molstar
Version:
A comprehensive macromolecular library.
56 lines (55 loc) • 1.85 kB
JavaScript
;
/**
* Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseXyz = parseXyz;
const db_1 = require("../../../mol-data/db");
const mol_task_1 = require("../../../mol-task");
const tokenizer_1 = require("../common/text/tokenizer");
const result_1 = require("../result");
function handleMolecule(tokenizer) {
let count = tokenizer.position >= tokenizer.data.length - 1 ? 0 : +tokenizer_1.Tokenizer.readLine(tokenizer);
if (isNaN(count))
count = 0;
const comment = tokenizer_1.Tokenizer.readLine(tokenizer);
const x = new Float64Array(count);
const y = new Float64Array(count);
const z = new Float64Array(count);
const type_symbol = new Array(count);
for (let i = 0; i < count; ++i) {
const line = tokenizer_1.Tokenizer.readLineTrim(tokenizer);
const fields = line.split(/\s+/g);
type_symbol[i] = fields[0];
x[i] = +fields[1];
y[i] = +fields[2];
z[i] = +fields[3];
}
return {
count,
comment,
x: db_1.Column.ofFloatArray(x),
y: db_1.Column.ofFloatArray(y),
z: db_1.Column.ofFloatArray(z),
type_symbol: db_1.Column.ofStringArray(type_symbol)
};
}
function parseInternal(data) {
const tokenizer = (0, tokenizer_1.Tokenizer)(data);
const molecules = [];
while (true) {
const mol = handleMolecule(tokenizer);
if (mol.count === 0)
break;
molecules.push(mol);
}
const result = { molecules };
return result_1.ReaderResult.success(result);
}
function parseXyz(data) {
return mol_task_1.Task.create('Parse Mol', async () => {
return parseInternal(data);
});
}