From 22190c178c7cbddcca30c7608d97383b9dfca51c Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 18 Apr 2018 22:24:29 +0200
Subject: [PATCH] Renamed ElementGroup.id to key
---
src/mol-geo/representation/structure/index.ts | 4 +--
.../structure/structure/element/group.ts | 7 ++--
src/perf-tests/structure.ts | 35 ++++++++++++++++---
3 files changed, 36 insertions(+), 10 deletions(-)
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 9b1750019..3ee1a5502 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -34,11 +34,11 @@ export class StructureRepresentation {
const { elements, units } = structure;
const uniqueGroups = EquivalenceClasses<number, ElementGroup>(
ElementGroup.hashCode,
- (a, b) => units[a.id].model.id === units[b.id].model.id && OrderedSet.areEqual(a.elements, b.elements));
+ (a, b) => units[a.key].model.id === units[b.key].model.id && OrderedSet.areEqual(a.elements, b.elements));
for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
const group = ElementSet.unitGetByIndex(elements, i);
- uniqueGroups.add(group.id, group);
+ uniqueGroups.add(group.key, group);
}
diff --git a/src/mol-model/structure/structure/element/group.ts b/src/mol-model/structure/structure/element/group.ts
index ab1d18146..ff542066d 100644
--- a/src/mol-model/structure/structure/element/group.ts
+++ b/src/mol-model/structure/structure/element/group.ts
@@ -9,7 +9,8 @@ import Unit from '../unit'
interface ElementGroup {
elements: OrderedSet,
- id: number
+ // Unique identifier of the group, usable as partial key for various "caches".
+ key: number
}
namespace ElementGroup {
@@ -20,7 +21,7 @@ namespace ElementGroup {
}
export function createNew(elements: OrderedSet): ElementGroup {
- return { id: nextId(), elements };
+ return { key: nextKey(), elements };
}
export function create(unit: Unit, elements: OrderedSet): ElementGroup {
@@ -61,7 +62,7 @@ namespace ElementGroup {
}
let _id = 0;
- function nextId() {
+ function nextKey() {
const ret = _id;
_id = (_id + 1) % 0x3fffffff;
return ret;
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index cddec0a7a..e27ae3f04 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,11 +11,12 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Element, ElementGroup, ElementSet, Selection, Symmetry } from 'mol-model/structure'
-import { Segmentation } from 'mol-data/int'
+import { Structure, Model, Queries as Q, Element, ElementGroup, ElementSet, Selection, Symmetry, Unit } from 'mol-model/structure'
+import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
import { Run } from 'mol-task';
+import { EquivalenceClasses } from 'mol-data/util';
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
@@ -100,7 +101,7 @@ async function ensureBcifAvailable(pdbId: string) {
}
}
-async function getBcif(pdbId: string) {
+export async function getBcif(pdbId: string) {
await ensureBcifAvailable(pdbId);
return await readCIF(getBcifPath(pdbId));
}
@@ -301,11 +302,35 @@ export namespace PropertyAccess {
console.log('exported');
}
+ export function testGrouping(structure: Structure) {
+ const { elements, units } = Symmetry.buildAssembly(structure, '1');
+ console.log('grouping', units.length);
+ console.log('built asm');
+
+ const uniqueGroups = EquivalenceClasses<number, { unit: Unit, group: ElementGroup }>(
+ ({ unit, group }) => ElementGroup.hashCode(group),
+ (a, b) => a.unit.model.id === b.unit.model.id && (a.group.key === b.group.key && OrderedSet.areEqual(a.group.elements, b.group.elements))
+ );
+
+ for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
+ const group = ElementSet.unitGetByIndex(elements, i);
+ const unitId = ElementSet.unitGetId(elements, i);
+ uniqueGroups.add(unitId, { unit: units[unitId], group });
+ }
+
+ console.log('group count', uniqueGroups.groups.length);
+ }
+
export async function run() {
- const { structures, models/*, mmcif*/ } = await getBcif('1cbs');
+ //const { structures, models/*, mmcif*/ } = await getBcif('1cbs');
// const { structures, models } = await getBcif('3j3q');
- //const { structures, models, mmcif } = await readCIF('e:/test/quick/1cbs_updated.cif');
+ const { structures, models /*, mmcif*/ } = await readCIF('e:/test/quick/1hrv_updated.cif');
+ const { structures: s1, /*, mmcif*/ } = await readCIF('e:/test/quick/1tqn_updated.cif');
+
+ testGrouping(structures[0]);
+ console.log('------');
+ testGrouping(s1[0]);
//const { structures, models/*, mmcif*/ } = await readCIF('e:/test/quick/5j7v_updated.cif');
//console.log(mmcif.pdbx_struct_oper_list.matrix.toArray());
--
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