Preserve unknown auth_seq_num in poly_seq_scheme

If the poly_seq_scheme table maps a given seq_id
to an auth_seq_num of ? then preserve that mapping
on output, so we don't lose any information on
not-modeled residues in that table.

ihm/dumper.py

@@ -744,6 +744,10 @@ def dump(self, system, writer):
                             # See, e.g., https://files.rcsb.org/view/8QB4.cif
                             auth_comp_id = ihm.unknown
                             auth_seq_num = ihm.unknown
+                        elif auth_seq_num is ihm.unknown:
+                            # If we don't know the seq num, we can't know
+                            # the component ID either
+                            auth_comp_id = ihm.unknown
                         lp.write(asym_id=asym._id,
                                  pdb_strand_id=asym.strand_id,
                                  entity_id=entity._id, seq_id=num,

src/ihm_format.i

@@ -437,7 +437,7 @@ static void handle_poly_seq_scheme_data(struct ihm_reader *reader,
                                         void *data, struct ihm_error **err)
 {
   int i, seq_id, pdb_seq_num, auth_seq_num;
-  char *seq_id_endptr, *pdb_seq_num_endptr;
+  char *seq_id_endptr, *pdb_seq_num_endptr, *auth_seq_num_endptr;
   struct category_handler_data *hd = data;
   struct ihm_keyword **keys;
 
@@ -451,9 +451,11 @@ static void handle_poly_seq_scheme_data(struct ihm_reader *reader,
     return;
   }
 
-  for (i = 0, keys = hd->keywords; i < 3; ++i, ++keys) {
-    /* Do nothing if any of asym_id, seq_id, or pdb_seq_num are missing */
+  for (i = 0, keys = hd->keywords; i < 4; ++i, ++keys) {
+    /* Call Python handler if any of asym_id, seq_id, pdb_seq_num,
+       or auth_seq_num are missing */
     if (!(*keys)->in_file || (*keys)->omitted || (*keys)->unknown) {
+      handle_category_data(reader, data, err);
       return;
     }
   }
@@ -464,15 +466,9 @@ static void handle_poly_seq_scheme_data(struct ihm_reader *reader,
      nothing needs to be done */
   seq_id = strtol(hd->keywords[1]->data, &seq_id_endptr, 10);
   pdb_seq_num = strtol(hd->keywords[2]->data, &pdb_seq_num_endptr, 10);
-  if (!hd->keywords[3]->in_file || hd->keywords[3]->omitted
-      || hd->keywords[3]->unknown) {
-    /* If auth_seq_num is missing, assume identical to pdb_seq_num */
-    auth_seq_num = pdb_seq_num;
-  } else {
-    auth_seq_num = strtol(hd->keywords[3]->data, &pdb_seq_num_endptr, 10);
-  }
-  if (!*seq_id_endptr && !*pdb_seq_num_endptr && seq_id == pdb_seq_num
-      && seq_id == auth_seq_num
+  auth_seq_num = strtol(hd->keywords[3]->data, &auth_seq_num_endptr, 10);
+  if (!*seq_id_endptr && !*pdb_seq_num_endptr && !*auth_seq_num_endptr
+      && seq_id == pdb_seq_num && seq_id == auth_seq_num
       && (!hd->keywords[4]->in_file || hd->keywords[4]->omitted
           || hd->keywords[4]->unknown)) {
     return;

test/test_dumper.py

@@ -980,6 +980,40 @@ def test_poly_seq_scheme_dumper(self):
 D 4 1 DA 1 1 DA DA X A
 D 4 2 DC 1 1 DC DC X B
 #
+""")
+
+    def test_poly_seq_scheme_unknown_auth_seq(self):
+        """Test PolySeqSchemeDumper with explicit unknown auth_seq_num"""
+        system = ihm.System()
+        e1 = ihm.Entity('ACGT')
+        system.entities.append(e1)
+        a1 = ihm.AsymUnit(e1, 'foo',
+                          orig_auth_seq_id_map={1: 3, 2: 4,
+                                                3: ihm.unknown, 4: 6})
+        system.asym_units.append(a1)
+        ihm.dumper._EntityDumper().finalize(system)
+        ihm.dumper._StructAsymDumper().finalize(system)
+        dumper = ihm.dumper._PolySeqSchemeDumper()
+        out = _get_dumper_output(dumper, system)
+        # If auth_seq_num is ?, so should pdb_mon_id and auth_mon_id;
+        # see, e.g. PDB ID 8qb4
+        self.assertEqual(out, """#
+loop_
+_pdbx_poly_seq_scheme.asym_id
+_pdbx_poly_seq_scheme.entity_id
+_pdbx_poly_seq_scheme.seq_id
+_pdbx_poly_seq_scheme.mon_id
+_pdbx_poly_seq_scheme.pdb_seq_num
+_pdbx_poly_seq_scheme.auth_seq_num
+_pdbx_poly_seq_scheme.pdb_mon_id
+_pdbx_poly_seq_scheme.auth_mon_id
+_pdbx_poly_seq_scheme.pdb_strand_id
+_pdbx_poly_seq_scheme.pdb_ins_code
+A 1 1 ALA 1 3 ALA ALA A .
+A 1 2 CYS 2 4 CYS CYS A .
+A 1 3 GLY 3 ? ? ? A .
+A 1 4 THR 4 6 THR THR A .
+#
 """)
 
     def test_poly_seq_scheme_dumper_not_modeled(self):

test/test_reader.py

@@ -2832,6 +2832,26 @@ def test_poly_seq_scheme_handler_incon_off(self):
         self.assertIsNone(asym.residue(1).ins_code)
         self.assertIsNone(asym.orig_auth_seq_id_map)
 
+    def test_poly_seq_scheme_handler_unknown_auth_seq(self):
+        """Test PolySeqSchemeHandler with explicit unknown auth_seq_num"""
+        fh = StringIO(ASYM_ENTITY + """
+loop_
+_pdbx_poly_seq_scheme.asym_id
+_pdbx_poly_seq_scheme.entity_id
+_pdbx_poly_seq_scheme.seq_id
+_pdbx_poly_seq_scheme.pdb_seq_num
+_pdbx_poly_seq_scheme.auth_seq_num
+_pdbx_poly_seq_scheme.pdb_strand_id
+A 1 1 1 1 A
+A 1 2 2 2 A
+A 1 3 3 ? A
+A 1 4 4 4 A
+""")
+        s, = ihm.reader.read(fh)
+        asym, = s.asym_units
+        self.assertEqual(asym.auth_seq_id_map, 0)
+        self.assertEqual(asym.orig_auth_seq_id_map, {3: ihm.unknown})
+
     def test_poly_seq_scheme_handler_str_seq_id(self):
         """Test PolySeqSchemeHandler with a non-integer pdb_seq_num"""
         fh = StringIO(ASYM_ENTITY + """