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import unittest, os, sys
import ost
from ost import conop
from ost import io, mol, seq, settings
# check if we can import: fails if numpy or scipy not available
try:
import numpy as np
from ost.mol.alg.contact_score import *
from ost.mol.alg.chain_mapping import *
except ImportError:
print("Failed to import contact_score.py. Happens when numpy or scipy "\
"missing. Ignoring contact_score.py tests.")
sys.exit(0)
def _LoadFile(file_name):
"""Helper to avoid repeating input path over and over."""
return io.LoadPDB(os.path.join('testfiles', file_name))
class TestContactScore(unittest.TestCase):
def test_ContactEntity(self):
self.maxDiff = None
ent = _LoadFile("3l1p.1.pdb")
cent = ContactEntity(ent)
self.assertEqual(cent.GetChain("A").GetName(), "A")
self.assertEqual(cent.GetChain("B").GetName(), "B")
self.assertEqual(cent.GetChain("C").GetName(), "C")
self.assertEqual(cent.GetChain("D").GetName(), "D")
self.assertRaises(Exception, cent.GetChain, "E")
self.assertEqual(cent.chain_names, ["A", "B", "C", "D"])
self.assertEqual(cent.GetSequence("A"), "DMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR")
self.assertEqual(cent.GetSequence("B"), "KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS")
self.assertEqual(cent.GetSequence("C"), "TCCACATTTGAAAGGCAAATGGA")
self.assertEqual(cent.GetSequence("D"), "ATCCATTTGCCTTTCAAATGTGG")
self.assertEqual(cent.contact_mode, "aa")
self.assertEqual(cent.contact_d, 5.0)
self.assertEqual(sorted(cent.interacting_chains), [('A', 'B'),
('A', 'C'),
('A', 'D'),
('B', 'C'),
('B', 'D'),
('C', 'D')])
exp_contacts = sorted(list(cent.contacts[('A', 'C')]))
self.assertEqual(exp_contacts, [(40, 9), (41, 8), (41, 9), (42, 8),
(42, 9), (42, 10), (43, 12), (44, 9),
(44, 10), (44, 11), (45, 8), (45, 9),
(48, 8), (48, 9), (54, 8), (55, 6),
(55, 7), (57, 7), (58, 7), (58, 8),
(62, 8), (91, 8), (91, 9), (91, 10),
(93, 8), (93, 9), (93, 10), (95, 10),
(95, 11), (113, 2), (113, 3), (115, 2),
(134, 1), (139, 5), (141, 2), (141, 3),
(142, 4), (142, 5), (142, 6), (145, 4)])
def test_ContactScorer(self):
target = _LoadFile("3l1p.1.pdb")
model = _LoadFile("3l1p.1_model.pdb")
# we need to derive a chain mapping prior to scoring
mapper = ChainMapper(target)
res = mapper.GetRMSDMapping(model, strategy="greedy_iterative")
contact_scorer = ContactScorer.FromMappingResult(res)
score_result = contact_scorer.ScoreICS(res.mapping)
self.assertAlmostEqual(score_result.precision, 0.583, places=2)
self.assertAlmostEqual(score_result.recall, 0.288, places=2)
self.assertAlmostEqual(score_result.ics, 0.386, places=2)
score_result = contact_scorer.ScoreIPS(res.mapping)
self.assertAlmostEqual(score_result.precision, 0.779, places=2)
self.assertAlmostEqual(score_result.recall, 0.493, places=2)
self.assertAlmostEqual(score_result.ips, 0.432, places=2)
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound lib available. Ignoring contact_score.py tests.')
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