107811..5188c1397 100644
--- a/src/mol-model/structure/query/queries/internal.ts
+++ b/src/mol-model/structure/query/queries/internal.ts
@@ -35,7 +35,7 @@ export function atomicSequence(): StructureQuery {
units.push(unit);
}
- return StructureSelection.Singletons(inputStructure, new Structure(units));
+ return StructureSelection.Singletons(inputStructure, new Structure(units, inputStructure.assemblyName));
};
}
@@ -54,7 +54,7 @@ export function water(): StructureQuery {
if (P.entity.type(l) !== 'water') continue;
units.push(unit);
}
- return StructureSelection.Singletons(inputStructure, new Structure(units));
+ return StructureSelection.Singletons(inputStructure, new Structure(units, inputStructure.assemblyName));
};
}
@@ -84,7 +84,7 @@ export function atomicHet(): StructureQuery {
units.push(unit);
}
- return StructureSelection.Singletons(inputStructure, new Structure(units));
+ return StructureSelection.Singletons(inputStructure, new Structure(units, inputStructure.assemblyName));
};
}
@@ -97,6 +97,6 @@ export function spheres(): StructureQuery {
if (unit.kind !== Unit.Kind.Spheres) continue;
units.push(unit);
}
- return StructureSelection.Singletons(inputStructure, new Structure(units));
+ return StructureSelection.Singletons(inputStructure, new Structure(units, inputStructure.assemblyName));
};
}
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index b25717071..69aba9fa2 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -109,7 +109,7 @@ namespace StructureSelection {
const { elements } = unit;
for (let i = 0, _i = elements.length; i < _i; i++) {
// TODO: optimize this somehow???
- const s = Structure.create([unit.getChild(SortedArray.ofSingleton(elements[i]))]);
+ const s = Structure.create([unit.getChild(SortedArray.ofSingleton(elements[i]))], sel.structure.assemblyName);
fn(s, idx++);
}
}
diff --git a/src/mol-model/structure/query/utils/structure-set.ts b/src/mol-model/structure/query/utils/structure-set.ts
index 858674195..46a5c0f43 100644
--- a/src/mol-model/structure/query/utils/structure-set.ts
+++ b/src/mol-model/structure/query/utils/structure-set.ts
@@ -80,7 +80,7 @@ export function structureIntersect(sA: Structure, sB: Structure): Structure {
}
}
- return Structure.create(units);
+ return Structure.create(units, sA.assemblyName === sB.assemblyName ? sA.assemblyName : '');
}
export function structureSubtract(a: Structure, b: Structure): Structure {
@@ -100,5 +100,5 @@ export function structureSubtract(a: Structure, b: Structure): Structure {
}
}
- return Structure.create(units);
+ return Structure.create(units, a.assemblyName === b.assemblyName ? a.assemblyName : '');
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index cab555fd9..a61046ff2 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { IntMap, SortedArray, Iterator, Segmentation } from 'mol-data/int'
@@ -48,7 +49,8 @@ class Structure {
transformHash: number,
elementCount: number,
polymerResidueCount: number,
- } = { hashCode: -1, transformHash: -1, elementCount: 0, polymerResidueCount: 0 };
+ assemblyName: string
+ } = { hashCode: -1, transformHash: -1, elementCount: 0, polymerResidueCount: 0, assemblyName: '' };
subsetBuilder(isSorted: boolean) {
return new StructureSubsetBuilder(this, isSorted);
@@ -64,6 +66,11 @@ class Structure {
return this._props.polymerResidueCount;
}
+ /** Name of the assembly given by `_pdbx_struct_assembly.id` when applicable */
+ get assemblyName() {
+ return this._props.assemblyName;
+ }
+
/** Coarse structure, defined as Containing less than twice as many elements as polymer residues */
get isCoarse() {
const ec = this.elementCount
@@ -169,7 +176,7 @@ class Structure {
return SortedArray.has(this.unitMap.get(e.unit.id).elements, e.element);
}
- constructor(units: ArrayLike<Unit>) {
+ constructor(units: ArrayLike<Unit>, assemblyName: string) {
const map = IntMap.Mutable<Unit>();
let elementCount = 0;
let polymerResidueCount = 0;
@@ -188,6 +195,7 @@ class Structure {
this.units = units as ReadonlyArray<Unit>;
this._props.elementCount = elementCount;
this._props.polymerResidueCount = polymerResidueCount;
+ this._props.assemblyName = assemblyName
}
}
@@ -278,7 +286,7 @@ function getUniqueAtomicResidueIndices(structure: Structure): ReadonlyMap<UUID,
}
namespace Structure {
- export const Empty = new Structure([]);
+ export const Empty = new Structure([], '');
/** Represents a single structure */
export interface Loci {
@@ -297,7 +305,7 @@ namespace Structure {
return a.structure === b.structure
}
- export function create(units: ReadonlyArray<Unit>): Structure { return new Structure(units); }
+ export function create(units: ReadonlyArray<Unit>, assemblyName: string): Structure { return new Structure(units, assemblyName); }
/**
* Construct a Structure from a model.
@@ -338,7 +346,7 @@ namespace Structure {
}
}
- return builder.getStructure();
+ return builder.getStructure('deposited');
}
function isWaterChain(model: Model, chainIndex: ChainIndex, indices: SortedArray) {
@@ -380,7 +388,7 @@ namespace Structure {
units.push(u.applyOperator(u.id, op));
}
- return new Structure(units);
+ return new Structure(units, s.assemblyName);
}
export class StructureBuilder {
@@ -399,8 +407,8 @@ namespace Structure {
return newUnit;
}
- getStructure(): Structure {
- return create(this.units);
+ getStructure(assemblyName: string): Structure {
+ return create(this.units, assemblyName);
}
get isEmpty() {
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 5af14696a..2acbf7d87 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -42,7 +42,7 @@ namespace StructureSymmetry {
}
}
- return assembler.getStructure();
+ return assembler.getStructure(asmName);
});
}
@@ -118,7 +118,7 @@ function assembleOperators(structure: Structure, operators: ReadonlyArray<Symmet
assembler.addWithOperator(unit, oper);
}
}
- return assembler.getStructure();
+ return assembler.getStructure(structure.assemblyName);
}
async function _buildNCS(ctx: RuntimeContext, structure: Structure) {
@@ -173,7 +173,7 @@ async function findMatesRadius(ctx: RuntimeContext, structure: Structure, radius
}
- return assembler.getStructure();
+ return assembler.getStructure(structure.assemblyName);
}
export default StructureSymmetry;
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/util/subset-builder.ts b/src/mol-model/structure/structure/util/subset-builder.ts
index 77c228902..608bae0de 100644
--- a/src/mol-model/structure/structure/util/subset-builder.ts
+++ b/src/mol-model/structure/structure/util/subset-builder.ts
@@ -90,7 +90,7 @@ export class StructureSubsetBuilder {
newUnits[newUnits.length] = child;
}
- return Structure.create(newUnits);
+ return Structure.create(newUnits, this.parent.assemblyName);
}
getStructure() {
diff --git a/src/mol-model/structure/structure/util/unique-subset-builder.ts b/src/mol-model/structure/structure/util/unique-subset-builder.ts
index bc18e6519..f19ecace7 100644
--- a/src/mol-model/structure/structure/util/unique-subset-builder.ts
+++ b/src/mol-model/structure/structure/util/unique-subset-builder.ts
@@ -85,7 +85,7 @@ export class StructureUniqueSubsetBuilder {
newUnits[newUnits.length] = child;
}
- return Structure.create(newUnits);
+ return Structure.create(newUnits, this.parent.assemblyName);
}
get isEmpty() {
--
GitLab