simplify tests

modules/io/tests/test_io_mmcif.py

@@ -141,14 +141,14 @@ class TestMMCifInfo(unittest.TestCase):
                                      seqres=True,
                                      info=True)
     pdb_ent = info.GetBioUnits()[0].PDBize(ent)
-    pdb_seqres_ent = info.GetBioUnits()[0].PDBize(ent, seqres)
     chains = pdb_ent.chains
-    self.assertEquals([c.name for c in chains], 
-                      ['A', '_', '-', 'B', 'C', 'D'])
+    self.assertEquals(''.join([c.name for c in chains]), 
+                      'A_-BCD')
     ligand_chain = chains[1]
     ligand_residues = ligand_chain.residues
     self.assertEquals([r.number for r in ligand_residues],
                       [mol.ResNum(1), mol.ResNum(2), mol.ResNum(3), mol.ResNum(4)])
+
   def test_mmcifinfo_biounit_pdbize(self):
     ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
                                      seqres=True,
@@ -156,60 +156,16 @@ class TestMMCifInfo(unittest.TestCase):
     pdb_ent = info.GetBioUnits()[0].PDBize(ent)
     pdb_seqres_ent = info.GetBioUnits()[0].PDBize(ent, seqres)
 
-    # chains
-    self.assertEquals(str(pdb_ent.GetChainList()[0]), 'A')
-    self.assertEquals(str(pdb_ent.GetChainList()[1]), 'B')
-    self.assertEquals(str(pdb_ent.GetChainList()[2]), '_')
-    self.assertEquals(str(pdb_ent.GetChainList()[3]), '-')
-    self.assertEquals(str(pdb_ent.GetChainList()[4]), 'C')
-    self.assertEquals(str(pdb_ent.GetChainList()[5]), 'D')
-    self.assertEquals(str(pdb_ent.GetChainList()[6]), 'E')
-    self.assertEquals(str(pdb_ent.GetChainList()[7]), 'F')
-    self.assertEquals(str(pdb_ent.GetChainList()[8]), 'G')
-    self.assertEquals(str(pdb_ent.GetChainList()[9]), 'H')
-    # size of chains
-    self.assertEquals(len(pdb_ent.GetChainList()[0].GetResidueList()),  415)
-    self.assertEquals(len(pdb_ent.GetChainList()[1].GetResidueList()),  414)
-    self.assertEquals(len(pdb_ent.GetChainList()[2].GetResidueList()),   64)
-    self.assertEquals(len(pdb_ent.GetChainList()[3].GetResidueList()), 3816)
-    self.assertEquals(len(pdb_ent.GetChainList()[4].GetResidueList()),  415)
-    self.assertEquals(len(pdb_ent.GetChainList()[5].GetResidueList()),  414)
-    self.assertEquals(len(pdb_ent.GetChainList()[6].GetResidueList()),  415)
-    self.assertEquals(len(pdb_ent.GetChainList()[7].GetResidueList()),  414)
-    self.assertEquals(len(pdb_ent.GetChainList()[8].GetResidueList()),  415)
-    self.assertEquals(len(pdb_ent.GetChainList()[9].GetResidueList()),  414)
-
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[0]), 'A')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[1]), 'B')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[2]), '_')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[3]), '-')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[4]), 'C')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[5]), 'D')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[6]), 'E')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[7]), 'F')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[8]), 'G')
-    self.assertEquals(str(pdb_seqres_ent.GetChainList()[9]), 'H')
+    self.assertEquals(''.join([c.name for c in pdb_ent.chains]),
+                      'AB_-CDEFGH')
+                      
+    self.assertEquals([c.residue_count for c in pdb_ent.chains],
+                      [415, 414, 64, 3816, 415,414,415,414,415,414])
 
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[0].GetResidueList()),
-                      415)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[1].GetResidueList()),
-                      414)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[2].GetResidueList()),
-                      64)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[3].GetResidueList()),
-                      3816)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[4].GetResidueList()),
-                      415)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[5].GetResidueList()),
-                      414)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[6].GetResidueList()),
-                      415)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[7].GetResidueList()),
-                      414)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[8].GetResidueList()),
-                      415)
-    self.assertEquals(len(pdb_seqres_ent.GetChainList()[9].GetResidueList()),
-                      414)
+    self.assertEquals(''.join([c.name for c in pdb_seqres_ent.chains]),
+                      'AB_-CDEFGH')
+    self.assertEquals([c.residue_count for c in pdb_seqres_ent.chains],
+                      [415, 414, 64, 3816, 415,414,415,414,415,414])
 
   def test_mmcifinfo_biounit_pdbize_transformation(self):
     ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3hqv.cif.gz",
@@ -226,36 +182,6 @@ class TestMMCifInfo(unittest.TestCase):
                                            0,0,0,1),
                                  epsilon=0.01), True)
 
-  def test_mmcifinfo_biounit_pdbize_multi_transformations(self):
-    # in case we have more than one set of chains & transformations,
-    # ligand/ water chains may mess up
-    ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/2ast.cif.gz",
-                                     seqres=True,
-                                     info=True)
-    pdb_ent = info.GetBioUnits()[2].PDBize(ent, seqres=seqres)
-    # chains
-    self.assertEquals(str(pdb_ent.GetChainList()[0]), 'A')
-    self.assertEquals(str(pdb_ent.GetChainList()[1]), 'B')
-    self.assertEquals(str(pdb_ent.GetChainList()[2]), '_')
-    self.assertEquals(str(pdb_ent.GetChainList()[3]), '-')
-    self.assertEquals(str(pdb_ent.GetChainList()[4]), 'C')
-    self.assertEquals(str(pdb_ent.GetChainList()[5]), 'D')
-    self.assertEquals(str(pdb_ent.GetChainList()[6]), 'E')
-    self.assertEquals(str(pdb_ent.GetChainList()[7]), 'F')
-    self.assertEquals(str(pdb_ent.GetChainList()[8]), 'G')
-    self.assertEquals(str(pdb_ent.GetChainList()[9]), 'H')
-    # size of chains
-    self.assertEquals(len(pdb_ent.GetChainList()[0].GetResidueList()),  142)
-    self.assertEquals(len(pdb_ent.GetChainList()[1].GetResidueList()),  325)
-    self.assertEquals(len(pdb_ent.GetChainList()[2].GetResidueList()),    4)
-    self.assertEquals(len(pdb_ent.GetChainList()[3].GetResidueList()),  530)
-    self.assertEquals(len(pdb_ent.GetChainList()[4].GetResidueList()),  142)
-    self.assertEquals(len(pdb_ent.GetChainList()[5].GetResidueList()),  325)
-    self.assertEquals(len(pdb_ent.GetChainList()[6].GetResidueList()),   69)
-    self.assertEquals(len(pdb_ent.GetChainList()[7].GetResidueList()),   10)
-    self.assertEquals(len(pdb_ent.GetChainList()[8].GetResidueList()),   69)
-    self.assertEquals(len(pdb_ent.GetChainList()[9].GetResidueList()),   10)
-
   def test_mmcifinfo_structdetails(self):
     d = io.MMCifInfoStructDetails()