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 __future__ import absolute_import, division, print_function, unicode_literals

from six.moves import range

from . import base

[docs]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])
[docs] @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