gnina docking

Setup

Setup gnina

Below are the commands to setup

# !sudo apt install -yq openbabel
# !wget https://github.com/gnina/gnina/releases/download/v1.0.3/gnina #check the latest version please
# !chmod +x gnina
# !./gnina

Alternatively, use python script to setup:

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setup_gnina_local

 setup_gnina_local (version='v1.3')

Download and install gnina in the current directory

# setup_gnina_local('v1.1')

def delete_gnina(gnina_path="gnina"):
    "Remove gnina after finish"
    path=Path(gnina_path)
    if path.exists() and path.is_file():
        path.unlink()
        print('Deleted!')
    else: print('Not exist!')

# delete_gnina()

Deleted!

If local is not successful, use docker

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setup_gnina_docker

 setup_gnina_docker ()

Pull gnina docker image

# setup_gnina_docker()

Pulling GNINA Docker image: gnina/gnina
GNINA Docker image is ready.

Get protein and ligand

# #nature medicine paper, mrtx
# !wget http://files.rcsb.org/download/7T47.pdb

# # get ligand
# !grep 6IC 7T47.pdb > lig.pdb

# # get protein
# # !grep ATOM 7T47.pdb > rec.pdb #not as good as the one below

# !grep -v 6IC 7T47.pdb > rec.pdb

Gnina affinity

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extract_gnina_dock

 extract_gnina_dock (gnina_output)

Extract values from gnina output

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gnina_dock

 gnina_dock (receptor, ligand, autobox_ligand, output='docked.sdf',
             seed=0, exhaustiveness=None)

	Type	Default	Details
receptor			receptor file
ligand			ligand file
autobox_ligand			ligand file isolated from the complex
output	str	docked.sdf	output file (sdf or sdf.gz) to be saved
seed	int	0	set seeds
exhaustiveness	NoneType	None	number of MC chains, default is 8 if None, the higher the better (16,32); for whole protein, use 64

# df = Data.get_g12d_dedup()[:10]

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gnina_dock

 gnina_dock (df, ID_col='ID', smi_col='SMILES', output_dir='gnina_docked')

# out = gnina_dock_df(df)

TODO: make it parallel

End