A batteries-included toolkit of analysis modules and helper functions
Project description
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
-
Install MDHelper and its dependencies using
pip install mdhelper
Install using Anaconda or Miniconda
-
Add the conda-forge channel using
conda config --add channels conda-forge
-
Install MDHelper and its dependencies using
conda install mdhelper
Build from source
-
Ensure that the latest version of the Python build frontend,
build
, is installed:python3 -m pip install --upgrade build
-
Create a local copy of the MDHelper repository on your machine using
git clone https://github.com/bbye98/mdhelper.git
-
Enter the root directory of MDHelper using
cd mdhelper
-
Build the MDHelper wheel using
python3 -m build
The Python wheel will be placed in the
dist
directory. -
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
-
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.
-
Create a local copy of the MDHelper repository on your machine using
git clone https://github.com/bbye98/mdhelper.git
-
Enter the root directory of MDHelper using
cd mdhelper
-
Install the dependencies using
pip install -r requirements.txt
or
conda install --file requirements.txt
-
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
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