mdhelper 0.0.2

A batteries-included toolkit of analysis modules and helper functions

MDHelper

MDHelper is a batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.

• Documentation: https://bbye98.github.io/mdhelper/
• Python Package Index (PyPI): https://pypi.org/project/mdhelper/

Note that MDHelper is currently an experimental library that has only been tested on Linux and may contain bugs and issues. If you come across one, please submit a new issue. If you would like to contribute to MDHelper, please submit a pull request.

Features

• algorithm: Efficient NumPy algorithms for data wrangling and evaluating structural and dynamical properties.
• analysis: Serial and parallel data analysis tools built on top of the MDAnalysis framework.
• fit: Two-dimensional curve fitting models for use with SciPy.
• openmm: Extensions to the high-performance OpenMM toolkit, such as custom bond/pair potentials, support for NetCDF trajectories, and much more.
• plot: Settings and additional functionality for Matplotlib figures.
• utility: General utility functions.

Installation and usage

Prerequisites

If you use pip to manage your Python packages or plan on using OpenMM with third-party extensions, such as constvplugin for the method of image charges, you must compile and install OpenMM prior to installing MDHelper. See the "Compiling OpenMM from Source Code" for more section of the OpenMM User Guide for more information. This additional step is necessary since precompiled versions of OpenMM do not expose their header files, which are needed to link against custom plugins. Otherwise, the lastest precompiled version of OpenMM on conda-forge will be installed during the installation of MDHelper.

Virtual environment

It is recommended, but not necessary, that you create a virtual environment to prevent dependency conflicts.

If you are using pip to manage Python packages, use

virtualenv venv
source venv/bin/activate

where venv is the name of the new environment.

If you are using Anaconda or Miniconda, use

conda create --name venv
conda activate venv

Install using pip

1. Install MDHelper and its dependencies using

   pip install mdhelper

Install using Anaconda or Miniconda

1. Add the conda-forge channel using

   conda config --add channels conda-forge
   

2. Install MDHelper and its dependencies using

   conda install mdhelper
   

Build from source

1. Ensure that the latest version of the Python build frontend, build, is installed:

   python3 -m pip install --upgrade build
   

2. Create a local copy of the MDHelper repository on your machine using

   git clone https://github.com/bbye98/mdhelper.git
   

3. Enter the root directory of MDHelper using

   cd mdhelper
   

4. Build the MDHelper wheel using

   python3 -m build
   

   The Python wheel will be placed in the dist directory.

5. Install MDHelper using

   python3 -m pip install dist/mdhelper-<version>-py3-none-any.whl
   

   where <version> is the version of MDHelper you are installing.

Portable package

1. Change to the directory where you want to store a copy of MDHelper using

   cd <directory>
   

   where <directory> is the relative path to the desired directory.

   If you are already in the correct location, skip this step.

2. Create a local copy of the MDHelper repository on your machine using

   git clone https://github.com/bbye98/mdhelper.git
   

3. Enter the root directory of MDHelper using

   cd mdhelper
   

4. Install the dependencies using

   pip install -r requirements.txt
   

   or

   conda install --file requirements.txt
   

5. Once done, you can use MDHelper by first adding the path to the src directory in your Python scripts:

   import sys
   sys.path.insert(0, "/path/to/mdhelper/src")
   import mdhelper