Fix out-of-range fragments

Fragments should start numbering at 1, not 0.
This is now checked by python-ihm.

test/test_mmcif.py

@@ -1916,10 +1916,10 @@ def get_seq_dif(self):
     def test_beads_fragment(self):
         """Test _BeadsFragment class"""
         system = ihm.System()
-        e = ihm.Entity('A' * 40)
+        e = ihm.Entity('A' * 50)
         asym = ihm.AsymUnit(e)
         m = None
-        bf1 = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=0,
+        bf1 = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=1,
                                            end=10, count=2, hier=None,
                                            asym_unit=asym)
         bf2 = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=11,
@@ -1931,11 +1931,11 @@ def test_beads_fragment(self):
         self.assertFalse(bf1.combine(None))
         self.assertFalse(bf1.combine(bf3))
         self.assertTrue(bf1.combine(bf2))
-        self.assertEqual(bf1.asym_unit.seq_id_range[0], 0)
+        self.assertEqual(bf1.asym_unit.seq_id_range[0], 1)
         self.assertEqual(bf1.asym_unit.seq_id_range[1], 30)
         self.assertEqual(bf1.count, 5)
         self.assertTrue(bf1.combine(bf3))
-        self.assertEqual(bf1.asym_unit.seq_id_range[0], 0)
+        self.assertEqual(bf1.asym_unit.seq_id_range[0], 1)
         self.assertEqual(bf1.asym_unit.seq_id_range[1], 50)
         self.assertEqual(bf1.count, 9)
 
@@ -1949,14 +1949,14 @@ def test_model_repr_dump_add_frag(self):
         state2 = 'state2'
         rep1 = ihm.representation.Representation()
         d = IMP.pmi1.mmcif._AllModelRepresentations(EmptyObject())
-        b = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=0,
+        b = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=1,
                                          end=10, count=2, hier=None,
                                          asym_unit=asym)
         d.add_fragment(state1, rep1, b)
         self.assertEqual(len(d.fragments[id(rep1)]['comp1']), 1)
         self.assertEqual(len(d.fragments[id(rep1)]['comp1'][state1]), 1)
         frag = d.fragments[id(rep1)]['comp1'][state1][0]
-        self.assertEqual(frag.asym_unit.seq_id_range[0], 0)
+        self.assertEqual(frag.asym_unit.seq_id_range[0], 1)
         self.assertEqual(frag.asym_unit.seq_id_range[1], 10)
 
         b = IMP.pmi1.mmcif._BeadsFragment(m, 'comp1', start=11,
@@ -1966,7 +1966,7 @@ def test_model_repr_dump_add_frag(self):
         self.assertEqual(len(d.fragments[id(rep1)]['comp1']), 1)
         self.assertEqual(len(d.fragments[id(rep1)]['comp1'][state1]), 1)
         frag = d.fragments[id(rep1)]['comp1'][state1][0]
-        self.assertEqual(frag.asym_unit.seq_id_range[0], 0)
+        self.assertEqual(frag.asym_unit.seq_id_range[0], 1)
         self.assertEqual(frag.asym_unit.seq_id_range[1], 30)
 
         d.add_fragment(state2, rep1, b)