Set sequence offset on mmCIF file read

When reading an mmCIF file, set each chain's
sequence offset using the internal and author
provided numbering of its first residue (rather
than leaving it as zero). This gives us a better
chance of having the correct seq_id in any future
output mmCIF file.

modules/atom/src/mmcif.cpp

@@ -133,8 +133,9 @@ class AtomSiteCategory : public Category {
     return true;
   }
 
-  void get_chain_particle(const std::string &chain,
+  bool get_chain_particle(const std::string &chain,
                           const std::string &label_asym_id) {
+    bool new_chain = false;
     if (cp_ == nullptr || chain != curr_chain_) {
       curr_chain_ = chain;
       std::pair<Particle *, std::string> root_chain(root_p_, chain);
@@ -144,11 +145,13 @@ class AtomSiteCategory : public Category {
         Chain(cp_).set_label_asym_id(label_asym_id);
         Hierarchy(root_p_).add_child(Chain(cp_));
         chain_map_[root_chain] = cp_;
+        new_chain = true;
       } else {
         cp_ = chain_map_[root_chain];
       }
       rp_ = nullptr; // make sure we get a new residue
     }
+    return new_chain;
   }
 
   // Replace at most maxlen chars in dest, starting at pos, with repl
@@ -178,10 +181,11 @@ class AtomSiteCategory : public Category {
 
     // Use author-provided chain ID if available
     std::string label_asym_id = chain_.as_str();
+    bool new_chain;
     if (strlen(auth_chain_.as_str()) > 0) {
-      get_chain_particle(auth_chain_.as_str(), label_asym_id);
+      new_chain = get_chain_particle(auth_chain_.as_str(), label_asym_id);
     } else {
-      get_chain_particle(label_asym_id, label_asym_id);
+      new_chain = get_chain_particle(label_asym_id, label_asym_id);
     }
     std::string auth_seq_id_str = auth_seq_id_.as_str();
     // Check if new residue
@@ -200,6 +204,12 @@ class AtomSiteCategory : public Category {
       // if auth_seq_id is blank, use seq_id instead
       if (endptr == start) auth_seq_id = seq_id;
       char one_icode = 32; // default insertion code (space)
+
+      // Set the chain's sequence offset based on the first residue numbering
+      if (new_chain) {
+        Chain(cp_).set_sequence_offset(auth_seq_id - seq_id);
+      }
+
       // if auth_seq_id is not blank and contains something after the number,
       // use the first character of that as the insertion code
       if (endptr != start && *endptr) {

modules/atom/test/test_mmcif.py

@@ -415,6 +415,16 @@ def test_chain_selector_multi_char(self):
                   for x in IMP.atom.get_by_type(mp, IMP.atom.CHAIN_TYPE)]
         self.assertEqual([c.get_id() for c in chains], ['ZB'])
 
+    def test_chain_read_offset(self):
+        """Check reading of chain sequence offset from an mmCIF file"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('chaintest.cif'), m,
+                                 IMP.atom.ChainPDBSelector(["ZK"]))
+        chains = [IMP.atom.Chain(x)
+                  for x in IMP.atom.get_by_type(mp, IMP.atom.CHAIN_TYPE)]
+        self.assertEqual(chains[0].get_sequence_offset(), 286)
+
 
 if __name__ == '__main__':
     IMP.test.main()