Add ins code to output pdbx_branch_scheme table

ihmwg · Feb 10, 2024 · 34aba4a · 34aba4a
1 parent 4a01eba
commit 34aba4a
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 9 deletions.
diff --git a/ihm/dumper.py b/ihm/dumper.py
@@ -745,7 +745,7 @@ class _BranchSchemeDumper(Dumper):
     def dump(self, system, writer):
         with writer.loop("_pdbx_branch_scheme",
                          ["asym_id", "entity_id", "mon_id", "num",
-                          "pdb_seq_num", "auth_seq_num",
+                          "pdb_seq_num", "pdb_ins_code", "auth_seq_num",
                           "auth_mon_id", "pdb_mon_id", "pdb_asym_id"]) as lp:
             for asym in system.asym_units:
                 entity = asym.entity
@@ -758,7 +758,7 @@ def dump(self, system, writer):
                     lp.write(asym_id=asym._id, pdb_asym_id=asym.strand_id,
                              entity_id=entity._id,
                              num=num + 1,
-                             pdb_seq_num=pdb_seq_num,
+                             pdb_seq_num=pdb_seq_num, pdb_ins_code=ins,
                              auth_seq_num=auth_seq_num,
                              mon_id=comp.id, auth_mon_id=comp.id,
                              pdb_mon_id=comp.id)

diff --git a/test/test_dumper.py b/test/test_dumper.py
@@ -5112,12 +5112,17 @@ def test_branch_scheme_dumper(self):
                          ihm.SaccharideChemComp('FUC')])
         e2 = ihm.Entity([ihm.SaccharideChemComp('FUC'),
                          ihm.SaccharideChemComp('BGC')])
+        e3 = ihm.Entity([ihm.SaccharideChemComp('NAG'),
+                         ihm.SaccharideChemComp('BGC')])
         # Non-branched entity
-        e3 = ihm.Entity('ACT')
-        system.entities.extend((e1, e2, e3))
+        e4 = ihm.Entity('ACT')
+        system.entities.extend((e1, e2, e3, e4))
         system.asym_units.append(ihm.AsymUnit(e1, 'foo'))
         system.asym_units.append(ihm.AsymUnit(e2, 'bar', auth_seq_id_map=5))
-        system.asym_units.append(ihm.AsymUnit(e3, 'baz'))
+        system.asym_units.append(ihm.AsymUnit(
+            e3, 'bar', auth_seq_id_map={1: 6, 2: (7, 'A')},
+            orig_auth_seq_id_map={1: 100}))
+        system.asym_units.append(ihm.AsymUnit(e4, 'baz'))
         ihm.dumper._EntityDumper().finalize(system)
         ihm.dumper._StructAsymDumper().finalize(system)
         dumper = ihm.dumper._BranchSchemeDumper()
@@ -5129,14 +5134,17 @@ def test_branch_scheme_dumper(self):
 _pdbx_branch_scheme.mon_id
 _pdbx_branch_scheme.num
 _pdbx_branch_scheme.pdb_seq_num
+_pdbx_branch_scheme.pdb_ins_code
 _pdbx_branch_scheme.auth_seq_num
 _pdbx_branch_scheme.auth_mon_id
 _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
+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
+C 3 NAG 1 6 . 100 NAG NAG C
+C 3 BGC 2 7 A 7 BGC BGC C
 #
 """)