Xponge 1.2.6.2

A Python package to perform pre- and post-processing of molecular simulations

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, 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

pip install Xponge

2. source setup

• 2.1 download or clone the source of the gitee or github repository

  The gitee repository is here. The github repository is here.

• 2.2 open the directory where you download or clone the repository

• 2.3 run the command

  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:

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.

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.