From 7be99f6bcbb0c69b09cb50faaa3e2ee17b568648 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 15:38:30 +0100
Subject: [PATCH] basic unit tests for TMAlign and TMScore
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_tmtools.py | 59 ++++++++++++++++++++++++++
2 files changed, 60 insertions(+)
create mode 100644 modules/bindings/tests/test_tmtools.py
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index b5a44d108..089f1ae9b 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_kclust.py
test_naccess.py
test_cadscore.py
+ test_tmtools.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_tmtools.py b/modules/bindings/tests/test_tmtools.py
new file mode 100644
index 000000000..148e6263c
--- /dev/null
+++ b/modules/bindings/tests/test_tmtools.py
@@ -0,0 +1,59 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import testutils
+from ost.seq.alg import SequenceIdentity
+from ost.bindings import tmtools
+
+class TestTMBindings(unittest.TestCase):
+
+ def setUp(self):
+ self.protein = io.LoadEntity("testfiles/testprotein.pdb")
+
+
+ def testTMAlign(self):
+
+ try:
+ cad_calc_path = settings.Locate('tmalign')
+ except:
+ print("Could not find tmalign executable: ignoring unit tests")
+ return
+
+ tm_result = tmtools.TMAlign(self.protein, self.protein)
+
+ # model and reference are the same, we expect pretty good results
+ self.assertEqual(tm_result.rmsd, 0.0)
+ self.assertEqual(tm_result.tm_score, 1.0)
+ self.assertEqual(tm_result.aligned_length, len(self.protein.chains[0].residues))
+ self.assertEqual(SequenceIdentity(tm_result.alignment), 100.0)
+
+ # transformation should be identity matrix (no transformation at all...)
+ identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(tm_result.transform, identity)
+
+
+ def testTMScore(self):
+
+ try:
+ cad_calc_path = settings.Locate('tmscore')
+ except:
+ print("Could not find tmalign executable: ignoring unit tests")
+ return
+
+ tm_result = tmtools.TMScore(self.protein, self.protein)
+
+ # model and reference are the same, we expect pretty good results
+ self.assertEqual(tm_result.rmsd_common, 0.0)
+ self.assertEqual(tm_result.tm_score, 1.0)
+ self.assertEqual(tm_result.max_sub, 1.0)
+ self.assertEqual(tm_result.gdt_ts, 1.0)
+ self.assertEqual(tm_result.gdt_ha, 1.0)
+ self.assertEqual(tm_result.rmsd_below_five, 0.0)
+
+ # transformation should be identity matrix (no transformation at all...)
+ identity = geom.Mat4(1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1)
+ self.assertEqual(tm_result.transform, identity)
+
+
+if __name__ == "__main__":
+ testutils.RunTests()
--
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