Install¶
System Requirements¶
A 64-bit operating system
A Python 3 installation with version ≥ 3.7
Conda Installation¶
The easiest method to install is with Anaconda or Miniconda, which works on all operating systems. It is highly recommended to install MD DaVis in a virtual environment. The environment.yml is provided to ease the process.
conda env create -f environment.yml -n md_davis_env
This automatically creates a conda environment called md_davis_env with all required dependencies.
Activate the environment and install MD DaVis in it using:
conda activate md_davis_env
pip install md-davis
If you don’t have pip installed, this Python installation guide can guide you through the process.
Finally, obtain the Delphi and MSMS if you intend to perform electrostatics analysis.
Installation in the base conda environment¶
If you do not want to use the environment.yml file or if you want to install it in the base environment. Install mdtraj and pymol before installing md-davis.
conda install -c conda-forge mdtraj pymol-open-source
pip install md-davis
Linux Installation¶
MD DaVis can be installed on Linux with:
pip install md-davis
Note
PyMOL is required to run MD DaVis, which may be challenging to install in a virtual environment without conda. (see External Dependencies)
Windows Installation¶
On Windows, pip may fail to install MD DaVis due to errors with compiling dependencies. Please follow the instructions under Conda Installation.
Development Version¶
You can obtain the source code by cloning the public repository:
git clone git@github.com:djmaity/md-davis.git
or downloading the tarball:
curl -OL https://github.com/djmaity/md-davis/tarball/master
Once you have a copy of the source, it can be installed with:
python setup.py install
OR
pip install path/to/extracted/source/code
You can also install the development version directly with:
pip install https://github.com/djmaity/md-davis/archive/master.zip
External Dependencies¶
GROMACS¶
Currently, most analyses have to be performed with GROMACS, and the output is provided to MD DaVis for visualization. Other analysis tools may be used as long as the input to MD DaVis can be appropriately formatted.
PyMOL¶
PyMOL is not available in the python package index.
Therefore, it cannot be automatically installed with pip.
Open-Source PyMOL¶
Open-Source PyMOL available from conda-forge can be installed with:
conda install -c conda-forge pymol-open-source
Alternatively, on Linux, PyMOL can be installed with the system package manager, e.g., apt in Ubuntu or dnf in Fedora.
However, it is not possible to install PyMOL into a virtual environment using this method.
Therefore, MD DaVis must be installed in the system python as well.
On Windows, if you are not using conda, then pre-built Open-Source PyMOL can be downloaded from
Christoph Gohlke’s page
distributing unofficial windows binaries for python extension packages.
Commercial/Educational PyMOL¶
Commercial/Educational PyMOL from Schrödinger can be installed with:
conda install -c schrodinger pymol-bundle
DelPhi and MSMS¶
Python dependencies are automatically installed. However, the electrostatics calculation requires the following two programs, which must be obtained separately.
Uninstall¶
MD DaVis can be easily uninstalled like any other python package, with:
pip uninstall md-davis
As with any python package, this does not remove the dependencies installed by MD DaVis. That is why it is recommended to install MD DaVis in a virtual environment. Then, the virtual environment may be entirely removed without affecting other python packages on the system.
Note
On Linux, if MD DaVis was installed as root or with sudo, the uninstall command should be run with sudo.