From 822ea40e7db481a2745f01d3b6c0899ac749e634 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 18 Nov 2022 10:42:33 +0100
Subject: [PATCH] stereocheck: extend unit tests
---
modules/mol/alg/tests/test_stereochemistry.py | 26 +++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/modules/mol/alg/tests/test_stereochemistry.py b/modules/mol/alg/tests/test_stereochemistry.py
index c394b6d87..ae458d4b5 100644
--- a/modules/mol/alg/tests/test_stereochemistry.py
+++ b/modules/mol/alg/tests/test_stereochemistry.py
@@ -181,6 +181,32 @@ class TestStereochemistry(unittest.TestCase):
self.assertEqual(sorted(["N", "CA", "C", "O"]),
sorted(phe_atoms))
+ # reload and trigger the case where the nucleotide backbone remains
+ ent = _LoadFile("10b2.pdb")
+ c_B_75 = ent.FindResidue("B", mol.ResNum(75))
+ ser_A_219 = ent.FindResidue("A", mol.ResNum(219))
+ c_at = c_B_75.FindAtom("O2")
+ ser_at = ser_A_219.FindAtom("O")
+ ed = ent.EditXCS()
+ new_pos = ser_at.GetPos() + 0.6*(c_at.GetPos()-ser_at.GetPos())
+ ed.SetAtomPos(ser_at, new_pos)
+
+ stereochecked_ent, clashes, bad_bonds, bad_angles = \
+ stereochemistry.StereoCheck(ent)
+
+ self.assertEqual(len(clashes), 1)
+ self.assertEqual(len(bad_bonds), 1)
+ self.assertEqual(len(bad_angles), 1)
+
+ c_B_75 = stereochecked_ent.FindResidue("B", mol.ResNum(75))
+ self.assertTrue(c_B_75.IsValid())
+ ser_A_219 = stereochecked_ent.FindResidue("A", mol.ResNum(219))
+ self.assertFalse(ser_A_219.IsValid())
+ c_atoms = [a.GetName() for a in c_B_75.atoms]
+ exp_c_atoms = ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "C3'",
+ "C2'", "C1'", "O4'", "O3'", "O2'"]
+ self.assertEqual(sorted(c_atoms), sorted(exp_c_atoms))
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():
--
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