HubLot / groio

A really simple library for gro files

groIO

A library to handle the reading and writing of a gro file.

Installation

pip install groio

Usage

import groio

#Read a gro file
title, atoms, box = groio.parse_file("filin.gro")

#Write a gro file
with open("filout.gro", "w") as f:
    for line in groio.write_gro(title, output_atoms, box):
        print(line, end='', file=f)

#Renumber the atoms to avoid number above 100 000
atoms = groio.renumber(atoms)

The function parse_file returns :

• title: the title of the system as written on line 1 of the file as a string
• atoms: a list of atom, each atom is stored as a dictionary
• box: the box description as written on the last line as a string

Run tests

Unit tests are available through nosetests python module.

nosetests tests/test_groio.py