stereochemistry unit tests

modules/mol/alg/tests/CMakeLists.txt

@@ -10,6 +10,7 @@ set(OST_MOL_ALG_UNIT_TESTS
   test_sec_struct.py
   test_lddt.py
   test_qsscore.py
+  test_stereochemistry.py
 )
 
 if (COMPOUND_LIB)

modules/mol/alg/tests/test_stereochemistry.py

+
+
+import unittest, os, sys
+import ost
+from ost import io, mol, settings, conop, seq
+# check if we can import: fails if numpy or scipy not available
+try:
+    from ost.mol.alg import stereochemistry
+except ImportError:
+    print("Failed to import stereochemistry. Happens when numpy missing. " \
+          "Ignoring test_stereochemistry.py tests.")
+    sys.exit(0)
+
+
+def _LoadFile(file_name):
+    """Helper to avoid repeating input path over and over."""
+    return io.LoadPDB(os.path.join('testfiles', file_name))
+
+class TestStereochemistry(unittest.TestCase):
+
+    def test_GetResidueType(self):
+        """ internal function in stereochemistry module, nevertheless crucial...
+        """
+        ent = _LoadFile("10b2.pdb")
+
+        # get some residues
+        ile_a_199 = ent.FindResidue("A", mol.ResNum(199))
+        self.assertEqual(ile_a_199.GetName(), "ILE")
+        pro_a_200 = ent.FindResidue("A", mol.ResNum(200))
+        self.assertEqual(pro_a_200.GetName(), "PRO")
+        glu_a_201 = ent.FindResidue("A", mol.ResNum(201))
+        self.assertEqual(glu_a_201.GetName(), "GLU")
+        pro_a_202 = ent.FindResidue("A", mol.ResNum(202))
+        self.assertEqual(pro_a_202.GetName(), "PRO")
+        ser_a_221 = ent.FindResidue("A", mol.ResNum(221))
+        self.assertEqual(ser_a_221.GetName(), "SER")
+        gly_a_222 = ent.FindResidue("A", mol.ResNum(222))
+        self.assertEqual(gly_a_222.GetName(), "GLY")
+        arg_a_223 = ent.FindResidue("A", mol.ResNum(223))
+        self.assertEqual(arg_a_223.GetName(), "ARG")
+        c_b_75 = ent.FindResidue("B", mol.ResNum(75))
+        self.assertEqual(c_b_75.GetName(), "C")
+        a_b_76 = ent.FindResidue("B", mol.ResNum(76))
+        self.assertEqual(a_b_76.GetName(), "A")
+
+        # check PRO_CIS
+        res_type = stereochemistry._GetResidueType([ile_a_199.FindAtom("C"),
+                                                    pro_a_200.FindAtom("N")])
+        self.assertEqual(res_type, "PRO_CIS")
+        res_type = stereochemistry._GetResidueType([pro_a_200.FindAtom("N"),
+                                                    ile_a_199.FindAtom("C")])
+        self.assertEqual(res_type, "PRO_CIS")
+        res_type = stereochemistry._GetResidueType([ile_a_199.FindAtom("O"),
+                                                    ile_a_199.FindAtom("C"),
+                                                    pro_a_200.FindAtom("N")])
+        self.assertEqual(res_type, "PRO_CIS")
+        res_type = stereochemistry._GetResidueType([pro_a_200.FindAtom("N"),
+                                                    ile_a_199.FindAtom("C"),
+                                                    ile_a_199.FindAtom("O")])
+        self.assertEqual(res_type, "PRO_CIS")
+
+        # check PRO_TRANS
+        res_type = stereochemistry._GetResidueType([glu_a_201.FindAtom("C"),
+                                                    pro_a_202.FindAtom("N")])
+        self.assertEqual(res_type, "PRO_TRANS")
+        res_type = stereochemistry._GetResidueType([pro_a_202.FindAtom("N"),
+                                                    glu_a_201.FindAtom("C")])
+        self.assertEqual(res_type, "PRO_TRANS")
+        res_type = stereochemistry._GetResidueType([glu_a_201.FindAtom("O"),
+                                                    glu_a_201.FindAtom("C"),
+                                                    pro_a_202.FindAtom("N")])
+        self.assertEqual(res_type, "PRO_TRANS")
+        res_type = stereochemistry._GetResidueType([pro_a_202.FindAtom("N"),
+                                                    glu_a_201.FindAtom("C"),
+                                                    glu_a_201.FindAtom("O")])
+        self.assertEqual(res_type, "PRO_TRANS")
+
+        # check GLY
+        res_type = stereochemistry._GetResidueType([ser_a_221.FindAtom("C"),
+                                                    gly_a_222.FindAtom("N")])
+        self.assertEqual(res_type, "GLY")
+        res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
+                                                    ser_a_221.FindAtom("C")])
+        self.assertEqual(res_type, "GLY")
+        res_type = stereochemistry._GetResidueType([ser_a_221.FindAtom("O"),
+                                                    ser_a_221.FindAtom("C"),
+                                                    gly_a_222.FindAtom("N")])
+        self.assertEqual(res_type, "GLY")
+        res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
+                                                    ser_a_221.FindAtom("C"),
+                                                    ser_a_221.FindAtom("O")])
+        self.assertEqual(res_type, "GLY")
+
+        # check PEPTIDE
+        res_type = stereochemistry._GetResidueType([arg_a_223.FindAtom("C"),
+                                                    gly_a_222.FindAtom("N")])
+        self.assertEqual(res_type, "PEPTIDE")
+        res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
+                                                    arg_a_223.FindAtom("C")])
+        self.assertEqual(res_type, "PEPTIDE")
+        res_type = stereochemistry._GetResidueType([arg_a_223.FindAtom("O"),
+                                                    arg_a_223.FindAtom("C"),
+                                                    gly_a_222.FindAtom("N")])
+        self.assertEqual(res_type, "PEPTIDE")
+        res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
+                                                    arg_a_223.FindAtom("C"),
+                                                    arg_a_223.FindAtom("O")])
+        self.assertEqual(res_type, "PEPTIDE")
+
+        # check NA
+        res_type = stereochemistry._GetResidueType([a_b_76.FindAtom("P"),
+                                                    c_b_75.FindAtom("O3'")])
+        self.assertEqual(res_type, "NA")
+        res_type = stereochemistry._GetResidueType([c_b_75.FindAtom("O3'"),
+                                                    a_b_76.FindAtom("P")])
+        self.assertEqual(res_type, "NA")
+        res_type = stereochemistry._GetResidueType([a_b_76.FindAtom("O5'"),
+                                                    a_b_76.FindAtom("P"),
+                                                    c_b_75.FindAtom("O3'")])
+        self.assertEqual(res_type, "NA")
+        res_type = stereochemistry._GetResidueType([c_b_75.FindAtom("O3'"),
+                                                    a_b_76.FindAtom("P"),
+                                                    a_b_76.FindAtom("O5'")])
+        self.assertEqual(res_type, "NA")
+
+    def test_FullParameters(self):
+        """ Tests whether we get parameters for each bond/angle
+        """
+        ent = _LoadFile("10b2.pdb")
+        data = stereochemistry.GetDefaultStereoData()
+        link_data = stereochemistry.GetDefaultStereoLinkData()
+        # do bonds
+        for b in ent.bonds:
+            param = stereochemistry.GetBondParam(b.first, b.second,
+                                                 stereo_data=data,
+                                                 stereo_link_data = link_data)
+            self.assertTrue(None not in param)
+        # do angles
+        angles = stereochemistry._GetAngles(ent.bonds)
+        for a in angles:
+            param = stereochemistry.GetAngleParam(a[0], a[1], a[2],
+                                                  stereo_data=data,
+                                                  stereo_link_data = link_data)
+            self.assertTrue(None not in param)
+
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+
+
+if __name__ == "__main__":
+    from ost import testutils
+    if testutils.SetDefaultCompoundLib():
+        testutils.RunTests()
+    else:
+        print('No compound library available. Ignoring test_stereochemistry.py tests.')
+
+