molstar
Version:
A comprehensive macromolecular library.
356 lines (355 loc) • 14.2 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>
*/
import { Task } from '../../../mol-task';
import { ReaderResult as Result } from '../result';
const MagicInts = new Uint32Array([
0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,
1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003,
16384, 20642, 26007, 32768, 41285, 52015, 65536, 82570, 104031,
131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561,
832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021,
4194304, 5284491, 6658042, 8388607, 10568983, 13316085, 16777216
]);
const FirstIdx = 9;
// const LastIdx = MagicInts.length
var Decoder;
(function (Decoder) {
function sizeOfInt(size) {
let num = 1;
let numOfBits = 0;
while (size >= num && numOfBits < 32) {
numOfBits++;
num <<= 1;
}
return numOfBits;
}
Decoder.sizeOfInt = sizeOfInt;
const _tmpBytes = new Uint8Array(32);
function sizeOfInts(numOfInts, sizes) {
let numOfBytes = 1;
let numOfBits = 0;
_tmpBytes[0] = 1;
for (let i = 0; i < numOfInts; i++) {
let bytecnt;
let tmp = 0;
for (bytecnt = 0; bytecnt < numOfBytes; bytecnt++) {
tmp += _tmpBytes[bytecnt] * sizes[i];
_tmpBytes[bytecnt] = tmp & 0xff;
tmp >>= 8;
}
while (tmp !== 0) {
_tmpBytes[bytecnt++] = tmp & 0xff;
tmp >>= 8;
}
numOfBytes = bytecnt;
}
let num = 1;
numOfBytes--;
while (_tmpBytes[numOfBytes] >= num) {
numOfBits++;
num *= 2;
}
return numOfBits + numOfBytes * 8;
}
Decoder.sizeOfInts = sizeOfInts;
const _buffer = new ArrayBuffer(8 * 3);
Decoder.buf = new Int32Array(_buffer);
const uint32view = new Uint32Array(_buffer);
function decodeBits(cbuf, offset, numOfBits1) {
let numOfBits = numOfBits1;
const mask = (1 << numOfBits) - 1;
let lastBB0 = uint32view[1];
let lastBB1 = uint32view[2];
let cnt = Decoder.buf[0];
let num = 0;
while (numOfBits >= 8) {
lastBB1 = (lastBB1 << 8) | cbuf[offset + cnt++];
num |= (lastBB1 >> lastBB0) << (numOfBits - 8);
numOfBits -= 8;
}
if (numOfBits > 0) {
if (lastBB0 < numOfBits) {
lastBB0 += 8;
lastBB1 = (lastBB1 << 8) | cbuf[offset + cnt++];
}
lastBB0 -= numOfBits;
num |= (lastBB1 >> lastBB0) & ((1 << numOfBits) - 1);
}
num &= mask;
Decoder.buf[0] = cnt;
Decoder.buf[1] = lastBB0;
Decoder.buf[2] = lastBB1;
return num;
}
Decoder.decodeBits = decodeBits;
function decodeByte(cbuf, offset) {
// special version of decodeBits with numOfBits = 8
// const mask = 0xff; // (1 << 8) - 1;
// let lastBB0 = uint32view[1];
let lastBB1 = uint32view[2];
const cnt = Decoder.buf[0];
lastBB1 = (lastBB1 << 8) | cbuf[offset + cnt];
Decoder.buf[0] = cnt + 1;
// buf[1] = lastBB0;
Decoder.buf[2] = lastBB1;
return (lastBB1 >> uint32view[1]) & 0xff;
}
const intBytes = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0];
// new Int32Array(32);
function decodeInts(cbuf, offset, numOfBits1, sizes, nums) {
let numOfBits = numOfBits1;
let numOfBytes = 0;
intBytes[0] = 0;
intBytes[1] = 0;
intBytes[2] = 0;
intBytes[3] = 0;
while (numOfBits > 8) {
// this is inversed??? why??? because of the endiannness???
intBytes[numOfBytes++] = decodeByte(cbuf, offset);
numOfBits -= 8;
}
if (numOfBits > 0) {
intBytes[numOfBytes++] = decodeBits(cbuf, offset, numOfBits);
}
for (let i = 2; i > 0; i--) {
let num = 0;
const s = sizes[i];
for (let j = numOfBytes - 1; j >= 0; j--) {
num = (num << 8) | intBytes[j];
const t = (num / s) | 0;
intBytes[j] = t;
num = num - t * s;
}
nums[i] = num;
}
nums[0] = intBytes[0] | (intBytes[1] << 8) | (intBytes[2] << 16) | (intBytes[3] << 24);
}
Decoder.decodeInts = decodeInts;
})(Decoder || (Decoder = {}));
function undefinedError() {
throw new Error('(xdrfile error) Undefined error.');
}
async function parseInternal(ctx, data) {
// https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/xtcio.cpp
// https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/libxdrf.cpp
const dv = new DataView(data.buffer, data.byteOffset);
const f = {
frames: [],
boxes: [],
times: [],
timeOffset: 0,
deltaTime: 0
};
const coordinates = f.frames;
const boxes = f.boxes;
const times = f.times;
const minMaxInt = [0, 0, 0, 0, 0, 0];
const sizeint = [0, 0, 0];
const bitsizeint = [0, 0, 0];
const sizesmall = [0, 0, 0];
const thiscoord = [0.1, 0.1, 0.1];
const prevcoord = [0.1, 0.1, 0.1];
let offset = 0;
const buf = Decoder.buf;
// const buf2 = new Uint32Array(buf.buffer);
while (true) {
let frameCoords;
// const magicnum = dv.getInt32(offset)
const natoms = dv.getInt32(offset + 4);
// const step = dv.getInt32(offset + 8)
offset += 12;
times.push(dv.getFloat32(offset));
offset += 4;
const box = new Float32Array(9);
for (let i = 0; i < 9; ++i) {
box[i] = dv.getFloat32(offset) * 10;
offset += 4;
}
boxes.push(box);
if (natoms <= 9) { // no compression
frameCoords = { count: natoms, x: new Float32Array(natoms), y: new Float32Array(natoms), z: new Float32Array(natoms) };
offset += 4;
for (let i = 0; i < natoms; ++i) {
frameCoords.x[i] = dv.getFloat32(offset);
frameCoords.y[i] = dv.getFloat32(offset + 4);
frameCoords.z[i] = dv.getFloat32(offset + 8);
offset += 12;
}
}
else {
buf[0] = buf[1] = buf[2] = 0;
sizeint[0] = sizeint[1] = sizeint[2] = 0;
sizesmall[0] = sizesmall[1] = sizesmall[2] = 0;
bitsizeint[0] = bitsizeint[1] = bitsizeint[2] = 0;
thiscoord[0] = thiscoord[1] = thiscoord[2] = 0;
prevcoord[0] = prevcoord[1] = prevcoord[2] = 0;
frameCoords = { count: natoms, x: new Float32Array(natoms), y: new Float32Array(natoms), z: new Float32Array(natoms) };
let lfp = 0;
const lsize = dv.getInt32(offset);
offset += 4;
const precision = dv.getFloat32(offset);
offset += 4;
minMaxInt[0] = dv.getInt32(offset);
minMaxInt[1] = dv.getInt32(offset + 4);
minMaxInt[2] = dv.getInt32(offset + 8);
minMaxInt[3] = dv.getInt32(offset + 12);
minMaxInt[4] = dv.getInt32(offset + 16);
minMaxInt[5] = dv.getInt32(offset + 20);
sizeint[0] = minMaxInt[3] - minMaxInt[0] + 1;
sizeint[1] = minMaxInt[4] - minMaxInt[1] + 1;
sizeint[2] = minMaxInt[5] - minMaxInt[2] + 1;
offset += 24;
let bitsize;
if ((sizeint[0] | sizeint[1] | sizeint[2]) > 0xffffff) {
bitsizeint[0] = Decoder.sizeOfInt(sizeint[0]);
bitsizeint[1] = Decoder.sizeOfInt(sizeint[1]);
bitsizeint[2] = Decoder.sizeOfInt(sizeint[2]);
bitsize = 0; // flag the use of large sizes
}
else {
bitsize = Decoder.sizeOfInts(3, sizeint);
}
let smallidx = dv.getInt32(offset);
offset += 4;
let tmpIdx = smallidx - 1;
tmpIdx = (FirstIdx > tmpIdx) ? FirstIdx : tmpIdx;
let smaller = (MagicInts[tmpIdx] / 2) | 0;
let smallnum = (MagicInts[smallidx] / 2) | 0;
sizesmall[0] = sizesmall[1] = sizesmall[2] = MagicInts[smallidx];
const adz = Math.ceil(dv.getInt32(offset) / 4) * 4;
offset += 4;
const invPrecision = 1.0 / precision;
let run = 0;
let i = 0;
// const buf8 = new Uint8Array(data.buffer, data.byteOffset + offset, 32 * 4); // 229...
thiscoord[0] = thiscoord[1] = thiscoord[2] = 0;
while (i < lsize) {
if (bitsize === 0) {
thiscoord[0] = Decoder.decodeBits(data, offset, bitsizeint[0]);
thiscoord[1] = Decoder.decodeBits(data, offset, bitsizeint[1]);
thiscoord[2] = Decoder.decodeBits(data, offset, bitsizeint[2]);
}
else {
Decoder.decodeInts(data, offset, bitsize, sizeint, thiscoord);
}
i++;
thiscoord[0] += minMaxInt[0];
thiscoord[1] += minMaxInt[1];
thiscoord[2] += minMaxInt[2];
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
const flag = Decoder.decodeBits(data, offset, 1);
let isSmaller = 0;
if (flag === 1) {
run = Decoder.decodeBits(data, offset, 5);
isSmaller = run % 3;
run -= isSmaller;
isSmaller--;
}
// if ((lfp-ptrstart)+run > size3){
// fprintf(stderr, "(xdrfile error) Buffer overrun during decompression.\n");
// return 0;
// }
if (run > 0) {
thiscoord[0] = thiscoord[1] = thiscoord[2] = 0;
for (let k = 0; k < run; k += 3) {
Decoder.decodeInts(data, offset, smallidx, sizesmall, thiscoord);
i++;
thiscoord[0] += prevcoord[0] - smallnum;
thiscoord[1] += prevcoord[1] - smallnum;
thiscoord[2] += prevcoord[2] - smallnum;
if (k === 0) {
// interchange first with second atom for
// better compression of water molecules
let tmpSwap = thiscoord[0];
thiscoord[0] = prevcoord[0];
prevcoord[0] = tmpSwap;
tmpSwap = thiscoord[1];
thiscoord[1] = prevcoord[1];
prevcoord[1] = tmpSwap;
tmpSwap = thiscoord[2];
thiscoord[2] = prevcoord[2];
prevcoord[2] = tmpSwap;
frameCoords.x[lfp] = prevcoord[0] * invPrecision;
frameCoords.y[lfp] = prevcoord[1] * invPrecision;
frameCoords.z[lfp] = prevcoord[2] * invPrecision;
lfp++;
}
else {
prevcoord[0] = thiscoord[0];
prevcoord[1] = thiscoord[1];
prevcoord[2] = thiscoord[2];
}
frameCoords.x[lfp] = thiscoord[0] * invPrecision;
frameCoords.y[lfp] = thiscoord[1] * invPrecision;
frameCoords.z[lfp] = thiscoord[2] * invPrecision;
lfp++;
}
}
else {
frameCoords.x[lfp] = thiscoord[0] * invPrecision;
frameCoords.y[lfp] = thiscoord[1] * invPrecision;
frameCoords.z[lfp] = thiscoord[2] * invPrecision;
lfp++;
}
smallidx += isSmaller;
if (isSmaller < 0) {
smallnum = smaller;
if (smallidx > FirstIdx) {
smaller = (MagicInts[smallidx - 1] / 2) | 0;
}
else {
smaller = 0;
}
}
else if (isSmaller > 0) {
smaller = smallnum;
smallnum = (MagicInts[smallidx] / 2) | 0;
}
sizesmall[0] = sizesmall[1] = sizesmall[2] = MagicInts[smallidx];
if (sizesmall[0] === 0 || sizesmall[1] === 0 || sizesmall[2] === 0) {
undefinedError();
}
}
offset += adz;
}
for (let c = 0; c < natoms; c++) {
frameCoords.x[c] *= 10;
frameCoords.y[c] *= 10;
frameCoords.z[c] *= 10;
}
coordinates.push(frameCoords);
if (ctx.shouldUpdate) {
await ctx.update({ current: offset, max: data.length });
}
if (offset >= data.length)
break;
}
if (times.length >= 1) {
f.timeOffset = times[0];
}
if (times.length >= 2) {
f.deltaTime = times[1] - times[0];
}
return f;
}
export function parseXtc(data) {
return Task.create('Parse XTC', async (ctx) => {
try {
ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
const file = await parseInternal(ctx, data);
return Result.success(file);
}
catch (e) {
return Result.error('' + e);
}
});
}