molstar
Version:
A comprehensive macromolecular library.
138 lines (137 loc) • 5.49 kB
JavaScript
"use strict";
/**
* 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getEntityData = getEntityData;
exports.getEntitiesWithPRD = getEntitiesWithPRD;
const db_1 = require("../../../mol-data/db");
const common_1 = require("../../../mol-model/structure/model/properties/common");
const types_1 = require("../../../mol-model/structure/model/types");
const schema_1 = require("./schema");
function getEntityData(data) {
let entityData;
if (!data.entity.id.isDefined) {
const entityIds = new Set();
const ids = [];
const types = [];
const { label_entity_id, label_comp_id } = data.atom_site;
for (let i = 0, il = data.atom_site._rowCount; i < il; i++) {
const entityId = label_entity_id.value(i);
if (!entityIds.has(entityId)) {
ids.push(entityId);
types.push((0, types_1.getEntityType)(label_comp_id.value(i)));
entityIds.add(entityId);
}
}
const { entity_id: sphere_entity_id } = data.ihm_sphere_obj_site;
for (let i = 0, il = data.ihm_sphere_obj_site._rowCount; i < il; i++) {
const entityId = sphere_entity_id.value(i);
if (!entityIds.has(entityId)) {
ids.push(entityId);
types.push('polymer');
entityIds.add(entityId);
}
}
const { entity_id: gaussian_entity_id } = data.ihm_gaussian_obj_site;
for (let i = 0, il = data.ihm_gaussian_obj_site._rowCount; i < il; i++) {
const entityId = gaussian_entity_id.value(i);
if (!entityIds.has(entityId)) {
ids.push(entityId);
types.push('polymer');
entityIds.add(entityId);
}
}
entityData = db_1.Table.ofPartialColumns(schema_1.BasicSchema.entity, {
id: db_1.Column.ofArray({ array: ids, schema: schema_1.BasicSchema.entity.id }),
type: db_1.Column.ofArray({ array: types, schema: schema_1.BasicSchema.entity.type }),
}, ids.length);
}
else {
entityData = data.entity;
}
const getEntityIndex = db_1.Column.createIndexer(entityData.id);
//
const subtypes = new Array(entityData._rowCount);
subtypes.fill('other');
const entityIds = new Set();
let assignSubtype = false;
if (data.entity_poly && data.entity_poly.type.isDefined) {
const { entity_id, type, _rowCount } = data.entity_poly;
for (let i = 0; i < _rowCount; ++i) {
const 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) {
const { entity_id, type, _rowCount } = data.pdbx_entity_branch;
for (let i = 0; i < _rowCount; ++i) {
const 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) {
const chemCompType = new Map();
if (data.chem_comp) {
const { id, type } = data.chem_comp;
for (let i = 0, il = data.chem_comp._rowCount; i < il; i++) {
chemCompType.set(id.value(i), type.value(i));
}
}
if (data.atom_site) {
const { label_entity_id, label_comp_id } = data.atom_site;
for (let i = 0, il = data.atom_site._rowCount; i < il; i++) {
const entityId = label_entity_id.value(i);
if (!entityIds.has(entityId)) {
const compId = label_comp_id.value(i);
const compType = chemCompType.get(compId) || 'other';
subtypes[getEntityIndex(entityId)] = (0, types_1.getEntitySubtype)(compId, compType);
entityIds.add(entityId);
}
}
}
// TODO how to handle coarse?
}
const subtypeColumn = db_1.Column.ofArray({ array: subtypes, schema: common_1.EntitySubtype });
return {
data: entityData,
subtype: subtypeColumn,
getEntityIndex
};
}
function getEntitiesWithPRD(data, entities, structAsymMap) {
var _a;
if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
return entities;
}
const prdIds = new Array(entities.data._rowCount);
prdIds.fill('');
const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
for (let i = 0; i < _rowCount; ++i) {
const asymId = asym_id.value(i);
const entityId = (_a = structAsymMap.get(asymId)) === null || _a === void 0 ? void 0 : _a.entity_id;
if (entityId !== undefined) {
prdIds[entities.getEntityIndex(entityId)] = prd_id.value(i);
}
}
const prdIdColumn = db_1.Column.ofArray({ array: prdIds, schema: db_1.Column.Schema.str });
return {
...entities,
prd_id: prdIdColumn
};
}