Install

install lazydock python package itself

pip install lazydock -U

pip install git+https://github.com/BHM-Bob/BA_PY.git

pip install git+https://gitee.com/BHM-Bob/BA_PY.git

dependencies
mbapy: coding base.
pygame: needed by mbapy.BaseInfo, part of coding base.
nicegui: needed by lazydock.pml_plugin to run web ui.
openbabel-wheel: needed by lazydock.scripts.prepare_gmx.py to center molecule, can be commented out if installed openbabel software.
networkx: needed by lazydock.gmx.thirdparty.cgenff_charmm2gmx.py, can be changed to other version if compatible.
DuIvyTools: needed by lazydock.scripts.run_gmx & ana_gmx to visualize gmx output.
lazydock_md_task: needed by lazydock.scripts.ana_gmx to run MD-TASK.
compas: needed by lazydock.pml.align_to_axis to calculate bonding box.
md-davis: needed by lazydock.scripts.ana_gmx to run MD-DaVis.
expect: a software for running shell command, needed by lazydock.gmx.run.Gromacs.
autodocktools-py3: a python package as AutoDockTooks.

In pymol plugin installation GUI, install path-to-site-packages/lazydock_pymol_plugin/__init__.py.

conda install -c conda-forge openbabel
pip install plip -U --no-deps

Now all needed functionality of MD-TASK for lazydock is included in lazydock_md_task package. Already installed by requirements.

pip install biopandas h5py
pip install md-davis -U --no-deps

Warning: gmx_MMPBSA is better to be installed in a separate conda environment to avoid lib conflicts.

conda install -c conda-forge "mpi4py==4.0.1" "ambertools<=23.3" "parmed==4.2.2" pocl
pip install gmx_MMPBSA -U --no-deps

Version are from gmx_MMPBSA's docs.

sudo apt install expect

pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3"