genice-cage 0.3

Cage detection plugin for GenIce.

genice-cage

A GenIce plugin to detect cage-like topologies.

version 0.3

Requirements

• countrings>=0.1.6
• genice>=0.25
• attrdict
• networkx
• numpy

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] 
    % genice CS2 -w tip4p -f cage[gromacs:-16:maxring=6]

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. (e.g. -4,6,8-10,16-) (default is 3-8)
    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.
    gromacs    Output in Gromacs format. (EXPERIMENTAL)

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