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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.qsscore import *
from ost.mol.alg.chain_mapping import *
except ImportError:
print("Failed to import qsscore.py. Happens when numpy or scipy "\
"missing. Ignoring qsscore.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 TestQSScore(unittest.TestCase):
def test_qsentity(self):
ent = _LoadFile("3l1p.1.pdb")
qsent = QSEntity(ent)
self.assertEqual(len(qsent.view.chains), 4)
self.assertEqual(qsent.GetChain("A").GetName(), "A")
self.assertEqual(qsent.GetChain("B").GetName(), "B")
self.assertEqual(qsent.GetChain("C").GetName(), "C")
self.assertEqual(qsent.GetChain("D").GetName(), "D")
self.assertRaises(Exception, qsent.GetChain, "E")
self.assertEqual(qsent.chain_names, ["A", "B", "C", "D"])
self.assertEqual(qsent.GetSequence("A"), "DMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR")
self.assertEqual(qsent.GetSequence("B"), "KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS")
self.assertEqual(qsent.GetSequence("C"), "TCCACATTTGAAAGGCAAATGGA")
self.assertEqual(qsent.GetSequence("D"), "ATCCATTTGCCTTTCAAATGTGG")
# check for a couple of positions with manually extracted values
# GLU
pos = qsent.GetPos("B")
self.assertAlmostEqual(pos[5,0], -1.661, places=3)
self.assertAlmostEqual(pos[5,1], 27.553, places=3)
self.assertAlmostEqual(pos[5,2], 12.774, places=3)
# GLY
pos = qsent.GetPos("A")
self.assertAlmostEqual(pos[23,0], 17.563, places=3)
self.assertAlmostEqual(pos[23,1], -4.082, places=3)
self.assertAlmostEqual(pos[23,2], 29.005, places=3)
# Cytosine
pos = qsent.GetPos("C")
self.assertAlmostEqual(pos[4,0], 14.796, places=3)
self.assertAlmostEqual(pos[4,1], 24.653, places=3)
self.assertAlmostEqual(pos[4,2], 59.318, places=3)
# check pairwise dist, chain names are always sorted =>
# A is rows, C is cols
dist_one = qsent.PairDist("A", "C")
dist_two = qsent.PairDist("C", "A")
self.assertTrue(np.array_equal(dist_one, dist_two))
self.assertEqual(dist_one.shape[0], len(qsent.GetSequence("A")))
self.assertEqual(dist_one.shape[1], len(qsent.GetSequence("C")))
# check some random distance between the Gly and Cytosine that we already
# checked above
self.assertAlmostEqual(dist_one[23,4], 41.86, places=2)
# all chains interact with each other... but hey, check nevertheless
self.assertEqual(qsent.interacting_chains, [("A", "B"), ("A", "C"),
("A", "D"), ("B", "C"),
("B", "D"), ("C", "D")])
def test_qsscorer(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")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.472, places=2)
def test_hetero_case_1(self):
# additional chains
ent_1 = _LoadFile('4ux8.1.pdb') # A2 B2 C2, symmetry: C2
ent_2 = _LoadFile('3fub.2.pdb') # A2 B2 , symmetry: C2
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.825, 2)
self.assertAlmostEqual(score_result.QS_best, 1.0, 2)
def test_hetero_case_1_switched_order(self):
# additional chains
ent_2 = _LoadFile('4ux8.1.pdb') # A2 B2 C2, symmetry: C2
ent_1 = _LoadFile('3fub.2.pdb') # A2 B2 , symmetry: C2
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.825, 2)
self.assertAlmostEqual(score_result.QS_best, 1.0, 2)
def test_HeteroCase1b(self):
# as above but with assymetric unit of 3fub
# -> no overlap found: check if extensive search can deal with it
ent_1 = _LoadFile('4ux8.1.pdb')
ent_2 = _LoadFile('3fub.au.pdb')
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.356, 2)
self.assertAlmostEqual(score_result.QS_best, 0.419, 2)
def test_HeteroCase1b_switched_order(self):
# chain mapping differs a bit when switching the order... I'm just
# too lazy...
pass
def test_hetero_case_2(self):
# different stoichiometry
ent_1 = _LoadFile('1efu.1.pdb') # A2 B2, symmetry: C2
ent_2 = _LoadFile('4pc6.1.pdb') # A B , no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.3191, 2)
self.assertAlmostEqual(score_result.QS_best, 0.9781, 2)
def test_hetero_case_2_switched_order(self):
# different stoichiometry
ent_2 = _LoadFile('1efu.1.pdb') # A2 B2, symmetry: C2
ent_1 = _LoadFile('4pc6.1.pdb') # A B , no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.3191, 2)
self.assertAlmostEqual(score_result.QS_best, 0.9781, 2)
def test_hetero_case_3(self):
# more chains
ent_1 = _LoadFile('2vjt.1.pdb') # A6 B6, symmetry: D3
ent_2 = _LoadFile('3dbj.1.pdb') # A3 B3, symmetry: C3
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.359, 2)
self.assertAlmostEqual(score_result.QS_best, 0.958, 2)
def test_hetero_case_3_switched_order(self):
# more chains
ent_2 = _LoadFile('2vjt.1.pdb') # A6 B6, symmetry: D3
ent_1 = _LoadFile('3dbj.1.pdb') # A3 B3, symmetry: C3
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.359, 2)
self.assertAlmostEqual(score_result.QS_best, 0.958, 2)
def test_hetero_case_4(self):
# inverted chains
ent_1 = _LoadFile('3ia3.1.pdb') # AB, no symmetry
ent_2 = _LoadFile('3ia3.2.pdb') # BA, no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.980, 2)
self.assertAlmostEqual(score_result.QS_best, 0.980, 2)
def test_hetero_case_4_switched_order(self):
# inverted chains
ent_2 = _LoadFile('3ia3.1.pdb') # AB, no symmetry
ent_1 = _LoadFile('3ia3.2.pdb') # BA, no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.980, 2)
self.assertAlmostEqual(score_result.QS_best, 0.980, 2)
def test_hetero_model(self):
# uncomplete model missing 2 third of the contacts
target = _LoadFile('1eud_ref.pdb') # AB, no symmetry
model = _LoadFile('1eud_mdl_partial-dimer.pdb') # BA, no symmetry
mapper = ChainMapper(target)
res = mapper.GetRMSDMapping(model, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.321, 2)
self.assertAlmostEqual(score_result.QS_best, 0.932, 2)
def test_hetero_model_switched_order(self):
# same as above but with switched order to test for symmetric behaviour
# of QS score
target = _LoadFile('1eud_mdl_partial-dimer.pdb') # BA, no symmetry
model = _LoadFile('1eud_ref.pdb') # AB, no symmetry
mapper = ChainMapper(target)
res = mapper.GetRMSDMapping(model, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 0.321, 2)
self.assertAlmostEqual(score_result.QS_best, 0.932, 2)
def test_homo_1(self):
# different stoichiometry SOD
ent_1 = _LoadFile('4dvh.1.pdb') # A2, symmetry: C2
ent_2 = _LoadFile('4br6.1.pdb') # A4, symmetry: D2
# original qsscoring uses other default values for gap_open and gap_extension
# penalties, let's use those to reproduce the old results as the alignments
# would differ otherwise
mapper = ChainMapper(ent_1, pep_gap_open = -5, pep_gap_ext = -2)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
# The alignments from parasail slightly differ. The sequence identities
# are in the range 40% but slightly lower for parasail alignments.
# however, the parasail alignments appear less gappy and "nicer".
# They nevertheless lead to lower QS-score.
if seq.alg.ParasailAvailable():
self.assertAlmostEqual(score_result.QS_global, 0.14757304498883386, 2)
self.assertAlmostEqual(score_result.QS_best, 0.7878766697963304, 2)
else:
self.assertAlmostEqual(score_result.QS_global, 0.14797023263299844, 2)
self.assertAlmostEqual(score_result.QS_best, 0.8666616636985371, 2)
def test_homo_1_switched_order(self):
# different stoichiometry SOD
ent_2 = _LoadFile('4dvh.1.pdb') # A2, symmetry: C2
ent_1 = _LoadFile('4br6.1.pdb') # A4, symmetry: D2
# original qsscoring uses other default values for gap_open and gap_extension
# penalties, let's use those to reproduce the old results as the alignments
# would differ otherwise
mapper = ChainMapper(ent_1, pep_gap_open = -5, pep_gap_ext = -2)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
# The alignments from parasail slightly differ. The sequence identities
# are in the range 40% but slightly lower for parasail alignments.
# however, the parasail alignments appear less gappy and "nicer".
# They nevertheless lead to lower QS-score.
if seq.alg.ParasailAvailable():
self.assertAlmostEqual(score_result.QS_global, 0.14757304498883386, 2)
self.assertAlmostEqual(score_result.QS_best, 0.7878766697963304, 2)
else:
self.assertAlmostEqual(score_result.QS_global, 0.14797023263299844, 2)
self.assertAlmostEqual(score_result.QS_best, 0.8666616636985371, 2)
def test_homo_2(self):
# broken cyclic symmetry
ent_1 = _LoadFile('4r7y.1.pdb') # A6, symmetry: C6
ent_2 = ent_1.Select('cname=A,B') # A2, no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 1/6, 2)
self.assertAlmostEqual(score_result.QS_best, 1.0, 2)
def test_homo_2_switched_order(self):
# same as above but with switched order to test for symmetric behaviour
# of QS score
ent_2 = _LoadFile('4r7y.1.pdb') # A6, symmetry: C6
ent_1 = ent_2.Select('cname=A,B') # A2, no symmetry
mapper = ChainMapper(ent_1)
res = mapper.GetRMSDMapping(ent_2, strategy="greedy_iterative")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
self.assertAlmostEqual(score_result.QS_global, 1/6, 2)
self.assertAlmostEqual(score_result.QS_best, 1.0, 2)
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound lib available. Ignoring test_qsscore.py tests.')
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