molstar
Version:
A comprehensive macromolecular library.
131 lines (130 loc) • 5.24 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getMissingResidues = getMissingResidues;
exports.getChemicalComponentMap = getChemicalComponentMap;
exports.getSaccharideComponentMap = getSaccharideComponentMap;
exports.getStructAsymMap = getStructAsymMap;
const db_1 = require("../../../mol-data/db");
const types_1 = require("../../../mol-model/structure/model/types");
const constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
const memoize_1 = require("../../../mol-util/memoize");
function getMissingResidues(data) {
const map = new Map();
const getKey = (model_num, asym_id, seq_id) => {
return `${model_num}|${asym_id}|${seq_id}`;
};
const c = data.pdbx_unobs_or_zero_occ_residues;
for (let i = 0, il = c._rowCount; i < il; ++i) {
const key = getKey(c.PDB_model_num.value(i), c.label_asym_id.value(i), c.label_seq_id.value(i));
map.set(key, { polymer_flag: c.polymer_flag.value(i), occupancy_flag: c.occupancy_flag.value(i) });
}
return {
has: (model_num, asym_id, seq_id) => {
return map.has(getKey(model_num, asym_id, seq_id));
},
get: (model_num, asym_id, seq_id) => {
return map.get(getKey(model_num, asym_id, seq_id));
},
size: map.size
};
}
function getChemicalComponentMap(data) {
const map = new Map();
if (data.chem_comp._rowCount > 0) {
const { id } = data.chem_comp;
for (let i = 0, il = id.rowCount; i < il; ++i) {
map.set(id.value(i), db_1.Table.getRow(data.chem_comp, i));
}
}
else {
const uniqueNames = getUniqueComponentNames(data);
uniqueNames.forEach(n => {
map.set(n, (0, types_1.getDefaultChemicalComponent)(n));
});
}
return map;
}
function getSaccharideComponentMap(data) {
const map = new Map();
if (data.pdbx_chem_comp_identifier._rowCount > 0) {
// note that `pdbx_chem_comp_identifier` does not contain
// a 'SNFG CARBOHYDRATE SYMBOL' entry for 'Unknown' saccharide components
// so we always need to check `chem_comp` for those
const { comp_id, type, identifier } = data.pdbx_chem_comp_identifier;
for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
if (type.value(i) === 'SNFG CARBOHYDRATE SYMBOL' ||
type.value(i) === 'SNFG CARB SYMBOL' // legacy, to be removed from mmCIF dictionary
) {
const snfgName = identifier.value(i);
const saccharideComp = constants_1.SaccharidesSnfgMap.get(snfgName);
if (saccharideComp) {
map.set(comp_id.value(i), saccharideComp);
}
else {
console.warn(`Unknown SNFG name '${snfgName}'`);
}
}
}
}
if (data.chem_comp._rowCount > 0) {
const { id, type } = data.chem_comp;
for (let i = 0, il = id.rowCount; i < il; ++i) {
const _id = id.value(i);
if (map.has(_id))
continue;
const _type = type.value(i);
if (constants_1.SaccharideCompIdMap.has(_id)) {
map.set(_id, constants_1.SaccharideCompIdMap.get(_id));
}
else if ((0, types_1.getMoleculeType)(_type, _id) === types_1.MoleculeType.Saccharide) {
map.set(_id, constants_1.UnknownSaccharideComponent);
}
}
}
else {
const uniqueNames = getUniqueComponentNames(data);
constants_1.SaccharideCompIdMap.forEach((v, k) => {
if (!map.has(k) && uniqueNames.has(k))
map.set(k, v);
});
}
return map;
}
const getUniqueComponentNames = (0, memoize_1.memoize1)((data) => {
const uniqueNames = new Set();
const { label_comp_id, auth_comp_id } = data.atom_site;
const comp_id = label_comp_id.isDefined ? label_comp_id : auth_comp_id;
for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
uniqueNames.add(comp_id.value(i));
}
return uniqueNames;
});
function getStructAsymMap(atomic, data) {
const map = new Map();
const { auth_asym_id, label_asym_id, label_entity_id } = atomic.chains;
for (let i = 0, _i = atomic.chains._rowCount; i < _i; i++) {
const id = label_asym_id.value(i);
map.set(id, { id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
}
// to get asym mapping for coarse/ihm data
if (data === null || data === void 0 ? void 0 : data.struct_asym._rowCount) {
const { id, entity_id } = data.struct_asym;
for (let i = 0, il = id.rowCount; i < il; ++i) {
const _id = id.value(i);
if (!map.has(_id)) {
map.set(_id, {
id: _id,
auth_id: '',
entity_id: entity_id.value(i)
});
}
}
}
return map;
}