genice-cage 0.2

Cage detection plugin for GenIce.

genice-cage

A GenIce plugin to detect cage-like topologies.

version 0.1

Requirements

• countrings>=0.1.6
• genice>=0.25

Installation from PyPI

% pip install genice_cage

Manual Installation

System-wide installation

% make install

Private installation

Copy the files in genice_cage/formats/ into your local formats/ folder.

Usage

Usage: 
    % genice CS1 -r 2 2 2 -f cage[12,14-16:maxring=6] 
    % genice CRN1 -f cage[3-10:json] 
    % genice CRN1 -f cage[3-10:yaplot] 

It may not work with a small structure. (In the example above, the unit cell of CS1 is extended to 2x2x2 so as to avoid detecting cell-spanning wierd cages.)

Options:
    Cage sizes to be listed, separated by commas and ranged with hyphens. (default is 3 to 8)
    maxring=x  Specify the maximum ring size (default=8).
    json       Output in [JSON](https://www.json.org/) format.
    yaplot     Visualize with [Yaplot](https://github.com/vitroid/Yaplot/). Cages are drawn in different layers according to the number of faces, and faces are colored according to the number of vertices.

Test in place

% make test

Algorithms

• M. Matsumoto, A. Baba, and I. Ohmine, Topological building blocks of hydrogen bond network in water, J. Chem. Phys. 127, 134504 (2007); doi:10.1063/1.2772627