Installation

Requirements:

• Python 3.8+.

• RDKit (2022.3.5+).

• Pandas.

• NumPy.

• tqdm.

• CReM (0.2.9+).

• Meeko.

• AutoDock-Vina.

Via pip (standard)

pip install

# To get the last "stable" version (strongly recommended). This project is still in beta state.
pip install moldrug

or:

# To get the version on development (not recommended)
pip install -U git+https://github.com/ale94mleon/moldrug.git@main

There are multiple methods to obtain AutoDock-Vina. You can use conda or download the latest release from the Vina Repository. We highly recommend using the last release posted on Vina Repository.

Via conda

moldrug is also available through conda. However, the pip installation is the recommended one.

conda create -n moldrug
conda activate moldrug
conda install -c ale94mleon -c conda-forge moldrug

Note

MacOS users may face some problems trying to install because of the AutoDock-Vina dependency. If that is the case, just download the executable as it is explained next.

If some dependencies are missing, please install them through pip. Some of them could be:

pip install meeko crem pyyaml scipy tqdm

AutoDock-Vina dependency and related software

Note

AutoDock-Vina is the only non-pip dependency required for moldrug. This section is useful in case you would like to use the build-in cost functions of moldrug from moldrug.fitness

AutoDock-Vina is an ongoing project, and it is advisable to stay up-to-date by regularly checking for the latest release. As of the creation of this documentation, the most recent version is v1.2.5. We will be using this version as a demonstration, but we strongly recommend using the most recent release for optimal performance and features. For detailed information, please visit: AutoDock-Vina installation Instruction.

Unix- and Linux-based OS

wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_linux_x86_64
chmod a+x vina_1.2.5_linux_x86_64
./vina_1.2.5_linux_x86_64 --help

MacOS

wget https://github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.5/vina_1.2.5_mac_x86_64
chmod a+x vina_1.2.5_mac_x86_64
./vina_1.2.5_mac_x86_64 --help

Note

MacOs users might need to allow the execution of the application on Privacy & Security depending on the MacOS version.

Windows

Please, download from release. Conda installation may not work.

Converting pdb to pdbqt

This step can be achieved through OpenBabel or ADFR. We recommend ADFR. Depending on the platform, you should be able to access the program prepare_receptor in different ways. In my case, it lies on /Users/klimt/ADFRsuite-1.0/bin/prepare_receptor. Then you can convert your pdb with:

/Users/klimt/ADFRsuite-1.0/bin/prepare_receptor -r your_protein.pdb -o your_protein.pdbqt

Check here for more information.

Getting box information

To perform the docking you must provide boxcenter (center for AutoDock-Vina) and boxsize (size for AutoDock-Vina) to the cost functions defined in moldrug.fitness. For that, two PyMol plugins are useful: GetBox and/or autodock. Details of their installation and use are not discussed here, please visit their corresponding repositories for more information.

Work with a docker container

1. Use the Docker configuration file on GitHub.

2. Visit the moldrug docker container.

Finally pip install moldrug inside it.