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poli.objective_repository.drd3_docking

poli.objective_repository.drd3_docking#

A wrapper around TDC’s DRD3 docking objective function.

Prerequisites#

There are several requirements for running this objective function. We expect you to

  • have AutoDock Vina installed in the path,

  • have the prepare_receptor binary from the ADFR suite installed and in the path,

  • have the poli__lambo environment created.

The rest of this description shows you how to do all this:

Installing AutoDock Vina#

  1. Download AutoDock Vina from the Center for Computational Structural Biology’s website (https://vina.scripps.edu/downloads/). Uncompress them.

  2. Add this to the path by including export PATH=path/to/AutoDock_vina/bin:$PATH in your ~/.bashrc or ~/.zshrc.

`bash # In your ~/.bashrc or ~/.zshrc export PATH=path/to/AutoDock_vina/bin:$PATH `

Installing the ADFR suite#

  1. Download the installable files (https://ccsb.scripps.edu/adfr/downloads/). It’s likely that you will have to run the ./install.sh script inside the folder, and thus you might have to change its permissions for execution using chmod +x

  2. After running ./install.sh, you should be able to find …/bin/prepare_receptor.

  3. For the docking to run, pyscreener needs access to the prepare_receptor binary. However, adding all of the ADFR bin folder is sometimes problematic, since it has a version of Python inside. Thus, we recommend creating a symlink. Write this in your ~/.bashrc or ~/.zshrc:

`bash # In your ~/.bashrc or ~/.zshrc ln -sf /path/to/ADFR/bin/prepare_receptor /path/to/AutoDock_vina/bin `

Create the poli__lambo environment#

This can easily be done by running

# From the base of the poli repo
conda env create --file src/poli/objective_repository/ddr3_docking/environment.yml

We also need lambo’s tasks to be available in Python’s path for poli__lambo:

git clone https://github.com/samuelstanton/lambo    # For reference, we use 431b052
cd lambo
pip install -e .

In particular, we need - lambo.tasks.proxy_rfp.proxy_rfp.ProxyRFPTask - the rfp data: see ~/lambo/assets/fpbase

And now you should be set! Running register.py and query_example.py should work.

Modules

poli.objective_repository.drd3_docking.register

Implements the DRD3 docking task using the TDC oracles [1].
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