Checked test_raw_modeling.py

meld/src/CMakeLists.txt

@@ -8,8 +8,11 @@ gap.hh
 model.hh
 )
 
-module(NAME meld HEADERS ${MELD_HEADERS} SOURCES ${MELD_SOURCES} DEPENDS_ON
-      promod3_core LINK ${OPENGL_LIBRARIES} ${OST_LIBRARIES} ${BOOST_LIBRARIES})
+module(NAME meld
+       HEADERS ${MELD_HEADERS}
+       SOURCES ${MELD_SOURCES}
+       DEPENDS_ON promod3_core
+       LINK ${OPENGL_LIBRARIES} ${OST_LIBRARIES} ${BOOST_LIBRARIES})
 
 if (QMEAN_ROOT)
   target_link_libraries(promod3_meld ${QMEAN_LIBRARIES})

meld/tests/CMakeLists.txt

@@ -20,4 +20,3 @@ set(MELD_TEST_DATA
 promod3_unittest(MODULE meld
                  SOURCES "${MELD_UNIT_TESTS}"
                  DATA "${MELD_TEST_DATA}")
-

meld/tests/test_raw_modeling.py

+"""
+Unit tests for meld.
+"""
 import unittest
 from promod3 import meld
 from ost import conop, seq, io, mol
 
 class RawModelingTests(unittest.TestCase):
-  def setUp(self):
-    compound_lib=conop.CompoundLib.Load('data/raw-modeling/compounds.chemlib')
-    conop.SetDefaultLib(compound_lib)
-    io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
+    def setUp(self):
+        compound_lib = conop.CompoundLib.Load(
+            'data/raw-modeling/compounds.chemlib')
+        conop.SetDefaultLib(compound_lib)
+        io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(
+            compound_lib)
 
-  def testRaiseNoAttachedView(self):
-    # test that BuildRawModel throws exception when no view is attached
-    aln=seq.CreateAlignment(seq.CreateSequence('A', 'acdef'), 
-                            seq.CreateSequence('B', 'ac-ef'))
-    self.assertRaises(RuntimeError, meld.BuildRawModel, aln)
-    
-  def testModeledSequence(self):
-    # test if the model has the sequence we want.
-    tpl=io.LoadPDB('data/raw-modeling/gly.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/seq.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    seq1=seq.SequenceFromChain('MODEL', result.model.chains[0])
-    self.assertEqual(seq1.string, aln.sequences[0].string)
+    def testRaiseNoAttachedView(self):
+        # test that BuildRawModel throws exception when no view is attached
+        aln = seq.CreateAlignment(seq.CreateSequence('A', 'acdef'),
+                                  seq.CreateSequence('B', 'ac-ef'))
+        self.assertRaises(RuntimeError, meld.BuildRawModel, aln)
 
-  def testDeletion(self):
-    # test if the result contains a "deletion" gap at the right spot.
-    tpl=io.LoadPDB('data/raw-modeling/gly.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/del.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    residues=result.model.residues
-    self.assertEqual(len(result.gaps), 1)
-    self.assertEqual(result.gaps[0].before, residues[2])
-    self.assertEqual(result.gaps[0].after, residues[3])
-    self.assertEqual(result.gaps[0].seq, '')
+    def testModeledSequence(self):
+        # test if the model has the sequence we want.
+        tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/seq.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        seq1 = seq.SequenceFromChain('MODEL', result.model.chains[0])
+        self.assertEqual(seq1.string, aln.sequences[0].string)
 
-  def testInsertion(self):
-    # test if the result contains an "insertion" gap at the right spot.
-    tpl=io.LoadPDB('data/raw-modeling/gly.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/ins.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    residues=result.model.residues
-    self.assertEqual(len(result.gaps), 1)
-    self.assertEqual(result.gaps[0].before, residues[1])
-    self.assertEqual(result.gaps[0].after, residues[2])
-    self.assertEqual(result.gaps[0].seq, 'AV')
-    
-  def testTer(self):
-    # test if the result contains two terminal gaps, one at the beginning, 
-    # one at the end
-    tpl=io.LoadPDB('data/raw-modeling/gly.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/ter.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    residues=result.model.residues
-    self.assertEqual(len(result.gaps), 2)
-    self.assertEqual(result.gaps[0].before, mol.ResidueHandle())
-    self.assertEqual(result.gaps[0].after, residues[0])
-    self.assertEqual(result.gaps[0].seq, 'G')
-    self.assertEqual(result.gaps[1].before, residues[-1])
-    self.assertEqual(result.gaps[1].after, mol.ResidueHandle())
-    self.assertEqual(result.gaps[1].seq, 'G')
+    def testDeletion(self):
+        # test if the result contains a "deletion" gap at the right spot.
+        tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/del.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        residues = result.model.residues
+        self.assertEqual(len(result.gaps), 1)
+        self.assertEqual(result.gaps[0].before, residues[2])
+        self.assertEqual(result.gaps[0].after, residues[3])
+        self.assertEqual(result.gaps[0].seq, '')
 
-  def testModified(self):
-    # test if we correctly strip off modifications
-    tpl=io.LoadPDB('data/raw-modeling/sep.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/sep.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    residues=result.model.residues
-    self.assertEqual(len(residues), 1)
-    self.assertEqual(len(residues[0].atoms), 6)
-    self.assertTrue(residues[0].FindAtom("N"))
-    self.assertTrue(residues[0].FindAtom("CA"))
-    self.assertTrue(residues[0].FindAtom("C"))
-    self.assertTrue(residues[0].FindAtom("O"))
-    self.assertTrue(residues[0].FindAtom("CB"))
-    self.assertTrue(residues[0].FindAtom("OG"))
+    def testInsertion(self):
+        # test if the result contains an "insertion" gap at the right spot.
+        tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/ins.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        residues = result.model.residues
+        self.assertEqual(len(result.gaps), 1)
+        self.assertEqual(result.gaps[0].before, residues[1])
+        self.assertEqual(result.gaps[0].after, residues[2])
+        self.assertEqual(result.gaps[0].seq, 'AV')
 
-  def testInsertCBeta(self):
-    # test if the dst residues contain cbeta, unless they are glycines
-    tpl=io.LoadPDB('data/raw-modeling/cbeta.pdb')
-    aln=io.LoadAlignment('data/raw-modeling/cbeta.fasta')
-    aln.AttachView(1, tpl.CreateFullView())
-    result=meld.BuildRawModel(aln)
-    residues=result.model.residues
-    assert not residues[0].FindAtom("CB").IsValid()
-    assert not residues[1].FindAtom("CB").IsValid()
-    assert residues[2].FindAtom("CB").IsValid()
-    assert residues[3].FindAtom("CB").IsValid()
+    def testTer(self):
+        # test if the result contains two terminal gaps, one at the beginning,
+        # one at the end
+        tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/ter.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        residues = result.model.residues
+        self.assertEqual(len(result.gaps), 2)
+        self.assertEqual(result.gaps[0].before, mol.ResidueHandle())
+        self.assertEqual(result.gaps[0].after, residues[0])
+        self.assertEqual(result.gaps[0].seq, 'G')
+        self.assertEqual(result.gaps[1].before, residues[-1])
+        self.assertEqual(result.gaps[1].after, mol.ResidueHandle())
+        self.assertEqual(result.gaps[1].seq, 'G')
+
+    def testModified(self):
+        # test if we correctly strip off modifications
+        tpl = io.LoadPDB('data/raw-modeling/sep.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/sep.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        residues = result.model.residues
+        self.assertEqual(len(residues), 1)
+        self.assertEqual(len(residues[0].atoms), 6)
+        self.assertTrue(residues[0].FindAtom("N"))
+        self.assertTrue(residues[0].FindAtom("CA"))
+        self.assertTrue(residues[0].FindAtom("C"))
+        self.assertTrue(residues[0].FindAtom("O"))
+        self.assertTrue(residues[0].FindAtom("CB"))
+        self.assertTrue(residues[0].FindAtom("OG"))
+
+    def testInsertCBeta(self):
+        # test if the dst residues contain cbeta, unless they are glycines
+        tpl = io.LoadPDB('data/raw-modeling/cbeta.pdb')
+        aln = io.LoadAlignment('data/raw-modeling/cbeta.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = meld.BuildRawModel(aln)
+        residues = result.model.residues
+        self.assertFalse(residues[0].FindAtom("CB").IsValid())
+        self.assertFalse(residues[1].FindAtom("CB").IsValid())
+        self.assertTrue(residues[2].FindAtom("CB").IsValid())
+        self.assertTrue(residues[3].FindAtom("CB").IsValid())
 
 
 if __name__ == "__main__":
-  from ost import testutils
-  testutils.RunTests()
+    from ost import testutils
+    testutils.RunTests()