Package: mdhelper
MDHelperMDHelper 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 anexperimentallibrary that has
only been tested on Linux and may contain bugs and issues. If you come
across one, pleasesubmit a new issue. If
you would like to contribute to MDHelper, pleasesubmit a pull request.Featuresalgorithm:
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 usagePrerequisitesIf you use pip to manage your Python packages or plan on using OpenMM
with third-party extensions, such asconstvpluginfor 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 environmentIt is recommended, but not necessary, that you create a virtual
environment to prevent dependency conflicts.If you are using pip to manage Python packages, usevirtualenv venv
source venv/bin/activatewherevenvis the name of the new environment.If you are using Anaconda or Miniconda, useconda create --name venv
conda activate venvInstall using pipInstall MDHelper and its dependencies usingpip install mdhelperInstall using Anaconda or MinicondaAdd the conda-forge channel usingconda config --add channels conda-forgeInstall MDHelper and its dependencies usingconda install mdhelperBuild from sourceEnsure that the latest version of the Python build frontend,build, is installed:python3 -m pip install --upgrade buildCreate a local copy of the MDHelper repository on your machine usinggit clone https://github.com/bbye98/mdhelper.gitEnter the root directory of MDHelper usingcd mdhelperBuild the MDHelper wheel usingpython3 -m buildThe Python wheel will be placed in thedistdirectory.Install MDHelper usingpython3 -m pip install dist/mdhelper-<version>-py3-none-any.whlwhere<version>is the version of MDHelper you are installing.Portable packageChange to the directory where you want to store a copy of MDHelper usingcd <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 usinggit clone https://github.com/bbye98/mdhelper.gitEnter the root directory of MDHelper usingcd mdhelperInstall the dependencies usingpip install -r requirements.txtorconda install --file requirements.txtOnce done, you can use MDHelper by first adding the path to thesrcdirectory in your Python scripts:import sys
sys.path.insert(0, "/path/to/mdhelper/src")
import mdhelper