"""Testing facility for conkit.io.CaspIO"""
__author__ = "Felix Simkovic"
__date__ = "17 Aug 2016"
import os
import unittest
from conkit.core.contact import Contact
from conkit.core.contactfile import ContactFile
from conkit.core.contactmap import ContactMap
from conkit.core.sequence import Sequence
from conkit.io.casp import CaspParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestCaspParser(ParserTestCase):
[docs] def test_read_1(self):
content = """PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQMSD
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(9, len(contact_map1))
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD", contact_map1.sequence.seq)
self.assertEqual("HLEG-IGILL-K-E-------------------", contact_map1.repr_sequence.seq)
[docs] def test_read_2(self):
content = """PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
MODEL 1
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(9, len(contact_map1))
self.assertIsNone(contact_map1.sequence)
with self.assertRaises(TypeError):
_ = contact_map1.repr_sequence
[docs] def test_read_3(self):
content = """PFRMAT RR
MODEL 1
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(9, len(contact_map1))
self.assertIsNone(contact_map1.sequence)
with self.assertRaises(TypeError):
_ = contact_map1.repr_sequence
[docs] def test_read_4(self):
content = """PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQMSD
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
ENDMDL
MODEL 2
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQM
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
ENDMDL
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
self.assertEqual(2, len(contact_file))
contact_map1 = contact_file[0]
self.assertEqual(9, len(contact_map1))
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD", contact_map1.sequence.seq)
self.assertEqual("HLEG-IGILL-K-E-------------------", contact_map1.repr_sequence.seq)
contact_map2 = contact_file["2"]
self.assertEqual(8, len(contact_map2))
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQM", contact_map2.sequence.seq)
self.assertEqual("HLEG-IGILL-K-E-----------------", contact_map2.repr_sequence.seq)
[docs] def test_read_5(self):
content = """PFRMAT RR
TARGET R9999
MODEL 1
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
ENDMDL
MODEL 2
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQMSD
1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
self.assertEqual(2, len(contact_file))
contact_map1 = contact_file["1"]
self.assertEqual(9, len(contact_map1))
self.assertIsNone(contact_map1.sequence)
contact_map2 = contact_file["2"]
self.assertEqual(9, len(contact_map2))
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD", contact_map2.sequence.seq)
self.assertEqual("HLEG-IGILL-K-E-------------------", contact_map2.repr_sequence.seq)
[docs] def test_read_6(self):
content = """1 9 0 8 0.70
1 10 0 8 0.70
1 12 0 8 0.60
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
"""
f_name = self.tempfile(content=content)
parser = CaspParser()
with open(f_name, "r") as f_in:
with self.assertRaises(ValueError):
CaspParser().read(f_in)
[docs] @unittest.skip("Not yet implemented")
def test_read_7(self):
content = """PFRMAT RR
TARGET R9999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQMSD
A1 B9 0 8 0.70
A1 B10 0 8 0.70
A1 B12 0 8 0.60
A1 B14 0 8 0.20
A1 B15 0 8 0.10
A1 B17 0 8 0.30
A1 B19 0 8 0.50
A2 B8 0 8 0.90
A3 B7 0 8 0.70
A3 B12 0 8 0.40
A3 B14 0 8 0.70
A3 B15 0 8 0.30
A4 B6 0 8 0.90
A7 B14 0 8 0.30
A9 B14 0 8 0.50
END
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CaspParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(15, len(contact_map1))
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD", contact_map1.sequence.seq)
self.assertEqual("HLEG-IGILL-K-E-------------------", contact_map1.repr_sequence.seq)
[docs] 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:
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)
[docs] def test_write_2(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)
contact_map.sequence = Sequence("1", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
f_name = self.tempfile()
with open(f_name, "w") as f_out:
CaspParser().write(f_out, contact_file)
content = [
"PFRMAT RR",
"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)
[docs] 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 = self.tempfile()
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)
[docs] def test_write_4(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)
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 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)
[docs] 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)
[docs] 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)
if __name__ == "__main__":
unittest.main(verbosity=2)
