Allow branched entities with same "sequence"

It is quite possible that a system may contain
multiple branched entities with the same "sequence"
but different connectivity, so relax our "entities
cannot have the same sequence" check for branched
entities. To be strictly correct, we should check
for branched entities that have both the same
sequence *and* the same connectivity, but that is not
handled here. Closes #126.

ihm/__init__.py

@@ -1330,12 +1330,21 @@ def residue(self, seq_id):
         """Get a :class:`Residue` at the given sequence position"""
         return Residue(entity=self, seq_id=seq_id)
 
-    # Entities are considered identical if they have the same sequence
+    # Entities are considered identical if they have the same sequence,
+    # unless they are branched
     def __eq__(self, other):
-        return isinstance(other, Entity) and self.sequence == other.sequence
+        if not isinstance(other, Entity):
+            return False
+        if self.is_branched() or other.is_branched():
+            return self is other
+        else:
+            return self.sequence == other.sequence
 
     def __hash__(self):
-        return hash(self.sequence)
+        if self.is_branched():
+            return hash(id(self))
+        else:
+            return hash(self.sequence)
 
     def __call__(self, seq_id_begin, seq_id_end):
         return EntityRange(self, seq_id_begin, seq_id_end)

test/test_dumper.py

@@ -414,13 +414,37 @@ def test_entity_dumper(self):
 """)
 
     def test_entity_duplicates(self):
-        """Test EntityDumper with duplicate entities"""
+        """Test EntityDumper with duplicate non-branched entities"""
         system = ihm.System()
         system.entities.append(ihm.Entity('AHC'))
         system.entities.append(ihm.Entity('AHC'))
         dumper = ihm.dumper._EntityDumper()
         self.assertRaises(ValueError, dumper.finalize, system)
 
+    def test_entity_duplicate_branched(self):
+        """Test EntityDumper with duplicate branched entities"""
+        system = ihm.System()
+        sacc = ihm.SaccharideChemComp('NAG')
+        system.entities.append(ihm.Entity([sacc]))
+        system.entities.append(ihm.Entity([sacc]))
+        dumper = ihm.dumper._EntityDumper()
+        dumper.finalize(system)  # Assign IDs
+        out = _get_dumper_output(dumper, system)
+        # Duplicate "sequences" are OK for branched entities
+        self.assertEqual(out, """#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.details
+1 branched man . . 0 .
+2 branched man . . 0 .
+#
+""")
+
     def test_entity_src_nat_dumper(self):
         """Test EntitySrcNatDumper"""
         system = ihm.System()

test/test_main.py

@@ -214,7 +214,7 @@ def test_chem_descriptor(self):
     def test_entity(self):
         """Test Entity class"""
         e1 = ihm.Entity('AHCD', description='foo')
-        # Should compare identical if sequences are the same
+        # Should compare identical if sequences are the same, if not branched
         e2 = ihm.Entity('AHCD', description='bar')
         e3 = ihm.Entity('AHCDE', description='foo')
         heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
@@ -223,6 +223,10 @@ def test_entity(self):
         self.assertNotEqual(e1, e3)
         self.assertEqual(e1.seq_id_range, (1, 4))
         self.assertEqual(e3.seq_id_range, (1, 5))
+        sugar2 = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        # Branched entities never compare equal unless they are the same object
+        self.assertEqual(sugar, sugar)
+        self.assertNotEqual(sugar, sugar2)
         # seq_id does not exist for nonpolymers
         self.assertEqual(heme.seq_id_range, (None, None))
         # We do have an internal seq_id_range for branched entities