"""Testing facility for conkit.io.map_align"""
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.mapalign import MapAlignParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestMapAlignParser(ParserTestCase):
[docs] def test_read_1(self):
content = """LEN 77
CON 10 14 1
CON 1 7 0.883
CON 10 13 0.871
CON 6 9 0.847
CON 5 71 0.816
CON 36 42 0.807
CON 1 73 0.806
CON 33 37 0.8
CON 21 68 0.563
CON 38 57 0.561
PRF 0 T X 0.0321 0.0078 0.0582 0.1021 0.0207 0.0384 0.038 0.0386 0.0697 0.0376 0.0586
PRF 1 M X 0.0228 0.0052 0.0103 0.0112 0.1236 0.0083 0.0106 0.1182 0.0104 0.3046 0.1922
PRF 2 K X 0.0322 0.0048 0.0563 0.128 0.0116 0.0481 0.0332 0.0319 0.1099 0.0366 0.0228
PRF 3 I X 0.0147 0.0062 0.0025 0.0034 0.2786 0.0058 0.0057 0.1876 0.0053 0.2779 0.0302
PRF 4 I X 0.0404 0.0057 0.1139 0.2398 0.0104 0.028 0.0275 0.0278 0.0491 0.0283 0.0051
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = MapAlignParser().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(
[1.0, 0.883, 0.871, 0.847, 0.816, 0.807, 0.806, 0.8, 0.563, 0.561], [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:
MapAlignParser().write(f_out, contact_file)
content = ["LEN 12", "CON 1 9 0.700000", "CON 1 10 0.700000", "CON 2 8 0.900000", "CON 3 12 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)
