Source code for MDAnalysis.coordinates.TXYZ

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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:
.. _Tinker:


.. autoclass:: TXYZReader

import numpy as np
import os
import errno

from ..lib import util
from . import base
from ..lib.util import openany, cached, store_init_arguments

[docs]class TXYZReader(base.ReaderBase): """Reads from a TXYZ file""" format = ['TXYZ', 'ARC'] # these are assumed! units = {'time': 'ps', 'length': 'Angstrom'} _Timestep = base.Timestep @store_init_arguments def __init__(self, filename, **kwargs): super(TXYZReader, self).__init__(filename, **kwargs) # the filename has been parsed to be either be or by # 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):[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