Core algorithms of GenIce2 It provides algorithms to generate directed graphs that satisfy the ice rules (hydrogen-disordered ice) from an undirected graph.
version 1.5.4
Python 3.10 or newer is required (see pyproject.toml).
- python
- networkx
- numpy
GenIce-core is registered to PyPI (Python Package Index). Install with pip3.
pip3 install genice-core
pip3 uninstall genice-core
API manual is here.
Make an ice graph from a given undirected graph.
import networkx as nx
import matplotlib
import genice_core
# np.random.seed(12345)
g = nx.dodecahedral_graph() # dodecahedral 20mer
pos = nx.spring_layout(g)
# set orientations of the hydrogen bonds.
dg = genice_core.ice_graph(g)
nx.draw_networkx(dg, pos)Additional examples can be found at https://github.com/vitroid/genice-core
The algorithms to make a depolarized hydrogen-disordered ice are explained in these papers:
M. Matsumoto, T. Yagasaki, and H. Tanaka, “GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.”, J. Chem. Phys. 160, 094101 (2024). DOI:10.1063/5.0198056
@article{Matsumoto:2024,
author = {Matsumoto, Masakazu and Yagasaki, Takuma and Tanaka, Hideki},
title = {GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures},
journal = {Journal of Chemical Physics},
volume = {160},
pages = {094101},
year = {2024}
}
GenIce has been available as open source software on GitHub since 2015. Feedback, suggestions for improvements and enhancements, bug fixes, etc., are sincerely welcome. Developers and test users are also welcome. If you have any publicly available ice that is not included in GenIce, please let us know.
Install dependencies (including dev and test groups):
poetry install
Run tests:
poetry run pytest
This project is licensed under the MIT License — see the LICENSE file for details.