Metadata-Version: 2.1
Name: genice2-twist
Version: 2.0
Summary: Twist analysis plugin for GenIce.
Home-page: https://github.com/vitroid/genice-twist/
Author: Masakazu Matsumoto
Author-email: vitroid@gmail.com
License: MIT
Keywords: genice,chirality
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
Requires-Dist: genice2
Requires-Dist: genice2-svg (>=0.7)
Requires-Dist: twist-op (>=0.2)
Requires-Dist: sklearn

<img src="sample.png">

```shell
genice2 CRN1 -f twist[svg] > sample.svg
```

# [genice2_twist](https://github.com/vitroid/genice-twist/)

Draw the structure with twist order parameter.

version 2.0

## Requirements


* genice2
* genice2-svg>=0.7
* twist-op>=0.2
* sklearn

## Installation from PyPI

```shell
% pip install genice2_twist
```

## Manual Installation

### System-wide installation

```shell
% make install
```

### Private installation

Copy the files in genice2_twist/formats/ into your local formats/ folder.


## Usage

    usage:
        genice II -f twist[options:separated:by:colons] > file

    Output the twist values for all the hydrogen-bonded pairs.

    options:
        png      Draw the hydrogen bonds with a rainbow palette according to the twist value in PNG format.
        png:CM   Draw the hydrogen bonds with color-mixing scheme in PNG format.
        png:DB   Draw the hydrogen bonds with decision-boundary coloring scheme in PNG format.
        png:SB   Draw the hydrogen bonds with simple boundary coloring scheme in PNG format.
        svg      Draw the hydrogen bonds with a rainbow palette according to the twist value in SVG format.
        svg:CM   Draw the hydrogen bonds with color-mixing scheme in SVG format.
        svg:DB   Draw the hydrogen bonds with decision-boundary coloring scheme in SVG format.
        svg:SB   Draw the hydrogen bonds with simple boundary coloring scheme in SVG format.
        yaplot   Draw the hydrogen bonds with a rainbow palette according to the twist value in YaPlot format.
        shadow   Draw shadows to the atoms (PNG and SVG)
        Ih=filename.twhist   Specify the (two-dimensional) histogram of twist parameter in pure ice Ih.
        Ic=filename.twhist   Specify the (two-dimensional) histogram of twist parameter in pure ice Ic.
        LDL=filename.twhist  Specify the (two-dimensional) histogram of twist parameter in pure LDL.
        HDL=filename.twhist  Specify the (two-dimensional) histogram of twist parameter in pure HDL.
        rotatex=30   Rotate the picture (SVG and PNG)
        rotatey=30   Rotate the picture (SVG and PNG)
        rotatez=30   Rotate the picture (SVG and PNG)


## Auxiliary Files

* IhST2.twhist
* IcST2.twhist
* LDLST2.twhist
* HDLST2.twhist

They are two-dimensional (i.e. real and imaginary) histograms of twist order parameter of ST2 water at 235 K, 0.98 g cm<sup>-3</sup>. You have to prepare the appropriate histogram if you want to apply CM (color-mixing) or DB (decision-boundary) coloring scheme to other water models or in other conditions.

## Test in place

```shell
% make test
```

## Reference

* Matsumoto, M., Yagasaki, T. & Tanaka, H. A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. J. Chem. Phys. 150, 214504 (2019).


