Installation

[Jameel9]

Dear DOCK team,

Thanks for providing free DOCK for academic users.
I already got the DOCK3.8 tarball but, unfortunately, I could not install it on a Ubuntu machine!
I don't have a degree in computer science and the README.md file was not easy to understand, even with help from AI. It looks more like developer notes than a clean user installation guide. The wiki pages are not different. For instance, This page seems to be for your HPC users only.
Adding extra lines to clarify the instructions would make our life easier!

Thanks for your support.

[bwhall61]

Hi Jameel,

Have you tried following the "Install the release" section of the README.md? If so, what specific error did you run into so that we may better help you?

[Jameel9]

Hi @bwhall61

Thanks for your reply.
This is the terminal output.

(base) user1@user1-Precision-3460:~/DOCK3.8$ export DOCK_INSTALL_PATH=/home/user1/DOCK3.8
(base) user1@user1-Precision-3460:~/DOCK3.8$ export DOCKBASE=/home/user1/DOCK3.8/legacy3
(base) user1@user1-Precision-3460:~/DOCK3.8$ python3 -m venv ${DOCK_INSTALL_PATH}/pydock_env
(base) user1@user1-Precision-3460:~/DOCK3.8$ source ${DOCK_INSTALL_PATH}/pydock_env/bin/activate
(pydock_env) (base) user1@user1-Precision-3460:~/DOCK3.8$ pip install ${DOCK_INSTALL_PATH}/pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl
Processing ./pydock3/dist/pydock3-0.1.0rc1-py3-none-any.whl
Collecting PyYAML<7.0,>=6.0 (from pydock3==0.1.0rc1)
  Using cached pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
Collecting fire<0.5.0,>=0.4.0 (from pydock3==0.1.0rc1)
  Using cached fire-0.4.0.tar.gz (87 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting joypy<0.3.0,>=0.2.6 (from pydock3==0.1.0rc1)
  Using cached joypy-0.2.6-py2.py3-none-any.whl.metadata (812 bytes)
Collecting matplotlib<4.0.0,>=3.5.1 (from pydock3==0.1.0rc1)
  Using cached matplotlib-3.10.6-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB)
Collecting networkx<3.0,>=2.8 (from pydock3==0.1.0rc1)
  Using cached networkx-2.8.8-py3-none-any.whl.metadata (5.1 kB)
Collecting numpy<2.0.0,>=1.21.5 (from pydock3==0.1.0rc1)
  Using cached numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting oyaml<2.0,>=1.0 (from pydock3==0.1.0rc1)
  Using cached oyaml-1.0-py2.py3-none-any.whl.metadata (1.2 kB)
Collecting pandas<2.0.0,>=1.4.2 (from pydock3==0.1.0rc1)
  Using cached pandas-1.5.3-cp312-cp312-linux_x86_64.whl
Collecting pillow<10.0.0,>=9.5.0 (from pydock3==0.1.0rc1)
  Using cached Pillow-9.5.0.tar.gz (50.5 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting plotly<6.0.0,>=5.14.1 (from pydock3==0.1.0rc1)
  Using cached plotly-5.24.1-py3-none-any.whl.metadata (7.3 kB)
Collecting python-dotenv<0.21.0,>=0.20.0 (from pydock3==0.1.0rc1)
  Using cached python_dotenv-0.20.0-py3-none-any.whl.metadata (19 kB)
INFO: pip is looking at multiple versions of pydock3 to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 1.21.2 Requires-Python >=3.7,<3.11; 1.21.3 Requires-Python >=3.7,<3.11; 1.21.4 Requires-Python >=3.7,<3.11; 1.21.5 Requires-Python >=3.7,<3.11; 1.21.6 Requires-Python >=3.7,<3.11
ERROR: Could not find a version that satisfies the requirement rdkit-pypi<2023.0.0,>=2022.3.2 (from pydock3) (from versions: none)

[notice] A new release of pip is available: 24.3.1 -> 25.2
[notice] To update, run: pip install --upgrade pip
ERROR: No matching distribution found for rdkit-pypi<2023.0.0,>=2022.3.2
(pydock_env) (base) user1@user1-Precision-3460:~/DOCK3.8$

I think the error says it's a python incompatibility thing (3.7 vs 3.12) that prevents installation of an RDKit version between 2022 and 2023. The questions now are:

• (1) If I created a new conda env with python==3.7, should I still follow the same instructions?
• (2) the first two commands (export DOCK_INSTALL_PATH & export DOCKBASE), should be ran every time DOCK3.8 is used? Or I can use Pydock directly from the conda env?

Thanks for your support!

[bwhall61]

Ah yes I will add that as a requirement.
(1) The pydock3 python package requires python >=3.8.1,<3.11. I will note that in the instructions when making the virtual environment. But yes if you have a conda env with python==3.9 for example you would follow the same instructions

(2) Pydock and DOCK3.8 don't explicitly need DOCK_INSTALL_PATH or DOCKBASE to run. These are mostly so that we can refer to paths in the installation and in the testing scripts (test_subdock.sh for example). There are also references to DOCKBASE in some of the lab's older papers so this is mostly for that.

[Jameel9]

Thank you @bwhall61!
One last question: Is there any way to convert sdf files (from rdkit, for example) to db2? I have seen some scripts on github to convert mol2, but I am avoiding Mol2 file format.