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Commit 321b7f05 authored by Studer Gabriel's avatar Studer Gabriel
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fix qsscoring unit test

parasail produces slightly different alignments for one test case
parent 99a1fdb2
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import unittest, os, sys import unittest, os, sys
import ost import ost
from ost import io, mol, settings from ost import io, mol, settings, seq
# check if we can import: fails if numpy or scipy not available # check if we can import: fails if numpy or scipy not available
try: try:
from ost.mol.alg.qsscoring import * from ost.mol.alg.qsscoring import *
...@@ -301,8 +301,18 @@ class TestQSscore(unittest.TestCase): ...@@ -301,8 +301,18 @@ class TestQSscore(unittest.TestCase):
ent_1 = _LoadFile('4dvh.1.pdb') # A2, symmetry: C2 ent_1 = _LoadFile('4dvh.1.pdb') # A2, symmetry: C2
ent_2 = _LoadFile('4br6.1.pdb') # A4, symmetry: D2 ent_2 = _LoadFile('4br6.1.pdb') # A4, symmetry: D2
qs_scorer = QSscorer(ent_1, ent_2) qs_scorer = QSscorer(ent_1, ent_2)
self.assertAlmostEqual(qs_scorer.global_score, 0.147, 2)
self.assertAlmostEqual(qs_scorer.best_score, 0.866, 2) # 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(qs_scorer.global_score, 0.14757304498883386, 2)
self.assertAlmostEqual(qs_scorer.best_score, 0.7878766697963304, 2)
else:
self.assertAlmostEqual(qs_scorer.global_score, 0.14797023263299844, 2)
self.assertAlmostEqual(qs_scorer.best_score, 0.8666616636985371, 2)
self._CheckScorer(qs_scorer) self._CheckScorer(qs_scorer)
# check properties # check properties
self.assertFalse(qs_scorer.calpha_only) self.assertFalse(qs_scorer.calpha_only)
......
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