Source code for gmso.formats.gro

import warnings
import datetime

import numpy as np
import unyt as u

from gmso.core.topology import Topology
from gmso.core.site import Site
from gmso.core.box import Box
from gmso.exceptions import NotYetImplementedWarning
from unyt.array import allclose_units

[docs]def read_gro(filename): """Provided a filepath to a gro file, generate a topology. 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 a 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)) resid = int(line[:5]) res_name = line[5:10] atom_name = line[10:15] atom_id = int(line[15:20]) coords[row] = u.nm * np.array([ float(line[20:28]), float(line[28:36]), float(line[36:44]), ]) site = Site(name=atom_name, position=coords[row]) top.add_site(site, update_types=False) 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]def write_gro(top, filename): """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. Notes ----- Multiple residue assignment has not been added, each `site` will belong to the same resid of 1 currently. """ top = _prepare_topology_to_gro(top) with open(filename, 'w') as out_file: out_file.write('{} written by topology at {}\n'.format( top.name if top.name is not None else '', str(datetime.datetime.now()))) out_file.write('{:d}\n'.format(top.n_sites)) for idx, site in enumerate(top.sites): warnings.warn('Residue information is not currently ' 'stored or written to GRO files.', NotYetImplementedWarning) # TODO: assign residues res_id = 1 res_name = 'X' atom_name = site.name atom_id = idx + 1 out_file.write('{0:5d}{1:5s}{2:5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}\n'.format( res_id, res_name, atom_name, atom_id, site.position[0].in_units(u.nm).value, site.position[1].in_units(u.nm).value, site.position[2].in_units(u.nm).value, )) if allclose_units(top.box.angles, u.degree * [90, 90, 90], rtol= 1e-5, atol=0.1*u.degree): out_file.write(' {: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_file.write(' {: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), ))
def _prepare_topology_to_gro(top): """Modify topology, as necessary, to fit limitations of the GRO format.""" if np.min(top.positions) < 0: warnings.warn('Topology contains some negative positions. Translating ' 'in order to ensure all coordinates are non-negative.') return top