def as_contact(self, distance_cutoff):
"""Create a :obj:`~conkit.core.contact.Contact` instance with the information in this
:obj:`~conkit.core.distance.Distance` instance.
Parameters
----------
distance_cutoff : int, float
The distance cutoff used to consider a residue pair within contact of each other
Returns
-------
:obj:`~conkit.core.contact.Contact`
A contact with the information present in this distance instance.
"""
if self.predicted_distance > distance_cutoff:
contact = Contact(self.res1_seq,
self.res2_seq,
0,
distance_bound=(0, distance_cutoff))
else:
contact = Contact(self.res1_seq,
self.res2_seq,
self.raw_score,
distance_bound=(0, distance_cutoff))
for attr in self.__slots__:
if hasattr(contact, attr):
setattr(contact, attr, getattr(self, attr))
return contact
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__to_dict_1(self):
contact = Contact(1, 2, 1.0)
answer_dict = {
'id': (1, 2),
'is_match': False,
'is_mismatch': False,
'is_unknown': True,
'distance_bound': (0.0, 8.0),
'lower_bound': 0.0,
'upper_bound': 8.0,
'raw_score': 1.0,
'res1': 'X',
'res2': 'X',
'res1_chain': '',
'res2_chain': '',
'res1_seq': 1,
'res2_seq': 2,
'res1_altseq': 0,
'res2_altseq': 0,
'scalar_score': 0.0,
'status': 0,
'weight': 1.0,
}
contact_dict = contact._to_dict()
for k in answer_dict.keys():
self.assertEqual(answer_dict[k], contact_dict[k],
"Key %s differs" % k)
def read(self, f_handle, f_id="freecontact"):
"""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`
"""
hierarchy = ContactFile(f_id)
contact_map = ContactMap("map_1")
hierarchy.add(contact_map)
for line in f_handle:
line = line.strip()
if line:
res1_seq, res1, res2_seq, res2, raw_score, _ = RE_SPLIT.split(
line)
contact = Contact(int(res1_seq), int(res2_seq),
float(raw_score))
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
hierarchy.method = "Contact map predicted using FreeContact"
return hierarchy
def test__to_dict_2(self):
contact = Contact(1, 2, 1.0)
contact.true_positive = True
contact.lower_bound = 4
answer_dict = {
"id": (1, 2),
"true_positive": True,
"false_positive": False,
"status_unknown": False,
"distance_bound": (4.0, 8.0),
"lower_bound": 4.0,
"upper_bound": 8.0,
"raw_score": 1.0,
"res1": "X",
"res2": "X",
"res1_chain": "",
"res2_chain": "",
"res1_seq": 1,
"res2_seq": 2,
"res1_altseq": 0,
"res2_altseq": 0,
"scalar_score": 0.0,
"status": 1,
"weight": 1.0,
}
contact_dict = contact._to_dict()
for k in answer_dict.keys():
self.assertEqual(answer_dict[k], contact_dict[k],
"Key {} differs".format(k))
def test_res2_chain_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual('', contact.res2_chain)
contact.res2_chain = 'b'
self.assertEqual('b', contact.res2_chain)
contact.res2_chain = 'X'
self.assertEqual('X', contact.res2_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_res2_chain_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual("", contact.res2_chain)
contact.res2_chain = "b"
self.assertEqual("b", contact.res2_chain)
contact.res2_chain = "X"
self.assertEqual("X", contact.res2_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 test_res2_seq_1(self):
contact = Contact(1, 2000000, 1.0)
self.assertEqual(2000000, contact.res2_seq)
contact.res2_seq = 1
self.assertEqual(1, contact.res2_seq)
contact.res2_seq = 2000
self.assertEqual(2000, contact.res2_seq)
contact.res2_seq = 5
self.assertEqual(5, contact.res2_seq)
def test_res1_seq_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual(1, contact.res1_seq)
contact.res1_seq = 2
self.assertEqual(2, contact.res1_seq)
contact.res1_seq = 5
self.assertEqual(5, contact.res1_seq)
contact.res1_seq = 1
self.assertEqual(1, contact.res1_seq)
def test_raw_score_1(self):
contact = Contact(1, 2, 1.0)
self.assertEqual(1.0, contact.raw_score)
contact.raw_score = 0.3
self.assertEqual(0.3, contact.raw_score)
contact.raw_score = -0.1
self.assertEqual(-0.1, contact.raw_score)
contact.raw_score = 1.0
self.assertEqual(1.0, contact.raw_score)
def test_distance_bound_3(self):
contact = Contact(1, 2, 1.0)
try:
contact.distance_bound = (1, 100)
except TypeError:
self.fail("contact.distance_bound raised TypeError unexpectedly")
with self.assertRaises(TypeError):
contact.distance_bound = 8
with self.assertRaises(TypeError):
contact.distance_bound = "test"
def read(self, f_handle, f_id="epcmap"):
"""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`
"""
hierarchy = ContactFile(f_id)
_map = ContactMap("map_1")
hierarchy.add(_map)
for line in f_handle:
line = line.strip().split()
if not line or line[0].isalpha():
continue
elif line[0].isdigit():
_contact = Contact(
int(line[0]), int(line[1]), float(line[4]), distance_bound=(float(line[2]), float(line[3]))
)
_map.add(_contact)
hierarchy.method = "Contact map predicted using EPC-Map"
return hierarchy
def read(self, f_handle, f_id="ccmpred"):
"""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_file.method = "Contact map predicted using CCMpred"
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
# Bits ripped from Stefan Seemayer's script shipped with CCMpred
mat = np.loadtxt(f_handle)
if mat.size > 0:
raw_contacts = self._get_contact_pairs(mat)
for res1_seq, res2_seq, raw_score in zip(raw_contacts[0],
raw_contacts[1],
mat[raw_contacts]):
if res1_seq > res2_seq:
continue
# Matrix starts count at 0 so increment numbers by one straight away
contact = Contact(int(res1_seq + 1), int(res2_seq + 1),
float(raw_score))
contact_map.add(contact)
return contact_file
def read(self, f_handle, f_id="plmdca"):
"""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 not line or line[0].isalpha():
continue
elif line[0].isdigit():
res1_seq, res2_seq, raw_score = line.split(',')
contact = Contact(int(res1_seq), int(res2_seq),
float(raw_score))
contact_map.add(contact)
contact_file.method = 'Contact map predicted using plmDCA'
return contact_file
def test_write_5(self):
contact_file = ContactFile("RR")
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 1.5), (1, 10, 0, 8, -0.3), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
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",
"1 9 0 8 1.000000",
"1 10 0 8 0.000000",
"2 8 0 8 0.666667",
"3 12 0 8 0.388889",
"ENDMDL",
"END",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def test_write_3(self):
contact_file = ContactFile('RR')
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
CaspParser().write(f_out, contact_file)
content = [
"PFRMAT RR",
"MODEL 1",
"1 9 0 8 0.700000",
"1 10 0 8 0.700000",
"2 8 0 8 0.900000",
"3 12 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="map_align"):
"""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`
"""
hierarchy = ContactFile(f_id)
_map = ContactMap("map_1")
hierarchy.add(_map)
for line in f_handle:
line = line.strip().split()
if line[0] == "CON" and line[1].isdigit() and line[2].isdigit():
_contact = Contact(int(line[1]), int(line[2]), float(line[3]))
_map.add(_contact)
hierarchy.method = "Contact map compatible with map_algin"
return hierarchy
def test_write_1(self):
contact_file = ContactFile('RR')
contact_file.target = 'R9999'
contact_file.author = '1234-5678-9000'
contact_file.remark = ['Predictor remarks']
contact_file.method = [
'Description of methods used', 'Description of methods used'
]
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence('1',
'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD')
contact_map.set_sequence_register()
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
ComsatParser().write(f_out, contact_file)
content = [
"1 H 9 L Hx-Hx",
"1 H 10 L Hx-Hx",
"2 L 8 I Hx-Hx",
"3 E 12 K Hx-Hx",
]
with open(f_name, 'r') as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
os.unlink(f_name)
def test_write_1(self):
contact_file = ContactFile("test")
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence(
"1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD"
)
f_name = self.tempfile()
# Not sure if bug in Python3 numpy or intended purpose [Implemented: 21.11.2016]
mode = "wb" if sys.version_info.major == 3 else "w"
with open(f_name, mode) as f_out:
CCMpredParser().write(f_out, contact_file)
content = [
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t6.999999999999999556e-01\t6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def test_write_1(self):
contact_file = ContactFile('RR')
contact_file.target = 'R9999'
contact_file.author = '1234-5678-9000'
contact_file.remark = ['Predictor remarks']
contact_file.method = ['Description of methods used', 'Description of methods used']
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence('1', 'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD')
contact_map.assign_sequence_register()
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
PsicovParser().write(f_out, contact_file)
content = [
"1 9 0 8 0.700000",
"1 10 0 8 0.700000",
"2 8 0 8 0.900000",
"3 12 0 8 0.400000",
"",
]
content = os.linesep.join(content)
with open(f_name, 'r') as f_in:
data = "".join(f_in.readlines())
self.assertEqual(content, data)
os.unlink(f_name)
def test_write_1(self):
contact_file = ContactFile('test')
contact_map = ContactMap('A')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence('1', 'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD')
contact_map.assign_sequence_register()
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
GremlinParser().write(f_out, contact_file)
content = [
"i j i_id j_id r_sco s_sco prob",
"1 9 1_H 9_L 0.7 1.0 1.0",
"1 10 1_H 10_L 0.7 1.0 1.0",
"2 8 2_L 8_I 0.9 1.3 1.0",
"3 12 3_E 12_K 0.4 0.6 1.0",
"",
]
content = os.linesep.join(content)
with open(f_name, 'r') as f_in:
data = "".join(f_in.readlines())
self.assertEqual(content, data)
os.unlink(f_name)
def read(self, f_handle, f_id="map_align"):
"""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`
"""
hierarchy = ContactFile(f_id)
_map = ContactMap("map_1")
hierarchy.add(_map)
for line in f_handle:
line = line.strip().split()
if len(line) == 2 and line[0].isdigit() and line[1].isdigit():
# Al-eigen has no score field so we assume score=0.5
_contact = Contact(int(line[0]), int(line[1]), 0.5)
_map.add(_contact)
hierarchy.method = "Contact map compatible with Al-Eigen"
return hierarchy
def test_write_1(self):
contact_file = ContactFile("test")
contact_map = ContactMap("A")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence(
"1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD"
)
contact_map.set_sequence_register()
f_name = self.tempfile()
with open(f_name, "w") as f_out:
GremlinParser().write(f_out, contact_file)
content = [
"i j i_id j_id r_sco s_sco prob",
"1 9 1_H 9_L 0.7 1.0 1.0",
"1 10 1_H 10_L 0.7 1.0 1.0",
"2 8 2_L 8_I 0.9 1.3 1.0",
"3 12 3_E 12_K 0.4 0.6 1.0",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def test__reconstruct_1(self):
hierarchy = Parser._reconstruct(Contact(1, 3, 1.0))
self.assertTrue(isinstance(hierarchy, ContactFile))
self.assertTrue(isinstance(hierarchy[0], ContactMap))
self.assertTrue(isinstance(hierarchy[0][0], Contact))
self.assertEqual((1, 3),
(hierarchy[0][0].res1_seq, hierarchy[0][0].res2_seq))
def test_write_1(self):
contact_file = ContactFile('test')
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence(
'1',
'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD'
)
f_name = create_tmp_f()
# Not sure if bug in Python3 numpy or intended purpose [Implemented: 21.11.2016]
mode = 'wb' if sys.version_info.major == 3 else 'w'
with open(f_name, mode) as f_out:
CCMpredParser().write(f_out, contact_file)
content = [
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t6.999999999999999556e-01\t6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00',
'0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00'
]
with open(f_name, 'r') as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
os.unlink(f_name)
def test_write_1(self):
contact_file = ContactFile("RR")
contact_file.target = "R9999"
contact_file.author = "1234-5678-9000"
contact_file.remark = ["Predictor remarks"]
contact_file.method = ["Description of methods used", "Description of methods used"]
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence("1", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
contact_map.set_sequence_register()
f_name = self.tempfile()
with open(f_name, "w") as f_out:
MemBrainParser().write(f_out, contact_file)
content = [
"Helix Position Residue Helix Position Residue Probability",
"Hx 1 H Hx 9 L 0.700000",
"Hx 1 H Hx 10 L 0.700000",
"Hx 2 L Hx 8 I 0.900000",
"Hx 3 E Hx 12 K 0.400000",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
def test_write_5(self):
contact_file = ContactFile('RR')
contact_map = ContactMap('1')
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 1.5), (1, 10, 0, 8, -0.3), (2, 8, 0, 8, 0.9),
(3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
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",
"1 9 0 8 1.000000",
"1 10 0 8 0.000000",
"2 8 0 8 0.666667",
"3 12 0 8 0.388889",
"ENDMDL",
"END",
"",
]
content = os.linesep.join(content)
with open(f_name, 'r') as f_in:
data = "".join(f_in.readlines())
self.assertEqual(content, data)
os.unlink(f_name)
def read(self, f_handle, f_id="membrain"):
"""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`
"""
hierarchy = ContactFile(f_id)
contact_map = ContactMap("map_1")
hierarchy.add(contact_map)
for line in f_handle:
line = line.rstrip()
if not line:
continue
if RE_HEADER.match(line):
continue
else:
_, res1_seq, res1, _, res2_seq, res2, raw_score = RE_SPLIT.split(
line)
contact = Contact(int(res1_seq), int(res2_seq),
float(raw_score))
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
hierarchy.method = 'Contact map predicted using MemBrain'
return hierarchy
