add basic OMF unit tests

modules/io/tests/CMakeLists.txt

 set(OST_IO_UNIT_TESTS
   test_io_pdb.py
   test_io_mmcif.py
+  test_io_omf.py
   test_clustal.cc
   test_io_pdb.cc
   test_io_crd.cc

modules/io/tests/test_io_omf.py

+import unittest
+from ost import geom
+from ost import io
+
+def compare_atoms(a1, a2):
+    if abs(a1.occupancy - a2.occupancy) > 0.01:
+        return False
+    if abs(a1.b_factor - a2.b_factor) > 0.01:
+        return False
+    if geom.Distance(a1.GetPos(), a2.GetPos()) > 0.001:
+        return False
+    if a1.is_hetatom != a2.is_hetatom:
+        return False
+    if a1.element != a2.element:
+        return False
+    return True
+
+def compare_residues(r1, r2):
+    if r1.GetName() != r2.GetName():
+        return False
+    if r1.GetNumber() != r2.GetNumber():
+        return False
+    if str(r1.GetSecStructure()) != str(r2.GetSecStructure()):
+        return False
+    if r1.one_letter_code != r2.one_letter_code:
+        return False
+    if r1.chem_type != r2.chem_type:
+        return False
+    if r1.chem_class != r2.chem_class:
+        return False
+    anames1 = [a.GetName() for a in r1.atoms]
+    anames2 = [a.GetName() for a in r2.atoms]
+    if sorted(anames1) != sorted(anames2):
+        return False
+    anames = anames1
+    for aname in anames:
+        a1 = r1.FindAtom(aname)
+        a2 = r2.FindAtom(aname)
+        if not compare_atoms(a1, a2):
+            return False
+    return True
+
+def compare_chains(ch1, ch2):
+    if len(ch1.residues) != len(ch2.residues):
+        return False
+    for r1, r2 in zip(ch1.residues, ch2.residues):
+        if not compare_residues(r1, r2):
+            return False
+    return True
+
+def compare_bonds(ent1, ent2):
+    bonds1 = list()
+    for b in ent1.bonds:
+        bond_partners = [str(b.first), str(b.second)]
+        bonds1.append([min(bond_partners), max(bond_partners), b.bond_order])
+    bonds2 = list()
+    for b in ent2.bonds:
+        bond_partners = [str(b.first), str(b.second)]
+        bonds2.append([min(bond_partners), max(bond_partners), b.bond_order])
+    return sorted(bonds1) == sorted(bonds2)
+
+def compare_ent(ent1, ent2):
+    chain_names_one = [ch.GetName() for ch in ent1.chains]
+    chain_names_two = [ch.GetName() for ch in ent2.chains]
+    if not sorted(chain_names_one) == sorted(chain_names_two):
+        return False
+    chain_names = chain_names_one
+    for chain_name in chain_names:
+        ch1 = ent1.FindChain(chain_name)
+        ch2 = ent2.FindChain(chain_name)
+        if not compare_chains(ch1, ch2):
+            return False
+    if not compare_bonds(ent1, ent2):
+        return False
+    return True
+
+class TestOMF(unittest.TestCase):
+    def test_AU(self):
+        ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz", 
+                                         seqres=True,
+                                         info=True)
+        omf = io.OMF.FromMMCIF(ent, info)
+        omf_bytes = omf.ToBytes()
+        loaded_omf = io.OMF.FromBytes(omf_bytes)
+        loaded_ent = loaded_omf.GetAU()
+        self.assertTrue(compare_ent(ent, loaded_ent))
+
+if __name__== '__main__':
+  from ost import testutils
+  testutils.RunTests()