molstar
Version:
A comprehensive macromolecular library.
115 lines (114 loc) • 5.08 kB
JavaScript
;
/**
* Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Ludovic Autin <ludovic.autin@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.compileIdListSelection = compileIdListSelection;
const builder_1 = require("../language/builder");
const base_1 = require("../runtime/query/base");
const generic_1 = require("../../mol-data/generic");
function residueEntriesToQuery(xs, kind) {
var _a;
const groups = [];
const asym_id_key = kind === 'auth' ? 'auth_asym_id' : 'label_asym_id';
const seq_id_key = kind === 'auth' ? 'auth_seq_id' : 'label_seq_id';
for (const x of xs) {
if (x.kind === 'range') {
groups.push(builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(asym_id_key), x.asym_id]),
'residue-test': builder_1.MolScriptBuilder.core.rel.inRange([builder_1.MolScriptBuilder.ammp(seq_id_key), x.seq_id_beg, x.seq_id_end])
}));
}
else {
const ins_code = ((_a = x.ins_code) !== null && _a !== void 0 ? _a : '').trim();
groups.push(builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(asym_id_key), x.asym_id]),
'residue-test': builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(seq_id_key), x.seq_id]),
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('pdbx_PDB_ins_code'), ins_code])
])
}));
}
}
const query = builder_1.MolScriptBuilder.struct.combinator.merge(groups);
return (0, base_1.compile)(query);
}
function atomEntriesToQuery(xs) {
const set = generic_1.UniqueArray.create();
for (const [a, b] of xs) {
for (let i = a; i <= b; i++) {
generic_1.UniqueArray.add(set, i, i);
}
}
const query = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set.array), builder_1.MolScriptBuilder.ammp('id')])
});
return (0, base_1.compile)(query);
}
function elementSymbolNumberEntriesToQuery(xs) {
const set = generic_1.UniqueArray.create();
for (const [a, b] of xs) {
for (let i = a; i <= b; i++) {
generic_1.UniqueArray.add(set, i.toString(), i.toString());
}
}
const query = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set.array), builder_1.MolScriptBuilder.acp('elementSymbol')])
});
return (0, base_1.compile)(query);
}
function elementSymbolStringEntriesToQuery(names) {
const query = builder_1.MolScriptBuilder.struct.generator.atomGroups({
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...names), builder_1.MolScriptBuilder.acp('elementSymbol')])
});
return (0, base_1.compile)(query);
}
function parseRange(c, s, e) {
if (!c || s.length === 0 || Number.isNaN(+s[0]))
return;
if (Number.isNaN(e)) {
return { kind: 'single', asym_id: c, seq_id: +s[0], ins_code: s[1] };
}
return { kind: 'range', asym_id: c, seq_id_beg: +s[0], seq_id_end: e };
}
function parseInsCode(e) {
if (!e)
return [];
return e.split(':');
}
function parseResidueListSelection(input) {
return input.split(',') // A 1-3, B 3 => [A 1-3, B 3]
.map(e => e.trim().split(/\s+|[-]/g).filter(e => !!e)) // [A 1-3, B 3] => [[A, 1, 3], [B, 3]]
.map(e => parseRange(e[0], parseInsCode(e[1]), +e[2]))
.filter(e => !!e);
}
function parseAtomListSelection(input) {
return input.split(',') // 1-3, 3 => [1-3, 3]
.map(e => e.trim().split(/\s+|[-]/g).filter(e => !!e)) // [1-3, 3] => [[1, 3], [3]]
.filter(e => e.length === 1 || e.length === 2)
.map(e => e.length === 1 ? [+e[0], +e[0]] : [+e[0], +e[1]]);
}
// parses a list of residue ranges, e.g. A 10-100, B 30, C 12:i
function compileIdListSelection(input, idType) {
if (idType === 'atom-id') {
const entries = parseAtomListSelection(input);
return atomEntriesToQuery(entries);
}
else if (idType === 'element-symbol') {
const containsLetters = /[a-zA-Z]/.test(input);
if (containsLetters) {
return elementSymbolStringEntriesToQuery(input.split(',').map(e => e.trim()));
}
else {
const entries = parseAtomListSelection(input);
return elementSymbolNumberEntriesToQuery(entries);
}
}
else {
const entries = parseResidueListSelection(input);
return residueEntriesToQuery(entries, idType);
}
}