diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index d5dcf651c7a7bc90a3079cbdc416b143a6e1364b..c7cb807bcca47a281aaa0b9e46b3a41724a6dcf9 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/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()
diff --git a/modules/io/tests/testfiles/mmcif/2ast.cif.gz b/modules/io/tests/testfiles/mmcif/2ast.cif.gz
deleted file mode 100644
index 5ed06c4312b953772f95a5f1fbdaaa3da5e98366..0000000000000000000000000000000000000000
Binary files a/modules/io/tests/testfiles/mmcif/2ast.cif.gz and /dev/null differ