VoronoiAnalysis
Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partial molar volume, and the number of waters associated with each side chain are calculated. This is specifically for PNIPAM but can be modified fairly easily to suit other polymers/protiens. The MDAnalysis library is used for parsing trajectories. Voronio polygons are created using the pyvoro wrapper of Voro++.
How to download and setup VoronoiAnalysis
Open terminal and run command
git clone https://github.com/madgal/VoronoiAnalysis.git
git clone is used to create a copy or clone of VoronoiAnalysis repositories.
You pass git clone a repository URL. it supports a few different network protocols and corresponding URL formats.
Also you may download zip file with VoronoiAnalysis https://github.com/madgal/VoronoiAnalysis/archive/master.zip
Or simply clone VoronoiAnalysis with SSH
[email protected]:madgal/VoronoiAnalysis.git
If you have some problems with VoronoiAnalysis
You may open issue on VoronoiAnalysis support forum (system) here: https://github.com/madgal/VoronoiAnalysis/issuesSimilar to VoronoiAnalysis repositories
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