def test_res1_altseq_1(self):
contact = Contact(1, 2000000, 1.0)
contact.res1_altseq = 1000
self.assertEqual(1000, contact.res1_altseq)
self.assertNotEqual(10, contact.res2_altseq)
def read(self, f_handle, f_id="casp"):
"""Read a contact file into a :obj:`conkit.core.contactfile.ContactFile` instance
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.contactfile.ContactFile>`
"""
lines = [l.strip() for l in f_handle.readlines()]
contact_file = ContactFile(f_id)
it = iter(lines)
while True:
try:
line = next(it)
except StopIteration:
break
if RE_PRFMAT.match(line):
continue
elif RE_TARGET.match(line):
contact_file.remark = RE_TARGET.match(line).group(1)
elif RE_AUTHOR.match(line):
contact_file.author = RE_AUTHOR.match(line).group(1)
elif RE_REMARK.match(line):
contact_file.remark = RE_REMARK.match(line).group(1)
elif RE_METHOD.match(line):
contact_file.method = RE_METHOD.match(line).group(1)
elif RE_MODEL.match(line):
contact_map = ContactMap(RE_MODEL.match(line).group(1))
seq_chunks = []
while True:
try:
line = next(it)
except StopIteration:
break
if not line:
break
if RE_ENDMDL.match(line):
break
elif RE_END.match(line):
break
elif RE_SEQ.match(line):
seq_chunks.append(line)
else:
res1_entry, res2_entry, lb, ub, raw_score = RE_SPLIT.split(line)
# Split in case we have chain in inter-molecular scenarios
res1_split = RE_RES.split(res1_entry)
if len(res1_split) == 1:
res1_chain, res1_seq = '', res1_split[0]
elif len(res1_split) == 4:
res1_chain, res1_seq = res1_split[1], res1_split[2]
res2_split = RE_RES.split(res2_entry)
if len(res2_split) == 1:
res2_chain, res2_seq = '', res2_split[0]
elif len(res2_split) == 4:
res2_chain, res2_seq = res2_split[1], res2_split[2]
contact = Contact(int(res1_seq), int(res2_seq), float(raw_score),
distance_bound=(float(lb), float(ub)))
contact.res1_chain = res1_chain
contact.res2_chain = res2_chain
contact.res1_altseq = int(res1_seq)
contact.res2_altseq = int(res2_seq)
contact_map.add(contact)
if seq_chunks:
seq = "".join(seq_chunks)
sequence = Sequence('seq_{0}'.format(contact_map.id), seq)
contact_map.sequence = sequence
contact_map.assign_sequence_register()
contact_file.add(contact_map)
elif RE_END.match(line):
break
else:
raise ValueError('Unrecognized line type. Please report this issue')
return contact_file
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.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]
