Classify single sugar as a nonpolymer, not branched

ihm/__init__.py

@@ -1402,7 +1402,7 @@ def is_polymeric(self):
     def is_branched(self):
         """Return True iff this entity is branched (generally
            an oligosaccharide)"""
-        return ((len(self.sequence) > 0
+        return ((len(self.sequence) > 1
                  and isinstance(self.sequence[0], SaccharideChemComp)) or
                 (len(self.sequence) == 0 and self._hint_branched))
 

test/test_dumper.py

@@ -426,9 +426,10 @@ def test_entity_duplicates(self):
     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]))
+        sacc1 = ihm.SaccharideChemComp('NAG')
+        sacc2 = ihm.SaccharideChemComp('FUC')
+        system.entities.append(ihm.Entity([sacc1, sacc2]))
+        system.entities.append(ihm.Entity([sacc1, sacc2]))
         dumper = ihm.dumper._EntityDumper()
         dumper.finalize(system)  # Assign IDs
         out = _get_dumper_output(dumper, system)
@@ -863,7 +864,8 @@ def test_entity_nonpoly_dumper(self):
         e2 = ihm.Entity([ihm.NonPolymerChemComp('HEM')], description='heme')
         e3 = ihm.Entity([ihm.WaterChemComp()])
         # Branched entity
-        e4 = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        e4 = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                         ihm.SaccharideChemComp('FUC')])
         system.entities.extend((e1, e2, e3, e4))
 
         ed = ihm.dumper._EntityDumper()
@@ -5064,7 +5066,8 @@ def test_entity_branch_list_dumper(self):
         """Test EntityBranchListDumper"""
         system = ihm.System()
         system.entities.append(ihm.Entity(
-            [ihm.SaccharideChemComp('NAG')]))
+            [ihm.SaccharideChemComp('NAG'),
+             ihm.SaccharideChemComp('FUC')]))
         # Non-branched entity
         system.entities.append(ihm.Entity('ACGT'))
         ed = ihm.dumper._EntityDumper()
@@ -5078,14 +5081,16 @@ def test_entity_branch_list_dumper(self):
 _pdbx_entity_branch_list.comp_id
 _pdbx_entity_branch_list.hetero
 1 1 NAG .
+1 2 FUC .
 #
 """)
 
     def test_entity_branch_dumper(self):
         """Test EntityBranchDumper"""
         system = ihm.System()
         system.entities.append(ihm.Entity(
-            [ihm.SaccharideChemComp('NAG')]))
+            [ihm.SaccharideChemComp('NAG'),
+             ihm.SaccharideChemComp('FUC')]))
         # Non-branched entity
         system.entities.append(ihm.Entity('ACGT'))
         ed = ihm.dumper._EntityDumper()
@@ -5103,8 +5108,10 @@ def test_entity_branch_dumper(self):
     def test_branch_scheme_dumper(self):
         """Test BranchSchemeDumper"""
         system = ihm.System()
-        e1 = ihm.Entity([ihm.SaccharideChemComp('NAG')])
-        e2 = ihm.Entity([ihm.SaccharideChemComp('FUC')])
+        e1 = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                         ihm.SaccharideChemComp('FUC')])
+        e2 = ihm.Entity([ihm.SaccharideChemComp('FUC'),
+                         ihm.SaccharideChemComp('BGC')])
         # Non-branched entity
         e3 = ihm.Entity('ACT')
         system.entities.extend((e1, e2, e3))
@@ -5127,7 +5134,9 @@ def test_branch_scheme_dumper(self):
 _pdbx_branch_scheme.pdb_mon_id
 _pdbx_branch_scheme.pdb_asym_id
 A 1 NAG 1 1 1 NAG NAG A
+A 1 FUC 2 2 2 FUC FUC A
 B 2 FUC 1 6 6 FUC FUC B
+B 2 BGC 2 7 7 BGC BGC B
 #
 """)
 

test/test_main.py

@@ -219,19 +219,21 @@ def test_entity(self):
         e2 = ihm.Entity('AHCD', description='bar')
         e3 = ihm.Entity('AHCDE', description='foo')
         heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
-        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                            ihm.SaccharideChemComp('FUC')])
         self.assertEqual(e1, e2)
         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')])
+        sugar2 = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                             ihm.SaccharideChemComp('FUC')])
         # 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
-        self.assertEqual(sugar.seq_id_range, (1, 1))
+        self.assertEqual(sugar.seq_id_range, (1, 2))
 
     def test_entity_weight(self):
         """Test Entity.formula_weight"""
@@ -246,7 +248,8 @@ def test_entity_type(self):
         protein = ihm.Entity('AHCD')
         heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
         water = ihm.Entity([ihm.WaterChemComp()])
-        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                            ihm.SaccharideChemComp('FUC')])
         self.assertEqual(protein.type, 'polymer')
         self.assertTrue(protein.is_polymeric())
         self.assertFalse(protein.is_branched())
@@ -260,6 +263,12 @@ def test_entity_type(self):
         self.assertFalse(sugar.is_polymeric())
         self.assertTrue(sugar.is_branched())
 
+        # A single sugar should be classified non-polymer
+        single_sugar = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        self.assertEqual(single_sugar.type, 'non-polymer')
+        self.assertFalse(single_sugar.is_polymeric())
+        self.assertFalse(single_sugar.is_branched())
+
         # A single amino acid should be classified non-polymer
         single_aa = ihm.Entity('A')
         self.assertEqual(single_aa.type, 'non-polymer')
@@ -475,7 +484,8 @@ def test_asym_range(self):
         """Test AsymUnitRange class"""
         e = ihm.Entity('AHCDAH')
         heme = ihm.Entity([ihm.NonPolymerChemComp('HEM')])
-        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG')])
+        sugar = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                            ihm.SaccharideChemComp('FUC')])
         a = ihm.AsymUnit(e, "testdetail")
         aheme = ihm.AsymUnit(heme)
         asugar = ihm.AsymUnit(sugar)
@@ -484,7 +494,7 @@ def test_asym_range(self):
         # seq_id is not defined for nonpolymers
         self.assertEqual(aheme.seq_id_range, (None, None))
         # We use seq_id internally for branched entities
-        self.assertEqual(asugar.seq_id_range, (1, 1))
+        self.assertEqual(asugar.seq_id_range, (1, 2))
         r = a(3, 4)
         self.assertEqual(r.seq_id_range, (3, 4))
         self.assertEqual(r._id, 42)