def test_scalar_score_1(self):
contact = Contact(1, 2000000, 1.0)
contact.scalar_score = 5.432
self.assertEqual(5.432, contact.scalar_score)
def test_scalar_score_2(self):
contact = Contact(1, 2000000, 1.0)
contact.scalar_score = 3
self.assertNotEqual(3, contact.res2_altseq)
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
