def test_res1_chain_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual('', contact.res1_chain)
contact.res1_chain = 'A'
self.assertEqual('A', contact.res1_chain)
contact.res1_chain = 'd'
self.assertEqual('d', contact.res1_chain)
def test_res1_chain_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual("", contact.res1_chain)
contact.res1_chain = "A"
self.assertEqual("A", contact.res1_chain)
contact.res1_chain = "d"
self.assertEqual("d", contact.res1_chain)
def test_write_6(self):
contact_file = ContactFile('RR')
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [('A', 1, 'B', 9, 0, 8, 0.7), ('A', 1, 'B', 10, 0, 8, 0.7),
('A', 2, 'B', 8, 0, 8, 0.9), ('A', 3, 'B', 12, 0, 8, 0.4)]:
contact = Contact(c[1], c[3], c[6], distance_bound=(c[4], c[5]))
contact.res1_chain = c[0]
contact.res2_chain = c[2]
contact_map.add(contact)
contact_map.sequence = Sequence(
'1',
'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD'
)
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
CaspParser().write(f_out, contact_file)
content = [
"PFRMAT RR",
"MODEL 1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVF",
"DGCHDFGRTYIWQMSD",
"A1 B9 0 8 0.700000",
"A1 B10 0 8 0.700000",
"A2 B8 0 8 0.900000",
"A3 B12 0 8 0.400000",
"ENDMDL",
"END",
]
with open(f_name, 'r') as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
os.unlink(f_name)
def read(self, f_handle, f_id="ncont"):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`~conkit.core.contactfile.ContactFile`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
for line in f_handle:
line = line.strip()
if RE_CONTACT.match(line):
matches = RE_CONTACT.match(line)
res1_seq = int(matches.group(2))
res2_seq = int(matches.group(5))
lb = ub = float(matches.group(7))
if (res1_seq, res2_seq) in contact_map:
msg = (
"This parser cannot handle multiple atoms of the same residue. "
"If your contact map contains such entries, only the first will be stored!"
)
warnings.warn(msg, Warning)
continue
contact = Contact(res1_seq,
res2_seq,
1.0,
distance_bound=(lb, ub))
contact.res1_chain = matches.group(1)
contact.res2_chain = matches.group(4)
contact.res1 = matches.group(3)
contact.res2 = matches.group(6)
contact_map.add(contact)
contact_file.method = "Contact map generated using Ncont"
return contact_file
def test_write_6(self):
contact_file = ContactFile("RR")
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [
("A", 1, "B", 9, 0, 8, 0.7),
("A", 1, "B", 10, 0, 8, 0.7),
("A", 2, "B", 8, 0, 8, 0.9),
("A", 3, "B", 12, 0, 8, 0.4),
]:
contact = Contact(c[1], c[3], c[6], distance_bound=(c[4], c[5]))
contact.res1_chain = c[0]
contact.res2_chain = c[2]
contact_map.add(contact)
contact_map.sequence = Sequence(
"1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD"
)
f_name = self.tempfile()
with open(f_name, "w") as f_out:
CaspParser().write(f_out, contact_file)
content = [
"PFRMAT RR",
"MODEL 1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVF",
"DGCHDFGRTYIWQMSD",
"A1 B9 0 8 0.700000",
"A1 B10 0 8 0.700000",
"A2 B8 0 8 0.900000",
"A3 B12 0 8 0.400000",
"ENDMDL",
"END",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
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]
def read(self, f_handle, f_id="gremlin"):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.contactfile.ContactFile>`
"""
hierarchy = ContactFile(f_id)
lines = iter([l.rstrip() for l in f_handle if l.rstrip()])
done = object()
line = next(lines, done)
inter = False
chain_list = set()
contact_list = []
while line is not done:
if RE_COMMENT.match(line):
hierarchy.remark = RE_COMMENT.match(line).group(1)
elif RE_HEADER_INTRA.match(line):
inter = False
elif RE_HEADER_INTER.match(line):
inter = True
else:
if inter:
res1_seq, res2_seq, chain, _, _, raw_score, scalar_score, _, _ = RE_SPLIT.split(line)
else:
res1_seq, res2_seq, _, _, raw_score, scalar_score, _ = RE_SPLIT.split(line)
chain = 'UNK'
c = Contact(int(res1_seq), int(res2_seq), float(raw_score))
c.scalar_score = float(scalar_score)
if chain == 'UNK':
chain_list.add('UNK')
elif len(chain) == 1:
c.res1_chain = chain[0]
c.res2_chain = chain[0]
chain_list.add((c.res1_chain, c.res2_chain))
elif len(chain) == 2:
c.res1_chain = chain[0]
c.res2_chain = chain[1]
chain_list.add((c.res1_chain, c.res2_chain))
elif len(chain) > 2:
raise ValueError('Cannot distinguish between chains')
contact_list.append(c)
line = next(lines, done)
chain_list = list(chain_list)
if len(chain_list) == 1 and chain_list[0] == 'UNK':
contact_map = ContactMap('1')
for c in contact_list:
contact_map.add(c)
hierarchy.add(contact_map)
elif len(chain_list) == 1:
chain = chain_list[0]
map_id = chain[0] if chain[0] == chain[1] else "".join(chain)
contact_map = ContactMap(map_id)
for c in contact_list:
contact_map.add(c)
hierarchy.add(contact_map)
else:
for chain in chain_list:
map_id = chain[0] if chain[0] == chain[1] else "".join(chain)
contact_map = ContactMap(map_id)
for c in contact_list:
if c.res1_chain == chain[0] and c.res2_chain == chain[1]:
contact_map.add(c)
hierarchy.add(contact_map)
hierarchy.sort('id', inplace=True)
return hierarchy
