diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 6a8ce63093eedd9d2c305346fbc74f06cdb75e08..304f34fc1c12f75910e19948202f2d0622660182 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -9,12 +9,11 @@ import * as argparse from 'argparse'
require('util.promisify').shim();
// import { Table } from 'mol-data/db'
-import CIF from 'mol-io/reader/cif'
-import { Model, Structure, Element, Unit, Queries } from 'mol-model/structure'
+import { CifFrame } from 'mol-io/reader/cif'
+import { Model, Structure, Element, Unit, Queries, Format } from 'mol-model/structure'
// import { Run, Progress } from 'mol-task'
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 { BitFlags } from 'mol-util';
import { SecondaryStructureType } from 'mol-model/structure/model/types';
@@ -24,12 +23,12 @@ import { UnitRings } from 'mol-model/structure/structure/unit/rings';
async function downloadFromPdb(pdb: string) {
// `https://files.rcsb.org/download/${pdb}.cif`
const parsed = await downloadCif(`http://www.ebi.ac.uk/pdbe/static/entry/${pdb}_updated.cif`, false);
- return CIF.schema.mmCIF(parsed.blocks[0]);
+ return parsed.blocks[0];
}
async function readPdbFile(path: string) {
const parsed = await openCif(path);
- return CIF.schema.mmCIF(parsed.blocks[0]);
+ return parsed.blocks[0];
}
export function atomLabel(model: Model, aI: number) {
@@ -189,8 +188,8 @@ export function printIHMModels(model: Model) {
console.log(Table.formatToString(model.coarseHierarchy.models));
}
-async function run(mmcif: mmCIF_Database) {
- const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
+async function run(frame: CifFrame) {
+ const models = await Model.create(Format.mmCIF(frame)).run();
const structure = Structure.ofModel(models[0]);
//printSequence(models[0]);
//printIHMModels(models[0]);
diff --git a/src/mol-data/util/buckets.ts b/src/mol-data/util/buckets.ts
index de409570912144fa1176004b45ed42161c6b3c01..1e8568a09cefa714427585147f261a62fa753815 100644
--- a/src/mol-data/util/buckets.ts
+++ b/src/mol-data/util/buckets.ts
@@ -54,7 +54,7 @@ function _makeBuckets(indices: Helpers.ArrayLike<number>,
}
if (sortBuckets && !sorted) {
- sort(bucketList, start, end, sortAsc, arraySwap);
+ sort(bucketList, 0, bucketList.length, sortAsc, arraySwap);
}
let offset = 0;
diff --git a/src/mol-model/structure/model/format.ts b/src/mol-model/structure/model/format.ts
index 2fa1f8ae1880d87643f6923b8a266c6693a151f5..d2053f170306e4e704fc6399dda1f0914a276b8e 100644
--- a/src/mol-model/structure/model/format.ts
+++ b/src/mol-model/structure/model/format.ts
@@ -6,6 +6,7 @@
// import { File as GroFile } from 'mol-io/reader/gro/schema'
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif'
+import CIF, { CifFrame } from 'mol-io/reader/cif';
type Format =
// | Format.gro
@@ -13,7 +14,11 @@ type Format =
namespace Format {
// export interface gro { kind: 'gro', data: GroFile }
- export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database }
+ export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database, frame: CifFrame }
+
+ export function mmCIF(frame: CifFrame, data?: mmCIF_Database): mmCIF {
+ return { kind: 'mmCIF', data: data || CIF.schema.mmCIF(frame), frame };
+ }
}
export default Format
\ No newline at end of file
diff --git a/src/mol-view/state/entity.ts b/src/mol-view/state/entity.ts
index a35ec66145f42af1a91551db8412450ad106a764..f987c4ada513dec65f4e0f1c822f2bc4cf6050a8 100644
--- a/src/mol-view/state/entity.ts
+++ b/src/mol-view/state/entity.ts
@@ -8,7 +8,7 @@ import { readFileAs, readUrlAs } from 'mol-util/read'
import { idFactory } from 'mol-util/id-factory'
import { StateContext } from './context';
import { getFileInfo } from 'mol-util/file-info';
-import { CifFile } from 'mol-io/reader/cif';
+import { CifFile, CifFrame } from 'mol-io/reader/cif';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { Model, Structure } from 'mol-model/structure';
import { StructureRepresentation } from 'mol-geo/representation/structure';
@@ -94,10 +94,10 @@ export namespace CifEntity {
}
}
-export type MmcifEntity = StateEntity<mmCIF_Database, 'mmcif'>
+export type MmcifEntity = StateEntity<{ db: mmCIF_Database, frame: CifFrame }, 'mmcif'>
export namespace MmcifEntity {
- export function ofMmcifDb(ctx: StateContext, db: mmCIF_Database): MmcifEntity {
- return StateEntity.create(ctx, 'mmcif', db)
+ export function ofMmcifDb(ctx: StateContext, mmCif: { db: mmCIF_Database, frame: CifFrame }): MmcifEntity {
+ return StateEntity.create(ctx, 'mmcif', mmCif)
}
}
diff --git a/src/mol-view/state/transform.ts b/src/mol-view/state/transform.ts
index ed4adbc48df82f0ac8af9be9720dd2bd5eeda63f..a618bdcca11906c5ca0dc6f5a2022c0cd1b26d03 100644
--- a/src/mol-view/state/transform.ts
+++ b/src/mol-view/state/transform.ts
@@ -6,7 +6,7 @@
import CIF from 'mol-io/reader/cif'
import { FileEntity, DataEntity, UrlEntity, CifEntity, MmcifEntity, ModelEntity, StructureEntity, SpacefillEntity, AnyEntity, NullEntity, BondEntity } from './entity';
-import { Model, Structure } from 'mol-model/structure';
+import { Model, Structure, Format } from 'mol-model/structure';
import { StateContext } from './context';
import Spacefill, { SpacefillProps } from 'mol-geo/representation/structure/spacefill';
@@ -55,13 +55,14 @@ export const DataToCif: DataToCif = StateTransform.create('data', 'cif', 'data-t
export type CifToMmcif = StateTransform<CifEntity, MmcifEntity, {}>
export const CifToMmcif: CifToMmcif = StateTransform.create('cif', 'mmcif', 'cif-to-mmcif',
async function (ctx: StateContext, cifEntity: CifEntity) {
- return MmcifEntity.ofMmcifDb(ctx, CIF.schema.mmCIF(cifEntity.value.blocks[0]))
+ const frame = cifEntity.value.blocks[0];
+ return MmcifEntity.ofMmcifDb(ctx, { frame, db: CIF.schema.mmCIF(frame) })
})
export type MmcifToModel = StateTransform<MmcifEntity, ModelEntity, {}>
export const MmcifToModel: MmcifToModel = StateTransform.create('mmcif', 'model', 'mmcif-to-model',
async function (ctx: StateContext, mmcifEntity: MmcifEntity) {
- const models = await Model.create({ kind: 'mmCIF', data: mmcifEntity.value }).run(ctx.log)
+ const models = await Model.create(Format.mmCIF(mmcifEntity.value.frame, mmcifEntity.value.db)).run(ctx.log)
return ModelEntity.ofModels(ctx, models)
})
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 957ce7c01c6be2e0c9b59db09dbab480302535cc..e2629a368096d45f6094e189888f9f60d8057078 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -2,7 +2,7 @@ import * as util from 'util'
import * as fs from 'fs'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model } from 'mol-model/structure'
+import { Structure, Model, Format } from 'mol-model/structure'
import { GridLookup3D } from 'mol-math/geometry';
// import { sortArray } from 'mol-data/util';
@@ -31,12 +31,11 @@ export async function readCIF(path: string) {
throw parsed;
}
- const data = parsed.result.blocks[0];
- const mmcif = CIF.schema.mmCIF(data);
- const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
+ const mmcif = Format.mmCIF(parsed.result.blocks[0]);
+ const models = await Model.create(mmcif).run();
const structures = models.map(Structure.ofModel);
- return { mmcif, models, structures };
+ return { mmcif: mmcif.data, models, structures };
}
export async function test() {
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index b2fea5b987fa7e53b58545ada38256da9a355dea..22914398f3b5edfff51467026b3dc3e156cef832 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,7 +11,7 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry, Query } from 'mol-model/structure'
+import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry, Query, Format } from 'mol-model/structure'
//import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
@@ -70,11 +70,11 @@ export async function readCIF(path: string) {
const data = parsed.result.blocks[0];
console.time('schema')
- const mmcif = CIF.schema.mmCIF(data);
+ const mmcif = Format.mmCIF(data);
console.timeEnd('schema')
console.time('buildModels')
- const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
+ const models = await Model.create(mmcif).run();
console.timeEnd('buildModels')
const structures = models.map(Structure.ofModel);
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 8e5d23e2bbda74e80c3da4829ae77b6725020ad8..ad6ba226db1d31154307b927b223846fc133aef7 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Structure, Model } from 'mol-model/structure';
+import { Structure, Model, Format } from 'mol-model/structure';
import { PerformanceMonitor } from 'mol-util/performance-monitor';
import { Cache } from './cache';
import Config from '../config';
@@ -89,10 +89,10 @@ async function readStructure(key: string, sourceId: string, entryId: string) {
const data = await readFile(filename);
perf.end('read');
perf.start('parse');
- const mmcif = CIF.schema.mmCIF((await parseCif(data)).blocks[0]);
+ const frame = (await parseCif(data)).blocks[0];
perf.end('parse');
perf.start('createModel');
- const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
+ const models = await Model.create(Format.mmCIF(frame)).run();
perf.end('createModel');
const structure = Structure.ofModel(models[0]);