From 358053327649047096637cdc07d1c7cf08f9e1d6 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 11 May 2018 10:19:28 +0200
Subject: [PATCH] Wrap Model.create in Task
---
src/apps/render-test/state.ts | 3 +-
src/apps/render-test/utils/index.ts | 4 +-
src/apps/structure-info/model.ts | 3 +-
.../structure/model/formats/mmcif.ts | 41 ++++++++++---------
.../structure/structure/structure.ts | 7 +---
src/perf-tests/lookup3d.ts | 2 +-
src/perf-tests/structure.ts | 2 +-
7 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index c0e92f901..58f3404e7 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -178,7 +178,8 @@ export default class State {
if (this.spacefillRepr) this.viewer.remove(this.spacefillRepr)
if (this.pdbId.length !== 4) return
this.loading.next(true)
- this.setModel((await getModelFromPdbId(this.pdbId))[0])
+ const models = await getModelFromPdbId(this.pdbId);
+ this.setModel(models[0])
}
setVolume(volume: Volume) {
diff --git a/src/apps/render-test/utils/index.ts b/src/apps/render-test/utils/index.ts
index 54486ffb3..b5eb271c7 100644
--- a/src/apps/render-test/utils/index.ts
+++ b/src/apps/render-test/utils/index.ts
@@ -29,7 +29,7 @@ export async function parseCif(data: string|Uint8Array) {
export async function getModelFromPdbId(pdbid: string) {
const cif = await downloadCif(`https://files.rcsb.org/download/${pdbid}.cif`, false)
- return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) })
+ return Run(Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }))
}
const readFileAsText = (file: File) => {
@@ -46,7 +46,7 @@ const readFileAsText = (file: File) => {
export async function getModelFromFile(file: File) {
const cif = await parseCif(await readFileAsText(file))
- return Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) })
+ return Run(Model.create({ kind: 'mmCIF', data: CIF.schema.mmCIF(cif.blocks[0]) }))
}
export type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 15ee55fd8..3f7957df8 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -16,6 +16,7 @@ import { OrderedSet } from 'mol-data/int';
import { Table } from 'mol-data/db';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { openCif, downloadCif } from './helpers';
+import { Run } from 'mol-task';
async function downloadFromPdb(pdb: string) {
@@ -117,7 +118,7 @@ export function printIHMModels(model: Model) {
}
async function run(mmcif: mmCIF_Database) {
- const models = Model.create({ kind: 'mmCIF', data: mmcif });
+ const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
const structure = Structure.ofModel(models[0]);
printSequence(models[0]);
printIHMModels(models[0]);
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 3f68d5444..d2a2338f3 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -21,6 +21,7 @@ import { getIHMCoarse } from './mmcif/ihm';
import { getSequence } from './mmcif/sequence';
import mmCIF_Format = Format.mmCIF
+import { Task } from 'mol-task';
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -154,25 +155,27 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
};
}
-function buildModels(format: mmCIF_Format): ReadonlyArray<Model> {
- const atomCount = format.data.atom_site._rowCount;
- const isIHM = format.data.ihm_model_list._rowCount > 0;
-
- if (atomCount === 0) {
- return isIHM
- ? [createModel(format, Interval.Empty, void 0)]
- : [];
- }
-
- const models: Model[] = [];
- let modelStart = 0;
- while (modelStart < atomCount) {
- const bounds = findModelBounds(format, modelStart);
- const model = createModel(format, bounds, models.length > 0 ? models[models.length - 1] : void 0);
- models.push(model);
- modelStart = Interval.end(bounds);
- }
- return models;
+function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
+ return Task.create('Create mmCIF Model', async ctx => {
+ const atomCount = format.data.atom_site._rowCount;
+ const isIHM = format.data.ihm_model_list._rowCount > 0;
+
+ if (atomCount === 0) {
+ return isIHM
+ ? [createModel(format, Interval.Empty, void 0)]
+ : [];
+ }
+
+ const models: Model[] = [];
+ let modelStart = 0;
+ while (modelStart < atomCount) {
+ const bounds = findModelBounds(format, modelStart);
+ const model = createModel(format, bounds, models.length > 0 ? models[models.length - 1] : void 0);
+ models.push(model);
+ modelStart = Interval.end(bounds);
+ }
+ return models;
+ });
}
export default buildModels;
\ 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 efe4e8bde..93d7d4b14 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -7,7 +7,7 @@
import { IntMap, SortedArray, Iterator } from 'mol-data/int'
import { UniqueArray } from 'mol-data/generic'
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
-import { Model, Format } from '../model'
+import { Model } from '../model'
import { sortArray, sort, arraySwap, hash1 } from 'mol-data/util';
import Element from './element'
import Unit from './unit'
@@ -85,11 +85,6 @@ namespace Structure {
export function create(units: ReadonlyArray<Unit>): Structure { return new Structure(units); }
- export function ofData(format: Format) {
- const models = Model.create(format);
- return models.map(ofModel);
- }
-
export function ofModel(model: Model): Structure {
const chains = model.atomicHierarchy.chainSegments;
const builder = new StructureBuilder();
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 3875a8c13..1245d80d4 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -34,7 +34,7 @@ export async function readCIF(path: string) {
const data = parsed.result.blocks[0];
const mmcif = CIF.schema.mmCIF(data);
- const models = Model.create({ kind: 'mmCIF', data: mmcif });
+ const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
const structures = models.map(Structure.ofModel);
return { mmcif, models, structures };
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 92831adec..e859ff78e 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -74,7 +74,7 @@ export async function readCIF(path: string) {
console.timeEnd('schema')
console.time('buildModels')
- const models = Model.create({ kind: 'mmCIF', data: mmcif });
+ const models = await Run(Model.create({ kind: 'mmCIF', data: mmcif }));
console.timeEnd('buildModels')
const structures = models.map(Structure.ofModel);
--
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