molstar
Version:
A comprehensive macromolecular library.
181 lines (180 loc) • 7.77 kB
JavaScript
"use strict";
/**
* Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
* @author Ludovic Autin <ludovic.autin@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseLammpsData = parseLammpsData;
const mol_task_1 = require("../../../../mol-task");
const tokenizer_1 = require("../../common/text/tokenizer");
const result_1 = require("../../result");
const token_1 = require("../../common/text/column/token");
const db_1 = require("../../../../mol-data/db");
const { readLine, skipWhitespace, eatValue, eatLine, markStart } = tokenizer_1.Tokenizer;
const reWhitespace = /\s+/;
function State(tokenizer, runtimeCtx) {
return {
tokenizer,
runtimeCtx,
};
}
async function handleAtoms(state, count, atom_style) {
const { tokenizer } = state;
// default atom style is atomic
// depending on the atom style the number of columns can change
const atomId = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const moleculeId = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const atomType = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const charge = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const x = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const y = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const z = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const columns = {
full: [atomId, moleculeId, atomType, charge, x, y, z],
atomic: [atomId, atomType, x, y, z],
bond: [atomId, moleculeId, atomType, x, y, z],
};
const n = columns[atom_style].length;
const { position } = tokenizer;
readLine(tokenizer).trim();
tokenizer.position = position;
const { length } = tokenizer;
let linesAlreadyRead = 0;
await (0, mol_task_1.chunkedSubtask)(state.runtimeCtx, 100000, void 0, chunkSize => {
const linesToRead = Math.min(count - linesAlreadyRead, chunkSize);
for (let i = 0; i < linesToRead; ++i) {
for (let j = 0; j < n; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
const column = columns[atom_style][j];
if (column) {
tokenizer_1.TokenBuilder.addUnchecked(column, tokenizer.tokenStart, tokenizer.tokenEnd);
}
}
// ignore any extra columns
eatLine(tokenizer);
markStart(tokenizer);
}
linesAlreadyRead += linesToRead;
return linesToRead;
}, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
return {
count,
atomId: (0, token_1.TokenColumnProvider)(atomId)(db_1.Column.Schema.int),
moleculeId: (0, token_1.TokenColumnProvider)(moleculeId)(db_1.Column.Schema.int),
atomType: (0, token_1.TokenColumnProvider)(atomType)(db_1.Column.Schema.int),
charge: (0, token_1.TokenColumnProvider)(charge)(db_1.Column.Schema.float),
x: (0, token_1.TokenColumnProvider)(x)(db_1.Column.Schema.float),
y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
};
}
async function handleBonds(state, count) {
const { tokenizer } = state;
const bondId = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const bondType = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const atomIdA = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const atomIdB = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
const { length } = tokenizer;
let bondsAlreadyRead = 0;
await (0, mol_task_1.chunkedSubtask)(state.runtimeCtx, 10, void 0, chunkSize => {
const bondsToRead = Math.min(count - bondsAlreadyRead, chunkSize);
for (let i = 0; i < bondsToRead; ++i) {
for (let j = 0; j < 4; ++j) {
skipWhitespace(tokenizer);
markStart(tokenizer);
eatValue(tokenizer);
switch (j) {
case 0:
tokenizer_1.TokenBuilder.addUnchecked(bondId, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 1:
tokenizer_1.TokenBuilder.addUnchecked(bondType, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 2:
tokenizer_1.TokenBuilder.addUnchecked(atomIdA, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
case 3:
tokenizer_1.TokenBuilder.addUnchecked(atomIdB, tokenizer.tokenStart, tokenizer.tokenEnd);
break;
}
}
}
bondsAlreadyRead += bondsToRead;
return bondsToRead;
}, ctx => ctx.update({ message: 'Parsing...', current: tokenizer.position, max: length }));
return {
count,
bondId: (0, token_1.TokenColumnProvider)(bondId)(db_1.Column.Schema.int),
bondType: (0, token_1.TokenColumnProvider)(bondType)(db_1.Column.Schema.int),
atomIdA: (0, token_1.TokenColumnProvider)(atomIdA)(db_1.Column.Schema.int),
atomIdB: (0, token_1.TokenColumnProvider)(atomIdB)(db_1.Column.Schema.int),
};
}
const AtomStyles = ['full', 'atomic', 'bond'];
async function parseInternal(data, ctx) {
const tokenizer = (0, tokenizer_1.Tokenizer)(data);
const state = State(tokenizer, ctx);
let atoms = undefined;
let bonds = undefined;
let numAtoms = 0;
let numBonds = 0;
let atom_style = 'full';
// full list of atom_style
// https://docs.lammps.org/atom_style.html
while (tokenizer.tokenEnd < tokenizer.length) {
const line = readLine(state.tokenizer).trim();
if (line.includes('atoms')) {
numAtoms = parseInt(line.split(reWhitespace)[0]);
}
else if (line.includes('bonds')) {
numBonds = parseInt(line.split(reWhitespace)[0]);
}
else if (line.includes('Masses')) {
// TODO: support masses
}
else if (line.includes('Atoms')) {
// usually atom style is indicated as a comment after Atoms. e.g. Atoms # full
const parts = line.split('#');
if (parts.length > 1) {
const atomStyle = parts[1].trim();
if (AtomStyles.includes(atomStyle)) {
atom_style = atomStyle;
}
else {
console.warn(`Unknown atom style: ${atomStyle}`);
}
}
atoms = await handleAtoms(state, numAtoms, atom_style);
}
else if (line.includes('Bonds')) {
bonds = await handleBonds(state, numBonds);
}
}
if (atoms === undefined) {
return result_1.ReaderResult.error('no atoms data');
}
if (bonds === undefined) {
bonds = {
count: 0,
bondId: db_1.Column.ofIntArray([]),
bondType: db_1.Column.ofIntArray([]),
atomIdA: db_1.Column.ofIntArray([]),
atomIdB: db_1.Column.ofIntArray([]),
};
}
const result = {
atoms,
bonds
};
return result_1.ReaderResult.success(result);
}
function parseLammpsData(data) {
return mol_task_1.Task.create('Parse LammpsData', async (ctx) => {
return await parseInternal(data, ctx);
});
}