genice-core 0.5.1

Core algorithms of GenIce2

GenIce-core

Core algorithms of GenIce2

version 0.5.1

Requirements

• numpy
• networkx

Installation

GenIce-core is registered to PyPI (Python Package Index). Install with pip3.

pip3 install genice-core

Uninstallation

pip3 uninstall genice-core

API

API manual is here.

Examples

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)

Algorithms and how to cite them.

The algorithms to make a depolarized hydrogen-disordered ice are explained in these papers:

M. Matsumoto, T. Yagasaki, and H. Tanaka,"GenIce: Hydrogen-Disordered Ice Generator", J. Comput. Chem. 39, 61-64 (2017). DOI: 10.1002/jcc.25077

@article{Matsumoto:2017bk,
    author = {Matsumoto, Masakazu and Yagasaki, Takuma and Tanaka, Hideki},
    title = {GenIce: Hydrogen-Disordered Ice Generator},
    journal = {Journal of Computational Chemistry},
	volume = {39},
	pages = {61-64},
    year = {2017}
}

M. Matsumoto, T. Yagasaki, and H. Tanaka, “Novel Algorithm to Generate Hydrogen-Disordered Ice Structures.”, J. Chem. Info. Modeling 61 (6): 2542–46 (2021). DOI:10.1021/acs.jcim.1c00440

@article{Matsumoto:2021,
    author = {Matsumoto, Masakazu and Yagasaki, Takuma and Tanaka, Hideki},
    title = {Novel Algorithm to Generate Hydrogen-Disordered Ice Structures},
    journal = {Journal of Chemical Information and Modeling},
    volume = {61},
    pages = {2542-2546},
    year = {2021}
}

How to contribute

GenIce has been available as open source software on GitHub(https://github.com/vitroid/GenIce) 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 ice that is publicly available but not included in GenIce, please let me know.