From 6217a51fa554f13d84c93b76fa6af1cc96a2dc85 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 29 Jul 2019 11:32:02 -0700
Subject: [PATCH] optimized `toScriptExpression`
---
src/mol-model/structure/structure/element.ts | 103 ++++++++++++++-----
1 file changed, 75 insertions(+), 28 deletions(-)
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 200f8b4c0..4b85cdc0f 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -16,7 +16,7 @@ import Structure from './structure';
import Unit from './unit';
import { Boundary } from './util/boundary';
import { StructureProperties } from '../structure';
-import { sortArray } from '../../../mol-data/util';
+import { sortArray, hashFnv32a, hash2 } from '../../../mol-data/util';
import Expression from '../../../mol-script/language/expression';
interface StructureElement<U = Unit> {
@@ -358,21 +358,81 @@ namespace StructureElement {
}
}
- const byOpName: Expression[] = [];
+ const opData: OpData[] = [];
const keys = sourceIndexMap.keys();
while (true) {
const k = keys.next();
if (k.done) break;
const e = sourceIndexMap.get(k.value)!;
- byOpName.push(getOpNameQuery(k.value, e.xs.array, models.length > 1, e.modelLabel, e.modelIndex));
+ opData.push(getOpData(k.value, e.xs.array, models.length > 1, e.modelLabel, e.modelIndex));
}
+ const opGroups = new Map<string, OpData>();
+ for (let i = 0, il = opData.length; i < il; ++i) {
+ const d = opData[i]
+ const hash = hash2(hashFnv32a(d.atom.ranges), hashFnv32a(d.atom.set))
+ const key = `${hash}|${d.entity ? (d.entity.modelLabel + d.entity.modelIndex) : ''}`
+ if (opGroups.has(key)) {
+ opGroups.get(key)!.chain.opName.push(...d.chain.opName)
+ } else {
+ opGroups.set(key, d)
+ }
+ }
+
+ const opQueries: Expression[] = [];
+ opGroups.forEach(d => {
+ const { ranges, set } = d.atom
+ const { opName } = d.chain
+
+ const opProp = MS.struct.atomProperty.core.operatorName()
+ const siProp = MS.struct.atomProperty.core.sourceIndex();
+ const tests: Expression[] = [];
+
+ // TODO: add set.ofRanges constructor to MolQL???
+ if (set.length > 0) {
+ tests[tests.length] = MS.core.set.has([MS.set.apply(null, set), siProp]);
+ }
+ for (let rI = 0, _rI = ranges.length / 2; rI < _rI; rI++) {
+ tests[tests.length] = MS.core.rel.inRange([siProp, ranges[2 * rI], ranges[2 * rI + 1]]);
+ }
+
+ if (d.entity) {
+ const { modelLabel, modelIndex } = d.entity
+ opQueries.push(MS.struct.generator.atomGroups({
+ 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
+ 'chain-test': opName.length > 1
+ ? MS.core.set.has([MS.set.apply(null, opName), opProp])
+ : MS.core.rel.eq([opProp, opName[0]]),
+ 'entity-test': MS.core.logic.and([
+ MS.core.rel.eq([MS.struct.atomProperty.core.modelLabel(), modelLabel]),
+ MS.core.rel.eq([MS.struct.atomProperty.core.modelIndex(), modelIndex]),
+ ])
+ }))
+ } else {
+ opQueries.push(MS.struct.generator.atomGroups({
+ 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
+ 'chain-test': opName.length > 1
+ ? MS.core.set.has([MS.set.apply(null, opName), opProp])
+ : MS.core.rel.eq([opProp, opName[0]])
+ }))
+ }
+ })
+
return MS.struct.modifier.union([
- byOpName.length === 1 ? byOpName[0] : MS.struct.combinator.merge(byOpName)
+ opQueries.length === 1
+ ? opQueries[0]
+ // Need to union before merge for fast performance
+ : MS.struct.combinator.merge(opQueries.map(q => MS.struct.modifier.union([ q ])))
]);
}
- function getOpNameQuery(opName: string, xs: number[], multimodel: boolean, modelLabel: string, modelIndex: number) {
+ type OpData = {
+ atom: { set: number[], ranges: number[] },
+ chain: { opName: string[] },
+ entity?: { modelLabel: string, modelIndex: number }
+ }
+
+ function getOpData(opName: string, xs: number[], multimodel: boolean, modelLabel: string, modelIndex: number): OpData {
sortArray(xs);
const ranges: number[] = [];
@@ -395,30 +455,17 @@ namespace StructureElement {
}
}
- const siProp = MS.struct.atomProperty.core.sourceIndex();
- const tests: Expression[] = [];
-
- // TODO: add set.ofRanges constructor to MolQL???
- if (set.length > 0) {
- tests[tests.length] = MS.core.set.has([MS.set.apply(null, set), siProp]);
- }
- for (let rI = 0, _rI = ranges.length / 2; rI < _rI; rI++) {
- tests[tests.length] = MS.core.rel.inRange([siProp, ranges[2 * rI], ranges[2 * rI + 1]]);
- }
-
return multimodel
- ? MS.struct.generator.atomGroups({
- 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
- 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.core.operatorName(), opName]),
- 'entity-test': MS.core.logic.and([
- MS.core.rel.eq([MS.struct.atomProperty.core.modelLabel(), modelLabel]),
- MS.core.rel.eq([MS.struct.atomProperty.core.modelIndex(), modelIndex]),
- ])
- })
- : MS.struct.generator.atomGroups({
- 'atom-test': tests.length > 1 ? MS.core.logic.or(tests) : tests[0],
- 'chain-test': MS.core.rel.eq([MS.struct.atomProperty.core.operatorName(), opName])
- });
+ ? {
+ atom: { set, ranges },
+ chain: { opName: [ opName ] },
+ entity: { modelLabel, modelIndex }
+ }
+ : {
+ atom: { set, ranges },
+ chain: { opName: [ opName ] },
+ }
+
}
}
}
--
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