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 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="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_top_map_3(self):
contact_file = ContactFile("test")
contact_map1 = ContactMap("foo")
contact_map2 = ContactMap("bar")
contact_file.add(contact_map1)
contact_file.add(contact_map2)
self.assertEqual(contact_map1, contact_file.top_map)
def test_method_3(self):
contact_file = ContactFile("test")
contact_file.method = "Hello"
contact_file.method = "5"
contact_file.method = "World"
contact_file.method = "!"
self.assertEqual(["Hello", "5", "World", "!"], contact_file.method)
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_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="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_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 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 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 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 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 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_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_remark_3(self):
contact_file = ContactFile("test")
contact_file.remark = "Hello"
contact_file.remark = "5"
contact_file.remark = "World"
contact_file.remark = "!"
self.assertEqual(["Hello", "5", "World", "!"], contact_file.remark)
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 test_sort_4(self):
contact_file = ContactFile("test")
for map in [ContactMap("foo"), ContactMap("bar"), ContactMap("doe")]:
contact_file.add(map)
contact_file_sorted = contact_file.sort("id",
reverse=True,
inplace=True)
self.assertEqual(["foo", "doe", "bar"],
[m.id for m in contact_file_sorted])
self.assertEqual(contact_file, contact_file_sorted)
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("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_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 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 read(self, f_handle, f_id="bbcontacts", del_one_two=False):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
del_one_two : bool
Remove one- & two-strand sheets
Returns
-------
:obj:`~conkit.core.contactfile.ContactFile`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
previous = "first"
for line in f_handle:
line = line.strip()
if line and not line.startswith("#"):
_, _, _, raw_score, _, current, res2_seq, res1_seq = line.split(
)
if del_one_two and previous == "first" and current == "last":
contact_map.child_list.pop()
elif any(value == "NA"
for value in [raw_score, res2_seq, res1_seq]):
pass
else:
contact = Contact(int(res1_seq), int(res2_seq),
float(raw_score))
contact_map.add(contact)
previous = current
if del_one_two and previous == "first" and len(contact_map) > 0:
contact_map.child_list.pop()
contact_file.method = "Contact map predicted using Bbcontacts"
return contact_file
def test_write_3(self):
contact_file = ContactFile("TEST")
contact_maps = [ContactMap("A"), ContactMap("AB"), ContactMap("B")]
contacts = [
(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9),
Contact(3, 12, 0.4)),
(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9),
Contact(3, 12, 0.4)),
(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9),
Contact(3, 12, 0.4)),
]
chains = [("A", "A"), ("A", "B"), ("B", "B")]
for contact_map, contacts, chain in zip(contact_maps, contacts,
chains):
contact_file.add(contact_map)
for c in contacts:
c.res1_chain = chain[0]
c.res2_chain = chain[1]
contact_map.add(c)
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 gene i_id j_id r_sco s_sco prob I_prob",
"1 9 A 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 A 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 A 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 A 3_E 12_K 0.4 0.6 1.0 N/A",
"1 9 AB 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 AB 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 AB 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 AB 3_E 12_K 0.4 0.6 1.0 N/A",
"1 9 B 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 B 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 B 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 B 3_E 12_K 0.4 0.6 1.0 N/A",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
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
def test_write_2(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]
with open(f_name, "w") as f_out:
if sys.version_info.major == 3:
with self.assertRaises(TypeError):
CCMpredParser().write(f_out, contact_file)
else:
self.assertTrue(True)
def test_write_2(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)
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_X 9_X 0.7 1.0 1.0",
"1 10 1_X 10_X 0.7 1.0 1.0",
"2 8 2_X 8_X 0.9 1.3 1.0",
"3 12 3_X 12_X 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_write_3(self):
contact_file = ContactFile('TEST')
contact_maps = [ContactMap('A'), ContactMap('AB'), ContactMap('B')]
contacts = [(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9), Contact(3, 12, 0.4)),
(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9), Contact(3, 12, 0.4)),
(Contact(1, 9, 0.7), Contact(1, 10, 0.7), Contact(2, 8, 0.9), Contact(3, 12, 0.4))]
chains = [('A', 'A'), ('A', 'B'), ('B', 'B')]
for contact_map, contacts, chain in zip(contact_maps, contacts, chains):
contact_file.add(contact_map)
for c in contacts:
c.res1_chain = chain[0]
c.res2_chain = chain[1]
contact_map.add(c)
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 gene i_id j_id r_sco s_sco prob I_prob",
"1 9 A 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 A 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 A 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 A 3_E 12_K 0.4 0.6 1.0 N/A",
"1 9 AB 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 AB 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 AB 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 AB 3_E 12_K 0.4 0.6 1.0 N/A",
"1 9 B 1_H 9_L 0.7 1.0 1.0 N/A",
"1 10 B 1_H 10_L 0.7 1.0 1.0 N/A",
"2 8 B 2_L 8_I 0.9 1.3 1.0 N/A",
"3 12 B 3_E 12_K 0.4 0.6 1.0 N/A",
"",
]
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_2(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)
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_X 9_X 0.7 1.0 1.0",
"1 10 1_X 10_X 0.7 1.0 1.0",
"2 8 2_X 8_X 0.9 1.3 1.0",
"3 12 3_X 12_X 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="comsat"):
"""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.rstrip()
if not line:
continue
else:
res1_seq, res1, res2_seq, res2, _ = RE_SPLIT.split(line)
contact = Contact(int(res1_seq), int(res2_seq), 0.0)
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
contact_file.method = "Contact map predicted using COMSAT"
return contact_file
