semvec/pypi-packages huggingface dataset:
genice-cage 0.4.6
Cage detection plugin for GenIce.
License: MIT
Keywords: genice,cage

# [genice-cage](https://github.com/vitroid/genice-cage/)

A [GenIce](https://github.com/vitroid/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](http://dx.doi.org/doi:10.1063/1.2772627)
schematics-to-swagger 1.4.7
Helper library to build Swagger Schema objects from Schematics models
License: MIT

[![Build Status](https://travis-ci.com/Alexei-Kornienko/schematics_to_swagger.svg?branch=master)](https://travis-ci.com/Alexei-Kornienko/schematics_to_swagger)

# Usecase

* I have a REST API built using aiohttp and schematics.
* I want to provide Swagger spec for it and I use aiohttp-swagger.
* I'm too lazy to describe models for swagger docs so I want to build this information automatically

## Usage

```
import schematics_to_swagger

from your_package import models

definitions = schematics_to_swagger.read_models_from_module(models)
```