"""Read and write Gromos87 (.GRO) file format."""
import datetime
import re
import warnings
import numpy as np
import unyt as u
from unyt.array import allclose_units
import gmso
from gmso.core.atom import Atom
from gmso.core.box import Box
from gmso.core.topology import Topology
from gmso.formats.formats_registry import loads_as, saves_as
[docs]
@loads_as(".gro")
def read_gro(filename):
"""Create a topology from a provided gro file.
The Gromos87 (gro) format is a common plain text structure file used
commonly with the GROMACS simulation engine. This file contains the
simulation box parameters, number of atoms, the residue and atom number for
each atom, as well as their positions and velocities (velocity is
optional). This method will receive a filepath representation either as a
string, or a file object and return a `topology`.
Parameters
----------
filename : str or file object
The path to the gro file either as a string, or a file object that
points to the gro file.
Returns
-------
gmso.core.topology
A `topology` object containing site information
Notes
-----
Gro files do not specify connections between atoms, the returned topology
will not have connections between sites either.
Currently this implementation does not support parsing velocities from a gro file or gro file
with more than 1 frame.
All residues and resid information from the gro file are currently lost
when converting to `topology`.
"""
top = Topology()
with open(filename, "r") as gro_file:
top.name = str(gro_file.readline().strip())
n_atoms = int(gro_file.readline())
coords = u.nm * np.zeros(shape=(n_atoms, 3))
for row, _ in enumerate(coords):
line = gro_file.readline()
if not line:
msg = (
"Incorrect number of lines in .gro file. Based on the "
"number in the second line of the file, {} rows of"
"atoms were expected, but at least one fewer was found."
)
raise ValueError(msg.format(n_atoms))
res_id = (
int(line[:5].strip()) - 1
) # reformat from 1 to 0 index in gmso
res_name = line[5:10].strip()
atom_name = line[10:15].strip()
atom_id = line[15:20].strip()
positions = line[20:].split()
coords[row] = u.nm * np.array(
[
float(positions[0]),
float(positions[1]),
float(positions[2]),
]
)
site = Atom(name=atom_name, position=coords[row])
site.molecule = (res_name, res_id)
site.residue = (res_name, res_id)
top.add_site(site, update_types=False)
if len(positions) == 6:
warnings.warn(
"Velocity information presents but will not be parsed."
)
top.update_topology()
# Box information
line = gro_file.readline().split()
top.box = Box(u.nm * np.array([float(val) for val in line[:3]]))
# Verify we have read the last line by ensuring the next line in blank
line = gro_file.readline()
if line:
msg = (
"Incorrect number of lines in input file. Based on the "
"number in the second line of the file, {} rows of atoms "
"were expected, but at least one more was found."
)
raise ValueError(msg.format(n_atoms))
return top
[docs]
@saves_as(".gro")
def write_gro(top, filename, n_decimals=3, shift_coord=False):
"""Write a topology to a gro file.
The Gromos87 (gro) format is a common plain text structure file used
commonly with the GROMACS simulation engine. This file contains the
simulation box parameters, number of atoms, the residue and atom number for
each atom, as well as their positions and velocities (velocity is
optional). This method takes a topology object and a filepath string or
file object and saves a Gromos87 (gro) to disk.
Parameters
----------
top : gmso.core.topology
The `topology` to write out to the gro file.
filename : str or file object
The location and name of file to save to disk.
n_decimals : int, optional, default=3
The number of sig fig to write out the position in.
shift_coord : bool, optional, default=False
If True, shift the coordinates of all sites by the minimum position
to ensure all sites have non-negative positions. This is not a requirement
for GRO files, but can be useful for visualizing.
Notes
-----
Multiple residue assignment has not been added, each `site` will belong to
the same resid of 1 currently.
Velocities are not written out.
"""
pos_array = np.ndarray.copy(top.positions)
if shift_coord:
pos_array = _validate_positions(pos_array)
with open(filename, "w") as out_file:
out_file.write(
"{} written by GMSO {} at {}\n".format(
top.name if top.name is not None else "",
gmso.__version__,
str(datetime.datetime.now()),
)
)
out_file.write("{:d}\n".format(top.n_sites))
out_file.write(_prepare_atoms(top, pos_array, n_decimals))
out_file.write(_prepare_box(top))
def _validate_positions(pos_array):
"""Modify coordinates, as necessary, to fit limitations of the GRO format."""
if np.min(pos_array) < 0:
warnings.warn(
"Topology contains some negative positions. Translating "
"in order to ensure all coordinates are non-negative."
)
min_xyz = np.min(pos_array, axis=0)
min_xyz0 = np.where(min_xyz < 0 * min_xyz.units, min_xyz, 0 * min_xyz.units)
pos_array -= min_xyz0
return pos_array
def _prepare_atoms(top, updated_positions, n_decimals):
out_str = str()
warnings.warn(
"Residue information is parsed from site.molecule,"
"or site.residue if site.molecule does not exist."
"Note that the residue idx will be bumped by 1 since GROMACS utilize 1-index."
)
# we need to sort through the sites to provide a unique number for each molecule/residue
# we will store the unique id in dictionary where the key is the idx
site_res_id = dict()
seen = dict()
for idx, site in enumerate(top.sites):
if site.molecule:
if site.molecule not in seen:
seen[site.molecule] = len(seen) + 1
site_res_id[idx] = seen[site.molecule]
elif site.residue:
if site.residue not in seen:
seen[site.residue] = len(seen) + 1
site_res_id[idx] = seen[site.residue]
else:
if "MOL" not in seen:
seen["MOL"] = len(seen) + 1
site_res_id[idx] = seen["MOL"]
for idx, (site, pos) in enumerate(zip(top.sites, updated_positions)):
if site.molecule:
res_id = site_res_id[idx]
res_name = (
site.molecule.name
if len(site.molecule.name) <= 5
else site.molecule.name[:5]
)
site.label = f"res_id: {res_id}, " + site.label
elif site.residue:
res_id = site_res_id[idx]
res_name = (
site.residue.name
if len(site.residue.name) <= 5
else site.residue.name[:5]
)
site.label = f"res_id: {res_id}, " + site.label
else:
res_id = site_res_id[idx]
res_name = "MOL"
site.label = f"res_id: {res_id}, " + site.label
atom_name = site.name if len(site.name) <= 5 else site.name[:5]
atom_id = idx + 1
# gromacs doesn't actually use the atom id in the .gro file
# so we will just loop back to 1 once we exceed 99999
# as is suggested in the FAQ in the manual.
max_val = 99999
atom_id = atom_id % max_val
res_id = res_id % max_val
varwidth = 5 + n_decimals
crdfmt = f"{{:{varwidth}.{n_decimals}f}}"
# preformat pos str
crt_x = crdfmt.format(pos[0].in_units(u.nm).value)[:varwidth]
crt_y = crdfmt.format(pos[1].in_units(u.nm).value)[:varwidth]
crt_z = crdfmt.format(pos[2].in_units(u.nm).value)[:varwidth]
out_str = out_str + "{0:5d}{1:5s}{2:>5s}{3:5d}{4}{5}{6}\n".format(
res_id,
res_name,
atom_name,
atom_id,
crt_x,
crt_y,
crt_z,
)
return out_str
def _prepare_box(top):
out_str = str()
if allclose_units(
top.box.angles,
u.degree * [90, 90, 90],
rtol=1e-5,
atol=0.1 * u.degree,
):
out_str = out_str + " {:0.5f} {:0.5f} {:0.5f}\n".format(
top.box.lengths[0].in_units(u.nm).value.round(6),
top.box.lengths[1].in_units(u.nm).value.round(6),
top.box.lengths[2].in_units(u.nm).value.round(6),
)
else:
# TODO: Work around GROMACS's triclinic limitations #30
vectors = top.box.get_vectors()
out_str = (
out_str
+ " {:0.5f} {:0.5f} {:0.5f} {:0.5f} {:0.5f} {:0.5f} {:0.5f} {:0.5f} {:0.5f} \n".format(
vectors[0, 0].in_units(u.nm).value.round(6),
vectors[1, 1].in_units(u.nm).value.round(6),
vectors[2, 2].in_units(u.nm).value.round(6),
vectors[0, 1].in_units(u.nm).value.round(6),
vectors[0, 2].in_units(u.nm).value.round(6),
vectors[1, 0].in_units(u.nm).value.round(6),
vectors[1, 2].in_units(u.nm).value.round(6),
vectors[2, 0].in_units(u.nm).value.round(6),
vectors[2, 1].in_units(u.nm).value.round(6),
)
)
return out_str