"""Testing facility for conkit.io.ComsatIO"""
__author__ = "Felix Simkovic"
__date__ = "14 Sep 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.comsat import ComsatParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestComsatParser(ParserTestCase):
[docs] def test_read_1(self):
content = """19 A 41 A H1-H2
19 A 42 C H1-H2
11 L 47 L H1-H2
11 L 48 L H1-H2
12 L 47 L H1-H2
12 L 48 L H1-H2
40 I 66 I H2-H3
41 A 66 I H2-H3
33 Y 73 H H2-H3
33 Y 74 A H2-H3
46 L 62 L H2-H3
47 L 62 L H2-H3
69 M 88 V H3-H4
69 M 89 A H3-H4
96 A 117 V H4-H5
96 A 118 A H4-H5
82 A 129 A H4-H5
82 A 130 G H4-H5
82 A 133 F H4-H5
83 F 133 F H4-H5
128 I 154 I H5-H6
129 A 154 I H5-H6
118 A 163 A H5-H6
119 V 163 A H5-H6
20 A 160 A H1-H6
21 L 160 A H1-H6
8 N 171 V H1-H6
9 V 171 V H1-H6
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = ComsatParser().read(f_in, "r")
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(28, len(contact_map1))
self.assertEqual(
[
19,
19,
11,
11,
12,
12,
40,
41,
33,
33,
46,
47,
69,
69,
96,
96,
82,
82,
82,
83,
128,
129,
118,
119,
20,
21,
8,
9,
],
[c.res1_seq 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:
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)
if __name__ == "__main__":
unittest.main(verbosity=2)
