Source code for MDAnalysis.coordinates.TRC
# -*- 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 GNU Public Licence, v2 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
#
"""GROMOS11 trajectory reader --- :mod:`MDAnalysis.coordinates.TRC`
====================================================================
Reads coordinates, timesteps and box-sizes from GROMOS11 TRC trajectories.
To load the trajectory into :class:`~MDAnalysis.core.universe.Universe`,
you need to provide topology information using a topology file such as
a PDB::
import MDAnalysis as mda
u = mda.Universe("topology.pdb", ["md_1.trc.gz","md_2.trc.gz"],
continuous=True)
.. Note::
The GROMOS trajectory format organizes its data in blocks. A block starts
with a blockname in capital letters (example: POSITIONRED) and ends with
a line containing only ''END''. Only the TITLE-block at the beginning of
each file is mandatory, others blocks can be chosen depending on the task.
The trajectory format as well as all permitted blocks and their data are
documented in the GROMOS Manual Vol. 4, chapter 2 and 4.
The manual can be downloaded here:
https://gromos.net/gromos11_pdf_manuals/vol4.pdf
This reader is designed to read the blocks "TIMESTEP", "POSITIONRED" and
"GENBOX" from the trajectory which covers the standard trajectories of most
simulations . If a trajectory includes other blocks, a warning is served
and the blocks are ignored.
.. Note::
MDAnalysis requires the blocks to be in the same order for each frame
and ignores non-supported blocks.
Classes
-------
.. autoclass:: TRCReader
:members:
"""
import pathlib
import errno
import warnings
import numpy as np
from . import base
from .timestep import Timestep
from ..lib import util
from ..lib.util import cached, store_init_arguments
import logging
logger = logging.getLogger("MDAnalysis.coordinates.GROMOS11")
[docs]
class TRCReader(base.ReaderBase):
"""Coordinate reader for the GROMOS11 format"""
format = "TRC"
units = {"time": "ps", "length": "nm"}
_Timestep = Timestep
SUPPORTED_BLOCKS = ["TITLE", "TIMESTEP", "POSITIONRED", "GENBOX"]
NOT_SUPPORTED_BLOCKS = [
"POSITION",
"REFPOSITION",
"VELOCITY",
"VELOCITYRED",
"FREEFORCE",
"FREEFORCERED",
"CONSFORCE",
"CONSFORCERED",
"SHAKEFAILPOSITION",
"SHAKEFAILPREVPOSITION",
"LATTICESHIFTS",
"COSDISPLACEMENTS",
"STOCHINT",
"NHCVARIABLES",
"ROTTRANSREFPOS",
"PERTDATA",
"DISRESEXPAVE",
"JVALUERESEXPAVE",
"JVALUERESEPS",
"JVALUEPERSCALE",
"ORDERPARAMRESEXPAVE",
"XRAYRESEXPAVE",
"LEUSBIAS",
"LEUSBIASBAS",
"ENERGY03",
"VOLUMEPRESSURE03",
"FREEENERGYDERIVS03",
"BFACTOR",
"AEDSS",
]
@store_init_arguments
def __init__(self, filename, convert_units=True, **kwargs):
super(TRCReader, self).__init__(filename, **kwargs)
# GROMOS11 trajectories are usually either *.trc or *.trc.gz.
# (trj suffix can come up when trajectory obtained from clustering)
ext = pathlib.Path(self.filename).suffix
if (ext[1:] == "trc") or (ext[1:] == "trj"):
self.compressed = None
else:
self.compressed = ext[1:]
self.trcfile = util.anyopen(self.filename)
self.convert_units = convert_units
# Read and calculate some information about the trajectory
self.traj_properties = self._read_traj_properties()
self._cache = {}
self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
self._reopen()
self.ts.dt = self.traj_properties["dt"]
self._read_frame(0)
@property
@cached("n_atoms")
def n_atoms(self):
"""The number of atoms in one frame."""
return self.traj_properties["n_atoms"]
@property
@cached("n_frames")
def n_frames(self):
"""The number of frames in the trajectory."""
return self.traj_properties["n_frames"]
def _frame_to_ts(self, frameDat, ts):
"""Convert a frame to a :class:`TimeStep`"""
ts.frame = self._frame
ts.time = frameDat["time"]
ts.data["time"] = frameDat["time"]
ts.data["step"] = frameDat["step"]
ts.dimensions = frameDat["dimensions"]
ts.positions = frameDat["positions"]
# Convert the units
if self.convert_units:
if ts.has_positions:
self.convert_pos_from_native(ts.positions)
if ts.dimensions is not None:
self.convert_pos_from_native(ts.dimensions[:3])
return ts
def _read_traj_properties(self):
"""
* Reads the number of atoms per frame (n_atoms)
* Reads the number of frames (n_frames)
* Reads the startposition of the timestep block
for each frame (l_blockstart_offset)
"""
traj_properties = {}
#
# Check which of the supported blocks comes first in the trajectory
#
first_block = None
with util.anyopen(self.filename) as f:
for line in iter(f.readline, ""):
for blockname in TRCReader.SUPPORTED_BLOCKS:
if (blockname == line.strip()) and (blockname != "TITLE"):
# Save the name of the first non-title block
# in the trajectory file
first_block = blockname
if first_block is not None:
break # First block found
#
# Calculate meta-data of the trajectory
#
in_positionred_block = False
lastline_was_timestep = False
atom_counter = 0
n_atoms = 0
frame_counter = 0
l_blockstart_offset = []
l_timestep_timevalues = []
with util.anyopen(self.filename) as f:
for line in iter(f.readline, ""):
#
# First block of frame
#
if first_block == line.strip():
l_blockstart_offset.append(f.tell() - len(line))
frame_counter += 1
#
# Timestep-block
#
if "TIMESTEP" == line.strip():
lastline_was_timestep = True
elif lastline_was_timestep is True:
l_timestep_timevalues.append(float(line.split()[1]))
lastline_was_timestep = False
#
# Coordinates-block
#
if "POSITIONRED" == line.strip():
in_positionred_block = True
elif (in_positionred_block is True) and (n_atoms == 0):
if len(line.split()) == 3:
atom_counter += 1
if ("END" == line.strip()) and (in_positionred_block is True):
n_atoms = atom_counter
in_positionred_block = False
if frame_counter == 0:
raise ValueError(
"No supported blocks were found within the GROMOS trajectory!"
)
traj_properties["n_atoms"] = n_atoms
traj_properties["n_frames"] = frame_counter
traj_properties["l_blockstart_offset"] = l_blockstart_offset
if len(l_timestep_timevalues) >= 2:
traj_properties["dt"] = l_timestep_timevalues[1] - l_timestep_timevalues[0]
else:
traj_properties["dt"] = 0
warnings.warn(
"The trajectory does not contain TIMESTEP blocks!", UserWarning
)
return traj_properties
def _read_GROMOS11_trajectory(self):
frameDat = {}
frameDat["step"] = int(self._frame)
frameDat["time"] = float(0.0)
frameDat["positions"] = None
frameDat["dimensions"] = None
self.periodic = False
# Read the trajectory
f = self.trcfile
for line in iter(f.readline, ""):
if "TIMESTEP" == line.strip():
tmp_step, tmp_time = f.readline().split()
frameDat["step"] = int(tmp_step)
frameDat["time"] = float(tmp_time)
elif "POSITIONRED" == line.strip():
tmp_buf = []
while True:
coords_str = f.readline()
if "#" in coords_str:
continue
elif "END" in coords_str:
break
else:
tmp_buf.append(coords_str.split())
if np.array(tmp_buf).shape[0] == self.n_atoms:
frameDat["positions"] = np.asarray(tmp_buf, dtype=np.float64)
else:
raise ValueError(
"The trajectory contains the wrong number of atoms!"
)
elif "GENBOX" == line.strip():
ntb_setting = int(f.readline())
if ntb_setting == 0:
frameDat["dimensions"] = None
self.periodic = False
elif ntb_setting in [1, 2]:
tmp_a, tmp_b, tmp_c = f.readline().split()
tmp_alpha, tmp_beta, tmp_gamma = f.readline().split()
frameDat["dimensions"] = [
float(tmp_a),
float(tmp_b),
float(tmp_c),
float(tmp_alpha),
float(tmp_beta),
float(tmp_gamma),
]
self.periodic = True
gb_line3 = f.readline().split()
if np.sum(np.abs(np.array(gb_line3).astype(np.float64))) > 1e-10:
raise ValueError(
"This reader doesnt't support a shifted origin!"
)
gb_line4 = f.readline().split()
if np.sum(np.abs(np.array(gb_line4).astype(np.float64))) > 1e-10:
raise ValueError(
"This reader "
"doesnt't support "
"yawed, pitched or "
"rolled boxes!"
)
else:
raise ValueError(
"This reader doesn't support "
"truncated-octahedral "
"periodic boundary conditions"
)
break
elif any(
non_supp_bn in line for non_supp_bn in TRCReader.NOT_SUPPORTED_BLOCKS
):
for non_supp_bn in TRCReader.NOT_SUPPORTED_BLOCKS:
if non_supp_bn == line.strip():
warnings.warn(
non_supp_bn + " block is not supported!", UserWarning
)
return frameDat
def _read_frame(self, i):
"""read frame i"""
self._frame = i - 1
# Move position in file just (-2 byte) before the start of the block
self.trcfile.seek(self.traj_properties["l_blockstart_offset"][i] - 2, 0)
return self._read_next_timestep()
def _read_next_timestep(self):
self._frame += 1
if self._frame >= self.n_frames:
raise IOError("Trying to go over trajectory limit")
raw_framedata = self._read_GROMOS11_trajectory()
self._frame_to_ts(raw_framedata, self.ts)
return self.ts
def _reopen(self):
"""Close and reopen the trajectory"""
self.close()
self.open_trajectory()
def open_trajectory(self):
if self.trcfile is not None:
raise IOError(errno.EALREADY, "TRC file already opened", self.filename)
# Reload trajectory file
self.trcfile = util.anyopen(self.filename)
# Reset ts
self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
# Set _frame to -1, so next timestep is zero
self._frame = -1
return self.trcfile
[docs]
def close(self):
"""Close the trc trajectory file if it was open."""
if self.trcfile is not None:
self.trcfile.close()
self.trcfile = None