Source code for MDAnalysis.coordinates.INPCRD

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"""INPCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
================================================================================

Read coordinates in Amber_ coordinate/restart file (suffix "inpcrd").

.. _Amber: http://ambermd.org/formats.html#restart


Classes
-------

.. autoclass:: INPReader
   :members:

"""

from . import base

class INPReader(base.SingleFrameReaderBase):
    """Reader for Amber restart files."""

    format = ['INPCRD', 'RESTRT']
    units = {'length': 'Angstrom'}

    def _read_first_frame(self):
        # Read header
        with open(self.filename, 'r') as inf:
            self.title = inf.readline().strip()
            line = inf.readline().split()
            self.n_atoms = int(line[0])

            self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
            try:
                time = float(line[1])
            except IndexError:
                pass
            else:
                self.ts.time = time
            self.ts.frame = 0

            for p in range(self.n_atoms // 2):
                line = inf.readline()
                # each float is f12.7, 6 floats a line
                for i, dest in enumerate([(2*p, 0), (2*p, 1), (2*p, 2),
                                          (2*p + 1, 0), (2*p + 1, 1), (2*p + 1, 2)]):
                    self.ts._pos[dest] = float(line[i*12:(i+1)*12])
            # Read last coordinate if necessary
            if self.n_atoms % 2:
                line = inf.readline()
                for i in range(3):
                    self.ts._pos[-1, i] = float(line[i*12:(i+1)*12])

    @staticmethod
    def parse_n_atoms(filename, **kwargs):
        with open(filename, 'r') as f:
            f.readline()
            n_atoms = int(f.readline().split()[0])
        return n_atoms