Source code for MDAnalysis.coordinates.NAMDBIN

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"""NAMDBIN files format --- :mod:`MDAnalysis.coordinates.NAMDBIN`
================================================================================

Read/Write coordinates in `NAMD double-precision binary format`_ (suffix "coor" or "namdbin").

.. _`NAMD double-precision binary format` : https://www.ks.uiuc.edu/Research/namd/2.10/ug/node11.html#SECTION00061500000000000000


Classes
-------

.. autoclass:: NAMDBINReader
   :members:

.. autoclass:: NAMDBINWriter
   :members:

"""
from struct import pack
import numpy as np

from . import base
from ..lib import util


class NAMDBINReader(base.SingleFrameReaderBase):
    """Reader for NAMD binary coordinate files.
    
    
    .. versionadded:: 1.0.0   
    """

    format = ['COOR', 'NAMDBIN']
    units = {'length': 'Angstrom'}

    def _read_first_frame(self):
        # Read header
        with open(self.filename, 'rb') as namdbin:
            self.n_atoms = np.fromfile(namdbin, dtype=np.int32, count=1)[0]
            self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
            self.ts.frame = 0
            coord_double = np.fromfile(namdbin,
                                       dtype=np.float64,
                                       count=self.n_atoms * 3)
            self.ts._pos[:] = np.array(
                coord_double, float).reshape(self.n_atoms, 3)

    @staticmethod
    def parse_n_atoms(filename, **kwargs):
        with open(filename, 'rb') as namdbin:
            n_atoms = np.fromfile(namdbin, dtype=np.int32, count=1)[0]
        return n_atoms

    def Writer(self, filename, **kwargs):
        """Returns a NAMDBINWriter for *filename*.

        Parameters
        ----------
        filename: str
            filename of the output NAMDBIN file

        Returns
        -------
        :class:`NAMDBINWriter`

        """
        return NAMDBINWriter(filename, **kwargs)


class NAMDBINWriter(base.WriterBase):
    """Writer for NAMD binary coordinate files.
    

    Note
    ----
    * Does not handle writing to bz2 or gz compressed file types.


    .. versionadded:: 1.0.0
    """
    format = ['COOR', 'NAMDBIN']
    units = {'time': None, 'length': 'Angstrom'}

    def __init__(self, filename, n_atoms=None, **kwargs):
        """
        Parameters
        ----------
        filename : str or :class:`~MDAnalysis.lib.util.NamedStream`
             name of the output file or a stream
        n_atoms  : int
            number of atoms for the output coordinate
        """
        self.filename = util.filename(filename)

    def _write_next_frame(self, obj):
        """Write information associated with ``obj`` at current frame into
        trajectory


        Parameters
        ----------
        obj : :class:`~MDAnalysis.core.groups.AtomGroup` or
              :class:`~MDAnalysis.core.universe.Universe`
              write coordinate information associated with `obj`


        .. versionchanged:: 1.0.0
           Renamed from `write` to `_write_next_frame`.
        .. versionchanged:: 2.0.0
           Deprecated support for Timestep argument has now been removed.
           Use AtomGroup or Universe as an input instead.
        """
        if hasattr(obj, 'atoms'):  # AtomGroup or Universe
            atoms = obj.atoms
            n_atoms = len(atoms)
            coor = atoms.positions.reshape(n_atoms*3)
        else:
            errmsg = "Input obj is neither an AtomGroup or Universe"
            raise TypeError(errmsg) from None

        with util.openany(self.filename, 'wb') as namdbin:
            # Write NUMATOMS
            namdbin.write(pack('i', n_atoms))
            # Write Coordinate
            namdbin.write(pack('{:d}d'.format(len(coor)), *coor))