Added first bit of struct_conf parsing to the mmCif parser, NO UNIT TESTS, yet

modules/io/src/mol/mmcif_reader.cc

@@ -80,6 +80,7 @@ void MMCifParser::ClearState()
   authors_map_.clear();
   bu_origin_map_.clear();
   bu_assemblies_.clear();
+  secstruct_list_.clear();
 }
 
 void MMCifParser::SetRestrictChains(const String& restrict_chains)
@@ -260,6 +261,20 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
        = header.GetIndex("pdbx_model_type_details");
     indices_[STRUCT_TITLE]               = header.GetIndex("title");
     cat_available = true;
+  } else if (header.GetCategory() == "struct_conf") {
+    category_ = STRUCT_CONF;
+    // mandatory items
+    this->TryStoreIdx(BEG_LABEL_ASYM_ID, "beg_label_asym_id", header);
+    this->TryStoreIdx(BEG_LABEL_COMP_ID, "beg_label_comp_id", header);
+    this->TryStoreIdx(BEG_LABEL_SEQ_ID,  "beg_label_seq_id", header);
+    this->TryStoreIdx(CONF_TYPE_ID,      "conf_type_id", header);
+    this->TryStoreIdx(END_LABEL_ASYM_ID, "end_label_asym_id", header);
+    this->TryStoreIdx(END_LABEL_COMP_ID, "end_label_comp_id", header);
+    this->TryStoreIdx(END_LABEL_SEQ_ID,  "end_label_seq_id", header);
+    this->TryStoreIdx(STRUCT_CONF_ID,    "id", header);
+    // optional items
+    indices_[BEG_AUTH_ASYM_ID] = header.GetIndex("beg_auth_asym_id");
+    cat_available = true;
   }
   category_counts_[category_]++;
   return cat_available;
@@ -1008,6 +1023,34 @@ void MMCifParser::ParseStruct(const std::vector<StringRef>& columns)
   info_.SetStructDetails(details);
 }
 
+void MMCifParser::ParseStructConf(const std::vector<StringRef>& columns)
+{
+  StringRef chain_name;
+  int s_res_num;
+  int e_res_num;
+  // fetch start and end
+  s_res_num = this->TryGetInt(columns[indices_[BEG_LABEL_SEQ_ID]],
+                              "struct_conf.beg_label_seq_id"); // unit test
+  e_res_num = this->TryGetInt(columns[indices_[END_LABEL_SEQ_ID]],
+                              "struct_conf.end_label_seq_id"); // unit test
+  if(auth_chain_id_) { // unit test both ways
+    if (indices_[BEG_AUTH_ASYM_ID] != -1) { // unit test
+      chain_name = columns[indices_[BEG_AUTH_ASYM_ID]];
+    } else { // unit test
+      throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+                                               "foo",
+                                               this->GetCurrentLinenum()));
+    }
+  } else { // unit test
+    chain_name = columns[indices_[BEG_LABEL_ASYM_ID]];
+  }
+  MMCifHSEntry hse = {to_res_num(s_res_num, ' '),
+                      to_res_num(e_res_num, ' '),
+                      chain_name.str(),
+                      columns[indices_[CONF_TYPE_ID]].str()};
+  secstruct_list_.push_back(hse);
+}
+
 void MMCifParser::OnDataRow(const StarLoopDesc& header, 
                             const std::vector<StringRef>& columns)
 {
@@ -1056,6 +1099,10 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
     LOG_TRACE("processing struct entry")
     this->ParseStruct(columns);
     break;
+  case STRUCT_CONF:
+    LOG_TRACE("processing struct_conf entry")
+    this->ParseStructConf(columns);
+    break;
   default:
     throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
                        "Uncatched category '"+ header.GetCategory() +"' found.",
@@ -1064,6 +1111,18 @@ void MMCifParser::OnDataRow(const StarLoopDesc& header,
   }
 }
 
+void MMCifParser::AssignSecStructure(mol::EntityHandle ent)
+{
+  // for each helix, take chain
+  // check for overlaps (visual artifacts)
+  // assign helix to chain
+
+  // for all strands
+  // take chain
+  // check for overlaps
+  // assign strand to chain
+}
+
 void MMCifParser::OnEndData()
 {
   mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT);
@@ -1155,6 +1214,8 @@ void MMCifParser::OnEndData()
   }
   bu_assemblies_.clear();
 
+  // create secondary structure from struct_conf info
+
   LOG_INFO("imported "
            << chain_count_ << " chains, "
            << residue_count_ << " residues, "

modules/io/src/mol/mmcif_reader.hh

@@ -270,6 +270,14 @@ protected:
   /// \param columns data row
   void ParseStruct(const std::vector<StringRef>& columns);
 
+  /// \brief Fetch MMCif struct_conf (secondary structure) information
+  ///
+  /// \param columns data row
+  void ParseStructConf(const std::vector<StringRef>& columns);
+
+  /// \brief Transform data from struct_conf entry into secondary structure
+  void AssignSecStructure(mol::EntityHandle ent);
+
 private:
   /// \enum magic numbers of this class
   typedef enum {
@@ -394,6 +402,19 @@ private:
      STRUCT_TITLE         ///< title for the data block
   } StructItems;
 
+  /// \enum items of the struct_conf category
+  typedef enum {
+    BEG_AUTH_ASYM_ID,  ///< Starting residue, points to atom_site.auth_asym_id
+    BEG_LABEL_ASYM_ID, ///< Starting residue, points to atom_site.label_asym_id
+    BEG_LABEL_COMP_ID, ///< Starting residue, points to atom_site.label_comp_id
+    BEG_LABEL_SEQ_ID,  ///< Starting residue, points to atom_site.label_seq_id
+    CONF_TYPE_ID,      ///< Pointer to struct_conf_type.id
+    END_LABEL_ASYM_ID, ///< Ending residue, points to atom_site.label_asym_id
+    END_LABEL_COMP_ID, ///< Ending residue, points to atom_site.label_comp_id
+    END_LABEL_SEQ_ID,  ///< Ending residue, points to atom_site.label_seq_id
+    STRUCT_CONF_ID,    ///< Unique identifier
+  } StructConfItems;
+
   /// \enum categories of the mmcif format
   typedef enum {
     ATOM_SITE,
@@ -407,6 +428,7 @@ private:
     PDBX_STRUCT_ASSEMBLY_GEN,
     PDBX_STRUCT_OPER_LIST,
     STRUCT,
+    STRUCT_CONF,
     DONT_KNOW
   } MMCifCategory;
 
@@ -429,6 +451,15 @@ private:
   typedef std::map<String, std::pair<std::vector<int>, std::vector<String> > >
     MMCifCitationAuthorMap;
 
+  /// \struct store struct_conf info (secondary structure)
+  typedef struct {
+    mol::ResNum start;
+    mol::ResNum end;
+    String chain_name;
+    String type;
+  } MMCifHSEntry;
+  typedef std::vector<MMCifHSEntry> MMCifHSVector;
+
   // members
   MMCifCategory category_;
   int category_counts_[DONT_KNOW+1]; ///< overall no. of atom_site loops
@@ -457,6 +488,7 @@ private:
   MMCifCitationAuthorMap authors_map_;
   MMCifBioUAssemblyVector bu_assemblies_;
   std::map<String, String> bu_origin_map_; ///< pdbx_struct_assembly.details
+  MMCifHSVector secstruct_list_; ///< for storing struct_conf sec.struct. data
 };
 
 }}

modules/io/tests/test_mmcif_reader.cc

@@ -724,8 +724,6 @@ BOOST_AUTO_TEST_CASE(mmcif_biounit_tests)
   tmmcif_h.Add(StringRef("matrix[3][2]", 12));
   tmmcif_h.Add(StringRef("matrix[3][3]", 12));
 
-
-
   tmmcif_p.OnBeginLoop(tmmcif_h);
 
   columns.pop_back();
@@ -940,6 +938,8 @@ BOOST_AUTO_TEST_CASE(mmcif_testreader)
     BOOST_CHECK_EQUAL(rs->GetNumber().GetNum(), i);
   }
 
+  // add checking of struct_conf info, here
+
   BOOST_MESSAGE("          done.");
 
   BOOST_MESSAGE("          reading data fields which should not fail...");

modules/io/tests/testfiles/mmcif/atom_site.mmcif

@@ -94,6 +94,27 @@ _struct.pdbx_formula_weight_method 'Good Guess'
 _struct.pdbx_model_details         'Even better guessing'
 _struct.pdbx_model_type_details    'Guess'
 
+loop_
+_struct_conf.id
+_struct_conf.conf_type_id
+_struct_conf.beg_label_comp_id
+_struct_conf.beg_label_asym_id
+_struct_conf.beg_label_seq_id
+_struct_conf.end_label_comp_id
+_struct_conf.end_label_asym_id
+_struct_conf.end_label_seq_id
+_struct_conf.details
+HELX1  HELX_RH_AL_P  ARG  A   87  GLN  A   92  .
+HELX2  HELX_RH_AL_P  ARG  B  287  GLN  B  292  .
+STRN1  STRN_P        PRO  A    1  LEU  A    5  .
+STRN2  STRN_P        CYS  B  295  PHE  B  299  .
+STRN3  STRN_P        CYS  A   95  PHE  A  299  .
+STRN4  STRN_P        PRO  B  201  LEU  B  205  .
+TURN1  TURN_TY1P_P   ILE  A   15  GLN  A   18  .
+TURN2  TURN_TY2_P    GLY  A   49  GLY  A   52  .
+TURN3  TURN_TY1P_P   ILE  A   55  HIS  A   69  .
+TURN4  TURN_TY1_P    THR  A   91  GLY  A   94  .
+
 loop_
 _atom_site.group_PDB
 _atom_site.type_symbol