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
"""

import errno
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 .. versionchanged:: 1.0.0 Added ability to use either AtomGroup or Universe. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. """ try: # Atomgroup? ts = ag.ts except AttributeError: try: # Universe? ts = ag.trajectory.ts except AttributeError: errmsg = "Input obj is neither an AtomGroup or Universe" raise TypeError(errmsg) from None 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 _read_next_timestep(self, ts=None): """ copy next frame into timestep versionadded:: 2.4.0 XTCReader implements this method so that it can use read_direct_x method of XTCFile to read the data directly into the timestep rather than copying it from a temporary array. """ if self._frame == self.n_frames - 1: raise IOError(errno.EIO, 'trying to go over trajectory limit') if ts is None: ts = self.ts if ts.has_positions: frame = self._xdr.read_direct_x(ts.positions) else: frame = self._xdr.read() self._frame += 1 self._frame_to_ts(frame, ts) return ts 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) if ts.dimensions is not None: self.convert_pos_from_native(ts.dimensions[:3]) return ts