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deulf / pdb_to_fasta.py
Created December 6, 2024 20:01
A Python script to extract protein/DNA/RNA sequences and ligands from a PDB file.
#!/usr/bin/env python
import sys
from prody import *
import pypdb
import requests
from pubchempy import get_compounds
AMINO_ACIDS = {
'ALA':'A','ARG':'R','ASN':'N','ASP':'D','CYS':'C','GLU':'E','GLN':'Q','GLY':'G','HIS':'H','ILE':'I',
'LEU':'L','LYS':'K','MET':'M','PHE':'F','PRO':'P','SER':'S','THR':'T','TRP':'W','TYR':'Y','VAL':'V',