This repo contains source code for the following set of MARA tools:

• Cleanup alternate locations for residues in a PDB file (cleanup_alternate_location.py)
• Save a protein-only PDB file (extract_protein_only_pdb.py)
• Find pockets for docking on the input protein (pocket_finding/main.py)
• Convert PDB to PDBQT for AutoDock Vina-based docking (convert_protein_to_pdbqt.py)
• Run docking using Smina (docking/run.py)
• Combine structures of a protein PDB and multiple ligands in SDF (show_structure_protein_multi_conf_ligand.py)
• Convert SMILES into Single Frame SDF (smiles_conversion.py)