molstar
Version:
A comprehensive macromolecular library.
67 lines • 4.24 kB
JavaScript
;
/**
* Copyright (c) 2019-2020 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.coordinatesFromDcd = void 0;
var tslib_1 = require("tslib");
var mol_task_1 = require("../../mol-task");
var coordinates_1 = require("../../mol-model/structure/coordinates");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
var misc_1 = require("../../mol-math/misc");
var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
var common_1 = require("../../mol-math/linear-algebra/3d/common");
var charmmTimeUnitFactor = 20.45482949774598;
function coordinatesFromDcd(dcdFile) {
var _this = this;
return mol_task_1.Task.create('Parse DCD', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var header, deltaTime, offsetTime, frames, i, il, dcdFrame, frame, c;
return (0, tslib_1.__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
? (0, coordinates_1.Time)(header.DELTA * charmmTimeUnitFactor, 'ps')
: (0, coordinates_1.Time)(1, 'step');
offsetTime = header.ISTART >= 1
? (0, coordinates_1.Time)((header.ISTART - 1) * deltaTime.value, deltaTime.unit)
: (0, coordinates_1.Time)(0, deltaTime.unit);
frames = [];
for (i = 0, il = dcdFile.frames.length; i < il; ++i) {
dcdFrame = dcdFile.frames[i];
frame = {
elementCount: dcdFrame.elementCount,
time: (0, coordinates_1.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_1.Cell.create(linear_algebra_1.Vec3.create(c[0], c[2], c[5]), linear_algebra_1.Vec3.create((0, misc_1.degToRad)(90 - Math.asin(c[1]) * 90 / misc_1.halfPI), (0, misc_1.degToRad)(90 - Math.asin(c[3]) * 90 / misc_1.halfPI), (0, misc_1.degToRad)(90 - Math.asin(c[4]) * 90 / misc_1.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_1.Cell.fromBasis(linear_algebra_1.Vec3.create(c[0], c[1], c[3]), linear_algebra_1.Vec3.create(c[1], c[2], c[4]), linear_algebra_1.Vec3.create(c[3], c[4], c[5]));
}
else {
frame.cell = cell_1.Cell.create(linear_algebra_1.Vec3.create(c[0], c[2], c[5]),
// interpret angles very close to 0 as 90 deg
linear_algebra_1.Vec3.create((0, misc_1.degToRad)((0, common_1.equalEps)(c[1], 0, common_1.EPSILON) ? 90 : c[1]), (0, misc_1.degToRad)((0, common_1.equalEps)(c[3], 0, common_1.EPSILON) ? 90 : c[3]), (0, misc_1.degToRad)((0, common_1.equalEps)(c[4], 0, common_1.EPSILON) ? 90 : c[4])));
}
}
frames.push(frame);
}
return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
}
});
}); });
}
exports.coordinatesFromDcd = coordinatesFromDcd;
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