molstar
Version:
A comprehensive macromolecular library.
87 lines (86 loc) • 5.45 kB
JavaScript
/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
*
* Adapted from MolQL project
*/
// https://pymol.org/dokuwiki/doku.php?id=selection:alpha
// https://pymolwiki.org/index.php/Selection_Algebra
// https://github.com/evonove/pymol/blob/master/pymol/layer3/Selector.cpp
import * as P from '../../../mol-util/monadic-parser';
import * as h from '../helper';
import { MolScriptBuilder } from '../../../mol-script/language/builder';
const B = MolScriptBuilder;
import { properties } from './properties';
import { operators } from './operators';
import { keywords } from './keywords';
const propertiesDict = h.getPropertyRules(properties);
const slash = P.MonadicParser.string('/');
function orNull(rule) {
return rule.or(P.MonadicParser.of(null));
}
function atomSelectionQuery(x) {
const tests = {};
const props = {};
for (const k in x) {
const ps = properties[k];
if (!ps) {
throw new Error(`property '${k}' not supported, value '${x[k]}'`);
}
if (x[k] === null)
continue;
if (!props[ps.level])
props[ps.level] = [];
props[ps.level].push(x[k]);
}
for (const p in props) {
tests[p] = h.andExpr(props[p]);
}
return B.struct.generator.atomGroups(tests);
}
const lang = P.MonadicParser.createLanguage({
Parens: function (r) {
return P.MonadicParser.alt(r.Parens, r.Operator, r.Expression).wrap(P.MonadicParser.string('('), P.MonadicParser.string(')'));
},
Expression: function (r) {
return P.MonadicParser.alt(r.Keywords, r.AtomSelectionMacro.map(atomSelectionQuery), r.NamedAtomProperties, r.Pepseq, r.Rep, r.Object);
},
AtomSelectionMacro: function (r) {
return P.MonadicParser.alt(slash.then(P.MonadicParser.alt(P.MonadicParser.seq(orNull(r.ObjectProperty).skip(slash), orNull(propertiesDict.segi).skip(slash), orNull(propertiesDict.chain).skip(slash), orNull(propertiesDict.resi).skip(slash), orNull(propertiesDict.name)).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3], name: x[4] }; }), P.MonadicParser.seq(orNull(r.ObjectProperty).skip(slash), orNull(propertiesDict.segi).skip(slash), orNull(propertiesDict.chain).skip(slash), orNull(propertiesDict.resi)).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3] }; }), P.MonadicParser.seq(orNull(r.ObjectProperty).skip(slash), orNull(propertiesDict.segi).skip(slash), orNull(propertiesDict.chain)).map(x => { return { object: x[0], segi: x[1], chain: x[2] }; }), P.MonadicParser.seq(orNull(r.ObjectProperty).skip(slash), orNull(propertiesDict.segi)).map(x => { return { object: x[0], segi: x[1] }; }), P.MonadicParser.seq(orNull(r.ObjectProperty)).map(x => { return { object: x[0] }; }))), P.MonadicParser.alt(P.MonadicParser.seq(orNull(r.ObjectProperty).skip(slash), orNull(propertiesDict.segi).skip(slash), orNull(propertiesDict.chain).skip(slash), orNull(propertiesDict.resi).skip(slash), orNull(propertiesDict.name)).map(x => { return { object: x[0], segi: x[1], chain: x[2], resi: x[3], name: x[4] }; }), P.MonadicParser.seq(orNull(propertiesDict.segi).skip(slash), orNull(propertiesDict.chain).skip(slash), orNull(propertiesDict.resi).skip(slash), orNull(propertiesDict.name)).map(x => { return { segi: x[0], chain: x[1], resi: x[2], name: x[3] }; }), P.MonadicParser.seq(orNull(propertiesDict.chain).skip(slash), orNull(propertiesDict.resi).skip(slash), orNull(propertiesDict.name)).map(x => { return { chain: x[0], resi: x[1], name: x[2] }; }), P.MonadicParser.seq(orNull(propertiesDict.resi).skip(slash), orNull(propertiesDict.name)).map(x => { return { resi: x[0], name: x[1] }; })));
},
NamedAtomProperties: function () {
return P.MonadicParser.alt(...h.getNamedPropertyRules(properties));
},
Keywords: () => P.MonadicParser.alt(...h.getKeywordRules(keywords)),
ObjectProperty: () => {
const w = h.getReservedWords(properties, keywords, operators)
.sort(h.strLenSortFn).map(h.escapeRegExp).join('|');
return P.MonadicParser.regexp(new RegExp(`(?!(${w}))[A-Z0-9_]+`, 'i'));
},
Object: (r) => {
return r.ObjectProperty.notFollowedBy(slash)
.map((x) => { throw new Error(`property 'object' not supported, value '${x}'`); });
},
// Selects peptide sequence matching upper-case one-letter
// sequence SEQ (see also FindSeq).
// PEPSEQ seq
Pepseq: () => {
return P.MonadicParser.regexp(/(PEPSEQ|ps\.)\s+([a-z]+)/i, 2)
.map(h.makeError(`operator 'pepseq' not supported`));
},
// Selects atoms which show representation rep.
// REP rep
Rep: () => {
return P.MonadicParser.regexp(/REP\s+(lines|spheres|mesh|ribbon|cartoon|sticks|dots|surface|labels|extent|nonbonded|nb_spheres|slice|extent|slice|dashes|angles|dihedrals|cgo|cell|callback|everything)/i, 1)
.map(h.makeError(`operator 'rep' not supported`));
},
Operator: function (r) {
return h.combineOperators(operators, P.MonadicParser.alt(r.Parens, r.Expression, r.Operator));
},
Query: function (r) {
return P.MonadicParser.alt(r.Operator, r.Parens, r.Expression).trim(P.MonadicParser.optWhitespace);
}
});
export const transpiler = str => lang.Query.tryParse(str);