## Copyright (c) 2017-2022, James Gayvert, Ruslan Tazhigulov, Ksenia Bravaya
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"""Parser used to parse PDB and MMCIF files.
Constructs an emap object containing parsed Bio.PDB.Structure and a list of customized Bio.PDB.Residue objects
corresponding to automatically identified electron transfer moieties.
"""
from Bio.PDB import PDBIO, FastMMCIFParser, PDBParser
from .custom_residues import process_custom_residues
from .data import res_name_to_char
from .emap import emap
from .pyemap_exceptions import *
import os
from pathlib import Path
import requests
def _download_pdb(pdbcode, datadir, downloadurl="https://files.rcsb.org/download/"):
"""
Downloads a PDB file from the Internet and saves it in a data directory.
:param pdbcode: The standard PDB ID e.g. '3ICB' or '3icb'
:param datadir: The directory where the downloaded file will be saved
:param downloadurl: The base PDB download URL, cf.
`https://www.rcsb.org/pages/download/http#structures` for details
:return: the full path to the downloaded PDB file or None if something went wrong
"""
pdbfn = pdbcode + ".pdb"
url = downloadurl + pdbfn
outfnm = os.path.join(datadir, pdbfn)
try:
R = requests.get(url, allow_redirects=True)
if R.status_code != 200:
raise ConnectionError('could not download {}\nerror code: {}'.format(url, R.status_code))
Path(outfnm).write_bytes(R.content)
return outfnm
except Exception as e:
print(e)
raise PyeMapParseException("Could not fetch PDB {}.".format(pdbcode)) from e
[docs]
def fetch_and_parse(pdb_id, dest="", quiet=False):
'''Fetches pdb from database and parses the file.
Parameters
----------
pdb_id: str
RCSB PDB ID
dest: str, optional
Full path to where file should be saved
quiet: bool, optional
Supresses output when set to true
Returns
-------
emap: :class:`~pyemap.emap`
emap object ready for processing.
'''
if not dest:
dest = os.getcwd()
if not quiet:
print("Fetching PDB " + pdb_id + " from RSCB Database...")
outfnm = _download_pdb(pdb_id, dest)
if not quiet:
print("Success!")
return parse(outfnm, quiet)
[docs]
def parse(filename, quiet=True):
'''Parses pdb file and returns emap object.
Parameters
----------
filename: str
Full path to file which needs to be parsed
quiet: bool, optional
Supresses output when set to true
Returns
-------
my_emap: :class:`~pyemap.emap`
emap object reading for parsing
'''
if not quiet:
print("Parsing file: " + str(filename))
try:
os.listdir()
parser = PDBParser()
structure = parser.get_structure("protein", filename)
except Exception as e:
try:
parser = FastMMCIFParser()
structure = parser.get_structure("protein", filename)
io = PDBIO()
fn = filename[:-4] + ".pdb"
io.set_structure(structure)
io.save(fn)
parser = PDBParser()
structure = parser.get_structure("protein", fn)
except Exception:
raise PyeMapParseException("Error: could not parse file {}.".format(filename)) from e
chain_list = []
sequences = {}
non_standard_residue_list = []
num_models = 0
for model in structure.get_models():
num_models += 1
if num_models < 1:
raise PyeMapParseException("Error: structure " + structure.header['idcode'] + " does not contain any models.")
if structure.header['idcode'] == "":
idcode = "CUST"
else:
idcode = structure.header['idcode']
for chain in structure[0]:
chain_list.append(chain.id)
seq = []
seq_idx = 1
for residue in chain:
if residue.resname in res_name_to_char:
seq.append(res_name_to_char[residue.resname])
residue.sequence_index = seq_idx
seq_idx += 1
else:
residue.get_full_id()
non_standard_residue_list.append(residue.copy())
residue.sequence_index = 'X'
seq_str = ">" + idcode + ":" + chain.id + "\n" + ''.join(seq)
sequences[chain.id] = seq_str
custom_residue_list = process_custom_residues(non_standard_residue_list)
if not quiet:
print("Identified " + str(len(custom_residue_list)) + " non-protein ET active moieties.")
my_emap = emap(filename, idcode, custom_residue_list, chain_list, sequences)
my_emap._structure = structure
return my_emap