Merge pull request #107 from molstar/remove-3dg

remove 3dg in favor of g3d (#93)

src/mol-io/reader/3dg/parser.ts

@@ -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 });
-    });
-}

src/mol-io/reader/_spec/3dg.spec.ts

@@ -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);
-    });
-});

src/mol-model-formats/structure/3dg.ts

@@ -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);
-    });
-}

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;

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 } |

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({