Python is used extensively in DOCK 3.8 scripts, and multiple versions of python are required to run the full suite of software.
top_poses.py : Python 3.8
top_poses.py makes use of python 3.8 specific features to perform its analysis. You can find a compatible install of python3.8 on Wynton and BKS clusters at these locations respectively:
/wynton/group/bks/soft/python-versions/python-3.8-install /nfs/soft/python/versions/python-3.8-install bash usage: source $INSTALL_DIR/python-3.8-install/bin/env.sh csh usage: source $INSTALL_DIR/python-3.8-install/bin/env.csh
3d building : Python 3.7
3D building scripts all use a special Python 3.7 version, packaged with openeye, rdkit, scipy, numpy, etc...
Note that you must source a valid openeye license to make use of openeye features. Like so:
export OE_LICENSE=<path to license>
This version can be found on Wynton and BKS at the following locations:
/wynton/group/bks/soft/python-versions/lig_build_py3-3.7.1 /nfs/soft/python/versions/lig_build_py3-3.7.1 bash usage: source $INSTALL_DIR/lig_build_py3-3.7.1/bin/activate
Keep in mind that many legacy scripts are kept around, and not all of them are written with python 3.7 in mind. The up-to-date pipeline will function with this version, e.g the following scripts:
$DOCKBASE/ligand/generate/build_ligands.py $DOCKBASE/ligand/mol2db2_py3_strain/* $DOCKBASE/ligand/omega/omega.py $DOCKBASE/ligand/*/*.py3.*
Other Python Versions
Older DOCK scripts may make use of python2, which is widely available by default on Wynton & BKS. You may try running these legacy scripts with a base install of python 2, however there may be pip requirements I am unaware of. If you are running these legacy scripts, you may wish to install your own version of python 2, run the scripts, then if there are any import errors, simply pip install the requirements to your own personal version. If you are doing this and you have found a script with a special requirement, please message me so I can update this page and make the python version widely available. My email is email@example.com.