精灵扭曲分析插件。
genice-twist的Python项目详细描述
genice-twist
使用扭曲顺序参数绘制结构。
版本0.1
要求
- 精灵=0.25
- 精灵SVG>；=0.4
- 旋转操作
从PYPI安装
% pip install genice_twist
手动安装
全系统安装
% make install
私人安装
以格式/将文件复制到本地格式/文件夹中。
用法
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)
- ihst2.twhist
- icst2.twhist
- ldlst2.twhist
- hdlst2.twhist
它们是235k，0.98g cm$^{-3}$下st2水扭曲序参数的二维（实和虚）直方图。如果要将CM（颜色混合）或DB（决策边界）着色方案应用于其他水模型或其他条件，则必须准备适当的直方图。
就地测试
% make test
参考
- Matsumoto，M.，Yagasaki，T.和Tanaka，H.用贝叶斯方法识别具有扭转阶参数的冰IH、冰IC、高密度和低密度液态水。化学杂志。菲斯。150214504（2019年）。
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