"""Testing facility for conkit.io.CCMpredIO"""
__author__ = "Felix Simkovic"
__date__ = "14 Sep 2016"
import os
import sys
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.ccmpred import CCMpredParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestCCMpredParser(ParserTestCase):
[docs] def test_read_1(self):
content = """0.00000000000000000000e+00 9.05865192413330078125e-01 4.48399752378463745117e-01 3.83993983268737792969e-02 7.80840754508972167969e-01 5.15280842781066894531e-01 2.66545146703720092773e-01 4.99921828508377075195e-01 4.54095661640167236328e-01 7.60651350021362304688e-01
9.05863702297210693359e-01 0.00000000000000000000e+00 7.22257912158966064453e-01 1.90076664090156555176e-01 1.08203485608100891113e-01 1.23369038105010986328e-01 5.28753221035003662109e-01 3.98827701807022094727e-01 7.34628140926361083984e-01 5.52688777446746826172e-01
4.48399752378463745117e-01 7.22256183624267578125e-01 0.00000000000000000000e+00 1.39001503586769104004e-01 8.06087076663970947266e-01 4.15808916091918945312e-01 3.66488158702850341797e-01 5.48547744750976562500e-01 3.75738739967346191406e-01 6.22575163841247558594e-01
3.83996069431304931641e-02 1.90076768398284912109e-01 1.39001443982124328613e-01 0.00000000000000000000e+00 3.90003859996795654297e-01 2.16557279229164123535e-01 4.70980733633041381836e-01 7.48713970184326171875e-01 3.39133590459823608398e-01 3.63562434911727905273e-01
7.80841588973999023438e-01 1.08203165233135223389e-01 8.06088566780090332031e-01 3.90004277229309082031e-01 0.00000000000000000000e+00 1.00000000000000000000e+00 4.70447808504104614258e-01 2.48236447572708129883e-01 1.31565973162651062012e-01 2.77379095554351806641e-01
5.15280425548553466797e-01 1.23368613421916961670e-01 4.15808051824569702148e-01 2.16556847095489501953e-01 9.99999344348907470703e-01 0.00000000000000000000e+00 4.25846457481384277344e-01 2.21113219857215881348e-01 9.12295103073120117188e-01 5.38769721984863281250e-01
2.66544729471206665039e-01 5.28752684593200683594e-01 3.66489529609680175781e-01 4.70980644226074218750e-01 4.70447897911071777344e-01 4.25846666097640991211e-01 0.00000000000000000000e+00 3.21736276149749755859e-01 5.99321126937866210938e-02 5.63172221183776855469e-01
4.99920457601547241211e-01 3.98826628923416137695e-01 5.48546612262725830078e-01 7.48714208602905273438e-01 2.48236656188964843750e-01 2.21113741397857666016e-01 3.21736931800842285156e-01 0.00000000000000000000e+00 6.80750489234924316406e-01 0.00000000000000000000e+00
4.54095035791397094727e-01 7.34628796577453613281e-01 3.75739067792892456055e-01 3.39132964611053466797e-01 1.31566718220710754395e-01 9.12294447422027587891e-01 5.99323771893978118896e-02 6.80750906467437744141e-01 0.00000000000000000000e+00 3.14438492059707641602e-01
7.60651111602783203125e-01 5.52687942981719970703e-01 6.22575819492340087891e-01 3.63562554121017456055e-01 2.77379721403121948242e-01 5.38770556449890136719e-01 5.63172996044158935547e-01 1.05407856665351573611e-07 3.14439445734024047852e-01 0.00000000000000000000e+00
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = CCMpredParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(55, len(contact_map1))
self.assertEqual(
sorted([1] * 10 + [2] * 9 + [3] * 8 + [4] * 7 + [5] * 6 + [6] * 5 + [7] * 4 + [8] * 3 + [9] * 2 + [10] * 1),
sorted([c.res1_seq for c in contact_map1]),
)
self.assertEqual(
[
1.0,
0.9122951030731201,
0.9058651924133301,
0.806087076663971,
0.7808407545089722,
0.7606513500213623,
0.7487139701843262,
0.7346281409263611,
0.7222579121589661,
0.6807504892349243,
0.6225751638412476,
0.5631722211837769,
0.5526887774467468,
0.5485477447509766,
0.5387697219848633,
0.5287532210350037,
0.5152808427810669,
0.4999218285083771,
0.4709807336330414,
0.4704478085041046,
0.45409566164016724,
0.44839975237846375,
0.4258464574813843,
0.41580891609191895,
0.3988277018070221,
0.39000385999679565,
0.3757387399673462,
0.36648815870285034,
0.3635624349117279,
0.3391335904598236,
0.32173627614974976,
0.31443849205970764,
0.2773790955543518,
0.2665451467037201,
0.24823644757270813,
0.22111321985721588,
0.21655727922916412,
0.19007666409015656,
0.1390015035867691,
0.13156597316265106,
0.12336903810501099,
0.10820348560810089,
0.05993211269378662,
0.03839939832687378,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
],
[c.raw_score for c in contact_map1],
)
[docs] def test_write_1(self):
contact_file = ContactFile("test")
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", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
f_name = self.tempfile()
# Not sure if bug in Python3 numpy or intended purpose [Implemented: 21.11.2016]
mode = "wb" if sys.version_info.major == 3 else "w"
with open(f_name, mode) as f_out:
CCMpredParser().write(f_out, contact_file)
content = [
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t6.999999999999999556e-01\t6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t9.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"6.999999999999999556e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
"0.000000000000000000e+00\t0.000000000000000000e+00\t4.000000000000000222e-01\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00\t0.000000000000000000e+00",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
[docs] def test_write_2(self):
contact_file = ContactFile("test")
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", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
f_name = self.tempfile()
# Not sure if bug in Python3 numpy or intended purpose [Implemented: 21.11.2016]
with open(f_name, "w") as f_out:
if sys.version_info.major == 3:
with self.assertRaises(TypeError):
CCMpredParser().write(f_out, contact_file)
else:
self.assertTrue(True)
if __name__ == "__main__":
unittest.main(verbosity=2)
