To install the PRauto, users can input the following command in the command-line interface:

   pip install PRauto

If you have problems with PyMOL dependency, try:

   conda install -c conda-forge pymol-open-source

   python -m prauto --sdf   or   python -m prauto

   python -m prauto.retriever

This tool allows users to retrieve the FASTA file of a target protein sequence via a search query in the UniProt API.
Additionally, using the UniProt accession number, PRauto retrieves the PDB files of target protein from the RCSB PDB API and
sdf files of ligands that interact with the target protein from the ChEMBL API.

1. the target protein sequences in a FASTA file format
2. PDB files of the target protein structures
3. sdf files of the ligands that interact with the target protein

   python -m prauto.prepauto

This tool processes PDB files that are located in a single directory.
It extracts only the chain(s) that correspond to the target protein and aligns them according to the reference PDB file.
It also removes any unnecessary molecules that are not involved in the binding of the primary ligand.
In a PSE PyMOL session, these unnecessary molecules are hidden rather than being removed.

1. preprocessed PDB files
2. PSE PyMOL session file.