diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index 352bd8a7ea68b7739d38bedbfb660f3438ae5a9d..bae20822d53b91a0b15532b84b2d34809b01da64 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -11,7 +11,7 @@ import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Ingredient, CellPacking, Cell } from './data';
import { getFromPdb, getFromCellPackDB } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../../../mol-model/structure';
-import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
+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';
import { SymmetryOperator } from '../../../../mol-math/geometry';
@@ -28,11 +28,10 @@ import { compile } from '../../../../mol-script/runtime/query/compiler';
import { UniformColorThemeProvider } from '../../../../mol-theme/color/uniform';
import { ThemeRegistryContext } from '../../../../mol-theme/theme';
import { ColorTheme } from '../../../../mol-theme/color';
-import { _parse_mmCif } from '../../../../mol-model-formats/structure/mmcif/parser';
-import { ModelFormat } from '../../../../mol-model-formats/structure/format';
import { CifCategory, CifField } from '../../../../mol-io/reader/cif';
import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
import { Column } from '../../../../mol-data/db';
+import { createModels } from '../../../../mol-model-formats/structure/basic/parser';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`
@@ -124,7 +123,10 @@ function getAssembly(transforms: Mat4[], structure: Structure) {
}
function getCifCurve(name: string, transforms: Mat4[], model: Model) {
- const d = model.sourceData.data.atom_site
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('mmcif source data needed')
+
+ const { db } = model.sourceData.data
+ const d = db.atom_site
const n = d._rowCount
const rowCount = n * transforms.length
@@ -201,8 +203,8 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
}
const categories = {
- entity: CifCategory.ofTable('entity', model.sourceData.data.entity),
- chem_comp: CifCategory.ofTable('chem_comp', model.sourceData.data.chem_comp),
+ entity: CifCategory.ofTable('entity', db.entity),
+ chem_comp: CifCategory.ofTable('chem_comp', db.chem_comp),
atom_site: CifCategory.ofFields('atom_site', _atom_site)
}
@@ -217,8 +219,8 @@ async function getCurve(name: string, transforms: Mat4[], model: Model) {
const cif = getCifCurve(name, transforms, model)
const curveModelTask = Task.create('Curve Model', async ctx => {
- const format = ModelFormat.mmCIF(cif)
- const models = await _parse_mmCif(format, ctx)
+ const format = MmcifFormat.fromFrame(cif)
+ const models = await createModels(format.data.db, format, ctx)
return models[0]
})
diff --git a/src/mol-model-formats/structure/3dg.ts b/src/mol-model-formats/structure/3dg.ts
index f72aff712cfc7d96f4bd3d7a33bd2d30d7942f17..74d5eba815f6560164c043e521319fb44401f6f8 100644
--- a/src/mol-model-formats/structure/3dg.ts
+++ b/src/mol-model-formats/structure/3dg.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,16 +7,15 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { Column } from '../../mol-data/db';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+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';
-function getCategories(table: File3DG['table']) {
+function getBasic(table: File3DG['table']) {
const entityIds = new Array<string>(table._rowCount)
const entityBuilder = new EntityBuilder()
@@ -33,47 +32,52 @@ function getCategories(table: File3DG['table']) {
seqIdEnds[i] = seqIdStarts[i] + stride - 1
}
- const ihm_sphere_obj_site: CifCategory.SomeFields<mmCIF_Schema['ihm_sphere_obj_site']> = {
- id: CifField.ofNumbers(fillSerial(new Uint32Array(table._rowCount))),
- entity_id: CifField.ofStrings(entityIds),
- seq_id_begin: CifField.ofNumbers(seqIdStarts),
- seq_id_end: CifField.ofNumbers(seqIdEnds),
- asym_id: CifField.ofColumn(table.chromosome),
+ 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: CifField.ofNumbers(Column.mapToArray(table.x, x => x * 10, Float32Array)),
- Cartn_y: CifField.ofNumbers(Column.mapToArray(table.y, y => y * 10, Float32Array)),
- Cartn_z: CifField.ofNumbers(Column.mapToArray(table.z, z => z * 10, Float32Array)),
+ 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: CifField.ofColumn(Column.ofConst(objectRadius, table._rowCount, Column.Schema.float)),
- rmsf: CifField.ofColumn(Column.ofConst(0, table._rowCount, Column.Schema.float)),
- model_id: CifField.ofColumn(Column.ofConst(1, table._rowCount, Column.Schema.int)),
- }
+ 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 {
- entity: entityBuilder.getEntityCategory(),
- ihm_model_list: CifCategory.ofFields('ihm_model_list', {
- model_id: CifField.ofNumbers([1]),
- model_name: CifField.ofStrings(['3DG Model']),
- }),
- ihm_sphere_obj_site: CifCategory.ofFields('ihm_sphere_obj_site', ihm_sphere_obj_site)
- }
+ 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
+ })
}
-async function mmCifFrom3dg(file3dg: File3DG) {
- const categories = getCategories(file3dg.table)
+//
+
+export { Format3dg }
- return {
- header: '3DG',
- categoryNames: Object.keys(categories),
- categories
- };
+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<Model.Trajectory> {
return Task.create('Parse 3DG', async ctx => {
- await ctx.update('Converting to mmCIF');
- const cif = await mmCifFrom3dg(file3dg);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = Format3dg.from3dg(file3dg);
+ const basic = getBasic(file3dg.table)
+ return createModels(basic, format, ctx);
})
}
diff --git a/src/mol-model-formats/structure/basic/parser.ts b/src/mol-model-formats/structure/basic/parser.ts
index 6dc6cc2e049eaba45bd9513a5e637b60f9f67c29..cf41cd1866c7c82aef5f6b339cdf6d5f28a8e402 100644
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -22,10 +22,11 @@ import { getProperties } from './properties';
import { getEntities } from './entities';
import { getModelGroupName } from './util';
-export async function _parse_basic(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
+export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
const properties = getProperties(data)
- const isIHM = data.ihm_model_list._rowCount > 0;
- return isIHM ? await readIntegrative(ctx, data, properties, format) : await readStandard(ctx, data, properties, format);
+ return data.ihm_model_list._rowCount > 0
+ ? await readIntegrative(ctx, data, properties, format)
+ : await readStandard(ctx, data, properties, format);
}
/** Standard atomic model */
@@ -87,8 +88,8 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
const label: string[] = []
if (entry) label.push(entry)
- if (format.data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(format.data.struct.title.value(0))
- if (ihm.model_group_name) label.push(ihm.model_name)
+ if (data.struct.title.valueKind(0) === Column.ValueKind.Present) label.push(data.struct.title.value(0))
+ if (ihm.model_name) label.push(ihm.model_name)
if (ihm.model_group_name) label.push(ihm.model_group_name)
return {
diff --git a/src/mol-model-formats/structure/basic/schema.ts b/src/mol-model-formats/structure/basic/schema.ts
index 5b4d2d41728bb932661a00717a2772b12faa1c98..dea7e328e8a9db387542f49ee8c057e7fb9f73aa 100644
--- a/src/mol-model-formats/structure/basic/schema.ts
+++ b/src/mol-model-formats/structure/basic/schema.ts
@@ -7,6 +7,9 @@
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { Table } from '../../../mol-data/db';
+// TODO split into conformation and hierarchy parts
+// TODO extract `pdbx_struct_mod_residue` as property?
+
export type Entry = Table<mmCIF_Schema['entry']>
export type Struct = Table<mmCIF_Schema['struct']>
export type StructAsym = Table<mmCIF_Schema['struct_asym']>
@@ -63,4 +66,16 @@ export interface BasicData {
ihm_sphere_obj_site: IhmSphereObjSite
ihm_gaussian_obj_site: IhmGaussianObjSite
pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues
+}
+
+export function createBasic(data: Partial<BasicData>): BasicData {
+ const basic = Object.create(null)
+ for (const name of Object.keys(BasicSchema)) {
+ if (name in data) {
+ basic[name] = data[name as keyof typeof BasicSchema]
+ } else {
+ basic[name] = Table.ofUndefinedColumns(BasicSchema[name as keyof typeof BasicSchema], 0)
+ }
+ }
+ return basic
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index 30f201b86c2f344560749e26fdd71ecdbb34f46a..483ac6e95369b33506deee7132a663104a8a7b91 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -1,15 +1,14 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { _parse_mmCif } from '../mmcif/parser';
-import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { Table, Column } from '../../../mol-data/db';
import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { WaterNames } from '../../../mol-model/structure/model/types';
import { SetUtils } from '../../../mol-util/set';
+import { BasicSchema } from '../basic/schema';
type Component = Table.Row<Pick<mmCIF_Schema['chem_comp'], 'id' | 'name' | 'type'>>
@@ -137,13 +136,12 @@ export class ComponentBuilder {
return this.get(compId)!
}
- getChemCompCategory() {
- const chemComp: CifCategory.SomeFields<mmCIF_Schema['chem_comp']> = {
- id: CifField.ofStrings(this.ids),
- name: CifField.ofStrings(this.names),
- type: CifField.ofStrings(this.types),
- }
- return CifCategory.ofFields('chem_comp', chemComp)
+ getChemCompTable() {
+ return Table.ofPartialColumns(BasicSchema.chem_comp, {
+ id: Column.ofStringArray(this.ids),
+ name: Column.ofStringArray(this.names),
+ type: Column.ofStringAliasArray(this.types),
+ }, this.ids.length)
}
setNames(names: [string, string][]) {
diff --git a/src/mol-model-formats/structure/common/entity.ts b/src/mol-model-formats/structure/common/entity.ts
index d44fefb2f7f9e7d5117333b80731f81d7181c604..3de2bfefd7c42951082f68b0f654d059d2dba716 100644
--- a/src/mol-model-formats/structure/common/entity.ts
+++ b/src/mol-model-formats/structure/common/entity.ts
@@ -1,20 +1,23 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { CifCategory, CifField } from '../../../mol-io/reader/cif';
import { MoleculeType, isPolymer } from '../../../mol-model/structure/model/types';
-import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+import { Column, Table } from '../../../mol-data/db';
+import { BasicSchema } from '../basic/schema';
export type EntityCompound = { chains: string[], description: string }
+// TODO add support for `branched`
+type EntityType = 'water' | 'polymer' | 'non-polymer'
+
export class EntityBuilder {
private count = 0
private ids: string[] = []
- private types: string[] = []
- private descriptions: string[] = []
+ private types: EntityType[] = []
+ private descriptions: string[][] = []
private compoundsMap = new Map<string, string>()
private namesMap = new Map<string, string>()
@@ -22,11 +25,11 @@ export class EntityBuilder {
private chainMap = new Map<string, string>()
private waterId?: string
- private set(type: string, description: string) {
+ private set(type: EntityType, description: string) {
this.count += 1
this.ids.push(`${this.count}`)
this.types.push(type)
- this.descriptions.push(description)
+ this.descriptions.push([description])
}
getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
@@ -55,13 +58,12 @@ export class EntityBuilder {
}
}
- getEntityCategory() {
- const entity: CifCategory.SomeFields<mmCIF_Schema['entity']> = {
- id: CifField.ofStrings(this.ids),
- type: CifField.ofStrings(this.types),
- pdbx_description: CifField.ofStrings(this.descriptions),
- }
- return CifCategory.ofFields('entity', entity)
+ getEntityTable() {
+ return Table.ofPartialColumns(BasicSchema.entity, {
+ id: Column.ofStringArray(this.ids),
+ type: Column.ofStringAliasArray(this.types),
+ pdbx_description: Column.ofStringListArray(this.descriptions),
+ }, this.count)
}
setCompounds(compounds: EntityCompound[]) {
diff --git a/src/mol-model-formats/structure/format.ts b/src/mol-model-formats/structure/format.ts
index efe82c0df900f2e7aec41bfec39e95cc55e8926c..a3cb77eb5327320f34972b02f43fc71995851534 100644
--- a/src/mol-model-formats/structure/format.ts
+++ b/src/mol-model-formats/structure/format.ts
@@ -5,22 +5,4 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
-import { CIF, CifFrame } from '../../mol-io/reader/cif';
-
-interface Format { readonly kind: string, name: string }
-
-type ModelFormat =
- | ModelFormat.mmCIF
-
-namespace ModelFormat {
- export interface mmCIF extends Format {
- readonly kind: 'mmCIF', data: mmCIF_Database, frame: CifFrame
- }
- export function mmCIF(frame: CifFrame, data?: mmCIF_Database): mmCIF {
- if (!data) data = CIF.schema.mmCIF(frame)
- return { kind: 'mmCIF', name: data._name, data, frame };
- }
-}
-
-export { ModelFormat }
\ No newline at end of file
+export interface ModelFormat<T = unknown> { readonly kind: string, name: string, data: T }
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index 8f141ea1c98305df18e3b54a5dd6ecf64a5b027a..c38beca49164cb7d98d322036b10db9d83a2a316 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,22 +7,21 @@
import { Model } from '../../mol-model/structure/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
import { GroFile, GroAtoms } from '../../mol-io/reader/gro/schema';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { Column } from '../../mol-data/db';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { Column, Table } from '../../mol-data/db';
import { guessElementSymbolString } from './util';
import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { ComponentBuilder } from './common/component';
import { getChainId } from './common/util';
import { EntityBuilder } from './common/entity';
+import { BasicData, BasicSchema, createBasic } from './basic/schema';
+import { createModels } from './basic/parser';
// TODO multi model files
-function getCategories(atoms: GroAtoms) {
- const auth_atom_id = CifField.ofColumn(atoms.atomName)
- const auth_comp_id = CifField.ofColumn(atoms.residueName)
+function getBasic(atoms: GroAtoms): BasicData {
+ const auth_atom_id = atoms.atomName
+ const auth_comp_id = atoms.residueName
const entityIds = new Array<string>(atoms.count)
const asymIds = new Array<string>(atoms.count)
@@ -69,57 +68,57 @@ function getCategories(atoms: GroAtoms) {
ids[i] = i
}
- const auth_asym_id = CifField.ofColumn(Column.ofStringArray(asymIds))
+ const auth_asym_id = Column.ofStringArray(asymIds)
- const atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+ const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id,
auth_atom_id,
auth_comp_id,
- auth_seq_id: CifField.ofColumn(atoms.residueNumber),
- B_iso_or_equiv: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_x: CifField.ofNumbers(Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
- Cartn_y: CifField.ofNumbers(Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
- Cartn_z: CifField.ofNumbers(Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
- group_PDB: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- id: CifField.ofColumn(Column.ofIntArray(ids)),
-
- label_alt_id: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
+ auth_seq_id: atoms.residueNumber,
+ Cartn_x: Column.ofFloatArray(Column.mapToArray(atoms.x, x => x * 10, Float32Array)),
+ Cartn_y: Column.ofFloatArray(Column.mapToArray(atoms.y, y => y * 10, Float32Array)),
+ Cartn_z: Column.ofFloatArray(Column.mapToArray(atoms.z, z => z * 10, Float32Array)),
+ id: Column.ofIntArray(ids),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
- label_seq_id: CifField.ofColumn(Column.ofIntArray(seqIds)),
- label_entity_id: CifField.ofColumn(Column.ofStringArray(entityIds)),
+ label_seq_id: Column.ofIntArray(seqIds),
+ label_entity_id: Column.ofStringArray(entityIds),
- occupancy: CifField.ofColumn(Column.ofConst(1, atoms.count, Column.Schema.float)),
- type_symbol: CifField.ofStrings(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+ occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+ type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
- pdbx_PDB_ins_code: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
- }
+ pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+ }, atoms.count)
- return {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
- atom_site: CifCategory.ofFields('atom_site', atom_site)
- }
+ return createBasic({
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
+ atom_site
+ })
}
-function groToMmCif(gro: GroFile) {
- const categories = getCategories(gro.structures[0].atoms)
+//
+
+export { GroFormat }
- return {
- header: gro.structures[0].header.title,
- categoryNames: Object.keys(categories),
- categories
- };
+type GroFormat = ModelFormat<GroFile>
+
+namespace GroFormat {
+ export function is(x: ModelFormat): x is GroFormat {
+ return x.kind === 'gro'
+ }
+
+ export function fromGro(gro: GroFile): GroFormat {
+ return { kind: 'gro', name: gro.structures[0].header.title, data: gro };
+ }
}
export function trajectoryFromGRO(gro: GroFile): Task<Model.Trajectory> {
return Task.create('Parse GRO', async ctx => {
- await ctx.update('Converting to mmCIF');
- const cif = groToMmCif(gro);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = GroFormat.fromGro(gro);
+ const basic = getBasic(gro.structures[0].atoms)
+ return createModels(basic, format, ctx);
})
}
diff --git a/src/mol-model-formats/structure/mmcif.ts b/src/mol-model-formats/structure/mmcif.ts
index ea8c6de0653c21bb9f0542f25e4fa69123be5462..d52f7898ce97b0431e80ea59a6e726efa58e3660 100644
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,9 +8,90 @@
import { Model } from '../../mol-model/structure/model/model';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
-import { CifFrame } from '../../mol-io/reader/cif';
+import { CifFrame, CIF } from '../../mol-io/reader/cif';
+import { mmCIF_Database, mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
+import { createModels } from './basic/parser';
+import { ModelSymmetry } from './property/symmetry';
+import { ModelSecondaryStructure } from './property/secondary-structure';
+import { Table } from '../../mol-data/db';
+import { AtomSiteAnisotrop } from './property/anisotropic';
+import { ComponentBond } from './property/bonds/comp';
+import { StructConn } from './property/bonds/struct_conn';
+import { ModelCrossLinkRestraint } from './property/pair-restraints/cross-links';
+
+function modelSymmetryFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ return ModelSymmetry.fromData(model.sourceData.data.db)
+}
+ModelSymmetry.Provider.formatRegistry.add('mmCIF', modelSymmetryFromMmcif)
+
+function secondaryStructureFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { struct_conf, struct_sheet_range } = model.sourceData.data.db
+ return ModelSecondaryStructure.fromStruct(struct_conf, struct_sheet_range, model.atomicHierarchy)
+}
+ModelSecondaryStructure.Provider.formatRegistry.add('mmCIF', secondaryStructureFromMmcif)
+
+function atomSiteAnisotropFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { atom_site_anisotrop } = model.sourceData.data.db
+ const data = Table.ofColumns(mmCIF_Schema['atom_site_anisotrop'], atom_site_anisotrop);
+ const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model, data)
+ return { data, elementToAnsiotrop }
+}
+AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif)
+
+function componentBondFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { chem_comp_bond } = model.sourceData.data.db;
+ if (chem_comp_bond._rowCount === 0) return;
+ return {
+ data: chem_comp_bond,
+ entries: ComponentBond.getEntriesFromChemCompBond(chem_comp_bond)
+ }
+}
+ComponentBond.Provider.formatRegistry.add('mmCIF', componentBondFromMmcif)
+
+function structConnFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { struct_conn } = model.sourceData.data.db;
+ if (struct_conn._rowCount === 0) return;
+ const entries = StructConn.getEntriesFromStructConn(struct_conn, model)
+ return {
+ data: struct_conn,
+ byAtomIndex: StructConn.getAtomIndexFromEntries(entries),
+ entries,
+ }
+}
+StructConn.Provider.formatRegistry.add('mmCIF', structConnFromMmcif)
+
+function crossLinkRestraintFromMmcif(model: Model) {
+ if (!MmcifFormat.is(model.sourceData)) return;
+ const { ihm_cross_link_restraint } = model.sourceData.data.db;
+ if (ihm_cross_link_restraint._rowCount === 0) return;
+ return ModelCrossLinkRestraint.fromTable(ihm_cross_link_restraint, model)
+}
+ModelCrossLinkRestraint.Provider.formatRegistry.add('mmCIF', crossLinkRestraintFromMmcif)
+
+//
+
+export { MmcifFormat }
+
+type MmcifFormat = ModelFormat<MmcifFormat.Data>
+
+namespace MmcifFormat {
+ export type Data = { db: mmCIF_Database, frame: CifFrame }
+ export function is(x: ModelFormat): x is MmcifFormat {
+ return x.kind === 'mmCIF'
+ }
+
+ export function fromFrame(frame: CifFrame, db?: mmCIF_Database): MmcifFormat {
+ if (!db) db = CIF.schema.mmCIF(frame)
+ return { kind: 'mmCIF', name: db._name, data: { db, frame } };
+ }
+}
export function trajectoryFromMmCIF(frame: CifFrame): Task<Model.Trajectory> {
- return Task.create('Create mmCIF Model', ctx => _parse_mmCif(ModelFormat.mmCIF(frame), ctx));
+ 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/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
deleted file mode 100644
index cbe1f50e134cdade04ed1ef90f5e0addc556587d..0000000000000000000000000000000000000000
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ /dev/null
@@ -1,78 +0,0 @@
-/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Table } from '../../../mol-data/db';
-import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { RuntimeContext } from '../../../mol-task';
-import { Model } from '../../../mol-model/structure/model/model';
-import { ModelFormat } from '../format';
-import mmCIF_Format = ModelFormat.mmCIF
-import { AtomSiteAnisotrop } from '../property/anisotropic';
-import { _parse_basic } from '../basic/parser';
-import { ModelSymmetry } from '../property/symmetry';
-import { ModelSecondaryStructure } from '../property/secondary-structure';
-import { ComponentBond } from '../property/bonds/comp';
-import { StructConn } from '../property/bonds/struct_conn';
-import { ModelCrossLinkRestraint } from '../property/pair-restraints/cross-links';
-
-export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
- return _parse_basic(format.data, format, ctx)
-}
-
-function modelSymmetryFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- return ModelSymmetry.fromData(model.sourceData.data)
-}
-ModelSymmetry.Provider.formatRegistry.add('mmCIF', modelSymmetryFromMmcif)
-
-function secondaryStructureFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- const { struct_conf, struct_sheet_range } = model.sourceData.data
- return ModelSecondaryStructure.fromStruct(struct_conf, struct_sheet_range, model.atomicHierarchy)
-}
-ModelSecondaryStructure.Provider.formatRegistry.add('mmCIF', secondaryStructureFromMmcif)
-
-function atomSiteAnisotropFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- const { atom_site_anisotrop } = model.sourceData.data
- const data = Table.ofColumns(mmCIF_Schema['atom_site_anisotrop'], atom_site_anisotrop);
- const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model, data)
- return { data, elementToAnsiotrop }
-}
-AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif)
-
-function componentBondFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- const { chem_comp_bond } = model.sourceData.data;
- if (chem_comp_bond._rowCount === 0) return;
- return {
- data: chem_comp_bond,
- entries: ComponentBond.getEntriesFromChemCompBond(chem_comp_bond)
- }
-}
-ComponentBond.Provider.formatRegistry.add('mmCIF', componentBondFromMmcif)
-
-function structConnFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- const { struct_conn } = model.sourceData.data;
- if (struct_conn._rowCount === 0) return;
- const entries = StructConn.getEntriesFromStructConn(struct_conn, model)
- return {
- data: struct_conn,
- byAtomIndex: StructConn.getAtomIndexFromEntries(entries),
- entries,
- }
-}
-StructConn.Provider.formatRegistry.add('mmCIF', structConnFromMmcif)
-
-function crossLinkRestraintFromMmcif(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') return;
- const { ihm_cross_link_restraint } = model.sourceData.data;
- if (ihm_cross_link_restraint._rowCount === 0) return;
- return ModelCrossLinkRestraint.fromTable(ihm_cross_link_restraint, model)
-}
-ModelCrossLinkRestraint.Provider.formatRegistry.add('mmCIF', crossLinkRestraintFromMmcif)
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/pdb.ts b/src/mol-model-formats/structure/pdb.ts
index 525ec39cccfa76c405fbb2d44b231b213ab0a946..c77392ec26435bf213bec83521a7f74f95836c17 100644
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.ts
@@ -1,21 +1,22 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
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 { ModelFormat } from './format';
-import { _parse_mmCif } from './mmcif/parser';
+import { MmcifFormat } from './mmcif';
+import { createModels } from './basic/parser';
export function trajectoryFromPDB(pdb: PdbFile): Task<Model.Trajectory> {
return Task.create('Parse PDB', async ctx => {
await ctx.update('Converting to mmCIF');
const cif = await pdbToMmCif(pdb);
- const format = ModelFormat.mmCIF(cif);
- return _parse_mmCif(format, ctx);
+ const format = MmcifFormat.fromFrame(cif)
+ return createModels(format.data.db, format, ctx)
})
}
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index cf967d4359bbb2a6437f4973a3eb3a20069646b8..05e0f8592689d7a48a0d44b3cac74e06f83284d5 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -162,8 +162,8 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
const categories = {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
atom_site: CifCategory.ofFields('atom_site', getAtomSite(atomSite)),
atom_site_anisotrop: CifCategory.ofFields('atom_site_anisotrop', getAnisotropic(anisotropic))
} as any;
diff --git a/src/mol-model-formats/structure/psf.ts b/src/mol-model-formats/structure/psf.ts
index ab4eae3e12a7c9c2a7d441f554fbe9d9b80dc59d..88e5a53d64a8e3f6dfdf798b15f8e61f580dccbf 100644
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -1,26 +1,24 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { PsfFile } from '../../mol-io/reader/psf/parser';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
-import { Column } from '../../mol-data/db';
+import { Column, Table } from '../../mol-data/db';
import { EntityBuilder } from './common/entity';
import { ComponentBuilder } from './common/component';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
import { guessElementSymbolString } from './util';
import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { getChainId } from './common/util';
import { Task } from '../../mol-task';
import { ModelFormat } from './format';
import { Topology } from '../../mol-model/structure/topology/topology';
+import { createBasic, BasicSchema } from './basic/schema';
-// TODO: shares most of the code with ./gro.ts#getCategories
-function getCategories(atoms: PsfFile['atoms']) {
- const auth_atom_id = CifField.ofColumn(atoms.atomName)
- const auth_comp_id = CifField.ofColumn(atoms.residueName)
+function getBasic(atoms: PsfFile['atoms']) {
+ const auth_atom_id = atoms.atomName
+ const auth_comp_id = atoms.residueName
const entityIds = new Array<string>(atoms.count)
const asymIds = new Array<string>(atoms.count)
@@ -62,57 +60,54 @@ function getCategories(atoms: PsfFile['atoms']) {
ids[i] = i
}
- const auth_asym_id = CifField.ofColumn(Column.ofStringArray(asymIds))
+ const auth_asym_id = Column.ofStringArray(asymIds)
- const atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+ const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
auth_asym_id,
auth_atom_id,
auth_comp_id,
- auth_seq_id: CifField.ofColumn(atoms.residueId),
- B_iso_or_equiv: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_x: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_y: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- Cartn_z: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.float)),
- group_PDB: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- id: CifField.ofColumn(Column.ofIntArray(ids)),
-
- label_alt_id: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
+ auth_seq_id: atoms.residueId,
+ id: Column.ofIntArray(ids),
label_asym_id: auth_asym_id,
label_atom_id: auth_atom_id,
label_comp_id: auth_comp_id,
- label_seq_id: CifField.ofColumn(Column.ofIntArray(seqIds)),
- label_entity_id: CifField.ofColumn(Column.ofStringArray(entityIds)),
+ label_seq_id: Column.ofIntArray(seqIds),
+ label_entity_id: Column.ofStringArray(entityIds),
- occupancy: CifField.ofColumn(Column.ofConst(1, atoms.count, Column.Schema.float)),
- type_symbol: CifField.ofStrings(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+ occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
+ type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
- pdbx_PDB_ins_code: CifField.ofColumn(Column.Undefined(atoms.count, Column.Schema.str)),
- pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst('1', atoms.count, Column.Schema.str)),
- }
+ pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
+ }, atoms.count)
- return {
- entity: entityBuilder.getEntityCategory(),
- chem_comp: componentBuilder.getChemCompCategory(),
- atom_site: CifCategory.ofFields('atom_site', atom_site)
- }
+ return createBasic({
+ entity: entityBuilder.getEntityTable(),
+ chem_comp: componentBuilder.getChemCompTable(),
+ atom_site
+ })
}
-function psfToMmCif(psf: PsfFile) {
- const categories = getCategories(psf.atoms)
+//
+
+export { PsfFormat }
- return {
- header: psf.id,
- categoryNames: Object.keys(categories),
- categories
- };
+type PsfFormat = ModelFormat<PsfFile>
+
+namespace PsfFormat {
+ export function is(x: ModelFormat): x is PsfFormat {
+ return x.kind === 'psf'
+ }
+
+ export function fromPsf(psf: PsfFile): PsfFormat {
+ return { kind: 'psf', name: psf.id, data: psf };
+ }
}
export function topologyFromPsf(psf: PsfFile): Task<Topology> {
return Task.create('Parse PSF', async ctx => {
- const label = psf.id
- const cif = psfToMmCif(psf);
- const format = ModelFormat.mmCIF(cif);
+ const format = PsfFormat.fromPsf(psf);
+ const basic = getBasic(psf.atoms)
const { atomIdA, atomIdB } = psf.bonds
@@ -130,6 +125,6 @@ export function topologyFromPsf(psf: PsfFile): Task<Topology> {
order: Column.ofConst(1, psf.bonds.count, Column.Schema.int)
}
- return Topology.create(label, format, bonds)
+ return Topology.create(psf.id, basic, bonds, format)
})
}
\ No newline at end of file
diff --git a/src/mol-model-props/common/wrapper.ts b/src/mol-model-props/common/wrapper.ts
index 21c57e124e18ad5ab3193eb9a67774cc8a0abd51..7f3523515dbfc88602fe798e05c7a6c79328b8f0 100644
--- a/src/mol-model-props/common/wrapper.ts
+++ b/src/mol-model-props/common/wrapper.ts
@@ -7,6 +7,7 @@
import { CifWriter } from '../../mol-io/writer/cif';
import { Model } from '../../mol-model/structure';
import { dateToUtcString } from '../../mol-util/date';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
interface PropertyWrapper<Data> {
info: PropertyWrapper.Info,
@@ -40,11 +41,11 @@ namespace PropertyWrapper {
];
export function tryGetInfoFromCif(categoryName: string, model: Model): Info | undefined {
- if (model.sourceData.kind !== 'mmCIF' || !model.sourceData.frame.categoryNames.includes(categoryName)) {
+ if (!MmcifFormat.is(model.sourceData) || !model.sourceData.data.frame.categoryNames.includes(categoryName)) {
return;
}
- const timestampField = model.sourceData.frame.categories[categoryName].getField('updated_datetime_utc');
+ const timestampField = model.sourceData.data.frame.categories[categoryName].getField('updated_datetime_utc');
if (!timestampField || timestampField.rowCount === 0) return;
return { timestamp_utc: timestampField.str(0) || dateToUtcString(new Date()) };
diff --git a/src/mol-model-props/computed/secondary-structure.ts b/src/mol-model-props/computed/secondary-structure.ts
index 40015d7d0e999271e802b7a0bb1883809fb7f8dc..d80c58b383b9a8725daed90eb9632203986e2f17 100644
--- a/src/mol-model-props/computed/secondary-structure.ts
+++ b/src/mol-model-props/computed/secondary-structure.ts
@@ -12,6 +12,7 @@ import { Unit } from '../../mol-model/structure/structure';
import { CustomStructureProperty } from '../common/custom-structure-property';
import { CustomProperty } from '../common/custom-property';
import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
function getSecondaryStructureParams(data?: Structure) {
let defaultType = 'mmcif' as 'mmcif' | 'dssp'
@@ -19,10 +20,10 @@ function getSecondaryStructureParams(data?: Structure) {
defaultType = 'dssp'
for (let i = 0, il = data.models.length; i < il; ++i) {
const m = data.models[i]
- if (m.sourceData.kind === 'mmCIF') {
- if (data.model.sourceData.data.struct_conf.id.isDefined ||
- data.model.sourceData.data.struct_sheet_range.id.isDefined ||
- data.model.sourceData.data.database_2.database_id.isDefined
+ if (MmcifFormat.is(m.sourceData)) {
+ if (m.sourceData.data.db.struct_conf.id.isDefined ||
+ m.sourceData.data.db.struct_sheet_range.id.isDefined ||
+ m.sourceData.data.db.database_2.database_id.isDefined
) {
// if there is any secondary structure definition given or if there is
// an archival model, don't calculate dssp by default
diff --git a/src/mol-model-props/pdbe/preferred-assembly.ts b/src/mol-model-props/pdbe/preferred-assembly.ts
index f156953280d95914287c3aa286eca830241452a5..ebc7fb081c24c9e50396450f84618f0a06a09b99 100644
--- a/src/mol-model-props/pdbe/preferred-assembly.ts
+++ b/src/mol-model-props/pdbe/preferred-assembly.ts
@@ -9,6 +9,7 @@ import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export namespace PDBePreferredAssembly {
export type Property = string
@@ -47,8 +48,8 @@ export namespace PDBePreferredAssembly {
});
function fromCifData(model: Model): string | undefined {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const cat = model.sourceData.frame.categories.pdbe_preferred_assembly;
+ if (!MmcifFormat.is(model.sourceData)) return void 0;
+ const cat = model.sourceData.data.frame.categories.pdbe_preferred_assembly;
if (!cat) return void 0;
return toTable(Schema.pdbe_preferred_assembly, cat).assembly_id.value(0) || getFirstFromModel(model);
}
diff --git a/src/mol-model-props/pdbe/struct-ref-domain.ts b/src/mol-model-props/pdbe/struct-ref-domain.ts
index 54a31131e8e6ecd75134ea49a17227dbda57b06b..db37fee7e8412b3d06e7f5e587aea9822483ebe9 100644
--- a/src/mol-model-props/pdbe/struct-ref-domain.ts
+++ b/src/mol-model-props/pdbe/struct-ref-domain.ts
@@ -9,6 +9,7 @@ import { toTable } from '../../mol-io/reader/cif/schema';
import { CifWriter } from '../../mol-io/writer/cif';
import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
import { PropertyWrapper } from '../common/wrapper';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export namespace PDBeStructRefDomain {
export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>
@@ -57,8 +58,8 @@ export namespace PDBeStructRefDomain {
});
function fromCifData(model: Model): Property['data'] {
- if (model.sourceData.kind !== 'mmCIF') return void 0;
- const cat = model.sourceData.frame.categories.pdbe_struct_ref_domain;
+ if (!MmcifFormat.is(model.sourceData)) return void 0;
+ const cat = model.sourceData.data.frame.categories.pdbe_struct_ref_domain;
if (!cat) return void 0;
return toTable(Schema.pdbe_struct_ref_domain, cat);
}
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 84bf3344aeae8a873ee1665a64bfa8c6cc4a5011..e153de014ba3749c37f0700edb55b9f0a01698b3 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -20,6 +20,7 @@ import { CustomModelProperty } from '../common/custom-model-property';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
import { CustomProperty } from '../common/custom-property';
import { arraySetAdd } from '../../mol-util/array';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export { StructureQualityReport }
@@ -37,8 +38,8 @@ namespace StructureQualityReport {
export function isApplicable(model?: Model): boolean {
return (
!!model &&
- model.sourceData.kind === 'mmCIF' &&
- (model.sourceData.data.database_2.database_id.isDefined ||
+ MmcifFormat.is(model.sourceData) &&
+ (model.sourceData.data.db.database_2.database_id.isDefined ||
model.entryId.length === 4)
)
}
@@ -103,10 +104,10 @@ namespace StructureQualityReport {
}
function getCifData(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.');
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF.');
return {
- residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues),
- groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.frame.categories.pdbe_structure_quality_report_issue_types),
+ residues: toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issues),
+ groups: toTable(Schema.pdbe_structure_quality_report_issue_types, model.sourceData.data.frame.categories.pdbe_structure_quality_report_issue_types),
}
}
}
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index 562ad1bb4bcbb2f657c742d31af02b9d8da39077..6dce3e871e3ebd414256ecc7fb2af5825fe524f6 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -14,6 +14,7 @@ import { GraphQLClient } from '../../mol-util/graphql-client';
import { CustomProperty } from '../common/custom-property';
import { NonNullableArray } from '../../mol-util/type-helpers';
import { CustomStructureProperty } from '../common/custom-structure-property';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
const BiologicalAssemblyNames = new Set([
'author_and_software_defined_assembly',
@@ -29,11 +30,11 @@ export namespace AssemblySymmetry {
export function isApplicable(structure?: Structure): boolean {
// check if structure is from pdb entry
- if (!structure || structure.models.length !== 1 || structure.models[0].sourceData.kind !== 'mmCIF' || (!structure.models[0].sourceData.data.database_2.database_id.isDefined &&
+ if (!structure || structure.models.length !== 1 || !MmcifFormat.is(structure.models[0].sourceData) || (!structure.models[0].sourceData.data.db.database_2.database_id.isDefined &&
structure.models[0].entryId.length !== 4)) return false
// check if assembly is 'biological'
- const mmcif = structure.models[0].sourceData.data
+ const mmcif = structure.models[0].sourceData.data.db
if (!mmcif.pdbx_struct_assembly.details.isDefined) return false
const id = structure.units[0].conformation.operator.assembly.id
const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id)
diff --git a/src/mol-model-props/rcsb/validation-report.ts b/src/mol-model-props/rcsb/validation-report.ts
index c2a2b054f8dab317d739a391fef2823b56658b0f..ada844656b5fd832507d19efae31e330cbe3d98c 100644
--- a/src/mol-model-props/rcsb/validation-report.ts
+++ b/src/mol-model-props/rcsb/validation-report.ts
@@ -18,6 +18,7 @@ import { IntMap, SortedArray } from '../../mol-data/int';
import { arrayMax } from '../../mol-util/array';
import { equalEps } from '../../mol-math/linear-algebra/3d/common';
import { Vec3 } from '../../mol-math/linear-algebra';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
export { ValidationReport }
@@ -90,8 +91,8 @@ namespace ValidationReport {
export function isApplicable(model?: Model): boolean {
return (
!!model &&
- model.sourceData.kind === 'mmCIF' &&
- (model.sourceData.data.database_2.database_id.isDefined ||
+ MmcifFormat.is(model.sourceData) &&
+ (model.sourceData.data.db.database_2.database_id.isDefined ||
model.entryId.length === 4)
)
}
diff --git a/src/mol-model/structure/export/categories/utils.ts b/src/mol-model/structure/export/categories/utils.ts
index 091e92172dcbfeefa10bb7e069c717103474a05a..4f500efbf56d9dfe93322614ca74b4b1d1958e47 100644
--- a/src/mol-model/structure/export/categories/utils.ts
+++ b/src/mol-model/structure/export/categories/utils.ts
@@ -13,10 +13,11 @@ import { UniqueArray } from '../../../../mol-data/generic';
import { sortArray } from '../../../../mol-data/util';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { CifExportContext } from '../mmcif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
- if (model.sourceData.kind !== 'mmCIF') return;
- return model.sourceData.data[name];
+ if (!MmcifFormat.is(model.sourceData)) return;
+ return model.sourceData.data.db[name];
}
export function getUniqueResidueNamesFromStructures(structures: Structure[]) {
@@ -50,9 +51,9 @@ export function copy_mmCif_category(name: keyof mmCIF_Schema, condition?: (struc
if (condition && !condition(structures[0])) return CifWriter.Category.Empty;
const model = structures[0].model;
- if (model.sourceData.kind !== 'mmCIF') return CifWriter.Category.Empty;
+ if (!MmcifFormat.is(model.sourceData)) return CifWriter.Category.Empty;
- const table = model.sourceData.data[name];
+ const table = model.sourceData.data.db[name];
if (!table || !table._rowCount) return CifWriter.Category.Empty;
return CifWriter.Category.ofTable(table);
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 0fe77b75e9bd9f7a52517b5d9af6de3c82edbc36..04dd2a0dd482c28713a5bb4c68686bf244752153 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -18,9 +18,9 @@ import { Vec3 } from '../../../mol-math/linear-algebra';
import { Mutable } from '../../../mol-util/type-helpers';
import { Coordinates } from '../coordinates';
import { Topology } from '../topology';
-import { _parse_mmCif } from '../../../mol-model-formats/structure/mmcif/parser';
import { Task } from '../../../mol-task';
import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
+import { createModels } from '../../../mol-model-formats/structure/basic/parser';
/**
* Interface to the "source data" of the molecule.
@@ -107,7 +107,7 @@ export namespace Model {
export function trajectoryFromTopologyAndCoordinates(topology: Topology, coordinates: Coordinates): Task<Trajectory> {
return Task.create('Create Trajectory', async ctx => {
- const model = (await _parse_mmCif(topology.format, ctx))[0];
+ const model = (await createModels(topology.basic, topology.sourceData, ctx))[0];
if (!model) throw new Error('found no model')
const trajectory = trajectoryFromModelAndCoordinates(model, coordinates)
const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount }
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index ec2cef78ee5d63986e7a0a1943be96dca50a2205..48ab835a516d3c50613ad4e5004389db0f6d53a8 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -62,7 +62,7 @@ function _compId(l: StructureElement.Location) {
function compId(l: StructureElement.Location) {
if (!Unit.isAtomic(l.unit)) notAtomic()
if (!hasMicroheterogeneity(l)) return _compId(l)
- return l.unit.model.sourceData.data.atom_site.label_comp_id.value(l.element)
+ return l.unit.model.atomicHierarchy.residues.label_comp_id.value(l.unit.residueIndex[l.element])
}
function seqId(l: StructureElement.Location) {
diff --git a/src/mol-model/structure/topology/topology.ts b/src/mol-model/structure/topology/topology.ts
index d5e6dbac27cde544ce95dc6784bbb880a2eeab67..6ef843f72f937e518baaa489571ca361759bc377 100644
--- a/src/mol-model/structure/topology/topology.ts
+++ b/src/mol-model/structure/topology/topology.ts
@@ -1,11 +1,12 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { UUID } from '../../../mol-util';
import { Column } from '../../../mol-data/db';
+import { BasicData } from '../../../mol-model-formats/structure/basic/schema';
import { ModelFormat } from '../../../mol-model-formats/structure/format';
export { Topology }
@@ -14,7 +15,8 @@ interface Topology {
readonly id: UUID
readonly label: string
- readonly format: ModelFormat
+ readonly basic: BasicData
+ readonly sourceData: ModelFormat
readonly bonds: {
readonly indexA: Column<number>,
@@ -47,11 +49,12 @@ interface Topology {
}
namespace Topology {
- export function create(label: string, format: ModelFormat, bonds: Topology['bonds']): Topology {
+ export function create(label: string, basic: BasicData, bonds: Topology['bonds'], format: ModelFormat): Topology {
return {
id: UUID.create22(),
label,
- format,
+ basic,
+ sourceData: format,
bonds
}
}
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
index ea703fe3691773819183ba7f215374de547d1af7..0f1d5ecca749050a9ef7e3f7e0aa388d53e21dd5 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -9,30 +9,31 @@ import { Structure, Model } from '../../../../mol-model/structure';
import { VolumeServerInfo } from './model';
import { PluginContext } from '../../../../mol-plugin/context';
import { RuntimeContext } from '../../../../mol-task';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.Kind = 'x-ray'): VolumeServerInfo.Kind {
if (!s) return defaultKind;
const model = s.models[0];
- if (model.sourceData.kind !== 'mmCIF') return defaultKind;
+ if (!MmcifFormat.is(model.sourceData)) return defaultKind;
- const { data } = model.sourceData;
+ const { db } = model.sourceData.data;
// prefer EMDB entries over structure-factors (SF) e.g. for 'ELECTRON CRYSTALLOGRAPHY' entries
// like 6axz or 6kj3 for which EMDB entries are available but map calculation from SF is hard
- for (let i = 0, il = data.pdbx_database_related._rowCount; i < il; ++i) {
- if (data.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
+ for (let i = 0, il = db.pdbx_database_related._rowCount; i < il; ++i) {
+ if (db.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
return 'em'
}
}
- if (data.pdbx_database_status.status_code_sf.isDefined && data.pdbx_database_status.status_code_sf.value(0) === 'REL') {
+ if (db.pdbx_database_status.status_code_sf.isDefined && db.pdbx_database_status.status_code_sf.value(0) === 'REL') {
return 'x-ray'
}
// fallbacks
- for (let i = 0; i < data.exptl.method.rowCount; i++) {
- const v = data.exptl.method.value(i).toUpperCase();
+ for (let i = 0; i < db.exptl.method.rowCount; i++) {
+ const v = db.exptl.method.value(i).toUpperCase();
if (v.indexOf('MICROSCOPY') >= 0) return 'em';
}
return defaultKind;
@@ -41,9 +42,9 @@ export function getStreamingMethod(s?: Structure, defaultKind: VolumeServerInfo.
/** Returns EMD ID when available, otherwise falls back to PDB ID */
export function getEmIds(model: Model): string[] {
const ids: string[] = []
- if (model.sourceData.kind !== 'mmCIF') return [ model.entryId ]
+ if (!MmcifFormat.is(model.sourceData)) return [ model.entryId ]
- const { db_id, db_name, content_type } = model.sourceData.data.pdbx_database_related
+ const { db_id, db_name, content_type } = model.sourceData.data.db.pdbx_database_related
if (!db_name.isDefined) return [ model.entryId ]
for (let i = 0, il = db_name.rowCount; i < il; ++i) {
diff --git a/src/mol-theme/color/entity-source.ts b/src/mol-theme/color/entity-source.ts
index c38d9f14a2776eaf61953b61bc99816856bed500..3e94e70ed7f33ba312240bfd19de769bfc12a812 100644
--- a/src/mol-theme/color/entity-source.ts
+++ b/src/mol-theme/color/entity-source.ts
@@ -16,6 +16,7 @@ import { getPaletteParams, getPalette } from '../../mol-util/color/palette';
import { TableLegend, ScaleLegend } from '../../mol-util/legend';
import { isInteger } from '../../mol-util/number';
import { ColorLists } from '../../mol-util/color/lists';
+import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
const DefaultList = 'dark-2'
const DefaultColor = Color(0xFAFAFA)
@@ -100,8 +101,8 @@ function getMaps(models: ReadonlyArray<Model>) {
for (let i = 0, il = models.length; i <il; ++i) {
const m = models[i]
- if (m.sourceData.kind !== 'mmCIF') continue
- const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
+ if (!MmcifFormat.is(m.sourceData)) continue
+ const { entity_src_gen, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data.db
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_scientific_name, entity_src_gen.plasmid_name, entity_src_gen.pdbx_gene_src_gene)
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat, entity_src_nat.pdbx_organism_scientific, entity_src_nat.pdbx_plasmid_name)
addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn, pdbx_entity_src_syn.organism_scientific)
diff --git a/src/mol-theme/color/uncertainty.ts b/src/mol-theme/color/uncertainty.ts
index b715369f10fb8db503a5c89c3745a07b8382e44d..d7511cb0533f6554bf50d9d92797ef1b0df223f5 100644
--- a/src/mol-theme/color/uncertainty.ts
+++ b/src/mol-theme/color/uncertainty.ts
@@ -67,5 +67,5 @@ export const UncertaintyColorThemeProvider: ColorTheme.Provider<UncertaintyColor
factory: UncertaintyColorTheme,
getParams: getUncertaintyColorThemeParams,
defaultValues: PD.getDefaultValues(UncertaintyColorThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.sourceData.data.ihm_sphere_obj_site.rmsf.isDefined)
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
}
\ No newline at end of file
diff --git a/src/mol-theme/size/uncertainty.ts b/src/mol-theme/size/uncertainty.ts
index 78e4dc41c8d915d8904b8c3c4d6bb47696dfe122..5f9da065b4b8331ac620db16e6e4b806446ac176 100644
--- a/src/mol-theme/size/uncertainty.ts
+++ b/src/mol-theme/size/uncertainty.ts
@@ -57,5 +57,5 @@ export const UncertaintySizeThemeProvider: SizeTheme.Provider<UncertaintySizeThe
factory: UncertaintySizeTheme,
getParams: getUncertaintySizeThemeParams,
defaultValues: PD.getDefaultValues(UncertaintySizeThemeParams),
- isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.sourceData.data.ihm_sphere_obj_site.rmsf.isDefined)
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => m.atomicConformation.B_iso_or_equiv.isDefined || m.coarseHierarchy.isDefined)
}
\ No newline at end of file
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 8df122b3e8f708a35d22e50f4ddf8ce927e34a9d..c4f7c19b319e039d08a2220ef925fc05b1cab758 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -7,7 +7,7 @@ import { Structure } from '../mol-model/structure'
import { GridLookup3D } from '../mol-math/geometry';
// import { sortArray } from 'mol-data/util';
import { OrderedSet } from '../mol-data/int';
-import { trajectoryFromMmCIF } from '../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure/mmcif';
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
@@ -35,14 +35,14 @@ export async function readCIF(path: string) {
const models = await trajectoryFromMmCIF(parsed.result.blocks[0]).run();
const structures = models.map(Structure.ofModel);
- return { mmcif: models[0].sourceData.data, models, structures };
+ return { mmcif: models[0].sourceData.data as MmcifFormat.Data, models, structures };
}
export async function test() {
const { mmcif, structures } = await readCIF('e:/test/quick/1tqn_updated.cif');
- const lookup = GridLookup3D({ x: mmcif.atom_site.Cartn_x.toArray(), y: mmcif.atom_site.Cartn_y.toArray(), z: mmcif.atom_site.Cartn_z.toArray(),
- indices: OrderedSet.ofBounds(0, mmcif.atom_site._rowCount),
+ const lookup = GridLookup3D({ x: mmcif.db.atom_site.Cartn_x.toArray(), y: mmcif.db.atom_site.Cartn_y.toArray(), z: mmcif.db.atom_site.Cartn_z.toArray(),
+ indices: OrderedSet.ofBounds(0, mmcif.db.atom_site._rowCount),
// radius: [1, 1, 1, 1]
// indices: [1]
});
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 8f7d1ac4e6cd3db684566a39004a2e485c5ed0c5..d67f811cea1d544b23efbc7495d1bb6fce2b98e0 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -16,7 +16,7 @@ import { Structure, Model, Queries as Q, StructureElement, StructureSelection, S
import to_mmCIF from '../mol-model/structure/export/mmcif'
import { Vec3 } from '../mol-math/linear-algebra';
-import { trajectoryFromMmCIF } from '../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF, MmcifFormat } from '../mol-model-formats/structure/mmcif';
// import { printUnits } from '../apps/structure-info/model';
// import { EquivalenceClasses } from '../mol-data/util';
@@ -106,8 +106,8 @@ export async function getBcif(pdbId: string) {
export namespace PropertyAccess {
function baseline(model: Model) {
- if (model.sourceData.kind !== 'mmCIF') throw new Error('Model must be mmCIF');
- const atom_site = model.sourceData.data.atom_site;
+ if (!MmcifFormat.is(model.sourceData)) throw new Error('Model must be mmCIF');
+ const atom_site = model.sourceData.data.db.atom_site;
const id = atom_site.id.value;
let s = 0;
for (let i = 0, _i = atom_site._rowCount; i < _i; i++) {