diff --git a/src/mol-geo/representation/structure/units-representation.ts b/src/mol-geo/representation/structure/units-representation.ts
index 766845896c9f491b0a225218409ab9512bdf9a8c..79a9c480645714079b51d38c571d7da268f82ced 100644
--- a/src/mol-geo/representation/structure/units-representation.ts
+++ b/src/mol-geo/representation/structure/units-representation.ts
@@ -34,6 +34,7 @@ export function UnitsRepresentation<P extends StructureProps>(label: string, vis
if (!_structure && !structure) {
throw new Error('missing structure')
} else if (structure && !_structure) {
+ // console.log('initial structure')
// First call with a structure, create visuals for each group.
_groups = structure.unitSymmetryGroups;
for (let i = 0; i < _groups.length; i++) {
@@ -43,6 +44,7 @@ export function UnitsRepresentation<P extends StructureProps>(label: string, vis
visuals.set(group.hashCode, { visual, group })
}
} else if (structure && _structure.hashCode !== structure.hashCode) {
+ // console.log('_structure.hashCode !== structure.hashCode')
// Tries to re-use existing visuals for the groups of the new structure.
// Creates additional visuals if needed, destroys left-over visuals.
_groups = structure.unitSymmetryGroups;
@@ -77,6 +79,7 @@ export function UnitsRepresentation<P extends StructureProps>(label: string, vis
// })
// unusedVisuals.forEach(visual => visual.destroy())
} else if (structure && _structure.hashCode === structure.hashCode) {
+ // console.log('_structure.hashCode === structure.hashCode')
// Expects that for structures with the same hashCode,
// the unitSymmetryGroups are the same as well.
// Re-uses existing visuals for the groups of the new structure.
@@ -92,6 +95,7 @@ export function UnitsRepresentation<P extends StructureProps>(label: string, vis
}
}
} else {
+ // console.log('no new structure')
// No new structure given, just update all visuals with new props.
visuals.forEach(async ({ visual, group }) => {
await visual.createOrUpdate(ctx, _props, { group, structure: _structure })
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index 66c2817fd01f326ee6dc36403768f27b0418a69c..f7d82a34a3de4967a425a480c6355dea118ee598 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -103,8 +103,8 @@ function markLink(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Inter
let changed = false
if (Unit.isAtomic(unit) && Link.isLoci(loci)) {
for (const b of loci.links) {
- const unitIdx = Unit.findUnitById(b.aUnit.id, group.units)
- if (unitIdx !== -1) {
+ const unitIdx = group.unitIndexMap.get(b.aUnit.id)
+ if (unitIdx !== undefined) {
const idx = unit.links.getDirectedEdgeIndex(b.aIndex, b.bIndex)
if (idx !== -1) {
if (apply(Interval.ofSingleton(idx))) changed = true
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 704b0632e25ede6b55cd1354539597b937cd5cfe..0de1861eefddaeac2d28b8d6e8f20790f4eca963 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -57,8 +57,8 @@ export function markElement(loci: Loci, group: Unit.SymmetryGroup, apply: (inter
let changed = false
if (StructureElement.isLoci(loci)) {
for (const e of loci.elements) {
- const unitIdx = Unit.findUnitById(e.unit.id, group.units)
- if (unitIdx !== -1) {
+ const unitIdx = group.unitIndexMap.get(e.unit.id)
+ if (unitIdx !== undefined) {
if (Interval.is(e.indices)) {
const start = unitIdx * elementCount + Interval.start(e.indices);
const end = unitIdx * elementCount + Interval.end(e.indices);
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 22972c0bbc454cd188d365921c5203a0b0c62337..c8a66c6a42613d6925a71a40cc0e296f852f859b 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -32,6 +32,8 @@ export function getGapRanges(unit: Unit): SortedRanges<ElementIndex> {
}
}
+// polymer element
+
export function getPolymerElementCount(unit: Unit) {
let count = 0
const { elements } = unit
@@ -108,6 +110,8 @@ export namespace PolymerLocationIterator {
}
}
+// polymer gap
+
export function getPolymerGapCount(unit: Unit) {
let count = 0
const { elements } = unit
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index f14a7eec3522fdf24749d89ffa449a9a884b6f6b..dcdfaba17fd5422b31985f78f69385209f91fb2c 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -25,7 +25,9 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { idFactory } from 'mol-util/id-factory';
class Structure {
+ /** Maps unit.id to unit */
readonly unitMap: IntMap<Unit>;
+ /** Array of all units in the structure, sorted by unit.id */
readonly units: ReadonlyArray<Unit>;
private _props: {
@@ -67,6 +69,7 @@ class Structure {
return hash;
}
+ /** Returns a new element location iterator */
elementLocations(): Iterator<StructureElement> {
return new Structure.ElementLocationIterator(this);
}
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index e3e9c4b6b4b3a8fa45a5a8dc8aef1f7ded41598b..1b35f8341f75d86dccf08e88b08cc8a475e3506f 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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 Structure from './structure'
@@ -10,7 +11,7 @@ import { ModelSymmetry } from '../model'
import { Task, RuntimeContext } from 'mol-task';
import { SortedArray } from 'mol-data/int';
import Unit from './unit';
-import { EquivalenceClasses, hash2 } from 'mol-data/util';
+import { EquivalenceClasses } from 'mol-data/util';
import { Vec3 } from 'mol-math/linear-algebra';
import { SymmetryOperator, Spacegroup, SpacegroupCell } from 'mol-math/geometry';
@@ -58,16 +59,12 @@ namespace StructureSymmetry {
return Task.create('Build NCS', ctx => _buildNCS(ctx, structure));
}
- function hashUnit(u: Unit) {
- return hash2(u.invariantId, SortedArray.hashCode(u.elements));
- }
-
export function areUnitsEquivalent(a: Unit, b: Unit) {
return a.invariantId === b.invariantId && a.model.id === b.model.id && SortedArray.areEqual(a.elements, b.elements);
}
export function UnitEquivalenceBuilder() {
- return EquivalenceClasses<number, Unit>(hashUnit, areUnitsEquivalent);
+ return EquivalenceClasses<number, Unit>(Unit.hashUnit, areUnitsEquivalent);
}
export function computeTransformGroups(s: Structure): ReadonlyArray<Unit.SymmetryGroup> {
@@ -76,12 +73,7 @@ namespace StructureSymmetry {
const ret: Unit.SymmetryGroup[] = [];
for (const eqUnits of groups.groups) {
- const first = s.unitMap.get(eqUnits[0]);
- ret.push({
- elements: first.elements,
- units: eqUnits.map(id => s.unitMap.get(id)),
- hashCode: hashUnit(first)
- });
+ ret.push(Unit.SymmetryGroup(eqUnits.map(id => s.unitMap.get(id))))
}
return ret;
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 5cb3aeae4f8157afa51b5804caad28b311f3ec4a..c7014ae582fd6cc11ebddfc028bd50f974f51c0b 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.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 { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
@@ -13,6 +14,8 @@ import { ValueRef } from 'mol-util';
import { UnitRings } from './unit/rings';
import StructureElement from './element'
import { ChainIndex, ResidueIndex } from '../model/indexing';
+import { IntMap, SortedArray } from 'mol-data/int';
+import { hash2 } from 'mol-data/util';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -36,21 +39,44 @@ namespace Unit {
/** A group of units that differ only by symmetry operators. */
export type SymmetryGroup = {
- readonly elements: StructureElement.Set,
+ readonly elements: StructureElement.Set
readonly units: ReadonlyArray<Unit>
+ /** Maps unit.id to index of unit in units array */
+ readonly unitIndexMap: IntMap<number>
readonly hashCode: number
}
+ function getUnitIndexMap(units: Unit[]) {
+ const unitIndexMap = IntMap.Mutable<number>();
+ for (let i = 0, _i = units.length; i < _i; i++) {
+ unitIndexMap.set(units[i].id, i);
+ }
+ return unitIndexMap
+ }
+
+ export function SymmetryGroup(units: Unit[]) {
+ const props: {
+ unitIndexMap?: IntMap<number>
+ } = {}
+
+ return {
+ elements: units[0].elements,
+ units,
+ get unitIndexMap () {
+ if (props.unitIndexMap) return props.unitIndexMap
+ props.unitIndexMap = getUnitIndexMap(units)
+ return props.unitIndexMap
+ },
+ hashCode: hashUnit(units[0])
+ }
+ }
+
export function conformationId (unit: Unit) {
return Unit.isAtomic(unit) ? unit.model.atomicConformation.id : unit.model.coarseConformation.id
}
- /** Find index of unit with given id, returns -1 if not found */
- export function findUnitById(id: number, units: ReadonlyArray<Unit>) {
- for (let i = 0, il = units.length; i < il; ++i) {
- if (units[i].id === id) return i
- }
- return -1
+ export function hashUnit(u: Unit) {
+ return hash2(u.invariantId, SortedArray.hashCode(u.elements));
}
export interface Base {