ExpectozJJ / pyGH

Python Package to compute Gromov-Hausdorff ultrametrics

pyGH

A Python tool to compare protein structures using Gromov-Hausdorff ultrametrics. The implementation is adapted from the MATLAB code in https://arxiv.org/abs/1912.00564. Here, we apply pyGH to distinguish between different protein conformers and different types of organic-inorganic halide perovskites.

Installation via pip

pip install pyGH

Upgrading via pip install --upgrade pyGH

Package Requirement

• NumPy
• SciPy
• Matplotlib

Simple Example

from pyGH.GH import uGH, plot_uGH

ux = np.array([[ 0, 5.0225,    5.4539,    4.8977,    5.3575],
    [5.0225,         0,    5.2971,    5.4132,    5.2084],
    [5.4539,    5.2971,         0,    5.2856,    4.5969],
    [4.8977,    5.4132,    5.2856,         0,    5.6365],
    [5.3575,    5.2084,    4.5969,    5.6365,         0]])
uy = np.array([[0, 4.89878009143743,	4.73993109215105],
[4.89878009143743,	0,	5.0687],
[4.73993109215105,	5.0687,	0]])

plot_uGH(ux,uy)