diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 2fd6246b1479a6d1d91188fbd9444c5685e62e49..a5bd282a71e1590a01d77ee55d17c0854289b32c 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -153,6 +153,24 @@ class TestQSscore(unittest.TestCase):
self.assertAlmostEqual(qs_scorer.best_score, 0.419, 2)
self._CheckScorer(qs_scorer)
+ # enforce different chain mapping
+ enforced_cm = {'C': 'C', 'E': 'A', 'D': 'D', 'F': 'B'}
+ qs_scorer_2 = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
+ qs_scorer_2.chain_mapping = enforced_cm
+ self.assertAlmostEqual(qs_scorer_2.global_score, 0.356, 2)
+ self.assertAlmostEqual(qs_scorer_2.best_score, 0.419, 2)
+ self.assertEqual(qs_scorer_2.chain_mapping, enforced_cm)
+ self._CheckScorer(qs_scorer_2)
+
+ # check if we get same mapping with restricted max_ca_per_chain_for_cm
+ qs_scorer_2 = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
+ qs_scorer_2.max_ca_per_chain_for_cm = 50
+ self.assertEqual(qs_scorer_2.chain_mapping, qs_scorer.chain_mapping)
+ self.assertAlmostEqual(qs_scorer_2.global_score, qs_scorer.global_score, 2)
+ self.assertAlmostEqual(qs_scorer_2.best_score, qs_scorer.best_score, 2)
+ self._CheckScorer(qs_scorer_2)
+
+
def test_HeteroCase2(self):
# different stoichiometry
ent_1 = _LoadFile('1efu.1.pdb') # A2 B2, symmetry: C2
@@ -221,6 +239,7 @@ class TestQSscore(unittest.TestCase):
qs_scorer_tst = QSscorer(qs_scorer.qs_ent_1, ent_2_almost_no_ca)
qs_scorer_tst.global_score
+
def test_HeteroModel(self):
# uncomplete model missing 2 third of the contacts
ent_1 = _LoadFile('1eud_ref.pdb') # AB, no symmetry
@@ -251,6 +270,13 @@ class TestQSscore(unittest.TestCase):
self.assertAlmostEqual(qs_scorer.global_score, 1/6., 2)
# without penalties the interface is the same
self.assertAlmostEqual(qs_scorer.best_score, 1.0, 2)
+ # check properties
+ self.assertFalse(qs_scorer.calpha_only)
+ self.assertEqual(qs_scorer.chem_mapping,
+ {('A', 'B', 'C', 'D', 'E', 'F'): ('A', 'B')})
+ self.assertEqual(sorted(qs_scorer.symm_1), [('A', 'B', 'C', 'D', 'E', 'F')])
+ self.assertEqual(sorted(qs_scorer.symm_2), [('B', 'A')])
+ self.assertEqual(qs_scorer.chain_mapping, {'A': 'A', 'B': 'B'})
self._CheckScorer(qs_scorer)
# using user symmetry groups
symm_1 = [('A', 'B'), ('C', 'D'), ('E', 'F')]
@@ -260,8 +286,47 @@ class TestQSscore(unittest.TestCase):
qs_scorer_symm.SetSymmetries(symm_1, symm_2)
self.assertEqual(qs_scorer_symm.global_score, qs_scorer.global_score)
self.assertEqual(qs_scorer_symm.best_score, qs_scorer.best_score)
+ # check properties
+ self.assertFalse(qs_scorer_symm.calpha_only)
+ self.assertEqual(qs_scorer_symm.chem_mapping, qs_scorer.chem_mapping)
+ self.assertEqual(qs_scorer_symm.symm_1, symm_1)
+ self.assertEqual(qs_scorer_symm.symm_2, symm_2)
+ self.assertEqual(qs_scorer_symm.chain_mapping, qs_scorer.chain_mapping)
self._CheckScorer(qs_scorer_symm)
+ # try to put invalid symmetries
+ qs_scorer_symm = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
+ triv_1 = [tuple(ch.name for ch in qs_scorer_symm.ent_to_cm_1.chains)]
+ triv_2 = [tuple(ch.name for ch in qs_scorer_symm.ent_to_cm_2.chains)]
+ qs_scorer_symm.SetSymmetries([], [])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ qs_scorer_symm.SetSymmetries([('A', 'B', 'C'), ('D', 'E', 'F')],
+ [('A', 'B')])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ qs_scorer_symm.SetSymmetries([('A', 'B'), ('C', 'D'), ('E', 'F')],
+ [('A', 'C')])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ qs_scorer_symm.SetSymmetries([('A', 'B'), ('C', 'D')],
+ [('A', 'B')])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ qs_scorer_symm.SetSymmetries([('A', 'B'), ('C', 'D'), ('A', 'B')],
+ [('A', 'B')])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ qs_scorer_symm.SetSymmetries([('A', 'B'), ('C', 'D', 'E', 'F')],
+ [('A', 'B')])
+ self.assertEqual(qs_scorer_symm.symm_1, triv_1)
+ self.assertEqual(qs_scorer_symm.symm_2, triv_2)
+ # check cleaning of extra chains
+ qs_scorer_symm.SetSymmetries([('A','B'), ('C','D'), ('E','F'), ('G','H')],
+ [('A', 'B', 'C')])
+ self.assertEqual(qs_scorer_symm.symm_1, [('A','B'), ('C','D'), ('E','F')])
+ self.assertEqual(qs_scorer_symm.symm_2, [('A', 'B')])
+
# TEST EXTRA SCORES
@@ -273,14 +338,14 @@ class TestQSscore(unittest.TestCase):
self.assertAlmostEqual(qs_scorer.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer.best_score, 1.00, 2)
self.assertAlmostEqual(qs_scorer.lddt_score, 1.00, 2)
- self._CheckScorer(qs_scorer)
+ self._CheckScorerLDDT(qs_scorer)
# flip them (use QSscoreEntity to go faster)
qs_scorer2 = QSscorer(qs_scorer.qs_ent_2, qs_scorer.qs_ent_1)
self.assertAlmostEqual(qs_scorer2.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer2.best_score, 1.00, 2)
self.assertAlmostEqual(qs_scorer2.lddt_score, 0.483, 2)
- self._CheckScorer(qs_scorer)
-
+ self._CheckScorerLDDT(qs_scorer)
+
# TEST BIG STUFF and FANCY SYMMETRIES
@@ -444,6 +509,33 @@ class TestQSscore(unittest.TestCase):
self.assertLessEqual(qs_scorer.global_score, 1.0)
+ def _CheckScorerLDDT(self, qs_scorer):
+ # check if we live up to our promises (assume: we did global and lddt score)
+ self._CheckScorer(qs_scorer)
+ # check lddt_mdl and lddt_ref
+ self.assertEqual(qs_scorer.lddt_mdl.chain_count, 1)
+ self.assertEqual(qs_scorer.lddt_ref.chain_count, 1)
+ # unique resnum?
+ resnum_mdl = [r.number.num for r in qs_scorer.lddt_mdl.residues]
+ resnum_mdl_set = set(resnum_mdl)
+ self.assertEqual(len(resnum_mdl), len(resnum_mdl_set))
+ resnum_ref = [r.number.num for r in qs_scorer.lddt_ref.residues]
+ resnum_ref_set = set(resnum_ref)
+ self.assertEqual(len(resnum_ref), len(resnum_ref_set))
+ # independent shared residues count from mapped_residues
+ num_shared = sum(len(v) for _,v in qs_scorer.mapped_residues.iteritems())
+ shared_set = resnum_ref_set.intersection(resnum_mdl_set)
+ self.assertEqual(len(shared_set), num_shared)
+ # "lddt" prop on residues and B-factors?
+ for r in qs_scorer.lddt_mdl.residues:
+ if r.number.num in shared_set:
+ self.assertTrue(r.HasProp('lddt'))
+ r_lddt = r.GetFloatProp('lddt')
+ else:
+ r_lddt = 0
+ self.assertTrue(all([a.b_factor == r_lddt for a in r.atoms]))
+
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():