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Description:

genicecage 0.4.6

genice-cage
A GenIce plugin to detect cage-like topologies.
version 0.4.6
Requirements

countrings>=0.1.7
genice>=0.25
attrdict
networkx
numpy
yaplotlib>=0.1.2
jinja2

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:ring=-6]
% genice CRN1 -f cage[3-10:json]
% genice CRN1 -f cage[3-10:yaplot]
% genice CS2 -w tip4p -f cage[gromacs:-16:ring=5,6]
% analice traj.gro -O OW -H HW[12] -w tip4p -f cage[quad]
% analice traj.gro -O OW -H HW[12] -w tip4p -f cage[quad: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. (e.g. -4,6,8-10,16-) (default is 3-16)
ring=3,5-6 Specify the ring sizes that cages are built of (default is 3-8, maximum is 8).
json Output values in [JSON](https://www.json.org/) format.
yaplot Visualize cages 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 individual cages in Gromacs format. (EXPERIMENTAL)
quad Quadcage order parameter to identify the Frank-Kasper-type crystal structures.[JMM2011] Cages sizes and maximum ring size are set appropriately automatically.
python Output cage types in python format convenient for GenIce lattice modules.
* [JMM2011] Jacobson, L. C., Matsumoto, M. & Molinero, V. Order parameters for the multistep crystallization of clathrate hydrates. J. Chem. Phys. 135, 074501 (2011).[doi:10.1063/1.3613667](https://doi.org/10.1063/1.3613667)

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