"""Testing facility for conkit.io.MemBrainIO"""
__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.tests.helpers import ParserTestCase
from conkit.io.membrain import MemBrainParser
[docs]class TestMemBrainParser(ParserTestCase):
[docs] def test_read_1(self):
content = """Helix Position Residue Helix Position Residue Probability
H1 30 F H2 55 F 1.000000
H1 33 L H2 51 A 0.944091
H1 18 G H2 65 C 0.942259
H1 30 F H2 54 G 0.919241
H1 26 I H2 57 L 0.817638
H1 18 G H2 58 S 0.797449
H1 33 L H2 63 L 0.795520
H1 12 A H2 68 V 0.795462
H1 29 V H2 55 F 0.791829
H1 24 I H2 51 A 0.790044
H1 19 L H2 62 G 0.784613
H1 19 L H2 55 F 0.782741
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = MemBrainParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(12, len(contact_map1))
self.assertEqual([30, 33, 18, 30, 26, 18, 33, 12, 29, 24, 19, 19], [c.res1_seq for c in contact_map1])
self.assertEqual([55, 51, 65, 54, 57, 58, 63, 68, 55, 51, 62, 55], [c.res2_seq for c in contact_map1])
self.assertEqual(
[
1.000000,
0.944091,
0.942259,
0.919241,
0.817638,
0.797449,
0.795520,
0.795462,
0.791829,
0.790044,
0.784613,
0.782741,
],
[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:
MemBrainParser().write(f_out, contact_file)
content = [
"Helix Position Residue Helix Position Residue Probability",
"Hx 1 H Hx 9 L 0.700000",
"Hx 1 H Hx 10 L 0.700000",
"Hx 2 L Hx 8 I 0.900000",
"Hx 3 E Hx 12 K 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)
