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import ampal
import gzip
from pathlib import Path
import string
import urllib
def gly_resid(pdb: Path, chain:chr):
"""Rewrite PDB,change all amino acids to Glycine.
Parameters
----------
pdb: Path
Location of pdb file
chain: chr
Chain identifier, only this chain will be changed to polyG."""
with open(pdb,'r') as file:
text=file.readlines()
for i,line in enumerate(text):
if line[21]==chain:
text[i]='ATOM '+text[i][6:17]+'GLY'+text[i][20:]
with open(pdb,'w') as file:
file.writelines(text)
def fetch_pdb(
pdb_code: str,
output_folder:Path,
pdb_request_url: str = "https://files.rcsb.org/download/" ,
is_pdb:bool=False,
) -> None:
"""
Downloads a specific pdb file into a specific folder.
Parameters
----------
pdb_code : str
Code of the PDB file to be downloaded.
output_folder : Path
Output path to save the PDB file.
pdb_request_url : str
Base URL to download the PDB files.
is_pdb:bool=False
If True, get .pdb, else get biological assembly.
"""
if is_pdb:
pdb_code_with_extension = f"{pdb_code[:4]}.pdb.gz"
else:
pdb_code_with_extension = f"{pdb_code[:4]}.pdb1.gz"
print(f'{pdb_code_with_extension} is missing and will be downloaded!')
urllib.request.urlretrieve(pdb_request_url + pdb_code_with_extension,filename=output_folder / pdb_code_with_extension)
def polyglycine(dataset:Path,path_to_assemblies:Path,working_dir:Path,is_pdb:bool=False):
"""Converts protein chains into polyglycine chains.
Parameters
-----------
dataset:Path
Path to the dataset list containing PDB+chain info (e.g. 1a2bA)
path_to_assemblies:Path
Path to the directory with protein structure files; missing files will be downloaded automatically.
working_dir:Path
Path to the directory where polyglycine structures will be saved.
is_pdb:bool
If True, expects and downloads PDBs. If False, expects/downloads biological assembly."""
with open(dataset,'r') as file:
structures = [x.strip("\n") for x in file.readlines()]
if is_pdb:
suffix='.pdb.gz'
else:
suffix='.pdb1.gz'
for protein in structures:
if not Path(path_to_assemblies / (protein[:4]+suffix)).exists():
fetch_pdb(protein,path_to_assemblies,is_pdb=is_pdb)
with gzip.open(path_to_assemblies / (protein[:4]+suffix)) as file:
assembly = ampal.load_pdb(file.read().decode(), path=False)
protein_chain=protein[-1]
if not is_pdb:
flag=0
# fuse all states of the assembly into one state.
empty_polymer = ampal.Assembly()
chain_id = []
for polymer in assembly:
for chain in polymer:
#remove side chains from the chain of interest
#some assemblies have multiple chains with the same id, use flag to remove side chains only from the first one.
if chain.id==protein_chain and flag==0:
empty_polymer.append(chain.backbone)
flag=1
else:
empty_polymer.append(chain)
chain_id.append(chain.id)
# relabel chains to avoid repetition, remove ligands.
str_list = string.ascii_uppercase.replace(protein_chain, "")
#assemblies such as viral capsids are longer than the alphabet
if len(empty_polymer)>=len(str_list):
str_list=str_list*10
index = chain_id.index(protein_chain)
chain_id = list(str_list[: len(chain_id)])
chain_id[index] = protein_chain
empty_polymer.relabel_polymers(chain_id)
else:
empty_polymer = ampal.Assembly()
#pick first state of NMR
if isinstance(assembly, ampal.assembly.AmpalContainer):
assembly=assembly[0]
for chain in assembly:
if chain.id==protein_chain:
empty_polymer.append(chain.backbone)
else:
empty_polymer.append(chain)
# writing new pdb with AMPAL fixes most of the errors with EvoEF2 and Rosetta.
pdb_text = empty_polymer.make_pdb(alt_states=False, ligands=False)
with open((working_dir / protein[:4]).with_suffix(".pdb"), "w") as pdb_file:
pdb_file.write(pdb_text)
#change res ids to GLY for the backbone-only chain
gly_resid((working_dir / protein[:4]).with_suffix(".pdb"),protein_chain)
if __name__=='__main__':
#biological assemblies of crystal structures
polyglycine(Path("/home/s1706179/Rosetta/data/set.txt"), Path("/home/s1706179/Rosetta/assemblies/"),Path("/home/s1706179/Rosetta/empty_backbones/"),False)
#first state of NMR structures
#polyglycine(Path("/home/s1706179/Rosetta/data/nmr_set.txt"), Path("/home/s1706179/Rosetta/nmr_structures/"),Path("/home/s1706179/Rosetta/empty_nmr_backbones/"),True) |