Cage detection plugin for GenIce.
Project description
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]
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 format.
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
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