"""Testing facility for conkit.io.EVfold"""
__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.evfold import EVfoldParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestEVfoldParser(ParserTestCase):
[docs] def test_read_1(self):
content = """1 M 2 V 0 0.0338619
1 M 3 G 0 0.0307956
1 M 4 L 0 0.0268079
1 M 5 T 0 0.0219783
1 M 6 T 0 0.0222061
1 M 7 L 0 0.0213079
1 M 8 F 0 0.0119054
1 M 9 W 0 0.0275182
1 M 10 L 0 0.0134577
1 M 11 G 0 0.0234555
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = EVfoldParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(10, len(contact_map1))
self.assertEqual([1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [c.res1_seq for c in contact_map1])
self.assertEqual([2, 3, 4, 5, 6, 7, 8, 9, 10, 11], [c.res2_seq for c in contact_map1])
self.assertEqual(
[
0.0338619,
0.0307956,
0.0268079,
0.0219783,
0.0222061,
0.0213079,
0.0119054,
0.0275182,
0.0134577,
0.0234555,
],
[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:
EVfoldParser().write(f_out, contact_file)
content = ["1 H 9 L 0 0.7", "1 H 10 L 0 0.7", "2 L 8 I 0 0.9", "3 E 12 K 0 0.4"]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
