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


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)


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