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.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.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('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('sequence_1',
'HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD')
contact_map.assign_sequence_register()
f_name = create_tmp_f()
with open(f_name, 'w') as f_out:
PconsParser().write(f_out, contact_file)
content = [
"##############################################################################",
"PconsC3 result file",
"Generated using ConKit",
"##############################################################################",
"Sequence number: 1",
"Sequence name: sequence_1",
"Sequence length: 33 aa.",
"Sequence:",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD",
"",
"",
"Predicted contacts:",
"Res1 Res2 Score",
" 1 9 0.700000",
" 1 10 0.700000",
" 2 8 0.900000",
" 3 12 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("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("sequence_1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
contact_map.set_sequence_register()
f_name = self.tempfile()
with open(f_name, "w") as f_out:
PconsParser().write(f_out, contact_file)
content = [
"##############################################################################",
"PconsC3 result file",
"Generated using ConKit",
"##############################################################################",
"Sequence number: 1",
"Sequence name: sequence_1",
"Sequence length: 33 aa.",
"Sequence:",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD",
"",
"",
"Predicted contacts:",
"Res1 Res2 Score",
" 1 9 0.700000",
" 1 10 0.700000",
" 2 8 0.900000",
" 3 12 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.set_sequence_register()
f_name = self.tempfile()
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)
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:
CaspParser().write(f_out, contact_file)
content = [
"PFRMAT RR",
"TARGET R9999",
"AUTHOR 1234-5678-9000",
"REMARK Predictor remarks",
"METHOD Description of methods used",
"METHOD Description of methods used",
"MODEL 1",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD",
"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_target_2(self):
contact_file = ContactFile("test")
contact_file.target = "John Doe"
contact_file.target = "Jane Roe"
self.assertEqual("Jane Roe", contact_file.target)
