Source code for mdtraj.formats.gro

"""gro.py: Used for loading Gromacs GRO files."""

##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Robert McGibbon, Lee-Ping Wang, Peter Eastman
# Contributors: Jason Swails
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
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# This library is distributed in the hope that it will be useful,
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
#
# Portions of this code originate from the OpenMM molecular simulation
# toolkit, copyright (c) 2012 Stanford University and the Authors. Those
# portions are distributed under the following terms:
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import itertools
import os
import warnings
from re import findall, match, sub

import numpy as np

import mdtraj as md
from mdtraj.core import element as elem
from mdtraj.formats import pdb
from mdtraj.formats.registry import FormatRegistry
from mdtraj.utils import cast_indices, ensure_type, in_units_of


@FormatRegistry.register_loader(".gro")
def load_gro(filename, stride=None, atom_indices=None, frame=None, top=None):
    """Load a GROMACS GRO file.

    Parameters
    ----------
    filename : path-like
        Path to the GRO file on disk.
    stride : int, default=None
        Only read every stride-th model from the file
    atom_indices : array_like, optional
        If not none, then read only a subset of the atoms coordinates from the
        file. These indices are zero-based.
    frame : int, optional
        Use this option to load only a single frame from a trajectory on disk.
        If frame is None, the default, the entire trajectory will be loaded.
        If supplied, ``stride`` will be ignored.
    top : mdtraj.core.Topology, default=None
        if you give a topology as input the topology won't be parsed from the gro file
        it saves time if you have to parse a big number of files
    """

    with GroTrajectoryFile(filename, "r", top=top) as f:
        if frame is not None:
            f.seek(frame)
            n_frames = 1
        else:
            n_frames = None
        return f.read_as_traj(
            n_frames=n_frames,
            stride=stride,
            atom_indices=atom_indices,
        )


[docs] @FormatRegistry.register_fileobject(".gro") class GroTrajectoryFile: """Interface for reading and writing to GROMACS GRO files. Parameters ---------- filename : path-like The filename to open. A path to a file on disk. mode : {'r', 'w'} The mode in which to open the file, either 'r' for read or 'w' for write. force_overwrite : bool If opened in write mode, and a file by the name of `filename` already exists on disk, should we overwrite it? top : mdtraj.core.Topology, default=None if you give a topology as input the topology won't be parsed from the gro file it saves time if you have to parse a big number of files Attributes ---------- n_atoms : int The number of atoms in the file topology : md.Topology The topology. TODO(rmcgibbo) note about chain See Also -------- load_gro : High-level wrapper that returns a ``md.Trajectory`` """ distance_unit = "nanometers"
[docs] def __init__(self, filename, mode="r", force_overwrite=True, top=None): self._open = False self._file = None self._mode = mode self.topology = top if mode == "r": self._open = True self._frame_index = 0 self._file = open(filename) try: if self.topology is None: self.n_atoms, self.topology = self._read_topology() else: self.n_atoms = self.topology.n_atoms finally: self._file.seek(0) elif mode == "w": self._open = True if os.path.exists(filename) and not force_overwrite: raise OSError('"%s" already exists' % filename) self._frame_index = 0 self._file = open(filename, "w") else: raise ValueError("invalid mode: %s" % mode)
def write( self, coordinates, topology, time=None, unitcell_vectors=None, precision=3, ): """Write one or more frames of a molecular dynamics trajectory to disk in the GROMACS GRO format. Parameters ---------- coordinates : np.ndarray, dtype=np.float32, shape=(n_frames, n_atoms, 3) The cartesian coordinates of each atom, in units of nanometers. topology : mdtraj.Topology The Topology defining the model to write. time : np.ndarray, dtype=float32, shape=(n_frames), optional The simulation time corresponding to each frame, in picoseconds. If not supplied, the numbers 0..n_frames will be written. unitcell_vectors : np.ndarray, dtype=float32, shape=(n_frames, 3, 3), optional The periodic box vectors of the simulation in each frame, in nanometers. precision : int, optional The number of decimal places to print for coordinates. Default is 3 """ if not self._open: raise ValueError("I/O operation on closed file") if not self._mode == "w": raise ValueError("file not opened for writing") coordinates = ensure_type( coordinates, dtype=np.float32, ndim=3, name="coordinates", can_be_none=False, warn_on_cast=False, ) time = ensure_type( time, dtype=float, ndim=1, name="time", can_be_none=True, shape=(len(coordinates),), warn_on_cast=False, ) unitcell_vectors = ensure_type( unitcell_vectors, dtype=float, ndim=3, name="unitcell_vectors", can_be_none=True, shape=(len(coordinates), 3, 3), warn_on_cast=False, ) for i in range(coordinates.shape[0]): frame_time = None if time is None else time[i] frame_box = None if unitcell_vectors is None else unitcell_vectors[i] self._write_frame( coordinates[i], topology, frame_time, frame_box, precision, ) def read_as_traj(self, n_frames=None, stride=None, atom_indices=None): """Read a trajectory from a gro file Parameters ---------- n_frames : int, optional If positive, then read only the next `n_frames` frames. Otherwise read all of the frames in the file. stride : np.ndarray, optional Read only every stride-th frame. atom_indices : array_like, optional If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory. Returns ------- trajectory : Trajectory A trajectory object containing the loaded portion of the file. """ from mdtraj.core.trajectory import Trajectory topology = self.topology if atom_indices is not None: topology = topology.subset(atom_indices) coordinates, time, unitcell_vectors = self.read( stride=stride, atom_indices=atom_indices, ) if len(coordinates) == 0: return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology) coordinates = in_units_of( coordinates, self.distance_unit, Trajectory._distance_unit, inplace=True, ) unitcell_vectors = in_units_of( unitcell_vectors, self.distance_unit, Trajectory._distance_unit, inplace=True, ) traj = Trajectory(xyz=coordinates, topology=topology, time=time) traj.unitcell_vectors = unitcell_vectors return traj def read(self, n_frames=None, stride=None, atom_indices=None): """Read data from a molecular dynamics trajectory in the GROMACS GRO format. Parameters ---------- n_frames : int, optional If n_frames is not None, the next n_frames of data from the file will be read. Otherwise, all of the frames in the file will be read. stride : int, optional If stride is not None, read only every stride-th frame from disk. atom_indices : np.ndarray, dtype=int, optional The specific indices of the atoms you'd like to retrieve. If not supplied, all of the atoms will be retrieved. Returns ------- coordinates : np.ndarray, shape=(n_frames, n_atoms, 3) The cartesian coordinates of the atoms, in units of nanometers. time : np.ndarray, None The time corresponding to each frame, in units of picoseconds, or None if no time information is present in the trajectory. unitcell_vectors : np.ndarray, shape=(n_frames, 3, 3) The box vectors in each frame, in units of nanometers """ if not self._open: raise ValueError("I/O operation on closed file") if not self._mode == "r": raise ValueError("file not opened for reading") coordinates = [] unitcell_vectors = [] time = [] contains_time = True atom_indices = cast_indices(atom_indices) atom_slice = slice(None) if atom_indices is None else atom_indices if n_frames is None: frameiter = itertools.count() else: frameiter = range(n_frames) for i in frameiter: try: frame_xyz, frame_box, frame_time = self._read_frame() contains_time = contains_time and (frame_time is not None) coordinates.append(frame_xyz[atom_slice]) unitcell_vectors.append(frame_box) time.append(frame_time) except StopIteration: break coordinates, unitcell_vectors, time = map( np.array, (coordinates, unitcell_vectors, time), ) if not contains_time: time = None else: time = time[::stride] return coordinates[::stride], time, unitcell_vectors[::stride] def _read_topology(self): if not self._open: raise ValueError("I/O operation on closed file") if not self._mode == "r": raise ValueError("file not opened for reading") pdb.PDBTrajectoryFile._loadNameReplacementTables() n_atoms = None topology = md.Topology() chain = topology.add_chain() residue = None atomReplacements = {} # This is needed because sometimes # residue names get replaced and this # brings to wrong residue parsing old_resname = None for ln, line in enumerate(self._file): if ln == 1: n_atoms = int(line.strip()) elif ln > 1 and ln < n_atoms + 2: (thisresnum, thisresname, thisatomname, thisatomnum) = ( line[i * 5 : i * 5 + 5].strip() for i in range(4) ) thisresnum, thisatomnum = map(int, (thisresnum, thisatomnum)) if residue is None or residue.resSeq != thisresnum or old_resname != thisresname: if residue is not None and thisresnum == residue.resSeq: warnings.warn( f"WARNING: two consecutive residues with same number ({thisresname}, {old_resname})", ) old_resname = thisresname if thisresname in pdb.PDBTrajectoryFile._residueNameReplacements: thisresname = pdb.PDBTrajectoryFile._residueNameReplacements[thisresname] residue = topology.add_residue( thisresname, chain, resSeq=thisresnum, ) if thisresname in pdb.PDBTrajectoryFile._atomNameReplacements: atomReplacements = pdb.PDBTrajectoryFile._atomNameReplacements[thisresname] else: atomReplacements = {} thiselem = thisatomname if len(thiselem) > 1: thiselem = thiselem[0] + sub("[A-Z0-9]", "", thiselem[1:]) try: element = elem.get_by_symbol(thiselem) except KeyError: element = elem.virtual if thisatomname in atomReplacements: thisatomname = atomReplacements[thisatomname] topology.add_atom( thisatomname, element=element, residue=residue, serial=thisatomnum, ) topology.create_standard_bonds() return n_atoms, topology def _read_frame(self): if not self._open: raise ValueError("I/O operation on closed file") if not self._mode == "r": raise ValueError("file not opened for reading") atomcounter = itertools.count() comment = None boxvectors = None xyz = np.zeros((self.n_atoms, 3), dtype=np.float32) got_line = False firstDecimalPos = None atomindex = -1 for ln, line in enumerate(self._file): got_line = True if ln == 0: comment = line.strip() continue elif ln == 1: assert self.n_atoms == int(line.strip()) continue if firstDecimalPos is None: try: firstDecimalPos = line.index(".", 20) secondDecimalPos = line.index(".", firstDecimalPos + 1) except ValueError: firstDecimalPos = secondDecimalPos = None crd = _parse_gro_coord(line, firstDecimalPos, secondDecimalPos) if crd is not None and atomindex < self.n_atoms - 1: atomindex = next(atomcounter) xyz[atomindex, :] = (crd[0], crd[1], crd[2]) elif _is_gro_box(line) and ln == self.n_atoms + 2: sline = line.split() boxvectors = tuple([float(i) for i in sline]) # the gro_box line comes at the end of the record break else: raise Exception("Unexpected line in .gro file: " + line) if not got_line: raise StopIteration() time = None if "t=" in comment: # title string (free format string, optional time in ps after 't=') time = float(findall(r"t= *(\d+\.\d+)", comment)[-1]) # box vectors (free format, space separated reals), values: v1(x) v2(y) # v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y), the last 6 values may be # omitted (they will be set to zero). box = [boxvectors[i] if i < len(boxvectors) else 0 for i in range(9)] unitcell_vectors = np.array( [ [box[0], box[3], box[4]], [box[5], box[1], box[6]], [box[7], box[8], box[2]], ], ) return xyz, unitcell_vectors, time def _write_frame(self, coordinates, topology, time, box, precision): comment = "Generated with MDTraj" if time is not None: comment += ", t= %s" % time varwidth = precision + 5 fmt = "%%5d%%-5s%%5s%%5d%%%d.%df%%%d.%df%%%d.%df" % ( varwidth, precision, varwidth, precision, varwidth, precision, ) assert topology.n_atoms == coordinates.shape[0] lines = [comment, " %d" % topology.n_atoms] if box is None: box = np.zeros((3, 3)) for i in range(topology.n_atoms): atom = topology.atom(i) residue = atom.residue serial = atom.serial if serial is None: serial = atom.index if serial >= 100000: serial %= 100000 lines.append( fmt % ( residue.resSeq, residue.name, atom.name, serial, coordinates[i, 0], coordinates[i, 1], coordinates[i, 2], ), ) lines.append( f"{box[0, 0]:10.5f}{box[1, 1]:10.5f}{box[2, 2]:10.5f}" f"{box[0, 1]:10.5f}{box[0, 2]:10.5f}{box[1, 0]:10.5f}" f"{box[1, 2]:10.5f}{box[2, 0]:10.5f}{box[2, 1]:10.5f}", ) self._file.write("\n".join(lines)) self._file.write("\n") def seek(self, offset, whence=0): """Move to a new file position Parameters ---------- offset : int A number of frames. whence : {0, 1, 2} 0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported """ raise NotImplementedError() def tell(self): """Current file position Returns ------- offset : int The current frame in the file. """ return self._frame_index def close(self): "Close the file" if self._open: self._file.close() self._open = False def __enter__(self): "Support the context manager protocol" return self def __exit__(self, *exc_info): "Support the context manager protocol" self.close()
def _isint(word): """ONLY matches integers! If you have a decimal point? None shall pass! @param[in] word String (for instance, '123', '153.0', '2.', '-354') @return answer Boolean which specifies whether the string is an integer (only +/- sign followed by digits) """ return match("^[-+]?[0-9]+$", word) def _isfloat(word): """Matches ANY number; it can be a decimal, scientific notation, what have you CAUTION - this will also match an integer. @param[in] word String (for instance, '123', '153.0', '2.', '-354') @return answer Boolean which specifies whether the string is any number """ return match(r"^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$", word) def _parse_gro_coord(line, firstDecimal, secondDecimal): """Determines whether a line contains GROMACS data or not @param[in] line The line to be tested """ if firstDecimal is None or secondDecimal is None: return None digits = secondDecimal - firstDecimal try: return tuple(float(line[20 + i * digits : 20 + (i + 1) * digits]) for i in range(3)) except ValueError: return None def _is_gro_box(line): """Determines whether a line contains a GROMACS box vector or not @param[in] line The line to be tested """ sline = line.split() if len(sline) == 9 and all([_isfloat(i) for i in sline]): return 1 elif len(sline) == 3 and all([_isfloat(i) for i in sline]): return 1 else: return 0