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@@ -1,25 +1,30 @@
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/**
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- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ * Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* @author David Sehnal <david.sehnal@gmail.com>
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
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*/
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import { Model } from '../../mol-model/structure/model/model';
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-import { Task } from '../../mol-task';
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+import { RuntimeContext, Task } from '../../mol-task';
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import { ModelFormat } from '../format';
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import { CifFrame, CIF } from '../../mol-io/reader/cif';
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import { mmCIF_Database } from '../../mol-io/reader/cif/schema/mmcif';
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import { createModels } from './basic/parser';
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import { ModelSymmetry } from './property/symmetry';
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import { ModelSecondaryStructure } from './property/secondary-structure';
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-import { Table } from '../../mol-data/db';
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+import { Column, Table } from '../../mol-data/db';
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import { AtomSiteAnisotrop } from './property/anisotropic';
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import { ComponentBond } from './property/bonds/chem_comp';
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import { StructConn } from './property/bonds/struct_conn';
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-import { Trajectory } from '../../mol-model/structure';
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+import { ArrayTrajectory, Trajectory } from '../../mol-model/structure';
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import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
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-import { createBasic } from './basic/schema';
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+import { BasicSchema, createBasic } from './basic/schema';
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+import { CCD_Database } from '../../mol-io/reader/cif/schema/ccd';
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+import { EntityBuilder } from './common/entity';
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+import { MoleculeType } from '../../mol-model/structure/model/types';
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+import { ComponentBuilder } from './common/component';
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function modelSymmetryFromMmcif(model: Model) {
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if (!MmcifFormat.is(model.sourceData)) return;
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@@ -103,4 +108,136 @@ export function trajectoryFromMmCIF(frame: CifFrame): Task<Trajectory> {
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const format = MmcifFormat.fromFrame(frame);
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const basic = createBasic(format.data.db, true);
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return Task.create('Create mmCIF Model', ctx => createModels(basic, format, ctx));
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+}
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+
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+export { CCDFormat };
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+
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+type CCDFormat = ModelFormat<CCDFormat.Data>
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+
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+namespace CCDFormat {
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+ export type Data = {
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+ db: CCD_Database,
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+ frame: CifFrame
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+ }
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+
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+ const CoordinateTypeProp = '__CcdCoordinateType__';
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+ export type CoordinateType = 'ideal' | 'model'
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+ export const CoordinateType = {
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+ get(model: Model): CoordinateType | undefined {
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+ return model._staticPropertyData[CoordinateTypeProp];
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+ },
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+ set(model: Model, type: CoordinateType) {
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+ return model._staticPropertyData[CoordinateTypeProp] = type;
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+ }
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+ };
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+
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+ export function is(x?: ModelFormat): x is CCDFormat {
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+ return x?.kind === 'CCD';
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+ }
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+
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+ export function fromFrame(frame: CifFrame, db?: CCD_Database): CCDFormat {
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+ if (!db) db = CIF.schema.CCD(frame);
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+ return { kind: 'CCD', name: db._name, data: { db, frame } };
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+ }
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+}
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+
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+export function trajectoryFromCCD(frame: CifFrame): Task<Trajectory> {
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+ const format = CCDFormat.fromFrame(frame);
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+ return Task.create('Create CCD Models', ctx => createCcdModels(format.data.db, CCDFormat.fromFrame(frame), ctx));
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+}
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+
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+async function createCcdModels(data: CCD_Database, format: CCDFormat, ctx: RuntimeContext) {
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+ const ideal = await createCcdModel(data, format, { coordinateType: 'ideal', cartn_x: 'pdbx_model_Cartn_x_ideal', cartn_y: 'pdbx_model_Cartn_y_ideal', cartn_z: 'pdbx_model_Cartn_z_ideal' }, ctx);
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+ const model = await createCcdModel(data, format, { coordinateType: 'model', cartn_x: 'model_Cartn_x', cartn_y: 'model_Cartn_y', cartn_z: 'model_Cartn_z' }, ctx);
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+
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+ const models = [];
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+ if (ideal) models.push(ideal);
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+ if (model) models.push(model);
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+ for (let i = 0, il = models.length; i < il; ++i) {
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+ Model.TrajectoryInfo.set(models[i], { index: i, size: models.length });
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+ }
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+
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+ return new ArrayTrajectory(models);
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+}
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+
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+type CCDProps = { coordinateType: CCDFormat.CoordinateType, cartn_x: 'model_Cartn_x' | 'pdbx_model_Cartn_x_ideal', cartn_y: 'model_Cartn_y' | 'pdbx_model_Cartn_y_ideal', cartn_z: 'model_Cartn_z' | 'pdbx_model_Cartn_z_ideal' };
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+async function createCcdModel(data: CCD_Database, format: CCDFormat, props: CCDProps, ctx: RuntimeContext) {
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+ const { chem_comp, chem_comp_atom, chem_comp_bond } = data;
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+ const { coordinateType, cartn_x, cartn_y, cartn_z } = props;
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+
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+ const name = chem_comp.name.value(0);
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+ const id = chem_comp.id.value(0);
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+
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+ const { atom_id, charge, comp_id, pdbx_ordinal, type_symbol } = chem_comp_atom;
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+ const atomCount = chem_comp_atom._rowCount;
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+
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+ const filteredRows: number[] = [];
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+ for (let i = 0; i < atomCount; i++) {
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+ if (chem_comp_atom[cartn_x].valueKind(i) > 0) continue;
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+ filteredRows[filteredRows.length] = i;
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+ }
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+ const filteredRowCount = filteredRows.length;
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+
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+ const A = Column.ofConst('A', filteredRowCount, Column.Schema.str);
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+ const seq_id = Column.ofConst(1, filteredRowCount, Column.Schema.int);
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+ const entity_id = Column.ofConst('1', filteredRowCount, Column.Schema.str);
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+ const occupancy = Column.ofConst(1, filteredRowCount, Column.Schema.float);
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+ const model_num = Column.ofConst(1, filteredRowCount, Column.Schema.int);
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+
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+ const filteredAtomId = Column.view(atom_id, filteredRows);
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+ const filteredCompId = Column.view(comp_id, filteredRows);
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+ const filteredX = Column.view(chem_comp_atom[cartn_x], filteredRows);
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+ const filteredY = Column.view(chem_comp_atom[cartn_y], filteredRows);
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+ const filteredZ = Column.view(chem_comp_atom[cartn_z], filteredRows);
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+ const filteredId = Column.view(pdbx_ordinal, filteredRows);
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+ const filteredTypeSymbol = Column.view(type_symbol, filteredRows);
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+ const filteredCharge = Column.view(charge, filteredRows);
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+
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+ const model_atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
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+ auth_asym_id: A,
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+ auth_atom_id: filteredAtomId,
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+ auth_comp_id: filteredCompId,
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+ auth_seq_id: seq_id,
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+ Cartn_x: filteredX,
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+ Cartn_y: filteredY,
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+ Cartn_z: filteredZ,
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+ id: filteredId,
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+
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+ label_asym_id: A,
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+ label_atom_id: filteredAtomId,
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+ label_comp_id: filteredCompId,
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+ label_seq_id: seq_id,
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+ label_entity_id: entity_id,
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+
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+ occupancy,
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+ type_symbol: filteredTypeSymbol,
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+
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+ pdbx_PDB_model_num: model_num,
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+ pdbx_formal_charge: filteredCharge
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+ }, filteredRowCount);
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+
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+ const entityBuilder = new EntityBuilder();
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+ entityBuilder.setNames([[id, `${name} (${coordinateType})`]]);
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+ entityBuilder.getEntityId(id, MoleculeType.Unknown, 'A');
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+
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+ const componentBuilder = new ComponentBuilder(seq_id, type_symbol);
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+ componentBuilder.setNames([[id, `${name} (${coordinateType})`]]);
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+ componentBuilder.add(id, 0);
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+
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+ const basicModel = createBasic({
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+ entity: entityBuilder.getEntityTable(),
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+ chem_comp: componentBuilder.getChemCompTable(),
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+ atom_site: model_atom_site
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+ });
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+ const models = await createModels(basicModel, format, ctx);
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+
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+ // all ideal or model coordinates might be absent
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+ if (!models.representative) return;
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+
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+ const first = models.representative;
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+ const entries = ComponentBond.getEntriesFromChemCompBond(chem_comp_bond);
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+ ComponentBond.Provider.set(first, { data: chem_comp_bond, entries });
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+ CCDFormat.CoordinateType.set(first, coordinateType);
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+
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+ return models.representative;
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}
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Alexander Rose