PDB Manager

The PDBManager class is a tool designed for managing Protein Data Bank (PDB) files in Monviso. It leverages Biopython's capabilities to download, filter, and extract valuable information from PDB files.

Features

• Download PDB Files: Download PDB files from the Protein Data Bank.
• Extract Clean Chain: Extracts a specific chain from a PDB file, filtering out non-standard residues and atoms, and checks for resolution cutoffs.
• Extract FASTA Sequence: Extracts the FASTA sequence from a PDB file.

PDBManager

Manages the downloading, cleaning, and processing of PDB files.

Methods

• downloadPDB(pdb, out_path): Downloads a PDB file and saves it locally.
• extract_clean_chain(input_pdb_path, output_pdb_path, chain_letter, resolution_cutoff): Extracts a specific chain from a PDB file, ensuring it meets resolution quality standards.
• extract_fasta(pdb_name, pdb_path, output_fasta_path): Extracts the FASTA sequence from a PDB file.

Accessory class

ChainSelection(Select)

A subclass of Biopython's Select class for filtering specific chains and residues in a PDB file.

Methods

• accept_model(model): Accepts only the first model in a PDB file.
• accept_residue(residue): Filters residues to include only standard amino acids.
• accept_chain(chain): Filters for a specific chain.
• accept_atom(atom): Filters for standard atoms.