Provides basic routines to read and extract information included in hoomdxml files and GSD files, and provides routines to convert to mbuild Compounds. While there are other packages do support reading hoomdxml files, they do not parse all sections of the file. This code will also perform grouping of atoms into molecules based on connectivity.
Other relevant links:
Check out the source from the github repository:
$ git clone https://github.com/chrisiacovella/hoomdxml_reader.git
In the top level of hoomdxml_reader directory, use pip to install:
$ pip install -e .
The core functions of the module will require networkx to be installed.
To create an environment named hoomdxml_reader with this necessary package,
run the following from the top level of the hoomdxml_reader directory.
$ conda env create -f environment.yml
While not necessary to use the core functions of the Module, conversion to an mBuild Compound, requires mbuild to be installed.
$ conda install -c conda-forge mbuild
To visualize mbuild Compounds in Jupyter notebooks, install py3dmol:
$ conda install -c conda-forge py3dmol
git push origin HEAD:
Copyright (c) 2022, Chris Iacovella
Project based on the Computational Molecular Science Python Cookiecutter version 1.1.