Metadata-Version: 2.1
Name: DuIvyTools
Version: 0.5.3
Summary: A simple tool for GROMACS results analysis and visualization
Home-page: https://github.com/CharlesHahn/DuIvyTools
Author: CharlesHahn,杜艾维
Author-email: 
License: UNKNOWN
Download-URL: https://github.com/CharlesHahn/DuIvyTools
Description: DuIvyTools
        
        [![PyPI version](https://badge.fury.io/py/DuIvyTools.svg)](https://badge.fury.io/py/DuIvyTools)
        ![PyPI - Downloads](https://img.shields.io/pypi/dm/DuIvyTools)
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        [![Documentation Status](https://readthedocs.org/projects/duivytools/badge/?version=latest)](https://duivytools.readthedocs.io/zh_CN/latest/?badge=latest)
        [![commits-since](https://img.shields.io/github/commits-since/CharlesHahn/DuIvyTools/v0.5.0.svg)](https://github.com/CharlesHahn/DuIvyTools/compare/v0.5.0...master)
        [![Python Version](https://img.shields.io/pypi/pyversions/DuIvyTools.svg)](https://pypi.org/project/DuIvyTools)
        
        
        
        ```
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         /**////**         /**          **   **/////**///               /**
         /**    /** **   **/** **    **//** **     /**  ******   ****** /**  ******
         /**    /**/**  /**/**/**   /** //***      /** **////** **////**/** **//// 
         /**    /**/**  /**/**//** /**   /**       /**/**   /**/**   /**/**//***** 
         /**    ** /**  /**/** //****    **        /**/**   /**/**   /**/** /////**
         /*******  //******/**  //**    **         /**//****** //****** *** ****** 
         ///////    ////// //    //    //          //  //////   ////// /// //////
        ```
        
        DuIvyTools (DIT) is a simple analysis and visualization tool for GROMACS result
        files, designed for fasten your analysis of molecular dynamics simulations. 
        
        ## Intro
        
        The usage of DIT is similar to GMX, type `dit` and followed by commands and 
        parameters, like:
        
        ```bash
        dit xvg_show -f test.xvg
        dit xpm_show -f test.xpm
        ```
        
        Type `dit` for the commands supported. Type `dit <comman> -h` for detailed help information of each command. 
        
        The tutorials (in Chinese) of DIT can be found at https://duivytools.readthedocs.io/
        
        If you got any problem using DIT or suggestions, feel free to issue or contact me by 飞书 (Lark): https://applink.feishu.cn/client/chat/chatter/add_by_link?link_token=a22q9297-2060-43d5-8b28-73637c82cad6
        
        
        
        ## Install
        
        This tool is a python3 library which you can install it by `pip`.
        
        ```bash
        pip install DuIvyTools
        ```
        
        ## Commands
        
        DuIvyTools provides about 30 commands for visualization and processing of GMX result files like .xvg or .xpm.
        
        ```
        All commands are shown below:
        XVG:
            xvg_show              : easily show xvg file
            xvg_compare           : visualize xvg data
            xvg_ave               : calculate the averages of xvg data
            xvg_energy_compute    : calculate eneries between protein and ligand
            xvg_combine           : combine data of xvg files
            xvg_show_distribution : show distribution of xvg data
            xvg_show_scatter      : show xvg data by scatter plot
            xvg_show_stack        : show xvg data by stack area plot
            xvg_box_compare       : compare xvg data by violin and scatter plots
            xvg_ave_bar           : calculate and show the averages of parallelism
            xvg_rama              : draw ramachandran plot from xvg data
        XPM:
            xpm_show              : visualize xpm data
            xpm2csv               : convert xpm data into csv file in form (x, y, z)
            xpm2dat               : convert xpm data into dat file in form (N*N)
            xpm_diff              : calculate the difference of xpms
            xpm_merge             : merge two xpm by half and half
        Others:
            mdp_gen               : generate mdp file templates
            show_style            : show figure control style files
            find_center           : find geometric center of one group of atoms
            dccm_ascii            : convert dccm from ascii data file to xpm
            dssp                  : generate xpm and xvg from ascii file of gmx2023
            ndx_add               : new a index group to ndx file
            ndx_split             : split one index group into several groups
            ndx_show              : show the groupnames of index file
        
        You can type `dit <command> -h` for detailed help messages about each command, like: `dit xvg_show -h`.
        
        All possible parameters could be inspected by `dit -h` or `dit --help`.
        
        ```
        
        ## Cite
        
        If you used DuIvyTools in your research, cite it by doi please.
        
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6339993.svg)](https://doi.org/10.5281/zenodo.6339993)
        
        
        
        ## Todo
        
        - [ ] python unittest
        - [ ] better docs
        - [ ] unequal number of x and y ticks in xpm like fel.xpm
        
        
        ## Others
        
        A lot of time and money have been spent for developing DuIvyTools and improve it. If possible, **REWARD** to help me improve it. 
        
        
        ![reward](docs/static/reward.png)
        
        
Platform: cross-platform
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
Provides-Extra: test
