Installation#
FragBEST-Myo uses pixi to manage the packages and virtual environments.
Note
A virtual environment is created to ensure that all dependencies are effectively managed and kept separate from your system’s Python installation.
Prerequisite package: pixi.
System requirement: Linux.
FragBEST-Myo basically follows the same preparation protocol as MaSIF to generate chemical features and surface files, so some third-party libraries and programs are required, including msms, PyMesh, APBS, reduce.
However, in order to make the packages compatible with our workflow and python version (3.10), we modified some code in PyMesh and MaSIF (see pymesh change logs and masif change logs).
Additionally, FragBEST-Myo directly adapts code from DeepDrug3D and 3D U-Net pytorch implementation based on GPL-3.0 and MIT licenses, respectively. Other dependencies are shown in pyproject.toml.
Please check more details about the third-party dependencies used in this project:
To use FragBEST-Myo, start by installing the necessary dependencies. Please follow the steps below:
Important
The installation code will automatically download msms (check with
the author if you are a commercial user)
and APBS from the source links, install the adapted masif, and
FragBEST_pymol_plugin (adapted from MaSIF) from Github repo (as a submodule),
use our adapted DeepDrug3D
and adapted 3D U-Net pytorch implementation
(located in ./utils/thirdparty). Since PyMesh is officially unsupported for python 3.10, we installed
PyMesh by a pre-built wheel here
from our adapted PyMesh repo. reduce will be installed by pixi from bioconda channel.
# Clone the repository
git clone https://github.com/fornililab/FragBEST-Myo.git
# Build the virtual environment
cd FragBEST-Myo
pixi run build
To verify the success of the installation, execute the following code:
# Test the installation
pixi run poe test -n 4 # "-n 4" means using 4 threads to run the tests parallely
# Some warnings are expected, but all tests should pass.
# Test the installation of pymol environment
pixi run -e pymol pymol --help
# You should be able to view the help documentation for PyMOL.
Activate the environment#
To activate FragBEST-Myo’s environment, you have to be in ~/path/to/FragBEST-Myo or its subfolder to activate the virtual environment:
# Activate the virtual environment (pixi)
pixi shell
# in the virtual environment, it looks like:
# (FragBEST-Myo) username@servername:~/path/to/FragBEST-Myo$
Activate jupyter notebook#
WHen you are in the virtual environment, you can start jupyter notebooks. Here we demonstrate how to open the tutorial notebooks.
# (in the virtual environment) Go to the tutorial directory
cd tutorial
# (in the virtual environment) Activate jupyter notebook
jupyter notebook
# This will open the jupyter notebook interface in your default web browser.
# Then, you can open any notebook file (.ipynb) to start exploring FragBEST-Myo.
Leave the environment#
To leave the virtual environment, you can simly run:
# Leave the virtual environment (pixi)
exit
# return to:
# username@servername:~/path/to/FragBEST-Myo$