docktprep

Prepare and fix Protein Data Bank (PDB) files for molecular modeling and docking.

Installation

Clone this repository, create a virtual environment and install the required dependencies:

# clone this repository...
cd docktprep
python3.12 -m venv env  # use python >=3.10 
source env/bin/activate
python -m pip install -r requirements.txt

Run tests:

python -m pytest -vs tests/ --log-cli-level=INFO 

Run the app:

python -m docktprep.main --help

MODELLER installation

Some functionalities of this package depend on MODELLER, which is not included in this repository; you'll need to install it separately. Follow the installation instructions on the official MODELLER website.

Tip

Below, instructions for Debian/Ubuntu systems are provided:

wget https://salilab.org/modeller/10.7/modeller_10.7-1_amd64.deb
sudo env KEY_MODELLER=XXXX dpkg -i modeller_10.7-1_amd64.deb  # substitute 'XXXX' for the actual key
python3.12 -c "import modeller; print(modeller.__version__)"  # test the installation

Important

Once MODELLER is installed, you must create symbolic links to its files in the virtual environment’s site-packages directory to make the library available inside the venv.

Find the location of the MODELLER installation:

deactivate  # `deactivate` the virtual environment first, if it is active!
MODELLER_PATH=$(python3.12 -c "import modeller, os; print(os.path.dirname(modeller.__file__))")
MODELLER_PARENT=$(dirname -- "${MODELLER_PATH%/}")

Reactivate the virtual environment and create symbolic links:

source env/bin/activate
VENV_SITEPACKAGES=$(python -c "import site; print(site.getsitepackages()[0])")
ln -s "$MODELLER_PATH" "$VENV_SITEPACKAGES/modeller"
ln -s "$MODELLER_PARENT/_modeller.so" "$VENV_SITEPACKAGES/_modeller.so"

Test the installation inside the virtual environment:

python -c "import modeller; print(modeller.__version__)"