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# 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
#
"""
GRO file format --- :mod:`MDAnalysis.coordinates.GRO`
======================================================
Classes to read and write Gromacs_ GRO_ coordinate files; see the notes on the
`GRO format`_ which includes a conversion routine for the box.
Writing GRO files
-----------------
By default any written GRO files will renumber the atom ids to move sequentially
from 1. This can be disabled, and instead the original atom ids kept, by
using the `reindex=False` keyword argument. This is useful when writing a
subsection of a larger Universe while wanting to preserve the original
identities of atoms.
For example::
>>> u = mda.Universe()`
>>> u.atoms.write('out.gro', reindex=False)
# OR
>>> with mda.Writer('out.gro', reindex=False) as w:
... w.write(u.atoms)
Classes
-------
.. autoclass:: Timestep
:members:
.. autoclass:: GROReader
:members:
.. autoclass:: GROWriter
:members:
Developer notes: ``GROWriter`` format strings
---------------------------------------------
The :class:`GROWriter` class has a :attr:`GROWriter.fmt` attribute, which is a dictionary of different
strings for writing lines in ``.gro`` files. These are as follows:
``n_atoms``
For the first line of the gro file, supply the number of atoms in the system.
E.g.::
fmt['n_atoms'].format(42)
``xyz``
An atom line without velocities. Requires that the 'resid', 'resname',
'name', 'index' and 'pos' keys be supplied.
E.g.::
fmt['xyz'].format(resid=1, resname='SOL', name='OW2', index=2, pos=(0.0, 1.0, 2.0))
``xyz_v``
As above, but with velocities. Needs an additional keyword 'vel'.
``box_orthorhombic``
The final line of the gro file which gives box dimensions. Requires
the box keyword to be given, which should be the three cartesian dimensions.
E.g.::
fmt['box_orthorhombic'].format(box=(10.0, 10.0, 10.0))
``box_triclinic``
As above, but for a non orthorhombic box. Requires the box keyword, but this
time as a length 9 vector. This is a flattened version of the (3,3) triclinic
vector representation of the unit cell. The rearrangement into the odd
gromacs order is done automatically.
.. _Gromacs: http://www.gromacs.org
.. _GRO: http://manual.gromacs.org/current/online/gro.html
.. _GRO format: http://chembytes.wikidot.com/g-grofile
"""
import re
import itertools
import warnings
import numpy as np
from . import base
from .base import Timestep
from .core import triclinic_box, triclinic_vectors
from ..exceptions import NoDataError
from ..lib import util
"""unitcell dimensions (A, B, C, alpha, beta, gamma)
GRO::
8.00170 8.00170 5.65806 0.00000 0.00000 0.00000 0.00000 4.00085 4.00085
PDB::
CRYST1 80.017 80.017 80.017 60.00 60.00 90.00 P 1 1
XTC: c.trajectory.ts._unitcell::
array([[ 80.00515747, 0. , 0. ],
[ 0. , 80.00515747, 0. ],
[ 40.00257874, 40.00257874, 56.57218552]], dtype=float32)
"""
# unit cell line (from http://manual.gromacs.org/current/online/gro.html)
# v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
# 0 1 2 3 4 5 6 7 8
# This information now stored as _ts_order_x/y/z to keep DRY
_TS_ORDER_X = [0, 3, 4]
_TS_ORDER_Y = [5, 1, 6]
_TS_ORDER_Z = [7, 8, 2]
def _gmx_to_dimensions(box):
# convert gromacs ordered box to [lx, ly, lz, alpha, beta, gamma] form
x = box[_TS_ORDER_X]
y = box[_TS_ORDER_Y]
z = box[_TS_ORDER_Z] # this ordering is correct! (checked it, OB)
return triclinic_box(x, y, z)
[docs]class GROReader(base.SingleFrameReaderBase):
"""Reader for the Gromacs GRO structure format.
.. note::
This Reader will only read the first frame present in a file.
.. note::
GRO files with zeroed 3 entry unit cells (i.e. ``0.0 0.0 0.0``)
are read as missing unit cell information. In these cases ``dimensions``
will be set to ``None``.
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
.. versionchanged:: 2.0.0
Reader now only parses boxes defined with 3 or 9 fields.
Reader now reads a 3 entry zero unit cell (i.e. ``[0, 0, 0]``) as a
being without dimension information (i.e. will the timestep dimension
to ``None``).
"""
format = 'GRO'
units = {'time': None, 'length': 'nm', 'velocity': 'nm/ps'}
_Timestep = Timestep
def _read_first_frame(self):
with util.openany(self.filename, 'rt') as grofile:
# Read first two lines to get number of atoms
grofile.readline()
self.n_atoms = n_atoms = int(grofile.readline())
self.ts = ts = self._Timestep(n_atoms, **self._ts_kwargs)
# Always try, and maybe add them later
velocities = np.zeros((n_atoms, 3), dtype=np.float32)
missed_vel = False
# and the third line to get the spacing between coords (cs)
# (dependent upon the GRO file precision)
first_atomline = grofile.readline()
cs = first_atomline[25:].find('.') + 1
ts._pos[0] = [first_atomline[20 + cs * i:20 + cs * (i + 1)]
for i in range(3)]
try:
velocities[0] = [first_atomline[20 + cs * i:20 + cs * (i + 1)]
for i in range(3, 6)]
except ValueError:
# Remember that we got this error
missed_vel = True
# TODO: Handle missing unitcell?
for pos, line in enumerate(grofile, start=1):
# 2 header lines, 1 box line at end
if pos == n_atoms:
try:
unitcell = np.float32(line.split())
except ValueError:
# Try to parse floats with 5 digits if no spaces between values...
unitcell = np.float32(re.findall(r"(\d+\.\d{5})", line))
break
ts._pos[pos] = [line[20 + cs * i:20 + cs * (i + 1)] for i in range(3)]
try:
velocities[pos] = [line[20 + cs * i:20 + cs * (i + 1)] for i in range(3, 6)]
except ValueError:
# Remember that we got this error
missed_vel = True
if np.any(velocities):
ts.velocities = velocities
if missed_vel:
warnings.warn("Not all velocities were present. "
"Unset velocities set to zero.")
self.ts.frame = 0 # 0-based frame number
if len(unitcell) == 3:
# special case: a b c --> (a 0 0) (b 0 0) (c 0 0)
# see docstring above for format (!)
# Treat empty 3 entry boxes as not having a unit cell
if np.allclose(unitcell, [0., 0., 0.]):
wmsg = ("Empty box [0., 0., 0.] found - treating as missing "
"unit cell. Dimensions set to `None`.")
warnings.warn(wmsg)
self.ts.dimensions = None
else:
self.ts.dimensions = np.r_[unitcell, [90., 90., 90.]]
elif len(unitcell) == 9:
self.ts.dimensions = _gmx_to_dimensions(unitcell)
else: # raise an error for wrong format
errmsg = "GRO unitcell has neither 3 nor 9 entries."
raise ValueError(errmsg)
if self.convert_units:
self.convert_pos_from_native(self.ts._pos) # in-place !
if self.ts.dimensions is not None:
self.convert_pos_from_native(self.ts.dimensions[:3]) # in-place!
if self.ts.has_velocities:
# converts nm/ps to A/ps units
self.convert_velocities_from_native(self.ts._velocities)
[docs] def Writer(self, filename, n_atoms=None, **kwargs):
"""Returns a CRDWriter for *filename*.
Parameters
----------
filename: str
filename of the output GRO file
Returns
-------
:class:`GROWriter`
"""
if n_atoms is None:
n_atoms = self.n_atoms
return GROWriter(filename, n_atoms=n_atoms, **kwargs)
[docs]class GROWriter(base.WriterBase):
"""GRO Writer that conforms to the Trajectory API.
Will attempt to write the following information from the topology:
- atom name (defaults to 'X')
- resnames (defaults to 'UNK')
- resids (defaults to '1')
.. note::
The precision is hard coded to three decimal places.
.. note::
When dimensions are missing (i.e. set to `None`), a zero width
unit cell box will be written (i.e. [0.0, 0.0, 0.0]).
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
.. versionchanged:: 0.13.0
Now strictly writes positions with 3dp precision.
and velocities with 4dp.
Removed the `convert_dimensions_to_unitcell` method,
use `Timestep.triclinic_dimensions` instead.
Now now writes velocities where possible.
.. versionchanged:: 0.18.0
Added `reindex` keyword argument to allow original atom
ids to be kept.
.. versionchanged:: 2.0.0
Raises a warning when writing timestep with missing dimension
information (i.e. set to ``None``).
"""
format = 'GRO'
units = {'time': None, 'length': 'nm', 'velocity': 'nm/ps'}
gro_coor_limits = {'min': -999.9995, 'max': 9999.9995}
#: format strings for the GRO file (all include newline); precision
#: of 3 decimal places is hard-coded here.
fmt = {
'n_atoms': "{0:5d}\n", # number of atoms
# coordinates output format, see http://chembytes.wikidot.com/g-grofile
'xyz': "{resid:>5d}{resname:<5.5s}{name:>5.5s}{index:>5d}{pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}\n",
# unitcell
'box_orthorhombic': "{box[0]:10.5f} {box[1]:9.5f} {box[2]:9.5f}\n",
'box_triclinic': "{box[0]:10.5f} {box[4]:9.5f} {box[8]:9.5f} {box[1]:9.5f} {box[2]:9.5f} {box[3]:9.5f} {box[5]:9.5f} {box[6]:9.5f} {box[7]:9.5f}\n"
}
fmt['xyz_v'] = fmt['xyz'][:-1] + "{vel[0]:8.4f}{vel[1]:8.4f}{vel[2]:8.4f}\n"
def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
"""Set up a GROWriter with a precision of 3 decimal places.
Parameters
-----------
filename : str
output filename
n_atoms : int (optional)
number of atoms
convert_units : bool (optional)
units are converted to the MDAnalysis base format; [``True``]
reindex : bool (optional)
By default, all the atoms were reindexed to have a atom id starting
from 1. [``True``] However, this behaviour can be turned off by
specifying `reindex` ``=False``.
Note
----
To use the reindex keyword, user can follow the two examples given
below.::
u = mda.Universe()
Usage 1::
u.atoms.write('out.gro', reindex=False)
Usage 2::
with mda.Writer('out.gro', reindex=False) as w:
w.write(u.atoms)
"""
self.filename = util.filename(filename, ext='gro', keep=True)
self.n_atoms = n_atoms
self.reindex = kwargs.pop('reindex', True)
self.convert_units = convert_units # convert length and time to base units
[docs] def write(self, obj):
"""Write selection at current trajectory frame to file.
Parameters
-----------
obj : AtomGroup or Universe
Note
----
The GRO format only allows 5 digits for *resid* and *atom
number*. If these numbers become larger than 99,999 then this
routine will chop off the leading digits.
.. versionchanged:: 0.7.6
*resName* and *atomName* are truncated to a maximum of 5 characters
.. versionchanged:: 0.16.0
`frame` kwarg has been removed
.. versionchanged:: 2.0.0
Deprecated support for calling with Timestep has nwo been removed.
Use AtomGroup or Universe as an input instead.
"""
# write() method that complies with the Trajectory API
try:
# make sure to use atoms (Issue 46)
ag = obj.atoms
# can write from selection == Universe (Issue 49)
except AttributeError:
errmsg = "Input obj is neither an AtomGroup or Universe"
raise TypeError(errmsg) from None
try:
velocities = ag.velocities
except NoDataError:
has_velocities = False
else:
has_velocities = True
# Check for topology information
missing_topology = []
try:
names = ag.names
except (AttributeError, NoDataError):
names = itertools.cycle(('X',))
missing_topology.append('names')
try:
resnames = ag.resnames
except (AttributeError, NoDataError):
resnames = itertools.cycle(('UNK',))
missing_topology.append('resnames')
try:
resids = ag.resids
except (AttributeError, NoDataError):
resids = itertools.cycle((1,))
missing_topology.append('resids')
if not self.reindex:
try:
atom_indices = ag.ids
except (AttributeError, NoDataError):
atom_indices = range(1, ag.n_atoms+1)
missing_topology.append('ids')
else:
atom_indices = range(1, ag.n_atoms + 1)
if missing_topology:
warnings.warn(
"Supplied AtomGroup was missing the following attributes: "
"{miss}. These will be written with default values. "
"Alternatively these can be supplied as keyword arguments."
"".format(miss=', '.join(missing_topology)))
positions = ag.positions
if self.convert_units:
# Convert back to nm from Angstroms,
# Not inplace because AtomGroup is not a copy
positions = self.convert_pos_to_native(positions, inplace=False)
if has_velocities:
velocities = self.convert_velocities_to_native(velocities, inplace=False)
# check if any coordinates are illegal
# (checks the coordinates in native nm!)
if not self.has_valid_coordinates(self.gro_coor_limits, positions):
raise ValueError("GRO files must have coordinate values between "
"{0:.3f} and {1:.3f} nm: No file was written."
"".format(self.gro_coor_limits["min"],
self.gro_coor_limits["max"]))
with util.openany(self.filename, 'wt') as output_gro:
# Header
output_gro.write('Written by MDAnalysis\n')
output_gro.write(self.fmt['n_atoms'].format(ag.n_atoms))
# Atom descriptions and coords
# Dont use enumerate here,
# all attributes could be infinite cycles!
for atom_index, resid, resname, name in zip(
range(ag.n_atoms), resids, resnames, names):
truncated_atom_index = util.ltruncate_int(atom_indices[atom_index], 5)
truncated_resid = util.ltruncate_int(resid, 5)
if has_velocities:
output_gro.write(self.fmt['xyz_v'].format(
resid=truncated_resid,
resname=resname,
index=truncated_atom_index,
name=name,
pos=positions[atom_index],
vel=velocities[atom_index],
))
else:
output_gro.write(self.fmt['xyz'].format(
resid=truncated_resid,
resname=resname,
index=truncated_atom_index,
name=name,
pos=positions[atom_index]
))
# Footer: box dimensions
if (ag.dimensions is None or
np.allclose(ag.dimensions[3:], [90., 90., 90.])):
if ag.dimensions is None:
wmsg = ("missing dimension - setting unit cell to zeroed "
"box [0., 0., 0.]")
warnings.warn(wmsg)
box = np.zeros(3)
else:
box = self.convert_pos_to_native(
ag.dimensions[:3], inplace=False)
# orthorhombic cell, only lengths along axes needed in gro
output_gro.write(self.fmt['box_orthorhombic'].format(
box=box)
)
else:
try: # for AtomGroup/Universe
tri_dims = obj.universe.coord.triclinic_dimensions
except AttributeError: # for Timestep
tri_dims = obj.triclinic_dimensions
# full output
box = self.convert_pos_to_native(tri_dims.flatten(), inplace=False)
output_gro.write(self.fmt['box_triclinic'].format(box=box))