mmcif writer: updates

Reads PDB entry 1a0s (has peptide, water, non-polymer residues in same chain)
and dumps an mmcif file that can be successfully loaded in OpenStructure again.
Still no claim for completeness of the produced mmcif file but we have a
proof of concept implementation.

modules/io/src/mol/mmcif_writer.cc

@@ -22,7 +22,6 @@
 #include <ost/io/mol/mmcif_writer.hh>
 
 
-
 namespace {
 
   // generates as many chain names as you want (potentially multiple characters)
@@ -83,6 +82,64 @@ namespace {
                     char chem_class,
                     const ost::mol::ResidueHandleList& res_list,
                     std::vector<EntityInfo>& entity_infos) {
+
+
+    // deal with water
+    if(chem_class == ost::mol::ChemClass::WATER) {
+      for(size_t i = 0; i < entity_infos.size(); ++i) {
+        if(entity_infos[i].chem_class == ost::mol::ChemClass::WATER) {
+          entity_infos[i].asym_ids.push_back(asym_chain_name);
+          return i;
+        }
+      }
+      int entity_idx = entity_infos.size();
+      entity_infos.push_back(EntityInfo());
+      entity_infos.back().chem_class = ost::mol::ChemClass::WATER;
+      entity_infos.back().asym_ids.push_back(asym_chain_name);
+      entity_infos.back().mon_ids.push_back("HOH");
+      return entity_idx; 
+    }
+
+    // deal with NON_POLYMER
+    if(chem_class == ost::mol::ChemClass::NON_POLYMER) {
+      for(size_t i = 0; i < entity_infos.size(); ++i) {
+        if(entity_infos[i].chem_class == ost::mol::ChemClass::NON_POLYMER &&
+           res_list[0].GetName() == entity_infos[i].mon_ids[0]) {
+          entity_infos[i].asym_ids.push_back(asym_chain_name);
+          return i;
+        }
+      }
+      int entity_idx = entity_infos.size();
+      entity_infos.push_back(EntityInfo());
+      entity_infos.back().chem_class = ost::mol::ChemClass::NON_POLYMER;
+      entity_infos.back().asym_ids.push_back(asym_chain_name);
+      entity_infos.back().mon_ids.push_back(res_list[0].GetName());
+      return entity_idx;
+    }
+
+    // deal with UNKNOWN
+    if(chem_class == ost::mol::ChemClass::UNKNOWN) {
+      for(size_t i = 0; i < entity_infos.size(); ++i) {
+        if(entity_infos[i].chem_class == ost::mol::ChemClass::UNKNOWN &&
+           res_list[0].GetName() == entity_infos[i].mon_ids[0]) {
+          entity_infos[i].asym_ids.push_back(asym_chain_name);
+          return i;
+        }
+      }
+      int entity_idx = entity_infos.size();
+      entity_infos.push_back(EntityInfo());
+      entity_infos.back().chem_class = ost::mol::ChemClass::UNKNOWN;
+      entity_infos.back().asym_ids.push_back(asym_chain_name);
+      entity_infos.back().mon_ids.push_back(res_list[0].GetName());
+      return entity_idx;
+    }
+
+    // with the current code, the following chem classes are considered
+    // polymers: PEPTIDE_LINKING, D_PEPTIDE_LINKING, L_PEPTIDE_LINKING
+    // RNA_LINKING, DNA_LINKING, L_SACCHARIDE, D_SACCHARIDE, SACCHARIDE
+    // They're also considered polymers even if only one residue is there
+    // Needs checking...
+
     std::vector<String> mon_ids;
     for(auto res : res_list) {
       mon_ids.push_back(res.GetName());
@@ -131,6 +188,7 @@ namespace {
     desc.Add("auth_seq_id");
     desc.Add("auth_asym_id");
     desc.Add("id");
+    desc.Add("pdbx_PDB_ins_code");
     ost::io::StarLoop* sl = new ost::io::StarLoop(desc);
     return sl;
   }
@@ -211,6 +269,8 @@ namespace {
         at_data.push_back(ost::io::StarLoopDataItemDO(auth_asym_id));
         // id
         at_data.push_back(ost::io::StarLoopDataItemDO(atom_site_ptr->GetN()));
+        // pdbx_PDB_ins_code
+        at_data.push_back(ost::io::StarLoopDataItemDO(""));
         atom_site_ptr->AddData(at_data);
       }
       ++label_seq_id;
@@ -232,8 +292,11 @@ namespace {
       } else if(chem_class == ost::mol::ChemClass::NON_POLYMER) {
         ent_data.push_back(ost::io::StarLoopDataItemDO("non-polymer"));        
       } else if(chem_class.IsSaccharide()) {
-        // I doubt that this is correct
+        // NOT SURE WHETHER THIS MAKES ANY SENSE!
         ent_data.push_back(ost::io::StarLoopDataItemDO("branched"));
+      } else if(chem_class == ost::mol::ChemClass::UNKNOWN) {
+        // NOT SURE WHETHER THIS MAKES ANY SENSE!
+        ent_data.push_back(ost::io::StarLoopDataItemDO("non-polymer"));
       } else {
         throw ost::io::IOException("Entity type issue");
       }
@@ -556,7 +619,7 @@ void MMCifWriter::Process_atom_site(const ost::mol::EntityHandle& ent) {
   }
 
   // process UNKNOWN
-  for(auto res: N_chains) {
+  for(auto res: U_chains) {
     ost::mol::ResidueHandleList res_list;
     res_list.push_back(res);
     String chain_name = chain_name_gen.Get();