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"""
Parser module specific to Pdb files
"""
from __future__ import division
__author__ = "Felix Simkovic"
__date__ = "27 Sep 2016"
__version__ = "0.1"
import collections
import itertools
import sys
import warnings
if sys.version_info.major < 3:
from itertools import izip as zip
from Bio.PDB import MMCIFParser
from Bio.PDB import PDBParser
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
from conkit.core.sequence import Sequence, THREE_TO_ONE
ATOM = collections.namedtuple('Atom', 'resname resseq resseq_alt reschain')
[docs]class GenericStructureParser(ContactFileParser):
"""
Parent class to parse a PDB file and extract distance restraints
as residue-residue contacts
"""
def _build_sequence(self, chain):
"""Build a peptide using Biopython to extract the sequence"""
return Sequence(chain.id + '_seq', ''.join(THREE_TO_ONE[residue.resname] for residue in chain))
def _chain_contacts(self, chain1, chain2):
"""Determine the contact pairs intra- or inter-molecular
Parameters
----------
chain1 : :obj:`Bio.PDB.Chain`
A first chain object
chain2 : :obj:`Bio.PDB.Chain`
A second chain object
Yields
------
atom_comb : list
A list of tuples containing the contact information
"""
if chain1 == chain2:
range1 = range2 = list(range(1, len(chain1) + 1))
else:
range1 = list(range(1, len(chain1) + 1))
range2 = list(range(len(chain1) + 1, len(chain1) + len(chain2) + 1))
assert len(range1) == len(chain1) and len(range2) == len(chain2)
iterator = itertools.product(list(zip(range1, chain1)), list(zip(range2, chain2)))
for (resseq1_alt, residue1), (resseq2_alt, residue2) in iterator:
for atom1, atom2 in itertools.product(residue1, residue2):
if chain1 == chain2 and int(residue1.id[1]) >= int(residue2.id[1]):
continue
construct1 = ATOM(
resname=residue1.resname,
resseq=int(residue1.id[1]),
resseq_alt=resseq1_alt,
reschain=chain1.id,
)
construct2 = ATOM(
resname=residue2.resname,
resseq=int(residue2.id[1]),
resseq_alt=resseq2_alt,
reschain=chain2.id,
)
yield (construct1, construct2, atom1 - atom2)
def _remove_atom(self, chain, type):
"""Tidy up a chain removing all HETATM entries"""
for residue in chain.copy():
for atom in residue.copy():
if atom.is_disordered():
chain[residue.id].detach_child(atom.id)
elif residue.resname == 'GLY' and type == 'CB' and atom.id == 'CA':
continue
elif atom.id != type:
chain[residue.id].detach_child(atom.id)
def _remove_hetatm(self, chain):
"""Tidy up a chain removing all HETATM entries"""
for residue in chain.copy():
if residue.id[0].strip() and residue.resname not in THREE_TO_ONE:
chain.detach_child(residue.id)
def _read(self, structure, f_id, distance_cutoff, atom_type):
"""Read a contact file
Parameters
----------
structure
A :obj:`Structure <Bio.PDB.Structure.Structure>` instance
f_id : str
Unique contact file identifier
distance_cutoff : int
Distance cutoff for which to determine contacts
atom_type : str
Atom type between which distances are calculated
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
hierarchies = []
for model in structure:
hierarchy = ContactFile(f_id + '_' + str(model.id))
chains = list(chain for chain in model)
for chain in chains:
self._remove_hetatm(chain)
self._remove_atom(chain, atom_type)
for chain1, chain2 in itertools.product(chains, chains):
if chain1.id == chain2.id: # intra
contact_map = ContactMap(chain1.id)
else: # inter
contact_map = ContactMap(chain1.id + chain2.id)
for (atom1, atom2, distance) in self._chain_contacts(chain1, chain2):
contact = Contact(
atom1.resseq,
atom2.resseq,
round(1.0 - (distance / 100), 6),
distance_bound=(0., float(distance_cutoff)))
contact.res1_altseq = atom1.resseq_alt
contact.res2_altseq = atom2.resseq_alt
contact.res1 = atom1.resname
contact.res2 = atom2.resname
contact.res1_chain = atom1.reschain
contact.res2_chain = atom2.reschain
if distance_cutoff == 0 or distance < distance_cutoff:
contact.define_match()
contact_map.add(contact)
if contact_map.empty:
del contact_map
else:
if len(contact_map.id) == 1:
contact_map.sequence = self._build_sequence(chain1)
assert len(contact_map.sequence.seq) == len(chain1)
else:
contact_map.sequence = self._build_sequence(chain1) \
+ self._build_sequence(chain2)
assert len(contact_map.sequence.seq) \
== len(chain1) + len(chain2)
hierarchy.add(contact_map)
hierarchy.method = 'Contact map extracted from PDB ' + str(model.id)
hierarchy.remark = [
'The model id is the chain identifier, i.e XY equates to chain X and chain Y.',
'Residue numbers in column 1 are chain X, and numbers in column 2 are chain Y.'
]
hierarchies.append(hierarchy)
if len(hierarchies) > 1:
msg = "Super-level to contact file not yet implemented. " \
"Parser returns hierarchy for top model only!"
warnings.warn(msg, FutureWarning)
return hierarchies[0]
def _write(self, f_handle, hierarchy):
"""Write a contact file instance to to file
Raises
------
NotImplementedError
Write function not available
"""
raise NotImplementedError("Write function not available")
[docs]class MmCifParser(GenericStructureParser):
"""
Class to parse a mmCIF file and extract distance restraints
as residue-residue contacts
"""
def __init__(self):
super(MmCifParser, self).__init__()
[docs] def read(self, f_handle, f_id="mmcif", distance_cutoff=8, atom_type='CB'):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
distance_cutoff : int, optional
Distance cutoff for which to determine contacts [default: 8]
atom_type : str, optional
Atom type between which distances are calculated [default: CB]
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
structure = MMCIFParser(QUIET=True).get_structure("mmcif", f_handle)
return self._read(structure, f_id, distance_cutoff, atom_type)
[docs] def write(self, f_handle, hierarchy):
"""Write a contact file instance to to file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`ContactMap <conkit.core.Contact>`
Raises
------
NotImplementedError
Write function not available
"""
self._write(f_handle, hierarchy)
[docs]class PdbParser(GenericStructureParser):
"""
Class to parse a PDB file and extract distance restraints
as residue-residue contacts
"""
def __init__(self):
super(PdbParser, self).__init__()
[docs] def read(self, f_handle, f_id="pdb", distance_cutoff=8, atom_type='CB'):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
distance_cutoff : int, optional
Distance cutoff for which to determine contacts [default: 8]
atom_type : str, optional
Atom type between which distances are calculated [default: CB]
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
structure = PDBParser(QUIET=True).get_structure("pdb", f_handle)
return self._read(structure, f_id, distance_cutoff, atom_type)
[docs] def write(self, f_handle, hierarchy):
"""Write a contact file instance to to file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`ContactMap <conkit.core.Contact>`
Raises
------
NotImplementedError
Write function not available
"""
self._write(f_handle, hierarchy)
