molstar
Version:
A comprehensive macromolecular library.
129 lines • 5.53 kB
JavaScript
/**
* 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 { Column, Table } from '../../../mol-data/db';
import { EntitySubtype } from '../../../mol-model/structure/model/properties/common';
import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/model/types';
import { BasicSchema } from './schema';
export function getEntities(data, properties) {
var _a;
var entityData;
if (!data.entity.id.isDefined) {
var entityIds_1 = new Set();
var ids = [];
var types = [];
var _b = data.atom_site, label_entity_id = _b.label_entity_id, label_comp_id = _b.label_comp_id;
for (var i = 0, il = data.atom_site._rowCount; i < il; i++) {
var entityId = label_entity_id.value(i);
if (!entityIds_1.has(entityId)) {
ids.push(entityId);
types.push(getEntityType(label_comp_id.value(i)));
entityIds_1.add(entityId);
}
}
var sphere_entity_id = data.ihm_sphere_obj_site.entity_id;
for (var i = 0, il = data.ihm_sphere_obj_site._rowCount; i < il; i++) {
var entityId = sphere_entity_id.value(i);
if (!entityIds_1.has(entityId)) {
ids.push(entityId);
types.push('polymer');
entityIds_1.add(entityId);
}
}
var gaussian_entity_id = data.ihm_gaussian_obj_site.entity_id;
for (var i = 0, il = data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
var entityId = gaussian_entity_id.value(i);
if (!entityIds_1.has(entityId)) {
ids.push(entityId);
types.push('polymer');
entityIds_1.add(entityId);
}
}
entityData = Table.ofPartialColumns(BasicSchema.entity, {
id: Column.ofArray({ array: ids, schema: BasicSchema.entity.id }),
type: Column.ofArray({ array: types, schema: BasicSchema.entity.type }),
}, ids.length);
}
else {
entityData = data.entity;
}
var getEntityIndex = Column.createIndexer(entityData.id);
//
var subtypes = new Array(entityData._rowCount);
subtypes.fill('other');
var entityIds = new Set();
var assignSubtype = false;
if (data.entity_poly && data.entity_poly.type.isDefined) {
var _c = data.entity_poly, entity_id = _c.entity_id, type = _c.type, _rowCount = _c._rowCount;
for (var i = 0; i < _rowCount; ++i) {
var entityId = entity_id.value(i);
subtypes[getEntityIndex(entityId)] = type.value(i);
entityIds.add(entityId);
}
}
else {
assignSubtype = true;
}
if (data.pdbx_entity_branch && data.pdbx_entity_branch.entity_id.isDefined) {
var _d = data.pdbx_entity_branch, entity_id = _d.entity_id, type = _d.type, _rowCount = _d._rowCount;
for (var i = 0; i < _rowCount; ++i) {
var entityId = entity_id.value(i);
subtypes[getEntityIndex(entityId)] = type.value(i);
entityIds.add(entityId);
}
}
else {
assignSubtype = true;
}
if (entityIds.size < subtypes.length) {
// still unassigned subtypes, need to derive from component id/type
assignSubtype = true;
}
if (assignSubtype) {
var chemCompType = new Map();
if (data.chem_comp) {
var _e = data.chem_comp, id = _e.id, type = _e.type;
for (var i = 0, il = data.chem_comp._rowCount; i < il; i++) {
chemCompType.set(id.value(i), type.value(i));
}
}
if (data.atom_site) {
var _f = data.atom_site, label_entity_id = _f.label_entity_id, label_comp_id = _f.label_comp_id;
for (var i = 0, il = data.atom_site._rowCount; i < il; i++) {
var entityId = label_entity_id.value(i);
if (!entityIds.has(entityId)) {
var compId = label_comp_id.value(i);
var compType = chemCompType.get(compId) || '';
subtypes[getEntityIndex(entityId)] = getEntitySubtype(compId, compType);
entityIds.add(entityId);
}
}
}
// TODO how to handle coarse?
}
var subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype });
//
var prdIds = new Array(entityData._rowCount);
prdIds.fill('');
if (data.pdbx_molecule && data.pdbx_molecule.prd_id.isDefined) {
var _g = data.pdbx_molecule, asym_id = _g.asym_id, prd_id = _g.prd_id, _rowCount = _g._rowCount;
for (var i = 0; i < _rowCount; ++i) {
var asymId = asym_id.value(i);
var entityId = (_a = properties.structAsymMap.get(asymId)) === null || _a === void 0 ? void 0 : _a.entity_id;
if (entityId !== undefined) {
prdIds[getEntityIndex(entityId)] = prd_id.value(i);
}
}
}
var prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
return {
data: entityData,
subtype: subtypeColumn,
prd_id: prdIdColumn,
getEntityIndex: getEntityIndex
};
}
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