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src=\"sample.png\"\u003e\n\n```shell\ngenice2 CRN1 -f twist[svg] \u003e sample.svg\n```\n\n# [genice2_twist](https://github.com/vitroid/genice-twist/)\n\nDraw the structure with twist order parameter.\n\nversion 2.0\n\n## Requirements\n\n\n* genice2\n* genice2-svg\u003e=0.7\n* twist-op\u003e=0.2\n* sklearn\n\n## Installation from PyPI\n\n```shell\n% pip install genice2_twist\n```\n\n## Manual Installation\n\n### System-wide installation\n\n```shell\n% make install\n```\n\n### Private installation\n\nCopy the files in genice2_twist/formats/ into your local formats/ folder.\n\n\n## Usage\n        \n    usage:\n        genice II -f twist[options:separated:by:colons] \u003e 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\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\u003csup\u003e-3\u003c/sup\u003e. 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```shell\n% make test\n```\n\n## Reference\n\n* Matsumoto, M., Yagasaki, T. \u0026 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).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvitroid%2Fgenice-twist","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvitroid%2Fgenice-twist","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvitroid%2Fgenice-twist/lists"}