diff --git a/meld/src/CMakeLists.txt b/meld/src/CMakeLists.txt
index ca89294ebc990824b85927827e557a6d18d882a5..400084ac9af8e812bce22d36413e6f58cf8c1ad6 100644
--- a/meld/src/CMakeLists.txt
+++ b/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 ${QMEAN_LIBRARIES})
diff --git a/meld/tests/CMakeLists.txt b/meld/tests/CMakeLists.txt
index 331317e57404072ba4cf4432fdfd69d7f556c05e..d3c6a8f074ec5796cef9c771f906079277e8f6f0 100644
--- a/meld/tests/CMakeLists.txt
+++ b/meld/tests/CMakeLists.txt
@@ -20,4 +20,3 @@ set(MELD_TEST_DATA
promod3_unittest(MODULE meld
SOURCES "${MELD_UNIT_TESTS}"
DATA "${MELD_TEST_DATA}")
-
diff --git a/meld/tests/test_raw_modeling.py b/meld/tests/test_raw_modeling.py
index a99115ffdf86b456ea9a25932cb9f4dfed28ee8b..b18cc0e4c415d25309338e35ebeec799591bb576 100644
--- a/meld/tests/test_raw_modeling.py
+++ b/meld/tests/test_raw_modeling.py
@@ -1,97 +1,102 @@
+"""
+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()