#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Standard modules
import os
import gzip
# Local module
from .structure import Atom, Chain
# =============================================================================
# Data
# =============================================================================
# file extensions for PDB and PDBx/mmCIF files
PDB_EXTENSIONS = ('.pdb', '.PDB', '.pdb.gz', '.pdb.GZ', '.PDB.gz', '.PDB.GZ', '.ent', '.ENT4')
PDBx_EXTENSIONS = ('.cif', '.CIF', '.cif.gz', '.CIF.GZ')
[docs]class PDB:
"""
Class to read PDB files.
"""
def __init__(self, name):
"""
Default constructor for PDB file.
"""
self.filename = name
self.chains = []
# check that file exists
if not os.path.isfile(self.filename):
raise IOError("Cannot read {}: does not exist or is not a file."
.format(self.filename))
if self.filename.endswith(PDB_EXTENSIONS):
self.__read_PDB()
elif self.filename.endswith(PDBx_EXTENSIONS):
self.__read_PDBx()
else:
raise IOError("File extension is not a valid one. "
"Corrects one are {}".format(", ".join(PDB_EXTENSIONS + PDBx_EXTENSIONS)))
def __read_PDB(self):
"""
Read PDB file.
"""
# create new chain
chain = Chain()
# get chains from file
# A PDB file can have several models
# that can have several chains themselves.
if self.filename.endswith(('.gz', '.GZ')):
# for compressed file
f_in = gzip.open(self.filename, 'rt')
else:
f_in = open(self.filename, 'rt')
for line in f_in:
flag = line[0:6].strip()
if flag == "MODEL":
chain.set_model(line.split()[1])
if flag == "ATOM":
atom = Atom.read_from_PDB(line)
# store current chain and clean object
if chain.size() != 0 and chain.name != atom.chain:
self.chains.append(chain)
chain = Chain()
# append structure with atom
chain.add_atom(atom)
# store chain after end of model or chain
if chain.size() != 0 and flag in ["TER", "ENDMDL"]:
self.chains.append(chain)
chain = Chain()
# store last chain
if chain.size() != 0:
self.chains.append(chain)
f_in.close()
def __read_PDBx(self):
"""
Read PDBx/mmCIF file
"""
# create new chain
chain = Chain()
# get chains from file
# A PDBx file can have several models
# that can have several chains themselves.
atom_fields = []
atom_coordinates = []
if self.filename.endswith(('.gz', '.GZ')):
# for compressed file
f_in = gzip.open(self.filename, 'rt')
else:
f_in = open(self.filename, 'rt')
for line in f_in:
item = line.strip()
# then store atom field definitions
if item.startswith("_atom_site."):
atom_fields.append(item.replace("_atom_site.", ""))
# then store atom coordinates
if atom_fields and item.startswith('ATOM'):
atom_coordinates.append(item)
f_in.close()
# separate all chains and store atoms
chain = Chain()
for atom_line in atom_coordinates:
atom = Atom.read_from_PDBx(atom_line, atom_fields)
# define model at first atom
if chain.size() == 1:
chain.set_model(atom.model)
# store current chain when chain name changed
if chain.size() != 0 and chain.name != atom.chain:
# store model number only if there is more than one model
if chain.model == atom.model:
chain.set_model("")
self.chains.append(chain)
chain = Chain()
# store current chain when model number changed
if chain.size() != 0 and chain.model != atom.model:
self.chains.append(chain)
chain = Chain()
# append structure with atom
chain.add_atom(atom)
# store last chain
if chain.size() != 0:
self.chains.append(chain)
def get_chains(self):
"""
Give chains, one at a time.
Returns
-------
generator
Chains in PDB structure.
"""
for chain in self.chains:
yield chain
@property
def nb_chains(self):
"""
Give the number of chains
"""
return len(self.chains)