feat: high level toolkit for running ligand and docking

[sg-s]

changes

• high level toolkit functions
• support for scores for vina

usage

from deeporigin.tools import toolkit
csv_file = "/Users/srinivas/Downloads/ligands.csv"
column_name = "SMILES"
toolkit.prep_ligands(
    csv_file=csv_file,
    column_name=column_name,
)

^ this takes in a CSV file, converts every smiles string to a SDF file, uploads them to datahub, and preps them all using meeko (on deeporigin)

ligand_database_name = "ligand-prep-meeko"
ligand_column_name = "output-ligand"
protein_database_name = "protein"
protein_column_name = "protein"
protein_row = "protein-1"

search_space = {
    "center_x": 15.190,
    "center_y": 53.903,
    "center_z": 16.917,
    "size_x": 15.1,
    "size_y": 15.1,
    "size_z": 15.1,
}

docking = {
    "energy_range": 3.1,
    "exhaustiveness": 1,
    "num_modes": 3,
}

toolkit.dock_ligands_to_protein(
    docking=docking,
    search_space=search_space,
    protein_row=protein_row,
    protein_column_name=protein_column_name,
    ligand_database_name=ligand_database_name,
    ligand_column_name=ligand_column_name,
    protein_database_name=protein_database_name,
)

^ this takes a bunch of prepped ligands in a database (created using previous step), and a protein in a protein DB (that was previously prepped using tools) and docks them all in parallel.