File size: 3,067 Bytes
ef423c5 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 | import os
import glob
import pandas as pd
import subprocess
from difflib import SequenceMatcher
from Bio import SeqIO
from Bio.PDB import PDBParser, PDBIO, Chain, Select, is_aa
from Bio.PDB.Polypeptide import PPBuilder
from Bio.PDB import PDBParser
from Bio.SeqUtils import seq1
# def parse_pdb_chains(pdb_file):
# parser = PDBParser()
# structure = parser.get_structure("protein", pdb_file)
# pp_builder = PPBuilder()
# sequences = {}
# for model in structure:
# for chain in model:
# chain_id = chain.get_id()
# sequence = "".join([str(pp.get_sequence()) for pp in pp_builder.build_peptides(chain)])
# print(len(sequence))
# sequences[chain_id] = sequence
# return sequences
def get_fasta_from_pdb(pdb_file):
parser = PDBParser()
structure = parser.get_structure("pdb", pdb_file)
fasta_sequence = {}
for chain in structure.get_chains():
seq = ""
for residue in chain.get_residues():
seq += seq1(residue.get_resname())
fasta_sequence[chain.id] = seq
return fasta_sequence
def parse_fasta(file):
sequences = {}
with open(file, "r") as fasta_file:
for i, record in enumerate(SeqIO.parse(fasta_file, "fasta")):
sequences[i] = str(record.seq).split("/")
return sequences
def renumber_pdb(input_pdb, output_pdb):
parser = PDBParser()
structure = parser.get_structure("protein", input_pdb)
chain_dic = {}
for model in structure:
old_chains = []
new_chains = []
for chain in model: # this may include HEAATM atoms
new_chain_id = chain.id + "_renum"
new_chain = Chain.Chain(new_chain_id)
for i, residue in enumerate(chain):
new_residue = residue.copy()
new_residue_id = (residue.id[0], i + 1, residue.id[2])
new_residue.id = new_residue_id
new_chain.add(new_residue)
old_chains.append(chain)
new_chains.append(new_chain)
chain_dic[chain.id] = len(list(chain))
for chain, new_chain in zip(old_chains, new_chains):
model.detach_child(chain.id)
new_chain.id = chain.id
model.add(new_chain)
io = PDBIO()
io.set_structure(structure)
io.save(output_pdb)
return chain_dic
def get_chain_dic(input_pdb):
parser = PDBParser()
structure = parser.get_structure("protein", input_pdb)
chain_dic = {}
for model in structure:
for chain in model:
chain_dic[chain.id] = len([res for res in chain if is_aa(res) and res.has_id('CA')])
return chain_dic
def keep_backbone_atoms(input_file, output_file):
class BackboneSelect(Select):
def accept_atom(self, atom):
return atom.get_name() in ["N", "CA", "C", "O"]
parser = PDBParser()
io = PDBIO()
structure = parser.get_structure("protein", input_file)
io.set_structure(structure)
io.save(output_file, BackboneSelect()) |