Metadata-Version: 2.1
Name: Xponge
Version: 1.2.6.2
Summary: A Python package to perform pre- and post-processing of molecular simulations
Home-page: https://gitee.com/gao_hyp_xyj_admin/xponge
Author: Yijie Xia
Author-email: yijiexia@pku.edu.cn
License: UNKNOWN
Description: # Welcome to Use Xponge!
        
        ## What is Xponge?
        
        ``Xponge`` is a lightweight and easy-customizing python package to perform pre- and post-processing of molecular simulations.
        
        ## What can Xponge do?
        
        Xponge includes three major categories of functionality, namely, the simulation system construction, simulation data transformation and analysis, and automated workflows for complex simulations. ``Xponge`` is mainly designed for the molecular dynamics (MD) program [SPONGE](https://onlinelibrary.wiley.com/doi/epdf/10.1002/cjoc.202100456), but it can also output some general format files such as mol2 and PDB, so it may help the other molecular modelling programs too.
        
        ## How can I get Xponge?
        
        Xponge can be used on both Windows and Linux operating systems
        
        ### 1. pip install
        
        ```bash
        pip install Xponge
        ```
        
        ### 2. source setup
        
        - 2.1 download or clone the source of the gitee or github repository
        
            The gitee repository is [here](https://gitee.com/gao_hyp_xyj_admin/xponge).
            The github repository is [here](https://github.com/xia-yijie/xponge).
        
        - 2.2 open the directory where you download or clone the repository
        
        - 2.3 run the command
        
            ```bash
            python setup.py install
            ```
        
        ## How can I check whether I have installed Xponge correctly?
        
        There are some unit tests in ``Xponge``. You can do the basic test to check whether the installation is successful like this:
        
        ```bash
        Xponge test -do base -o test
        ```
        
        Here, ``Xponge`` can be replaced to ``python -m Xponge``, ``python3 -m Xponge`` and so on according to your settings of the environmental variables.
        
        ## Can you give me a example to use?
        
        Here is a simple example.
        
        ```python
        import Xponge
        # import the force field you need
        import Xponge.forcefield.amber.ff14sb
        # build the molecule
        peptide = ACE + ALA + NME
        # save it as your favorite format
        Xponge.save_pdb(peptide, "ala.pdb")
        Xponge.save_mol2(peptide, "ala.mol2")
        Xponge.save_sponge_input(peptide, "ala")
        ```
        
        ## Where can I see the complicated usage, the API documentation or the way to develop my own force field?
        
        All can be seen [here](https://spongemm.cn/xponge_doc/index.html).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Development Status :: 5 - Production/Stable
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
