diff --git a/src/cli/structure-info/model.ts b/src/cli/structure-info/model.ts
index 87ca5e63a04de70a7d5f856ab52ad17d2dde0664..55e7ef0874682ce642da7423afc2131f93158842 100644
--- a/src/cli/structure-info/model.ts
+++ b/src/cli/structure-info/model.ts
@@ -10,7 +10,7 @@ import * as argparse from 'argparse';
require('util.promisify').shim();
import { CifFrame } from '../../mol-io/reader/cif';
-import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure';
+import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing, Trajectory } from '../../mol-model/structure';
// import { Run, Progress } from '../../mol-task'
import { OrderedSet } from '../../mol-data/int';
import { openCif, downloadCif } from './helpers';
@@ -19,6 +19,7 @@ import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
import { Sequence } from '../../mol-model/sequence';
import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { Task } from '../../mol-task';
async function downloadFromPdb(pdb: string) {
@@ -183,10 +184,11 @@ export function printSymmetryInfo(model: Model) {
console.log(`NCS operators: ${symmetry.ncsOperators && symmetry.ncsOperators.map(a => a.name).join(', ')}`);
}
-export function printModelStats(models: ReadonlyArray<Model>) {
+export async function printModelStats(models: Trajectory) {
console.log('\nModels\n=============');
- for (const m of models) {
+ for (let i = 0; i < models.frameCount; i++) {
+ const m = await Task.resolveInContext(models.getFrameAtIndex(i));
if (m.coarseHierarchy.isDefined) {
console.log(`${m.label} ${m.modelNum}: ${m.atomicHierarchy.atoms._rowCount} atom(s), ${m.coarseHierarchy.spheres.count} sphere(s), ${m.coarseHierarchy.gaussians.count} gaussian(s)`);
} else {
@@ -198,7 +200,7 @@ export function printModelStats(models: ReadonlyArray<Model>) {
export async function getModelsAndStructure(frame: CifFrame) {
const models = await trajectoryFromMmCIF(frame).run();
- const structure = Structure.ofModel(models[0]);
+ const structure = Structure.ofModel(models.representative);
return { models, structure };
}
@@ -206,13 +208,13 @@ async function run(frame: CifFrame, args: Args) {
const { models, structure } = await getModelsAndStructure(frame);
if (args.models) printModelStats(models);
- if (args.seq) printSequence(models[0]);
+ if (args.seq) printSequence(models.representative);
if (args.units) printUnits(structure);
- if (args.sym) printSymmetryInfo(models[0]);
+ if (args.sym) printSymmetryInfo(models.representative);
if (args.rings) printRings(structure);
if (args.intraBonds) printBonds(structure, true, false);
if (args.interBonds) printBonds(structure, false, true);
- if (args.sec) printSecStructure(models[0]);
+ if (args.sec) printSecStructure(models.representative);
}
async function runDL(pdb: string, args: Args) {
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index cf6f2ef997772b37bebdfce9b704e5f4f2d4e9fd..2043f93f62e4f6b18f6edb8f54cf4a25a240129a 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -10,7 +10,7 @@ import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Ingredient, IngredientSource, CellPacking } from './data';
import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
-import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../mol-model/structure';
+import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit, Trajectory } from '../../mol-model/structure';
import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
@@ -36,8 +36,8 @@ function getCellPackModelUrl(fileName: string, baseUrl: string) {
}
class TrajectoryCache {
- private map = new Map<string, Model.Trajectory>();
- set(id: string, trajectory: Model.Trajectory) { this.map.set(id, trajectory); }
+ private map = new Map<string, Trajectory>();
+ set(id: string, trajectory: Trajectory) { this.map.set(id, trajectory); }
get(id: string) { return this.map.get(id); }
}
@@ -94,9 +94,9 @@ async function getModel(plugin: PluginContext, id: string, ingredient: Ingredien
trajectory = await plugin.runTask(trajectoryFromMmCIF(data.mmcif));
}
}
- trajCache.set(id, trajectory);
+ trajCache.set(id, trajectory!);
}
- const model = trajectory[modelIndex];
+ const model = await plugin.resolveTask(trajectory?.getFrameAtIndex(modelIndex)!);
return { model, assets };
}
@@ -303,7 +303,7 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
const curveModelTask = Task.create('Curve Model', async ctx => {
const format = MmcifFormat.fromFrame(cif);
const models = await createModels(format.data.db, format, ctx);
- return models[0];
+ return models.representative;
});
const curveModel = await plugin.runTask(curveModelTask);
diff --git a/src/extensions/g3d/model.ts b/src/extensions/g3d/model.ts
index 5ed757cb662be82d83a073c22869e90342fde493..353e8d3a10bd70862b0c01446bfba7438f2df5ee 100644
--- a/src/extensions/g3d/model.ts
+++ b/src/extensions/g3d/model.ts
@@ -4,7 +4,6 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { Column, Table } from '../../mol-data/db';
import { MoleculeType } from '../../mol-model/structure/model/types';
@@ -13,6 +12,7 @@ import { BasicSchema, createBasic } from '../../mol-model-formats/structure/basi
import { createModels } from '../../mol-model-formats/structure/basic/parser';
import { G3dDataBlock } from './data';
import { objectForEach } from '../../mol-util/object';
+import { Trajectory } from '../../mol-model/structure';
interface Columns {
entity_id: string[],
@@ -106,7 +106,7 @@ function getBasic(data: G3dDataBlock) {
});
}
-export function trajectoryFromG3D(data: G3dDataBlock): Task<Model.Trajectory> {
+export function trajectoryFromG3D(data: G3dDataBlock): Task<Trajectory> {
return Task.create('Parse G3D', async ctx => {
const basic = getBasic(data);
return createModels(basic, { kind: 'g3d', name: 'G3D', data }, ctx);
diff --git a/src/mol-model-formats/structure/3dg.ts b/src/mol-model-formats/structure/3dg.ts
index 0e829bdafa8ebaa753e5c7c4212178b5bce02529..18aeab4730f8c4897a90049795fc5136a81784f7 100644
--- a/src/mol-model-formats/structure/3dg.ts
+++ b/src/mol-model-formats/structure/3dg.ts
@@ -4,7 +4,6 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { ModelFormat } from '../format';
import { Column, Table } from '../../mol-data/db';
@@ -14,6 +13,7 @@ import { fillSerial } from '../../mol-util/array';
import { MoleculeType } from '../../mol-model/structure/model/types';
import { BasicSchema, createBasic } from './basic/schema';
import { createModels } from './basic/parser';
+import { Trajectory } from '../../mol-model/structure';
function getBasic(table: File3DG['table']) {
const entityIds = new Array<string>(table._rowCount);
@@ -74,7 +74,7 @@ namespace Format3dg {
}
}
-export function trajectoryFrom3DG(file3dg: File3DG): Task<Model.Trajectory> {
+export function trajectoryFrom3DG(file3dg: File3DG): Task<Trajectory> {
return Task.create('Parse 3DG', async ctx => {
const format = Format3dg.from3dg(file3dg);
const basic = getBasic(file3dg.table);
diff --git a/src/mol-model-formats/structure/basic/parser.ts b/src/mol-model-formats/structure/basic/parser.ts
index 3262dad5f0aea636590d70dde03c42c20e812a1e..d8a42f4195d6feb604775cbdc344791f96bc547c 100644
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -21,6 +21,7 @@ import { AtomSite, BasicData } from './schema';
import { getProperties } from './properties';
import { getEntities } from './entities';
import { getModelGroupName } from './util';
+import { ArrayTrajectory } from '../../../mol-model/structure/trajectory';
export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
const properties = getProperties(data);
@@ -32,7 +33,7 @@ export async function createModels(data: BasicData, format: ModelFormat, ctx: Ru
Model.TrajectoryInfo.set(models[i], { index: i, size: models.length });
}
- return models;
+ return new ArrayTrajectory(models);
}
/** Standard atomic model */
diff --git a/src/mol-model-formats/structure/cif-core.ts b/src/mol-model-formats/structure/cif-core.ts
index 532e1fb0f453407669fad09b82701ea0c89a786a..8c09d0fb28a0c442b4ac33da694d300479a5ee3d 100644
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -21,6 +21,7 @@ import { ModelSymmetry } from './property/symmetry';
import { IndexPairBonds } from './property/bonds/index-pair';
import { AtomSiteAnisotrop } from './property/anisotropic';
import { guessElementSymbolString } from './util';
+import { Trajectory } from '../../mol-model/structure';
function getSpacegroupNameOrNumber(space_group: CifCore_Database['space_group']) {
const groupNumber = space_group.IT_number.value(0);
@@ -45,7 +46,7 @@ function getSymmetry(db: CifCore_Database): Symmetry {
};
}
-async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: RuntimeContext): Promise<Model[]> {
+async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: RuntimeContext) {
const atomCount = db.atom_site._rowCount;
const MOL = Column.ofConst('MOL', atomCount, Column.Schema.str);
@@ -152,8 +153,10 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
const models = await createModels(basics, format, ctx);
- if (models.length > 0) {
- ModelSymmetry.Provider.set(models[0], symmetry);
+ if (models.frameCount > 0) {
+ const first = models.representative;
+
+ ModelSymmetry.Provider.set(first, symmetry);
const bondCount = db.geom_bond._rowCount;
if(bondCount > 0) {
@@ -179,7 +182,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
symmetryB[i] = site_symmetry_2.value(i) || '1_555';
}
- IndexPairBonds.Provider.set(models[0], IndexPairBonds.fromData({ pairs: {
+ IndexPairBonds.Provider.set(first, IndexPairBonds.fromData({ pairs: {
indexA: Column.ofIntArray(indexA),
indexB: Column.ofIntArray(indexB),
order: Column.ofIntArray(order),
@@ -238,7 +241,7 @@ namespace CifCoreFormat {
}
}
-export function trajectoryFromCifCore(frame: CifFrame): Task<Model.Trajectory> {
+export function trajectoryFromCifCore(frame: CifFrame): Task<Trajectory> {
const format = CifCoreFormat.fromFrame(frame);
return Task.create('Parse CIF Core', ctx => getModels(format.data.db, format, ctx));
}
diff --git a/src/mol-model-formats/structure/cube.ts b/src/mol-model-formats/structure/cube.ts
index 3b72a034b774b8378a99bf0a85c1984f2332fcba..9983693f094727d89f92e1e3e91708f7e8bb3cef 100644
--- a/src/mol-model-formats/structure/cube.ts
+++ b/src/mol-model-formats/structure/cube.ts
@@ -5,7 +5,6 @@
*/
import { Column, Table } from '../../mol-data/db';
-import { Model } from '../../mol-model/structure/model';
import { MoleculeType, getElementFromAtomicNumber, ElementSymbol } from '../../mol-model/structure/model/types';
import { RuntimeContext, Task } from '../../mol-task';
import { createModels } from './basic/parser';
@@ -14,8 +13,9 @@ import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
import { ModelFormat } from '../format';
import { CubeFile } from '../../mol-io/reader/cube/parser';
+import { Trajectory } from '../../mol-model/structure';
-async function getModels(cube: CubeFile, ctx: RuntimeContext): Promise<Model[]> {
+async function getModels(cube: CubeFile, ctx: RuntimeContext) {
const { atoms } = cube;
const MOL = Column.ofConst('MOL', cube.atoms.count, Column.Schema.str);
@@ -78,6 +78,6 @@ namespace MolFormat {
}
}
-export function trajectoryFromCube(cube: CubeFile): Task<Model.Trajectory> {
+export function trajectoryFromCube(cube: CubeFile): Task<Trajectory> {
return Task.create('Parse Cube', ctx => getModels(cube, ctx));
}
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index f0228eed99de42ce40e055167a8eab208803ea61..af13e6c015866896c1b37f4fde48c6e44a74647e 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -16,6 +16,8 @@ import { getChainId } from './common/util';
import { EntityBuilder } from './common/entity';
import { BasicData, BasicSchema, createBasic } from './basic/schema';
import { createModels } from './basic/parser';
+import { Trajectory } from '../../mol-model/structure';
+import { ArrayTrajectory } from '../../mol-model/structure/trajectory';
function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
const auth_atom_id = atoms.atomName;
@@ -116,15 +118,17 @@ namespace GroFormat {
// TODO reuse static model parts when hierarchy is identical
// need to pass all gro.structures as one table into createModels
-export function trajectoryFromGRO(gro: GroFile): Task<Model.Trajectory> {
+export function trajectoryFromGRO(gro: GroFile): Task<Trajectory> {
return Task.create('Parse GRO', async ctx => {
const format = GroFormat.fromGro(gro);
const models: Model[] = [];
for (let i = 0, il = gro.structures.length; i < il; ++i) {
const basic = getBasic(gro.structures[i].atoms, i + 1);
const m = await createModels(basic, format, ctx);
- if (m.length === 1) models.push(m[0]);
+ if (m.frameCount === 1) {
+ models.push(m.representative);
+ }
}
- return models;
+ return new ArrayTrajectory(models);
});
}
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index 9a4503f1d831ce8b7fbc492a9c5289fe20699625..48e9970cecf8844b86fe7a2312c9f2f1cbd1c55b 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -17,6 +17,7 @@ import { Table } from '../../mol-data/db';
import { AtomSiteAnisotrop } from './property/anisotropic';
import { ComponentBond } from './property/bonds/chem_comp';
import { StructConn } from './property/bonds/struct_conn';
+import { Trajectory } from '../../mol-model/structure';
function modelSymmetryFromMmcif(model: Model) {
if (!MmcifFormat.is(model.sourceData)) return;
@@ -86,7 +87,7 @@ namespace MmcifFormat {
}
}
-export function trajectoryFromMmCIF(frame: CifFrame): Task<Model.Trajectory> {
+export function trajectoryFromMmCIF(frame: CifFrame): Task<Trajectory> {
const format = MmcifFormat.fromFrame(frame);
return Task.create('Create mmCIF Model', ctx => createModels(format.data.db, format, ctx));
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mol.ts b/src/mol-model-formats/structure/mol.ts
index dbfc113907915813dc2667ae0e40a9d872c516a3..633d3ab820d4269dcdadf4f1b0f37732df19d0b5 100644
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -7,7 +7,6 @@
import { Column, Table } from '../../mol-data/db';
import { MolFile } from '../../mol-io/reader/mol/parser';
-import { Model } from '../../mol-model/structure/model';
import { MoleculeType } from '../../mol-model/structure/model/types';
import { RuntimeContext, Task } from '../../mol-task';
import { createModels } from './basic/parser';
@@ -16,8 +15,9 @@ import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
import { ModelFormat } from '../format';
import { IndexPairBonds } from './property/bonds/index-pair';
+import { Trajectory } from '../../mol-model/structure';
-async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
+async function getModels(mol: MolFile, ctx: RuntimeContext) {
const { atoms, bonds } = mol;
const MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
@@ -63,12 +63,12 @@ async function getModels(mol: MolFile, ctx: RuntimeContext): Promise<Model[]> {
const models = await createModels(basics, MolFormat.create(mol), ctx);
- if (models.length > 0) {
+ if (models.frameCount > 0) {
const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
const indexB = Column.ofIntArray(Column.mapToArray(bonds.atomIdxB, x => x - 1, Int32Array));
const order = Column.asArrayColumn(bonds.order, Int32Array);
const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: bonds.count });
- IndexPairBonds.Provider.set(models[0], pairBonds);
+ IndexPairBonds.Provider.set(models.representative, pairBonds);
}
return models;
@@ -90,6 +90,6 @@ namespace MolFormat {
}
}
-export function trajectoryFromMol(mol: MolFile): Task<Model.Trajectory> {
+export function trajectoryFromMol(mol: MolFile): Task<Trajectory> {
return Task.create('Parse MOL', ctx => getModels(mol, ctx));
}
diff --git a/src/mol-model-formats/structure/mol2.ts b/src/mol-model-formats/structure/mol2.ts
index 14f63fc85e96ff7e21b0ee91badbf0e877001dc0..d3ba36bdbd359790ea153bcfcc3db0e02788495f 100644
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/src/mol-model-formats/structure/mol2.ts
@@ -16,8 +16,9 @@ import { ModelFormat } from '../format';
import { IndexPairBonds } from './property/bonds/index-pair';
import { Mol2File } from '../../mol-io/reader/mol2/schema';
import { AtomPartialCharge } from './property/partial-charge';
+import { Trajectory, ArrayTrajectory } from '../../mol-model/structure';
-async function getModels(mol2: Mol2File, ctx: RuntimeContext): Promise<Model[]> {
+async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
const models: Model[] = [];
for (let i = 0, il = mol2.structures.length; i < il; ++i) {
@@ -64,23 +65,25 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext): Promise<Model[]>
const _models = await createModels(basics, Mol2Format.create(mol2), ctx);
- if (_models.length > 0) {
+ if (_models.frameCount > 0) {
const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
const indexB = Column.ofIntArray(Column.mapToArray(bonds.target_atom_id, x => x - 1, Int32Array));
const order = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => x === 'ar' ? 1 : parseInt(x), Int8Array));
const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: bonds.count });
- IndexPairBonds.Provider.set(_models[0], pairBonds);
- AtomPartialCharge.Provider.set(_models[0], {
+ const first = _models.representative;
+ IndexPairBonds.Provider.set(first, pairBonds);
+
+ AtomPartialCharge.Provider.set(first, {
data: atoms.charge,
type: molecule.charge_type
});
- models.push(_models[0]);
+ models.push(first);
}
}
- return models;
+ return new ArrayTrajectory(models);
}
//
@@ -99,6 +102,6 @@ namespace Mol2Format {
}
}
-export function trajectoryFromMol2(mol2: Mol2File): Task<Model.Trajectory> {
+export function trajectoryFromMol2(mol2: Mol2File): Task<Trajectory> {
return Task.create('Parse MOL2', ctx => getModels(mol2, ctx));
}
diff --git a/src/mol-model-formats/structure/pdb.ts b/src/mol-model-formats/structure/pdb.ts
index cd7388bd1e77e8ac2034c78dd0f3d786ac86b195..95ab30881f337ded93eba78090b018e55d408798 100644
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.ts
@@ -7,14 +7,14 @@
import { PdbFile } from '../../mol-io/reader/pdb/schema';
import { pdbToMmCif } from './pdb/to-cif';
-import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { MmcifFormat } from './mmcif';
import { createModels } from './basic/parser';
import { Column } from '../../mol-data/db';
import { AtomPartialCharge } from './property/partial-charge';
+import { Trajectory } from '../../mol-model/structure';
-export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
+export function trajectoryFromPDB(pdb: PdbFile): Task<Trajectory> {
return Task.create('Parse PDB', async ctx => {
await ctx.update('Converting to mmCIF');
const cif = await pdbToMmCif(pdb);
@@ -24,8 +24,9 @@ export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
if (partial_charge) {
// TODO works only for single, unsorted model, to work generally
// would need to do model splitting again
- if (models.length === 1) {
- const srcIndex = models[0].atomicHierarchy.atoms.sourceIndex;
+ if (models.frameCount === 1) {
+ const first = models.representative;
+ const srcIndex = first.atomicHierarchy.atoms.sourceIndex;
const isIdentity = Column.isIdentity(srcIndex);
const srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
@@ -34,7 +35,7 @@ export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
? Column.ofFloatArray(Column.mapToArray(srcIndex, i => q[i], Float32Array))
: Column.ofFloatArray(q);
- AtomPartialCharge.Provider.set(models[0], {
+ AtomPartialCharge.Provider.set(first, {
data: partialCharge,
type: 'GASTEIGER' // from PDBQT
});
diff --git a/src/mol-model/structure.ts b/src/mol-model/structure.ts
index d8ab4a1a8c79065037c93708cc2864720beda46d..3ee18d9b5118c062b74bae7139112221ef3e732d 100644
--- a/src/mol-model/structure.ts
+++ b/src/mol-model/structure.ts
@@ -9,4 +9,5 @@ export * from './structure/coordinates';
export * from './structure/topology';
export * from './structure/model';
export * from './structure/structure';
-export * from './structure/query';
\ No newline at end of file
+export * from './structure/query';
+export * from './structure/trajectory';
\ No newline at end of file
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index aee5a4411ec0cecb263ac558fe325d007eda4c04..46bbd7456614f497d79bd2b975cc373629b59cde 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -15,7 +15,6 @@ import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
import { ModelFormat } from '../../../mol-model-formats/format';
import { calcModelCenter, getAsymIdCount } from './util';
import { Vec3 } from '../../../mol-math/linear-algebra';
-import { Mutable } from '../../../mol-util/type-helpers';
import { Coordinates } from '../coordinates';
import { Topology } from '../topology';
import { Task } from '../../../mol-task';
@@ -27,6 +26,7 @@ import { SymmetryOperator } from '../../../mol-math/geometry';
import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
import { Column } from '../../../mol-data/db';
import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Trajectory, ArrayTrajectory } from '../trajectory';
/**
* Interface to the "source data" of the molecule.
@@ -86,10 +86,8 @@ export interface Model extends Readonly<{
} { }
export namespace Model {
- export type Trajectory = ReadonlyArray<Model>
-
function _trajectoryFromModelAndCoordinates(model: Model, coordinates: Coordinates) {
- const trajectory: Mutable<Model.Trajectory> = [];
+ const trajectory: Model[] = [];
const { frames } = coordinates;
const srcIndex = model.atomicHierarchy.atoms.sourceIndex;
@@ -117,7 +115,7 @@ export namespace Model {
}
export function trajectoryFromModelAndCoordinates(model: Model, coordinates: Coordinates): Trajectory {
- return _trajectoryFromModelAndCoordinates(model, coordinates).trajectory;
+ return new ArrayTrajectory(_trajectoryFromModelAndCoordinates(model, coordinates).trajectory);
}
export function invertIndex(xs: ArrayLike<number>) {
@@ -130,8 +128,9 @@ export namespace Model {
export function trajectoryFromTopologyAndCoordinates(topology: Topology, coordinates: Coordinates): Task<Trajectory> {
return Task.create('Create Trajectory', async ctx => {
- const model = (await createModels(topology.basic, topology.sourceData, ctx))[0];
- if (!model) throw new Error('found no model');
+ const models = await createModels(topology.basic, topology.sourceData, ctx);
+ if (models.frameCount === 0) throw new Error('found no model');
+ const model = models.representative;
const { trajectory, srcIndexArray } = _trajectoryFromModelAndCoordinates(model, coordinates);
// TODO: cache the inverted index somewhere?
@@ -152,7 +151,7 @@ export namespace Model {
IndexPairBonds.Provider.set(m, indexPairBonds);
TrajectoryInfo.set(m, { index: index++, size: trajectory.length });
}
- return trajectory;
+ return new ArrayTrajectory(trajectory);
});
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 020fe97332bc708f232eb50a85edf437ad3d4f9e..64d926486d2f0d3ca9a65be235e7edcc9f38b01a 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -31,6 +31,8 @@ import { StructureSelection } from '../query/selection';
import { getBoundary } from '../../../mol-math/geometry/boundary';
import { ElementSymbol } from '../model/types';
import { CustomStructureProperty } from '../../../mol-model-props/common/custom-structure-property';
+import { Trajectory } from '../trajectory';
+import { RuntimeContext, Task } from '../../../mol-task';
class Structure {
/** Maps unit.id to unit */
@@ -639,14 +641,17 @@ namespace Structure {
return new Structure(units, props);
}
- export function ofTrajectory(trajectory: ReadonlyArray<Model>): Structure {
- if (trajectory.length === 0) return Empty;
+ export async function ofTrajectory(trajectory: Trajectory, ctx: RuntimeContext): Promise<Structure> {
+ if (trajectory.frameCount === 0) return Empty;
const units: Unit[] = [];
+ let first: Model | undefined = void 0;
let count = 0;
- for (let i = 0, il = trajectory.length; i < il; ++i) {
- const structure = ofModel(trajectory[i]);
+ for (let i = 0, il = trajectory.frameCount; i < il; ++i) {
+ const frame = await Task.resolveInContext(trajectory.getFrameAtIndex(i), ctx);
+ if (!first) first = frame;
+ const structure = ofModel(frame);
for (let j = 0, jl = structure.units.length; j < jl; ++j) {
const u = structure.units[j];
const invariantId = u.invariantId + count;
@@ -657,7 +662,7 @@ namespace Structure {
count = units.length;
}
- return create(units, { representativeModel: trajectory[0], label: trajectory[0].label });
+ return create(units, { representativeModel: first!, label: first!.label });
}
const PARTITION = false;
diff --git a/src/mol-model/structure/trajectory.ts b/src/mol-model/structure/trajectory.ts
new file mode 100644
index 0000000000000000000000000000000000000000..69bcbaad3a591b94709e5c0e5bd0889cc77dd768
--- /dev/null
+++ b/src/mol-model/structure/trajectory.ts
@@ -0,0 +1,45 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Task } from '../../mol-task';
+import { Model } from '../structure';
+
+export type TrajectoryFrameType =
+ | { type: 'default' }
+ /** Returns the closest available frame to the requested index */
+ | { type: 'snap' }
+ /** Interpolates between two available adjacent frames */
+ | { type: 'interpolate', kind?: 'linear' }
+
+/**
+ * A generic interface for representing (partial) trajectories
+ */
+export interface Trajectory {
+ readonly duration: number,
+ readonly frameCount: number,
+
+ /** Statically available representative model. Required for example by certain UI actions. */
+ readonly representative: Model,
+
+ /** Allows to asynchronously query data from a server or interpolate frames on the fly */
+ getFrameAtIndex(i: number, type?: TrajectoryFrameType): Task<Model> | Model
+}
+
+export class ArrayTrajectory implements Trajectory {
+ readonly duration: number;
+ readonly frameCount: number;
+ readonly representative: Model;
+
+ getFrameAtIndex(i: number) {
+ return this.frames[i];
+ }
+
+ constructor(private frames: Model[]) {
+ this.frameCount = frames.length;
+ this.representative = frames[0];
+ this.duration = frames.length;
+ }
+}
\ No newline at end of file
diff --git a/src/mol-plugin-state/actions/structure.ts b/src/mol-plugin-state/actions/structure.ts
index a29f719eb48a1e26a620d27dd6e4ec8bb9f3f122..babb24352dcc51908914fc487727573317335ef3 100644
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -191,8 +191,8 @@ export const UpdateTrajectory = StateAction.build({
if (!parent || !parent.obj) continue;
const traj = parent.obj;
update.to(m).update(old => {
- let modelIndex = (old.modelIndex + params.by!) % traj.data.length;
- if (modelIndex < 0) modelIndex += traj.data.length;
+ let modelIndex = (old.modelIndex + params.by!) % traj.data.frameCount;
+ if (modelIndex < 0) modelIndex += traj.data.frameCount;
return { modelIndex };
});
}
diff --git a/src/mol-plugin-state/animation/built-in.ts b/src/mol-plugin-state/animation/built-in.ts
index a9b8244f50e7078a2c925cf56e25d2c0422e24f4..50ddce363099717234a445dda528fd56025170fa 100644
--- a/src/mol-plugin-state/animation/built-in.ts
+++ b/src/mol-plugin-state/animation/built-in.ts
@@ -28,7 +28,7 @@ export const AnimateModelIndex = PluginStateAnimation.create({
const models = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Model.ModelFromTrajectory));
for (const m of models) {
const parent = StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, [PluginStateObject.Molecule.Trajectory]);
- if (parent && parent.obj && parent.obj.data.length > 1) return { canApply: true };
+ if (parent && parent.obj && parent.obj.data.frameCount > 1) return { canApply: true };
}
return { canApply: false, reason: 'No trajectory to animate' };
},
@@ -57,10 +57,10 @@ export const AnimateModelIndex = PluginStateAnimation.create({
const parent = StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, [PluginStateObject.Molecule.Trajectory]);
if (!parent || !parent.obj) continue;
const traj = parent.obj;
- if (traj.data.length <= 1) continue;
+ if (traj.data.frameCount <= 1) continue;
update.to(m).update(old => {
- const len = traj.data.length;
+ const len = traj.data.frameCount;
if (len !== 1) {
allSingles = false;
} else {
diff --git a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
index e007906d1c82084e0cbe60bfacf235dce91a1c86..55bd35af41afe523566fdf2ed22419961d00efc5 100644
--- a/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
+++ b/src/mol-plugin-state/builder/structure/hierarchy-preset.ts
@@ -80,7 +80,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
description: 'Shows all models; colored by model-index.'
},
isApplicable: o => {
- return o.data.length > 1;
+ return o.data.frameCount > 1;
},
params: CommonParams,
async apply(trajectory, params, plugin) {
@@ -91,7 +91,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
const models = [], structures = [];
- for (let i = 0; i < tr.length; i++) {
+ for (let i = 0; i < tr.frameCount; i++) {
const model = await builder.createModel(trajectory, { modelIndex: i });
const modelProperties = await builder.insertModelProperties(model, params.modelProperties, { isCollapsed: true });
const structure = await builder.createStructure(modelProperties || model, { name: 'model', params: {} });
@@ -100,7 +100,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
models.push(model);
structures.push(structure);
- const quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.length }) : 'medium';
+ const quality = structure.obj ? getStructureQuality(structure.obj.data, { elementCountFactor: tr.frameCount }) : 'medium';
await builder.representation.applyPreset(structureProperties, params.representationPreset || 'auto', { theme: { globalName: 'model-index' }, quality });
}
@@ -145,7 +145,7 @@ const unitcell = TrajectoryHierarchyPresetProvider({
description: 'Shows the fully populated unit cell.'
},
isApplicable: o => {
- return Model.hasCrystalSymmetry(o.data[0]);
+ return Model.hasCrystalSymmetry(o.data.representative);
},
params: CrystalSymmetryParams,
async apply(trajectory, params, plugin) {
@@ -160,7 +160,7 @@ const supercell = TrajectoryHierarchyPresetProvider({
description: 'Shows the super cell, i.e. the central unit cell and all adjacent unit cells.'
},
isApplicable: o => {
- return Model.hasCrystalSymmetry(o.data[0]);
+ return Model.hasCrystalSymmetry(o.data.representative);
},
params: CrystalSymmetryParams,
async apply(trajectory, params, plugin) {
@@ -180,7 +180,7 @@ const crystalContacts = TrajectoryHierarchyPresetProvider({
description: 'Showsasymetric unit and chains from neighbours within 5 \u212B, i.e., symmetry mates.'
},
isApplicable: o => {
- return Model.hasCrystalSymmetry(o.data[0]);
+ return Model.hasCrystalSymmetry(o.data.representative);
},
params: CrystalContactsParams,
async apply(trajectory, params, plugin) {
diff --git a/src/mol-plugin-state/objects.ts b/src/mol-plugin-state/objects.ts
index a9b18d77da426094dc91deb5d34415de6973afe6..9c3fade63ea32e43f608e5554635389ba94f0f99 100644
--- a/src/mol-plugin-state/objects.ts
+++ b/src/mol-plugin-state/objects.ts
@@ -13,7 +13,7 @@ import { Dsn6File } from '../mol-io/reader/dsn6/schema';
import { PlyFile } from '../mol-io/reader/ply/schema';
import { PsfFile } from '../mol-io/reader/psf/parser';
import { ShapeProvider } from '../mol-model/shape/provider';
-import { Coordinates as _Coordinates, Model as _Model, Structure as _Structure, StructureElement, Topology as _Topology } from '../mol-model/structure';
+import { Coordinates as _Coordinates, Model as _Model, Structure as _Structure, Trajectory as _Trajectory, StructureElement, Topology as _Topology } from '../mol-model/structure';
import { Volume as _Volume } from '../mol-model/volume';
import { PluginBehavior } from '../mol-plugin/behavior/behavior';
import { Representation } from '../mol-repr/representation';
@@ -100,7 +100,7 @@ export namespace PluginStateObject {
export class Coordinates extends Create<_Coordinates>({ name: 'Coordinates', typeClass: 'Object' }) { }
export class Topology extends Create<_Topology>({ name: 'Topology', typeClass: 'Object' }) { }
export class Model extends Create<_Model>({ name: 'Model', typeClass: 'Object' }) { }
- export class Trajectory extends Create<ReadonlyArray<_Model>>({ name: 'Trajectory', typeClass: 'Object' }) { }
+ export class Trajectory extends Create<_Trajectory>({ name: 'Trajectory', typeClass: 'Object' }) { }
export class Structure extends Create<_Structure>({ name: 'Structure', typeClass: 'Object' }) { }
export namespace Structure {
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 91bc6cfd115075ec3d7e4ab9f7ff7f0ede7f1d86..4d3bd65152264f5cd4addb5803f5877e5ab3c9c5 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -17,7 +17,7 @@ import { trajectoryFromGRO } from '../../mol-model-formats/structure/gro';
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
import { topologyFromPsf } from '../../mol-model-formats/structure/psf';
-import { Coordinates, Model, Queries, QueryContext, Structure, StructureElement, StructureQuery, StructureSelection as Sel, Topology } from '../../mol-model/structure';
+import { Coordinates, Model, Queries, QueryContext, Structure, StructureElement, StructureQuery, StructureSelection as Sel, Topology, ArrayTrajectory, Trajectory } from '../../mol-model/structure';
import { PluginContext } from '../../mol-plugin/context';
import { MolScriptBuilder } from '../../mol-script/language/builder';
import Expression from '../../mol-script/language/expression';
@@ -142,7 +142,7 @@ const TrajectoryFromModelAndCoordinates = PluginStateTransform.BuiltIn({
return Task.create('Create trajectory from model/topology and coordinates', async ctx => {
const coordinates = dependencies![params.coordinatesRef].data as Coordinates;
const trajectory = await getTrajectory(ctx, dependencies![params.modelRef], coordinates);
- const props = { label: 'Trajectory', description: `${trajectory.length} model${trajectory.length === 1 ? '' : 's'}` };
+ const props = { label: 'Trajectory', description: `${trajectory.frameCount} model${trajectory.frameCount === 1 ? '' : 's'}` };
return new SO.Molecule.Trajectory(trajectory, props);
});
}
@@ -162,16 +162,25 @@ const TrajectoryFromBlob = PluginStateTransform.BuiltIn({
if (e.kind !== 'cif') continue;
const block = e.data.blocks[0];
const xs = await trajectoryFromMmCIF(block).runInContext(ctx);
- if (xs.length === 0) throw new Error('No models found.');
- for (const x of xs) models.push(x);
+ if (xs.frameCount === 0) throw new Error('No models found.');
+
+ for (let i = 0; i < xs.frameCount; i++) {
+ const x = await Task.resolveInContext(xs.getFrameAtIndex(i), ctx);
+ models.push(x);
+ }
}
const props = { label: 'Trajectory', description: `${models.length} model${models.length === 1 ? '' : 's'}` };
- return new SO.Molecule.Trajectory(models, props);
+ return new SO.Molecule.Trajectory(new ArrayTrajectory(models), props);
});
}
});
+function trajectoryProps(trajectory: Trajectory) {
+ const first = trajectory.representative;
+ return { label: `${first.entry}`, description: `${trajectory.frameCount} model${trajectory.frameCount === 1 ? '' : 's'}` };
+}
+
type TrajectoryFromMmCif = typeof TrajectoryFromMmCif
const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
name: 'trajectory-from-mmcif',
@@ -197,8 +206,8 @@ const TrajectoryFromMmCif = PluginStateTransform.BuiltIn({
const block = a.data.blocks.find(b => b.header === header);
if (!block) throw new Error(`Data block '${[header]}' not found.`);
const models = await trajectoryFromMmCIF(block).runInContext(ctx);
- if (models.length === 0) throw new Error('No models found.');
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ if (models.frameCount === 0) throw new Error('No models found.');
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -219,7 +228,7 @@ const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
const parsed = await parsePDB(a.data, a.label, params.isPdbqt).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
const models = await trajectoryFromPDB(parsed.result).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -237,7 +246,7 @@ const TrajectoryFromGRO = PluginStateTransform.BuiltIn({
const parsed = await parseGRO(a.data).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
const models = await trajectoryFromGRO(parsed.result).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -255,7 +264,7 @@ const TrajectoryFromMOL = PluginStateTransform.BuiltIn({
const parsed = await parseMol(a.data).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
const models = await trajectoryFromMol(parsed.result).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -273,7 +282,7 @@ const TrajectoryFromMOL2 = PluginStateTransform.BuiltIn({
const parsed = await parseMol2(a.data, a.label).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
const models = await trajectoryFromMol2(parsed.result).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -289,7 +298,7 @@ const TrajectoryFromCube = PluginStateTransform.BuiltIn({
apply({ a }) {
return Task.create('Parse MOL', async ctx => {
const models = await trajectoryFromCube(a.data).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -319,8 +328,8 @@ const TrajectoryFromCifCore = PluginStateTransform.BuiltIn({
const block = a.data.blocks.find(b => b.header === header);
if (!block) throw new Error(`Data block '${[header]}' not found.`);
const models = await trajectoryFromCifCore(block).runInContext(ctx);
- if (models.length === 0) throw new Error('No models found.');
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ if (models.frameCount === 0) throw new Error('No models found.');
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -338,7 +347,7 @@ const TrajectoryFrom3DG = PluginStateTransform.BuiltIn({
const parsed = await parse3DG(a.data).runInContext(ctx);
if (parsed.isError) throw new Error(parsed.message);
const models = await trajectoryFrom3DG(parsed.result).runInContext(ctx);
- const props = { label: `${models[0].entry}`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
+ const props = trajectoryProps(models);
return new SO.Molecule.Trajectory(models, props);
});
}
@@ -355,17 +364,19 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
if (!a) {
return { modelIndex: PD.Numeric(0, {}, { description: 'Zero-based index of the model' }) };
}
- return { modelIndex: PD.Converted(plus1, minus1, PD.Numeric(1, { min: 1, max: a.data.length, step: 1 }, { description: 'Model Index' })) };
+ return { modelIndex: PD.Converted(plus1, minus1, PD.Numeric(1, { min: 1, max: a.data.frameCount, step: 1 }, { description: 'Model Index' })) };
}
})({
- isApplicable: a => a.data.length > 0,
+ isApplicable: a => a.data.frameCount > 0,
apply({ a, params }) {
- let modelIndex = params.modelIndex % a.data.length;
- if (modelIndex < 0) modelIndex += a.data.length;
- const model = a.data[params.modelIndex];
- const label = `Model ${model.modelNum}`;
- const description = a.data.length === 1 ? undefined : `of ${a.data.length}`;
- return new SO.Molecule.Model(model, { label, description });
+ return Task.create('Model from Trajectory', async ctx => {
+ let modelIndex = params.modelIndex % a.data.frameCount;
+ if (modelIndex < 0) modelIndex += a.data.frameCount;
+ const model = await Task.resolveInContext(a.data.getFrameAtIndex(modelIndex), ctx);
+ const label = `Model ${modelIndex + 1}`;
+ let description = a.data.frameCount === 1 ? undefined : `of ${a.data.frameCount}`;
+ return new SO.Molecule.Model(model, { label, description });
+ });
},
dispose({ b }) {
b?.data.customProperties.dispose();
@@ -381,7 +392,7 @@ const StructureFromTrajectory = PluginStateTransform.BuiltIn({
})({
apply({ a }) {
return Task.create('Build Structure', async ctx => {
- const s = Structure.ofTrajectory(a.data);
+ const s = await Structure.ofTrajectory(a.data, ctx);
const props = { label: 'Ensemble', description: Structure.elementDescription(s) };
return new SO.Molecule.Structure(s, props);
});
diff --git a/src/mol-plugin-ui/controls.tsx b/src/mol-plugin-ui/controls.tsx
index a820782a29d2ca5233f02d9f002b8b8c3b127392..94b105c256babcb817080879a4313ee0b0549d4b 100644
--- a/src/mol-plugin-ui/controls.tsx
+++ b/src/mol-plugin-ui/controls.tsx
@@ -44,7 +44,7 @@ export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: bo
const parent = state.cells.get(m.sourceRef)!.obj as PluginStateObject.Molecule.Trajectory;
if (!parent) continue;
- if (parent.data.length > 1) {
+ if (parent.data.frameCount > 1) {
if (parents.has(m.sourceRef)) {
// do not show the controls if there are 2 models of the same trajectory present
this.setState({ show: false });
@@ -55,7 +55,7 @@ export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: bo
count++;
if (!label) {
const idx = (m.transform.params! as StateTransformer.Params<ModelFromTrajectory>).modelIndex;
- label = `Model ${idx + 1} / ${parent.data.length}`;
+ label = `Model ${idx + 1} / ${parent.data.frameCount}`;
}
}
}
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 5e7f67ae9c518506a90cc0436470f71fbb677b91..3f0d31f395c01abf7738dbe6cb3abe1b9545125e 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -62,6 +62,11 @@ import { filter, take } from 'rxjs/operators';
export class PluginContext {
runTask = <T>(task: Task<T>) => this.tasks.run(task);
+ resolveTask = <T>(object: Task<T> | T | undefined) => {
+ if (!object) return void 0;
+ if (Task.is(object)) return this.runTask(object);
+ return object;
+ }
private disposed = false;
private ev = RxEventHelper.create();
diff --git a/src/mol-task/task.ts b/src/mol-task/task.ts
index da0bf7228c7323c9b1220178d13150b6f5dab32d..d258948912370845ad7a19753e2c483218d854a3 100644
--- a/src/mol-task/task.ts
+++ b/src/mol-task/task.ts
@@ -71,6 +71,11 @@ namespace Task {
export function empty(): Task<void> { return create('', async ctx => {}); }
export function fail(name: string, reason: string): Task<any> { return create(name, async ctx => { throw new Error(reason); }); }
+ export function resolveInContext<T>(object: Task<T> | T, ctx?: RuntimeContext) {
+ if (is(object)) return ctx ? object.runInContext(ctx) : object.run();
+ return object;
+ }
+
export interface Progress {
taskId: number,
taskName: string,
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 1c4c45af5af92796714493be07430b47eb6b393d..81cbd9e9a8367a511c096a611f6b58f0f19bc1f4 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -34,9 +34,9 @@ export async function readCIF(path: string) {
}
const models = await trajectoryFromMmCIF(parsed.result.blocks[0]).run();
- const structures = models.map(Structure.ofModel);
+ const structures = [Structure.ofModel(models.representative)];
- return { mmcif: models[0].sourceData.data as MmcifFormat.Data, models, structures };
+ return { mmcif: models.representative.sourceData.data as MmcifFormat.Data, models, structures };
}
export async function test() {
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index e8314ec9647c93b1f02833ce801ab515567cd70f..c769e7aa0a80a567a01b70a1563c0aee7bd8fdb9 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -73,9 +73,9 @@ export async function readCIF(path: string) {
console.time('buildModels');
const models = await trajectoryFromMmCIF(data).run();
console.timeEnd('buildModels');
- const structures = models.map(Structure.ofModel);
+ const structures = [Structure.ofModel(models.representative)];
- return { mmcif: models[0].sourceData.data, models, structures };
+ return { mmcif: models.representative.sourceData.data, models, structures };
}
const DATA_DIR = './build/data';
@@ -411,7 +411,7 @@ export namespace PropertyAccess {
// return;
- console.log('bs', baseline(models[0]));
+ console.log('bs', baseline(models.representative));
console.log('sp', sumProperty(structures[0], l => l.unit.model.atomicConformation.atomId.value(l.element)));
// console.log(sumPropertySegmented(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
@@ -459,7 +459,7 @@ export namespace PropertyAccess {
console.log(StructureSelection.structureCount(q2r));
// console.log(q1(structures[0]));
- const col = models[0].atomicConformation.atomId.value;
+ const col = models.representative.atomicConformation.atomId.value;
const suite = new B.Suite();
suite
// .add('test q', () => q1(structures[0]))
diff --git a/src/servers/model/server/structure-wrapper.ts b/src/servers/model/server/structure-wrapper.ts
index 9fdb746a2c087034d363798f9ce5451ee37cfdaa..e1eb1fe848d91b41e2b9a100b296f8198d4f53b4 100644
--- a/src/servers/model/server/structure-wrapper.ts
+++ b/src/servers/model/server/structure-wrapper.ts
@@ -17,6 +17,7 @@ import { ConsoleLogger } from '../../../mol-util/console-logger';
import { ModelPropertiesProvider } from '../property-provider';
import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif';
import { fetchRetry } from '../utils/fetch-retry';
+import { Task } from '../../../mol-task';
require('util.promisify').shim();
@@ -160,11 +161,15 @@ function readOrFetch(jobId: string, key: string, sourceId: string | '_local_', e
export async function readStructureWrapper(key: string, sourceId: string | '_local_', entryId: string, jobId: string | undefined, propertyProvider: ModelPropertiesProvider | undefined) {
const { data, frame, isBinary } = await readOrFetch(jobId || '', key, sourceId, entryId);
perf.start('createModel');
- const models = await trajectoryFromMmCIF(frame).run();
+ const trajectory = await trajectoryFromMmCIF(frame).run();
perf.end('createModel');
+ const models: Model[] = [];
const modelMap = new Map<number, Model>();
- for (const m of models) {
+
+ for (let i = 0; i < trajectory.frameCount; i++) {
+ const m = await Task.resolveInContext(trajectory.getFrameAtIndex(i));
+ models.push(m);
modelMap.set(m.modelNum, m);
}
diff --git a/src/tests/browser/render-structure.ts b/src/tests/browser/render-structure.ts
index ab79a6f81ec764fbbdecaf63344b23cf694ceb5d..8e155735c17df92c6989bc9e5cf7cf6e39ed8140 100644
--- a/src/tests/browser/render-structure.ts
+++ b/src/tests/browser/render-structure.ts
@@ -127,7 +127,7 @@ async function init() {
const cif = await downloadFromPdb('3pqr');
const models = await getModels(cif);
- const structure = await getStructure(models[0]);
+ const structure = await getStructure(models.representative);
console.time('compute SecondaryStructure');
await SecondaryStructureProvider.attach(ctx, structure);