"""Testing facility for conkit.io.PsicovIO"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 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.psicov import PsicovParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestPsicovParser(ParserTestCase):
[docs] def test_read_1(self):
content = """46 78 0 8 9.301869
80 105 0 8 8.856009
111 129 0 8 7.252451
75 205 0 8 6.800462
19 44 0 8 6.588349
111 130 0 8 6.184269
23 41 0 8 6.163786
171 205 0 8 5.519271
53 126 0 8 5.440612
100 140 0 8 5.382865
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PsicovParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(10, len(contact_map1))
self.assertEqual([46, 80, 111, 75, 19, 111, 23, 171, 53, 100], [c.res1_seq for c in contact_map1])
self.assertEqual([78, 105, 129, 205, 44, 130, 41, 205, 126, 140], [c.res2_seq for c in contact_map1])
self.assertEqual(
[9.301869, 8.856009, 7.252451, 6.800462, 6.588349, 6.184269, 6.163786, 5.519271, 5.440612, 5.382865],
[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:
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"]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
