molstar
Version:
A comprehensive macromolecular library.
102 lines (101 loc) • 4.03 kB
JavaScript
;
/**
* 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.parseNctraj = void 0;
var tslib_1 = require("tslib");
var mol_task_1 = require("../../../mol-task");
var reader_1 = require("../../common/netcdf/reader");
var result_1 = require("../result");
function parseInternal(data) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var nc, f, _i, _a, c, velocities, _b, _c, v, forces, _d, _e, f_1, cell_lengths, _f, _g, l, cell_angles, _h, _j, a, time, _k, _l, t;
return tslib_1.__generator(this, function (_m) {
nc = new reader_1.NetcdfReader(data);
f = {
coordinates: [],
time: [],
timeOffset: 0,
deltaTime: 1
};
for (_i = 0, _a = nc.getDataVariable('coordinates'); _i < _a.length; _i++) {
c = _a[_i];
f.coordinates.push(c);
}
if (nc.hasDataVariable('velocities')) {
velocities = [];
for (_b = 0, _c = nc.getDataVariable('velocities'); _b < _c.length; _b++) {
v = _c[_b];
velocities.push(v);
}
f.velocities = velocities;
}
if (nc.hasDataVariable('forces')) {
forces = [];
for (_d = 0, _e = nc.getDataVariable('forces'); _d < _e.length; _d++) {
f_1 = _e[_d];
forces.push(f_1);
}
f.forces = forces;
}
if (nc.hasDataVariable('cell_lengths')) {
cell_lengths = [];
for (_f = 0, _g = nc.getDataVariable('cell_lengths'); _f < _g.length; _f++) {
l = _g[_f];
cell_lengths.push(l);
}
f.cell_lengths = cell_lengths;
}
if (nc.hasDataVariable('cell_angles')) {
cell_angles = [];
for (_h = 0, _j = nc.getDataVariable('cell_angles'); _h < _j.length; _h++) {
a = _j[_h];
cell_angles.push(a);
}
f.cell_angles = cell_angles;
}
if (nc.hasDataVariable('time')) {
time = [];
for (_k = 0, _l = nc.getDataVariable('time'); _k < _l.length; _k++) {
t = _l[_k];
time.push(t);
}
f.time = time;
}
if (f.time) {
if (f.time.length >= 1) {
f.timeOffset = f.time[0];
}
if (f.time.length >= 2) {
f.deltaTime = f.time[1] - f.time[0];
}
}
return [2 /*return*/, f];
});
});
}
function parseNctraj(data) {
var _this = this;
return mol_task_1.Task.create('Parse NCTRAJ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var file, e_1;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
_a.trys.push([0, 2, , 3]);
ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
return [4 /*yield*/, parseInternal(data)];
case 1:
file = _a.sent();
return [2 /*return*/, result_1.ReaderResult.success(file)];
case 2:
e_1 = _a.sent();
return [2 /*return*/, result_1.ReaderResult.error('' + e_1)];
case 3: return [2 /*return*/];
}
});
}); });
}
exports.parseNctraj = parseNctraj;