"""Testing facility for conkit.io.PlmDCAIO"""
__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.plmdca import PlmDCAParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestPlmDCAParser(ParserTestCase):
[docs] def test_read_1(self):
content = """1,2,0.12212
1,3,0.14004
1,4,0.12926
1,5,0.089211
1,6,0.079976
1,7,0.078954
1,8,0.052275
1,9,0.026012
1,10,0.049844
1,11,0.045109
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PlmDCAParser().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(
[0.12212, 0.14004, 0.12926, 0.089211, 0.079976, 0.078954, 0.052275, 0.026012, 0.049844, 0.045109],
[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:
PlmDCAParser().write(f_out, contact_file)
content = ["1,9,0.700000", "1,10,0.700000", "2,8,0.900000", "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)
