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| import os | |
| from argparse import FileType, ArgumentParser | |
| import numpy as np | |
| import pandas as pd | |
| from Bio.PDB import PDBParser | |
| from Bio.Seq import Seq | |
| from Bio.SeqRecord import SeqRecord | |
| from tqdm import tqdm | |
| from Bio import SeqIO | |
| def esm_embedding_prep(out_file, protein_path): | |
| biopython_parser = PDBParser() | |
| three_to_one = { | |
| "ALA": "A", | |
| "ARG": "R", | |
| "ASN": "N", | |
| "ASP": "D", | |
| "CYS": "C", | |
| "GLN": "Q", | |
| "GLU": "E", | |
| "GLY": "G", | |
| "HIS": "H", | |
| "ILE": "I", | |
| "LEU": "L", | |
| "LYS": "K", | |
| "MET": "M", | |
| "MSE": "M", # MSE this is almost the same AA as MET. The sulfur is just replaced by Selen | |
| "PHE": "F", | |
| "PRO": "P", | |
| "PYL": "O", | |
| "SER": "S", | |
| "SEC": "U", | |
| "THR": "T", | |
| "TRP": "W", | |
| "TYR": "Y", | |
| "VAL": "V", | |
| "ASX": "B", | |
| "GLX": "Z", | |
| "XAA": "X", | |
| "XLE": "J", | |
| } | |
| file_paths = [protein_path] | |
| sequences = [] | |
| ids = [] | |
| for file_path in tqdm(file_paths): | |
| structure = biopython_parser.get_structure("random_id", file_path) | |
| structure = structure[0] | |
| for i, chain in enumerate(structure): | |
| seq = "" | |
| for res_idx, residue in enumerate(chain): | |
| if residue.get_resname() == "HOH": | |
| continue | |
| residue_coords = [] | |
| c_alpha, n, c = None, None, None | |
| for atom in residue: | |
| if atom.name == "CA": | |
| c_alpha = list(atom.get_vector()) | |
| if atom.name == "N": | |
| n = list(atom.get_vector()) | |
| if atom.name == "C": | |
| c = list(atom.get_vector()) | |
| if ( | |
| c_alpha != None and n != None and c != None | |
| ): # only append residue if it is an amino acid | |
| try: | |
| seq += three_to_one[residue.get_resname()] | |
| except Exception as e: | |
| seq += "-" | |
| print( | |
| "encountered unknown AA: ", | |
| residue.get_resname(), | |
| " in the complex ", | |
| file_path, | |
| ". Replacing it with a dash - .", | |
| ) | |
| sequences.append(seq) | |
| ids.append(f"{os.path.basename(file_path)}_chain_{i}") | |
| records = [] | |
| for (index, seq) in zip(ids, sequences): | |
| record = SeqRecord(Seq(seq), str(index)) | |
| record.description = "" | |
| records.append(record) | |
| SeqIO.write(records, out_file, "fasta") | |