Source code for MDAnalysis.coordinates.TRC
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# Please cite your use of MDAnalysis in published work:
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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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# doi: 10.25080/majora-629e541a-00e
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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
#
"""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, ""):
stripped_line = line.strip()
if stripped_line in TRCReader.SUPPORTED_BLOCKS and (
stripped_line != "TITLE"
):
# Save the name of the first non-title block
# in the trajectory file
first_block = stripped_line
break
#
# Calculate meta-data of the trajectory
#
n_atoms = 0
frame_counter = 0
block_size = {}
block_size["POSITIONRED"] = None
inconsistent_size = False
l_blockstart_offset = []
l_timestep_timevalues = []
with util.anyopen(self.filename) as f:
for line in iter(f.readline, ""):
stripped_line = line.strip()
#
# First block of frame
#
if first_block == stripped_line:
l_blockstart_offset.append(f.tell() - len(line))
frame_counter += 1
#
# Timestep-block
#
if "TIMESTEP" == stripped_line:
l_timestep_timevalues.append(
float(f.readline().split()[1])
)
while stripped_line != "END":
stripped_line = f.readline().strip()
#
# Coordinates-block
#
if "POSITIONRED" == stripped_line:
# Only count the number of atoms in the first block
# Also stores the size of the POSITIONRED block which
# should be consistent in most cases.
if n_atoms == 0:
start = f.tell() - len(line)
while stripped_line != "END":
line = f.readline()
stripped_line = line.strip()
if len(stripped_line.split()) == 3:
n_atoms += 1
end = f.tell() - len(line)
block_size["POSITIONRED"] = end - start
elif inconsistent_size:
while stripped_line != "END":
stripped_line = f.readline().strip()
else:
# While it is allowed for trailing whitespace to exist
# in the trajectories, none of the GROMOS trajectory
# writers do actually produce trailing whitespace.
# By default we try to assume a consistent size of the
# POSITIONRED block. We then try to skip reading subsequent
# occurences of this block.
# If we end up somewhere unexpected, we will throw
# a warning and fall back to iterating over the file.
# instead of looping over the file, looking for an END
# we can seek to where the end of the block should be.
current_pos = f.tell() - len(line)
f.seek(
f.tell() - len(line) + block_size["POSITIONRED"]
)
# Check if we are at the correct position
# If not, set inconsistent_size to true and seek back
# to where we were before
if f.readline().strip() != "END":
inconsistent_size = True
warnmsg = f"Inconsistent POSITIONRED block size in file {f.name}. Falling back to slow reader."
warnings.warn(warnmsg, UserWarning)
logger.warning(warnmsg)
f.seek(current_pos)
if frame_counter == 0:
errormsg = (
"No supported blocks were found within the GROMOS trajectory!"
)
logger.error(errormsg)
raise ValueError(errormsg)
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
warnmsg = "The trajectory does not contain TIMESTEP blocks!"
warnings.warn(warnmsg, UserWarning)
logger.warning(warnmsg)
return traj_properties
def _read_GROMOS11_trajectory(self):
frameDat = {}
frameDat["step"] = int(self._frame)
frameDat["time"] = float(0.0)
frameDat["positions"] = np.zeros(
(self.traj_properties["n_atoms"], 3), dtype=np.float64
)
frameDat["dimensions"] = None
self.periodic = False
# Read the trajectory
f = self.trcfile
for line in iter(f.readline, ""):
stripped_line = line.strip()
if "TIMESTEP" == stripped_line:
tmp_step, tmp_time = f.readline().split()
frameDat["step"] = int(tmp_step)
frameDat["time"] = float(tmp_time)
elif "POSITIONRED" == stripped_line:
i = 0
buffer = []
while True:
coords_str = f.readline()
if "#" in coords_str:
continue
elif "END" in coords_str:
break
else:
buffer.append(coords_str)
i += 1
data = np.fromstring(
"".join(buffer),
sep=" ",
dtype=np.float64,
count=self.n_atoms * 3,
)
frameDat["positions"] = data.reshape(-1, 3)
if i != self.traj_properties["n_atoms"]:
errormsg = f"Found {i} atoms in step {self._frame}, but expected {self.traj_properties['n_atoms']}"
logger.error(errormsg)
raise ValueError(errormsg)
elif "GENBOX" == stripped_line:
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 = map(float, f.readline().split())
tmp_alpha, tmp_beta, tmp_gamma = map(
float, f.readline().split()
)
frameDat["dimensions"] = [
tmp_a,
tmp_b,
tmp_c,
tmp_alpha,
tmp_beta,
tmp_gamma,
]
self.periodic = True
# gb_line3
if (
sum(abs(float(v)) for v in f.readline().split())
> 1e-10
):
errormsg = (
"This reader doesnt't support a shifted origin!"
)
logger.error(errormsg)
raise ValueError(errormsg)
# gb_line4
if (
sum(abs(float(v)) for v in f.readline().split())
> 1e-10
):
errormsg = "This reader doesnt't support yawed, pitched or rolled boxes!"
logger.error(errormsg)
raise ValueError(errormsg)
else:
errormsg = "This reader does't support truncated-octahedral periodic boundary conditions"
logger.error(errormsg)
raise ValueError(errormsg)
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 == stripped_line:
warnmsg = non_supp_bn + " block is not supported!"
warnings.warn(warnmsg, UserWarning)
logger.warning(warnmsg)
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:
errormsg = "Trying to go over trajectory limit"
logger.error(errormsg)
raise IOError(errormsg)
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:
errormsg = errno.EALREADY, "TRC file already opened", self.filename
logger.error(errormsg)
raise IOError(errormsg)
# 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