"""Testing facility for conkit.io.aleigen"""
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.aleigen import AleigenParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestAleigenParser(ParserTestCase):
[docs] def test_read_1(self):
content = """77
10 14
1 7
10 13
6 9
5 71
36 42
1 73
33 37
21 68
38 57
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = AleigenParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(10, len(contact_map1))
self.assertEqual([10, 1, 10, 6, 5, 36, 1, 33, 21, 38], [c.res1_seq for c in contact_map1])
self.assertEqual([14, 7, 13, 9, 71, 42, 73, 37, 68, 57], [c.res2_seq for c in contact_map1])
self.assertEqual([0.5 for x in range(0, 10)], [c.raw_score for c in contact_map1])
[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:
AleigenParser().write(f_out, contact_file)
content = ["12", "1 9", "1 10", "2 8", "3 12"]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
