molstar
Version:
A comprehensive macromolecular library.
63 lines (62 loc) • 3.63 kB
JavaScript
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __awaiter, __generator } from "tslib";
import { Task } from '../../mol-task';
import { Coordinates, Time } from '../../mol-model/structure/coordinates';
import { Vec3 } from '../../mol-math/linear-algebra';
import { degToRad, halfPI } from '../../mol-math/misc';
import { Cell } from '../../mol-math/geometry/spacegroup/cell';
import { EPSILON, equalEps } from '../../mol-math/linear-algebra/3d/common';
var charmmTimeUnitFactor = 20.45482949774598;
export function coordinatesFromDcd(dcdFile) {
var _this = this;
return Task.create('Parse DCD', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
var header, deltaTime, offsetTime, frames, i, il, dcdFrame, frame, c;
return __generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
case 1:
_a.sent();
header = dcdFile.header;
deltaTime = header.DELTA
? Time(header.DELTA * charmmTimeUnitFactor, 'ps')
: Time(1, 'step');
offsetTime = header.ISTART >= 1
? Time((header.ISTART - 1) * deltaTime.value, deltaTime.unit)
: Time(0, deltaTime.unit);
frames = [];
for (i = 0, il = dcdFile.frames.length; i < il; ++i) {
dcdFrame = dcdFile.frames[i];
frame = {
elementCount: dcdFrame.elementCount,
time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit),
x: dcdFrame.x,
y: dcdFrame.y,
z: dcdFrame.z,
xyzOrdering: { isIdentity: true }
};
if (dcdFrame.cell) {
c = dcdFrame.cell;
if (c[1] >= -1 && c[1] <= 1 && c[3] >= -1 && c[3] <= 1 && c[4] >= -1 && c[4] <= 1) {
frame.cell = Cell.create(Vec3.create(c[0], c[2], c[5]), Vec3.create(degToRad(90 - Math.asin(c[1]) * 90 / halfPI), degToRad(90 - Math.asin(c[3]) * 90 / halfPI), degToRad(90 - Math.asin(c[4]) * 90 / halfPI)));
}
else if (c[0] < 0 || c[1] < 0 || c[2] < 0 || c[3] < 0 || c[4] < 0 || c[5] < 0 ||
c[3] > 180 || c[4] > 180 || c[5] > 180) {
frame.cell = Cell.fromBasis(Vec3.create(c[0], c[1], c[3]), Vec3.create(c[1], c[2], c[4]), Vec3.create(c[3], c[4], c[5]));
}
else {
frame.cell = Cell.create(Vec3.create(c[0], c[2], c[5]),
// interpret angles very close to 0 as 90 deg
Vec3.create(degToRad(equalEps(c[1], 0, EPSILON) ? 90 : c[1]), degToRad(equalEps(c[3], 0, EPSILON) ? 90 : c[3]), degToRad(equalEps(c[4], 0, EPSILON) ? 90 : c[4])));
}
}
frames.push(frame);
}
return [2 /*return*/, Coordinates.create(frames, deltaTime, offsetTime)];
}
});
}); });
}