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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""INPCRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
================================================================================
Read coordinates in Amber_ coordinate/restart file (suffix "inpcrd").
.. _Amber: https://ambermd.org/FileFormats.php
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
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