From 321b7f055a79a67a938a955c0cbb06b5b1f74019 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 27 Jun 2024 11:29:12 +0200
Subject: [PATCH] fix qsscoring unit test
parasail produces slightly different alignments for one test case
---
modules/mol/alg/tests/test_qsscoring.py | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index fc73c72d6..f24760929 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -1,6 +1,6 @@
import unittest, os, sys
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
try:
from ost.mol.alg.qsscoring import *
@@ -301,8 +301,18 @@ class TestQSscore(unittest.TestCase):
ent_1 = _LoadFile('4dvh.1.pdb') # A2, symmetry: C2
ent_2 = _LoadFile('4br6.1.pdb') # A4, symmetry: D2
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)
# check properties
self.assertFalse(qs_scorer.calpha_only)
--
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