Source code for MDAnalysis.coordinates.XTC

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"""
XTC trajectory files --- :mod:`MDAnalysis.coordinates.XTC`
==========================================================

Read and write GROMACS XTC trajectories.

See Also
--------
MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files.
MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats
"""
from __future__ import absolute_import

from . import base
from .XDR import XDRBaseReader, XDRBaseWriter
from ..lib.formats.libmdaxdr import XTCFile
from ..lib.mdamath import triclinic_vectors, triclinic_box


[docs]class XTCWriter(XDRBaseWriter): """Writer for the Gromacs XTC trajectory format. XTC is a compressed trajectory format from Gromacs. The trajectory is saved with reduced precision (3 decimal places by default) compared to other lossless formarts like TRR and DCD. The main advantage of XTC files is that they require significantly less disk space and the loss of precision is usually not a problem. """ format = 'XTC' multiframe = True units = {'time': 'ps', 'length': 'nm'} _file = XTCFile def __init__(self, filename, n_atoms, convert_units=True, precision=3, **kwargs): """ Parameters ---------- filename : str filename of the trajectory n_atoms : int number of atoms to write convert_units : bool (optional) convert into MDAnalysis units precision : float (optional) set precision of saved trjactory to this number of decimal places. """ super(XTCWriter, self).__init__(filename, n_atoms, convert_units, **kwargs) self.precision = precision def _write_next_frame(self, ag): """Write information associated with ``ag`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe See Also -------- <FormatWriter>.write(AtomGroup/Universe) The normal write() method takes a more general input .. deprecated:: 1.0.0 Deprecated using Timestep. To be removed in version 2.0. .. versionchanged:: 1.0.0 Added ability to use either AtomGroup or Universe. """ if isinstance(ag, base.Timestep): ts = ag else: try: # Atomgroup? ts = ag.ts except AttributeError: try: # Universe? ts = ag.trajectory.ts except AttributeError: raise TypeError("No Timestep found in ag argument") xyz = ts.positions.copy() time = ts.time step = ts.frame dimensions = ts.dimensions if self._convert_units: xyz = self.convert_pos_to_native(xyz, inplace=False) dimensions = self.convert_dimensions_to_unitcell(ts, inplace=False) box = triclinic_vectors(dimensions) # libmdaxdr will multiply the coordinates by precision. This means for # a precision of 3 decimal places we need to pass 1000.0 to the xdr # library. precision = 10.0 ** self.precision self._xdr.write(xyz, box, step, time, precision)
[docs]class XTCReader(XDRBaseReader): """Reader for the Gromacs XTC trajectory format. XTC is a compressed trajectory format from Gromacs. The trajectory is saved with reduced precision (3 decimal places) compared to other lossless formarts like TRR and DCD. The main advantage of XTC files is that they require significantly less disk space and the loss of precision is usually not a problem. Notes ----- See :ref:`Notes on offsets <offsets-label>` for more information about offsets. """ format = 'XTC' units = {'time': 'ps', 'length': 'nm'} _writer = XTCWriter _file = XTCFile def _frame_to_ts(self, frame, ts): """convert a xtc-frame to a mda TimeStep""" ts.frame = self._frame ts.time = frame.time ts.data['step'] = frame.step ts.dimensions = triclinic_box(*frame.box) if self._sub is not None: ts.positions = frame.x[self._sub] else: ts.positions = frame.x if self.convert_units: self.convert_pos_from_native(ts.positions) self.convert_pos_from_native(ts.dimensions[:3]) return ts