diff --git a/src/mol-io/reader/3dg/parser.ts b/src/mol-io/reader/3dg/parser.ts
deleted file mode 100644
index 1fc7b6a36b2aa1eb428a38015fcab3f48ad723ce..0000000000000000000000000000000000000000
--- a/src/mol-io/reader/3dg/parser.ts
+++ /dev/null
@@ -1,57 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ReaderResult as Result } from '../result';
-import { Task } from '../../../mol-task';
-import { parseCsv } from '../csv/parser';
-import { Column, Table } from '../../../mol-data/db';
-import { toTable } from '../cif/schema';
-
-import Schema = Column.Schema
-import { CsvTable } from '../csv/data-model';
-
-
-export const Schema3DG = {
- /** Chromosome name */
- chromosome: Schema.str,
- /** Base position */
- position: Schema.int,
- /** X coordinate */
- x: Schema.float,
- /** Y coordinate */
- y: Schema.float,
- /** Z coordinate */
- z: Schema.float,
-};
-export type Schema3DG = typeof Schema3DG
-
-export interface File3DG {
- table: Table<Schema3DG>
-}
-
-const FieldNames = [ 'chromosome', 'position', 'x', 'y', 'z' ];
-
-function categoryFromTable(name: string, table: CsvTable) {
- return {
- name,
- rowCount: table.rowCount,
- fieldNames: FieldNames,
- getField: (name: string) => {
- return table.getColumn(FieldNames.indexOf(name).toString());
- }
- };
-}
-
-export function parse3DG(data: string) {
- return Task.create<Result<File3DG>>('Parse 3DG', async ctx => {
- const opts = { quote: '', comment: '#', delimiter: '\t', noColumnNames: true };
- const csvFile = await parseCsv(data, opts).runInContext(ctx);
- if (csvFile.isError) return Result.error(csvFile.message, csvFile.line);
- const category = categoryFromTable('3dg', csvFile.result.table);
- const table = toTable(Schema3DG, category);
- return Result.success({ table });
- });
-}
\ No newline at end of file
diff --git a/src/mol-io/reader/_spec/3dg.spec.ts b/src/mol-io/reader/_spec/3dg.spec.ts
deleted file mode 100644
index 25f4dd4d6bd72261d34f018bdf53c8de8ff9773a..0000000000000000000000000000000000000000
--- a/src/mol-io/reader/_spec/3dg.spec.ts
+++ /dev/null
@@ -1,33 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { parse3DG } from '../3dg/parser';
-
-const basic3dgString = `1(mat) 1420000 0.791377837067 10.9947291355 -13.1882897693
-1(mat) 1440000 -0.268241283699 10.5200875887 -13.0896257278
-1(mat) 1460000 -1.3853075236 10.5513787498 -13.1440142173
-1(mat) 1480000 -1.55984101733 11.4340829129 -13.6026301209
-1(mat) 1500000 -0.770991778399 11.4758488546 -14.5881137222
-1(mat) 1520000 -0.0848245107875 12.2624690808 -14.354289628
-1(mat) 1540000 -0.458643807046 12.5985791771 -13.4701149287
-1(mat) 1560000 -0.810322906201 12.2461643989 -12.3172933413
-1(mat) 1580000 -2.08211172035 12.8886838656 -12.8742007778
-1(mat) 1600000 -3.52093948201 13.1850935438 -12.4118684428`;
-
-describe('3dg reader', () => {
- it('basic', async () => {
- const parsed = await parse3DG(basic3dgString).run();
- expect(parsed.isError).toBe(false);
-
- if (parsed.isError) return;
- const { chromosome, position, x, y, z } = parsed.result.table;
- expect(chromosome.value(0)).toBe('1(mat)');
- expect(position.value(1)).toBe(1440000);
- expect(x.value(5)).toBe(-0.0848245107875);
- expect(y.value(5)).toBe(12.2624690808);
- expect(z.value(5)).toBe(-14.354289628);
- });
-});
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/3dg.ts b/src/mol-model-formats/structure/3dg.ts
deleted file mode 100644
index 18aeab4730f8c4897a90049795fc5136a81784f7..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/3dg.ts
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Task } from '../../mol-task';
-import { ModelFormat } from '../format';
-import { Column, Table } from '../../mol-data/db';
-import { EntityBuilder } from './common/entity';
-import { File3DG } from '../../mol-io/reader/3dg/parser';
-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);
- const entityBuilder = new EntityBuilder();
-
- const seqIdStarts = table.position.toArray({ array: Uint32Array });
- const seqIdEnds = new Uint32Array(table._rowCount);
- const stride = seqIdStarts[1] - seqIdStarts[0];
-
- const objectRadius = stride / 3500;
-
- for (let i = 0, il = table._rowCount; i < il; ++i) {
- const chr = table.chromosome.value(i);
- const entityId = entityBuilder.getEntityId(chr, MoleculeType.DNA, chr);
- entityIds[i] = entityId;
- seqIdEnds[i] = seqIdStarts[i] + stride - 1;
- }
-
- const ihm_sphere_obj_site = Table.ofPartialColumns(BasicSchema.ihm_sphere_obj_site, {
- id: Column.ofIntArray(fillSerial(new Uint32Array(table._rowCount))),
- entity_id: Column.ofStringArray(entityIds),
- seq_id_begin: Column.ofIntArray(seqIdStarts),
- seq_id_end: Column.ofIntArray(seqIdEnds),
- asym_id: table.chromosome,
-
- Cartn_x: Column.ofFloatArray(Column.mapToArray(table.x, x => x * 10, Float32Array)),
- Cartn_y: Column.ofFloatArray(Column.mapToArray(table.y, y => y * 10, Float32Array)),
- Cartn_z: Column.ofFloatArray(Column.mapToArray(table.z, z => z * 10, Float32Array)),
-
- object_radius: Column.ofConst(objectRadius, table._rowCount, Column.Schema.float),
- rmsf: Column.ofConst(0, table._rowCount, Column.Schema.float),
- model_id: Column.ofConst(1, table._rowCount, Column.Schema.int),
- }, table._rowCount);
-
- return createBasic({
- entity: entityBuilder.getEntityTable(),
- ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
- model_id: Column.ofIntArray([1]),
- model_name: Column.ofStringArray(['3DG Model']),
- }, 1),
- ihm_sphere_obj_site
- });
-}
-
-//
-
-export { Format3dg };
-
-type Format3dg = ModelFormat<File3DG>
-
-namespace Format3dg {
- export function is(x: ModelFormat): x is Format3dg {
- return x.kind === '3dg';
- }
-
- export function from3dg(file3dg: File3DG): Format3dg {
- return { kind: '3dg', name: '3DG', data: file3dg };
- }
-}
-
-export function trajectoryFrom3DG(file3dg: File3DG): Task<Trajectory> {
- return Task.create('Parse 3DG', async ctx => {
- const format = Format3dg.from3dg(file3dg);
- const basic = getBasic(file3dg.table);
- return createModels(basic, format, ctx);
- });
-}
diff --git a/src/mol-plugin-state/formats/trajectory.ts b/src/mol-plugin-state/formats/trajectory.ts
index bfeddf182f650e060944be6eefb68a6c3e066716..b0494f01b5c7eeafd0c9c7620c4c58bbad4b332a 100644
--- a/src/mol-plugin-state/formats/trajectory.ts
+++ b/src/mol-plugin-state/formats/trajectory.ts
@@ -113,15 +113,6 @@ export const GroProvider: TrajectoryFormatProvider = {
visuals: defaultVisuals
};
-export const Provider3dg: TrajectoryFormatProvider = {
- label: '3DG',
- description: '3DG',
- category: TrajectoryFormatCategory,
- stringExtensions: ['3dg'],
- parse: directTrajectory(StateTransforms.Model.TrajectoryFrom3DG),
- visuals: defaultVisuals
-};
-
export const MolProvider: TrajectoryFormatProvider = {
label: 'MOL/SDF',
description: 'MOL/SDF',
@@ -146,7 +137,6 @@ export const BuiltInTrajectoryFormats = [
['pdb', PdbProvider] as const,
['pdbqt', PdbqtProvider] as const,
['gro', GroProvider] as const,
- ['3dg', Provider3dg] as const,
['mol', MolProvider] as const,
['mol2', Mol2Provider] as const,
] as const;
diff --git a/src/mol-plugin-state/objects.ts b/src/mol-plugin-state/objects.ts
index 9c3fade63ea32e43f608e5554635389ba94f0f99..403fa9669755c33dd187aa44dc32de8f8f64e82d 100644
--- a/src/mol-plugin-state/objects.ts
+++ b/src/mol-plugin-state/objects.ts
@@ -5,7 +5,6 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { File3DG } from '../mol-io/reader/3dg/parser';
import { Ccp4File } from '../mol-io/reader/ccp4/schema';
import { CifFile } from '../mol-io/reader/cif';
import { DcdFile } from '../mol-io/reader/dcd/parser';
@@ -83,7 +82,6 @@ export namespace PluginStateObject {
{ kind: 'cif', data: CifFile } |
{ kind: 'pdb', data: CifFile } |
{ kind: 'gro', data: CifFile } |
- { kind: '3dg', data: File3DG } |
{ kind: 'dcd', data: DcdFile } |
{ kind: 'ccp4', data: Ccp4File } |
{ kind: 'dsn6', data: Dsn6File } |
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 31bcef917f3a7fa3d432a131323e0411669d4085..a40cd78e5f676953cf9169d2cf2abecb213d153b 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -5,13 +5,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { parse3DG } from '../../mol-io/reader/3dg/parser';
import { parseDcd } from '../../mol-io/reader/dcd/parser';
import { parseGRO } from '../../mol-io/reader/gro/parser';
import { parsePDB } from '../../mol-io/reader/pdb/parser';
import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
import { shapeFromPly } from '../../mol-model-formats/shape/ply';
-import { trajectoryFrom3DG } from '../../mol-model-formats/structure/3dg';
import { coordinatesFromDcd } from '../../mol-model-formats/structure/dcd';
import { trajectoryFromGRO } from '../../mol-model-formats/structure/gro';
import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
@@ -52,7 +50,6 @@ export { TrajectoryFromMOL };
export { TrajectoryFromMOL2 };
export { TrajectoryFromCube };
export { TrajectoryFromCifCore };
-export { TrajectoryFrom3DG };
export { ModelFromTrajectory };
export { StructureFromTrajectory };
export { StructureFromModel };
@@ -339,24 +336,6 @@ const TrajectoryFromCifCore = PluginStateTransform.BuiltIn({
}
});
-type TrajectoryFrom3DG = typeof TrajectoryFrom3DG
-const TrajectoryFrom3DG = PluginStateTransform.BuiltIn({
- name: 'trajectory-from-3dg',
- display: { name: 'Parse 3DG', description: 'Parse 3DG string and create trajectory.' },
- from: [SO.Data.String],
- to: SO.Molecule.Trajectory
-})({
- apply({ a }) {
- return Task.create('Parse 3DG', async ctx => {
- 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 = trajectoryProps(models);
- return new SO.Molecule.Trajectory(models, props);
- });
- }
-});
-
const plus1 = (v: number) => v + 1, minus1 = (v: number) => v - 1;
type ModelFromTrajectory = typeof ModelFromTrajectory
const ModelFromTrajectory = PluginStateTransform.BuiltIn({