{ "info": { "author": "Masakazu Matsumoto", "author_email": "vitroid@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Programming Language :: Python", "Programming Language :: Python :: 3.5" ], "description": "# [genice-twist](https://github.com/vitroid/genice-twist/)\n\nDraw the structure with twist order parameter.\n\nversion 0.1.1\n\n## Requirements\n\n* genice>=0.25\n* genice-svg>=0.4\n* twist-op>=0.2\n\n## Installation from PyPI\n\n % pip install genice_twist\n\n## Manual Installation\n\n### System-wide installation\n\n % make install\n\n### Private Installation\n\nCopy the files in formats/ into your local formats/ folder.\n\n## Usage\n\n\n usage:\n genice II -f twist[options:separated:by:colons] > file\n\n Output the twist values for all the hydrogen-bonded pairs.\n\n options:\n png Draw the hydrogen bonds with a rainbow palette according to the twist value in PNG format.\n png:CM Draw the hydrogen bonds with color-mixing scheme in PNG format.\n png:DB Draw the hydrogen bonds with decision-boundary coloring scheme in PNG format.\n png:SB Draw the hydrogen bonds with simple boundary coloring scheme in PNG format.\n svg Draw the hydrogen bonds with a rainbow palette according to the twist value in SVG format.\n svg:CM Draw the hydrogen bonds with color-mixing scheme in SVG format.\n svg:DB Draw the hydrogen bonds with decision-boundary coloring scheme in SVG format.\n svg:SB Draw the hydrogen bonds with simple boundary coloring scheme in SVG format.\n yaplot Draw the hydrogen bonds with a rainbow palette according to the twist value in YaPlot format.\n shadow Draw shadows to the atoms (PNG and SVG)\n Ih=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure ice Ih.\n Ic=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure ice Ic.\n LDL=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure LDL.\n HDL=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure HDL.\n rotatex=30 Rotate the picture (SVG and PNG)\n rotatey=30 Rotate the picture (SVG and PNG)\n rotatez=30 Rotate the picture (SVG and PNG)\n\n## Auxiliary Files\n\n* IhST2.twhist\n* IcST2.twhist\n* LDLST2.twhist\n* HDLST2.twhist\n\nThey 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.\n\n## Test in place\n\n % make test\n\n## Reference\n\n* 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. 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