From e2a16931f71a78629c0e8ee5d2336fee10e2fb67 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 17 Nov 2022 22:44:56 +0100
Subject: [PATCH] stereochemistry unit tests
---
modules/mol/alg/tests/test_stereochemistry.py | 58 ++++++++++++-------
1 file changed, 38 insertions(+), 20 deletions(-)
diff --git a/modules/mol/alg/tests/test_stereochemistry.py b/modules/mol/alg/tests/test_stereochemistry.py
index 98889d650..c394b6d87 100644
--- a/modules/mol/alg/tests/test_stereochemistry.py
+++ b/modules/mol/alg/tests/test_stereochemistry.py
@@ -1,5 +1,3 @@
-
-
import unittest, os, sys
import ost
from ost import io, mol, settings, conop, seq
@@ -143,23 +141,45 @@ class TestStereochemistry(unittest.TestCase):
stereo_link_data = link_data)
self.assertTrue(None not in param)
+ def test_StereoCheck(self):
+ """ Test StereoCheck
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+ GetClashes, GetBadBonds and GetBadAngles get tested implicitely
+ """
+ ent = _LoadFile("10b2.pdb")
+ sterochecked_ent, clashes, bad_bonds, bad_angles = \
+ stereochemistry.StereoCheck(ent)
+
+ self.assertEqual(len(clashes), 0)
+ self.assertEqual(len(bad_bonds), 0)
+ self.assertEqual(len(bad_angles), 0)
+
+ phe_A_218 = ent.FindResidue("A", mol.ResNum(218))
+ c_B_75 = ent.FindResidue("B", mol.ResNum(75))
+
+ phe_at = phe_A_218.FindAtom("CD2")
+ c_at = c_B_75.FindAtom("C4'")
+ ed = ent.EditXCS()
+ ed.SetAtomPos(phe_at, 0.5*(phe_at.GetPos() + c_at.GetPos()))
+
+ stereochecked_ent, clashes, bad_bonds, bad_angles = \
+ stereochemistry.StereoCheck(ent)
+
+ self.assertEqual(len(clashes), 2)
+ self.assertEqual(len(bad_bonds), 2)
+ self.assertEqual(len(bad_angles), 2)
+
+ # c_B_75 gets completely removed as two backbone atoms are involved
+ # in clashes. phe_A_218 has the sidechain removed
+ self.assertEqual(len(ent.residues)-1,
+ len(stereochecked_ent.residues))
+ c_B_75 = stereochecked_ent.FindResidue("B", mol.ResNum(75))
+ self.assertFalse(c_B_75.IsValid())
+ phe_A_218 = stereochecked_ent.FindResidue("A", mol.ResNum(218))
+ self.assertTrue(phe_A_218.IsValid())
+ phe_atoms = [a.GetName() for a in phe_A_218.atoms]
+ self.assertEqual(sorted(["N", "CA", "C", "O"]),
+ sorted(phe_atoms))
if __name__ == "__main__":
from ost import testutils
@@ -167,5 +187,3 @@ if __name__ == "__main__":
testutils.RunTests()
else:
print('No compound library available. Ignoring test_stereochemistry.py tests.')
-
-
--
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