Source code for MDAnalysis.coordinates.TXYZ
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# 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
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
TXYZ file format --- :mod:`MDAnalysis.coordinates.TXYZ`
=======================================================
Coordinate reader for Tinker_ xyz files .txyz and trajectory .arc files.
Differences between Tinker format_ and normal xyz files:
- there is only one header line containing both the number of atoms and a comment
- column 1 contains atom numbers (starting from 1)
- column 6 contains atoms types
- the following columns indicate connectivity (atoms to which that particular atom is
bonded, according to numbering in column 1)
.. _format: http://chembytes.wikidot.com/tnk-tut00#toc2
.. _Tinker: https://dasher.wustl.edu/tinker/
Classes
-------
.. autoclass:: TXYZReader
:members:
:inherited-members:
"""
import numpy as np
import os
import errno
from ..lib import util
from . import base
from ..lib.util import openany, cached
[docs]class TXYZReader(base.ReaderBase):
"""Reads from a TXYZ file"""
format = ['TXYZ', 'ARC']
# these are assumed!
units = {'time': 'ps', 'length': 'Angstrom'}
_Timestep = base.Timestep
def __init__(self, filename, **kwargs):
super(TXYZReader, self).__init__(filename, **kwargs)
# the filename has been parsed to be either be foo.xyz or foo.xyz.bz2 by
# coordinates::core.py so the last file extension will tell us if it is
# bzipped or not
root, ext = os.path.splitext(self.filename)
self.xyzfile = util.anyopen(self.filename)
self._cache = dict()
# Check if file has box information saved
with util.openany(self.filename) as inp:
inp.readline()
line = inp.readline()
# If second line has float at second position, we have box info
try:
float(line.split()[1])
except ValueError:
self.periodic = False
else:
self.periodic = True
self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
self._read_next_timestep()
@property
@cached('n_atoms')
def n_atoms(self):
"""number of atoms in a frame"""
with util.anyopen(self.filename) as f:
n = f.readline().split()[0]
# need to check type of n
return int(n)
@property
@cached('n_frames')
def n_frames(self):
try:
return self._read_xyz_n_frames()
except IOError:
return 0
def _read_xyz_n_frames(self):
# the number of lines in the XYZ file will be 1 greater than the
# number of atoms
linesPerFrame = self.n_atoms + 1
if self.periodic:
linesPerFrame += 1
counter = 0
offsets = []
with util.anyopen(self.filename) as f:
line = True
while line:
if not counter % linesPerFrame:
offsets.append(f.tell())
line = f.readline()
counter += 1
# need to check this is an integer!
n_frames = int(counter / linesPerFrame)
self._offsets = offsets
return n_frames
def _read_frame(self, frame):
self.xyzfile.seek(self._offsets[frame])
self.ts.frame = frame - 1 # gets +1'd in next
return self._read_next_timestep()
def _read_next_timestep(self, ts=None):
# check that the timestep object exists
if ts is None:
ts = self.ts
f = self.xyzfile
try:
# we assume that there is only one header line per frame
f.readline()
if self.periodic:
ts.dimensions = f.readline().split()
# convert all entries at the end once for optimal speed
tmp_buf = []
for i in range(self.n_atoms):
tmp_buf.append(f.readline().split()[2:5])
ts.positions = tmp_buf
ts.frame += 1
return ts
except (ValueError, IndexError) as err:
raise EOFError(err) from None
def _reopen(self):
self.close()
self.open_trajectory()
def open_trajectory(self):
if self.xyzfile is not None:
raise IOError(
errno.EALREADY, 'TXYZ file already opened', self.filename)
self.xyzfile = util.anyopen(self.filename)
# reset ts
ts = self.ts
ts.frame = -1
return self.xyzfile
[docs] def close(self):
"""Close arc trajectory file if it was open."""
if self.xyzfile is None:
return
self.xyzfile.close()
self.xyzfile = None