# -*- 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 # """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") 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 def close(self): """Close the trc trajectory file if it was open.""" if self.trcfile is not None: self.trcfile.close() self.trcfile = None