molstar
Version:
A comprehensive macromolecular library.
304 lines (303 loc) • 12.7 kB
JavaScript
"use strict";
/**
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseTop = void 0;
var tslib_1 = require("tslib");
var mol_task_1 = require("../../../mol-task");
var tokenizer_1 = require("../common/text/tokenizer");
var result_1 = require("../result");
var token_1 = require("../common/text/column/token");
var db_1 = require("../../../mol-data/db");
// https://manual.gromacs.org/2021-current/reference-manual/file-formats.html#top
var AtomsSchema = {
nr: db_1.Column.Schema.Int(),
type: db_1.Column.Schema.Str(),
resnr: db_1.Column.Schema.Int(),
residu: db_1.Column.Schema.Str(),
atom: db_1.Column.Schema.Str(),
cgnr: db_1.Column.Schema.Int(),
charge: db_1.Column.Schema.Float(),
mass: db_1.Column.Schema.Float(),
};
var BondsSchema = {
ai: db_1.Column.Schema.Int(),
aj: db_1.Column.Schema.Int(),
};
var MoleculesSchema = {
compound: db_1.Column.Schema.Str(),
molCount: db_1.Column.Schema.Int(),
};
var readLine = tokenizer_1.Tokenizer.readLine, markLine = tokenizer_1.Tokenizer.markLine, skipWhitespace = tokenizer_1.Tokenizer.skipWhitespace, markStart = tokenizer_1.Tokenizer.markStart, eatValue = tokenizer_1.Tokenizer.eatValue, eatLine = tokenizer_1.Tokenizer.eatLine;
function State(tokenizer, runtimeCtx) {
return {
tokenizer: tokenizer,
runtimeCtx: runtimeCtx,
};
}
var reField = /\[ (.+) \]/;
var reWhitespace = /\s+/;
function handleMoleculetype(state) {
var tokenizer = state.tokenizer;
var molName = undefined;
while (tokenizer.tokenEnd < tokenizer.length) {
skipWhitespace(tokenizer);
var c = tokenizer.data[tokenizer.position];
if (c === '[')
break;
if (c === ';' || c === '*') {
markLine(tokenizer);
continue;
}
if (molName !== undefined)
throw new Error('more than one molName');
var line = readLine(tokenizer);
molName = line.split(reWhitespace)[0];
}
if (molName === undefined)
throw new Error('missing molName');
return molName;
}
function handleAtoms(state) {
var tokenizer = state.tokenizer;
var nr = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var type = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var resnr = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var residu = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var atom = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var cgnr = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var charge = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var mass = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
while (tokenizer.tokenEnd < tokenizer.length) {
skipWhitespace(tokenizer);
var c = tokenizer.data[tokenizer.position];
if (c === '[')
break;
if (c === ';' || c === '*') {
markLine(tokenizer);
continue;
}
for (var j = 0; j < 8; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
switch (j) {
case 0:
tokenizer_1.TokenBuilder.add(nr, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
tokenizer_1.TokenBuilder.add(type, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 2:
tokenizer_1.TokenBuilder.add(resnr, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 3:
tokenizer_1.TokenBuilder.add(residu, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 4:
tokenizer_1.TokenBuilder.add(atom, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 5:
tokenizer_1.TokenBuilder.add(cgnr, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 6:
tokenizer_1.TokenBuilder.add(charge, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 7:
tokenizer_1.TokenBuilder.add(mass, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
// ignore any extra columns
markLine(tokenizer);
}
return db_1.Table.ofColumns(AtomsSchema, {
nr: (0, token_1.TokenColumnProvider)(nr)(db_1.Column.Schema.int),
type: (0, token_1.TokenColumnProvider)(type)(db_1.Column.Schema.str),
resnr: (0, token_1.TokenColumnProvider)(resnr)(db_1.Column.Schema.int),
residu: (0, token_1.TokenColumnProvider)(residu)(db_1.Column.Schema.str),
atom: (0, token_1.TokenColumnProvider)(atom)(db_1.Column.Schema.str),
cgnr: (0, token_1.TokenColumnProvider)(cgnr)(db_1.Column.Schema.int),
charge: (0, token_1.TokenColumnProvider)(charge)(db_1.Column.Schema.float),
mass: (0, token_1.TokenColumnProvider)(mass)(db_1.Column.Schema.float),
});
}
function handleBonds(state) {
var tokenizer = state.tokenizer;
var ai = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var aj = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
while (tokenizer.tokenEnd < tokenizer.length) {
skipWhitespace(tokenizer);
var c = tokenizer.data[tokenizer.position];
if (c === '[')
break;
if (c === ';' || c === '*') {
markLine(tokenizer);
continue;
}
for (var j = 0; j < 2; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
switch (j) {
case 0:
tokenizer_1.TokenBuilder.add(ai, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
tokenizer_1.TokenBuilder.add(aj, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
// ignore any extra columns
markLine(tokenizer);
}
return db_1.Table.ofColumns(BondsSchema, {
ai: (0, token_1.TokenColumnProvider)(ai)(db_1.Column.Schema.int),
aj: (0, token_1.TokenColumnProvider)(aj)(db_1.Column.Schema.int),
});
}
function handleSystem(state) {
var tokenizer = state.tokenizer;
var system = undefined;
while (tokenizer.tokenEnd < tokenizer.length) {
skipWhitespace(tokenizer);
var c = tokenizer.data[tokenizer.position];
if (c === '[')
break;
if (c === ';' || c === '*') {
markLine(tokenizer);
continue;
}
if (system !== undefined)
throw new Error('more than one system');
system = readLine(tokenizer).trim();
}
if (system === undefined)
throw new Error('missing system');
return system;
}
function handleMolecules(state) {
var tokenizer = state.tokenizer;
var compound = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
var molCount = tokenizer_1.TokenBuilder.create(tokenizer.data, 64);
while (tokenizer.tokenEnd < tokenizer.length) {
skipWhitespace(tokenizer);
if (tokenizer.position >= tokenizer.length)
break;
var c = tokenizer.data[tokenizer.position];
if (c === '[')
break;
if (c === ';' || c === '*') {
markLine(tokenizer);
continue;
}
for (var j = 0; j < 2; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
switch (j) {
case 0:
tokenizer_1.TokenBuilder.add(compound, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
tokenizer_1.TokenBuilder.add(molCount, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
// ignore any extra columns
eatLine(tokenizer);
markStart(tokenizer);
}
return db_1.Table.ofColumns(MoleculesSchema, {
compound: (0, token_1.TokenColumnProvider)(compound)(db_1.Column.Schema.str),
molCount: (0, token_1.TokenColumnProvider)(molCount)(db_1.Column.Schema.int),
});
}
function parseInternal(data, ctx) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
function addMol() {
if (currentMolName && currentCompound.atoms) {
result.compounds[currentMolName] = currentCompound;
currentCompound = {};
currentMolName = '';
}
}
var t, state, result, prevPosition, currentCompound, currentMolName, line, fieldMatch, fieldName;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
t = (0, tokenizer_1.Tokenizer)(data);
state = State(t, ctx);
result = Object.create(null);
prevPosition = 0;
result.compounds = {};
currentCompound = {};
currentMolName = '';
_a.label = 1;
case 1:
if (!(t.tokenEnd < t.length)) return [3 /*break*/, 4];
if (!(t.position - prevPosition > 100000 && ctx.shouldUpdate)) return [3 /*break*/, 3];
prevPosition = t.position;
return [4 /*yield*/, ctx.update({ current: t.position, max: t.length })];
case 2:
_a.sent();
_a.label = 3;
case 3:
line = readLine(state.tokenizer).trim();
if (!line || line[0] === '*' || line[0] === ';') {
return [3 /*break*/, 1];
}
if (line.startsWith('#include')) {
throw new Error('#include statements not allowed');
}
if (line.startsWith('[')) {
fieldMatch = line.match(reField);
if (fieldMatch === null)
throw new Error('expected field name');
fieldName = fieldMatch[1];
if (fieldName === 'moleculetype') {
addMol();
currentMolName = handleMoleculetype(state);
}
else if (fieldName === 'atoms') {
currentCompound.atoms = handleAtoms(state);
}
else if (fieldName === 'bonds') {
currentCompound.bonds = handleBonds(state);
}
else if (fieldName === 'system') {
result.system = handleSystem(state);
}
else if (fieldName === 'molecules') {
addMol(); // add the last compound
result.molecules = handleMolecules(state);
}
else {
while (t.tokenEnd < t.length) {
if (t.data[t.position] === '[')
break;
markLine(t);
}
}
}
return [3 /*break*/, 1];
case 4: return [2 /*return*/, result_1.ReaderResult.success(result)];
}
});
});
}
function parseTop(data) {
var _this = this;
return mol_task_1.Task.create('Parse TOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, parseInternal(data, ctx)];
case 1: return [2 /*return*/, _a.sent()];
}
});
}); });
}
exports.parseTop = parseTop;