molstar
Version:
A comprehensive macromolecular library.
104 lines (103 loc) • 4.44 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Adapted from NGL.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseDx = parseDx;
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const mol_task_1 = require("../../../mol-task");
const string_like_1 = require("../../common/string-like");
const utf8_1 = require("../../common/utf8");
const number_parser_1 = require("../common/text/number-parser");
const tokenizer_1 = require("../common/text/tokenizer");
const result_1 = require("../result");
function readHeader(tokenizer) {
const header = { h: (0, linear_algebra_1.Vec3)() };
let headerByteCount = 0;
let deltaLineCount = 0;
const reWhitespace = /\s+/g;
while (true) {
const line = tokenizer_1.Tokenizer.readLine(tokenizer);
let ls;
if (line.startsWith('object 1')) {
ls = line.split(reWhitespace);
header.dim = linear_algebra_1.Vec3.create(parseInt(ls[5]), parseInt(ls[6]), parseInt(ls[7]));
}
else if (line.startsWith('origin')) {
ls = line.split(reWhitespace);
header.min = linear_algebra_1.Vec3.create(parseFloat(ls[1]), parseFloat(ls[2]), parseFloat(ls[3]));
}
else if (line.startsWith('delta')) {
ls = line.split(reWhitespace);
if (deltaLineCount === 0) {
header.h[0] = parseFloat(ls[1]);
}
else if (deltaLineCount === 1) {
header.h[1] = parseFloat(ls[2]);
}
else if (deltaLineCount === 2) {
header.h[2] = parseFloat(ls[3]);
}
deltaLineCount += 1;
}
else if (line.startsWith('object 3')) {
headerByteCount += line.length + 1;
break;
}
headerByteCount += line.length + 1;
}
return { header: header, headerByteCount };
}
function readValuesText(ctx, tokenizer, header) {
const N = header.dim[0] * header.dim[1] * header.dim[2];
const chunkSize = 100 * 100 * 100;
const data = new Float64Array(N);
let offset = 0;
return (0, mol_task_1.chunkedSubtask)(ctx, chunkSize, data, (count, data) => {
const max = Math.min(N, offset + count);
for (let i = offset; i < max; i++) {
tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
tokenizer.tokenStart = tokenizer.position;
tokenizer_1.Tokenizer.eatValue(tokenizer);
data[i] = (0, number_parser_1.parseFloat)(tokenizer.data, tokenizer.tokenStart, tokenizer.tokenEnd);
}
offset = max;
return max === N ? 0 : chunkSize;
}, (ctx, _, i) => ctx.update({ current: Math.min(i, N), max: N }));
}
async function parseText(taskCtx, data, name) {
await taskCtx.update('Reading header...');
const tokenizer = (0, tokenizer_1.Tokenizer)(data);
const { header } = readHeader(tokenizer);
await taskCtx.update('Reading values...');
const values = await readValuesText(taskCtx, tokenizer, header);
return result_1.ReaderResult.success({ header, values, name });
}
async function parseBinary(taskCtx, data, name) {
await taskCtx.update('Reading header...');
const headerString = (0, utf8_1.utf8Read)(data, 0, 1000);
const tokenizer = (0, tokenizer_1.Tokenizer)(headerString);
const { header, headerByteCount } = readHeader(tokenizer);
await taskCtx.update('Reading values...');
const size = header.dim[0] * header.dim[1] * header.dim[2];
const dv = new DataView(data.buffer, data.byteOffset + headerByteCount);
const values = new Float64Array(size);
for (let i = 0; i < size; i++) {
values[i] = dv.getFloat64(i * 8, true);
}
// TODO: why doesnt this work? throw "attempting to construct out-of-bounds TypedArray"
// const values = new Float64Array(data.buffer, data.byteOffset + headerByteCount, header.dim[0] * header.dim[1] * header.dim[2]);
return result_1.ReaderResult.success({ header, values, name });
}
function parseDx(data, name) {
return mol_task_1.Task.create('Parse DX', taskCtx => {
if (string_like_1.StringLike.is(data))
return parseText(taskCtx, data, name);
return parseBinary(taskCtx, data, name);
});
}