semvec/pypi-packages huggingface dataset:
genice-twist 0.1.2
Twist analysis plugin for GenIce.
License: MIT
Keywords: genice,chirality

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

Draw the structure with twist order parameter.

version 0.1.2

## Requirements

* genice<2.0
* genice-svg>=0.4
* twist-op>=0.2
* sklearn

## Installation from PyPI

    % pip install genice_twist

## Manual Installation

### System-wide installation

    % make install

### Private Installation

Copy the files in 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$^{-3}$. 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

    % 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).
genice-svg 0.6.1
SVG format plugin for GenIce.
License: MIT
Keywords: genice,SVG

<img src="4R.png">

    genice 4R -f png[shadow:rotatex=2:rotatey=88] > 4R.png


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

A [GenIce](https://github.com/vitroid/GenIce) plugin to illustrate the structure in SVG (and PNG) format.

version 0.6.1

## Requirements

* svgwrite
* genice<2.0
* pillow
* attrdict
* countrings>=0.1.7
* jinja2

## Installation from PyPI

    % pip install genice_svg

## Manual Installation

### System-wide installation

    % make install

### Private installation

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

## Usage
        
    Usage:
        % genice CS2 -r 3 3 3 -f svg[rotatex=30:shadow] > CS2.svg
    	
    Options:
        rotatex=30
        rotatey=30
        rotatez=30
        polygon        Draw polygons instead of a ball and stick model.
        shadow         Draw shadows behind balls.
        bg=#f00        Specify the background color.
        H=0            Size of the hydrogen atom
        O=0.06
        HB=0.4
        OH=0.5
        width=0        (Pixel)
        height=0       (Pixel)

Png is a quick alternative for svg. Use png if making svg is too slow.
        
    Usage:
        % genice CS2 -r 3 3 3 -f png[shadow:bg=#f00] > CS2.png
    	
    Options:
        rotatex=30
        rotatey=30
        rotatez=30
        shadow         Draw shadows behind balls.
        bg=#f00        Specify the background color.
        H=0            Size of the hydrogen atom
        O=0.06
        HB=0.4
        OH=0.5
        width=0        (Pixel)
        height=0       (Pixel)

## Test in place

    % make test
genice-rdf 0.3.3
RDF format plugin for GenIce.
License: MIT
Keywords: genice,RDF

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

A GenIce format plugin to calculate radial distribution functions.

version 0.3.3

## Requirements

* PairList>=0.2.3
* GenIce<2.0

## Installation from PyPI

    % pip install genice_rdf

## Manual Installation

### System-wide installation

    % make install

### Private installation

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

## Usage

    
    Usage: 
        % genice 1c -r 3 3 3 -w tip4p -f _RDF > 1c.rdf
        % genice 1c -r 3 3 3 -w tip4p -f _RDF[OW:H=HW1=HW2] > 1c.rdf
        % analice data.gro  -O OW -H HW[12] -w tip3p -f _RDF[OW:HW1=HW2] > data.rdf
    
    Options:
        Atom name
        Atom name and aliases chained with "=".
        json      Output in JSON format.
        range=x   Range of interest (0.9 nm)
        binw=x    Bin width (0.003 nm)
    
    Options must be separated with colons.
    
    You can specify the list of atom types to be calculated.
    
    For example, in the following case, TIP4P water has four different atom
    types (OW, HW1, HW2, and MW), so all the possible 10 combinations of 
    atom types will be examined.
    
        % genice 1c -r 3 3 3 -w tip4p -f _RDF > 1c.rdf
    
    If you just want the RDF of OW and H, and HW1 and HW2 should be 
    abbreviated by H, specify the option string like following.
    
        % genice 1c -r 3 3 3 -w tip4p -f _RDF[OW:H=HW1=HW2] > 1c.rdf

## Test in place

    % make test