moved chemdict parser from conop to io to avoid circular dependency

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2724 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/conop/src/CMakeLists.txt

@@ -8,11 +8,9 @@ compound_lib.hh
 module_config.hh
 rule_based_builder.hh
 ring_finder.hh
-chemdict_parser.hh
 )
 
 set(OST_CONOP_SOURCES
-chemdict_parser.cc
 builder.cc
 conop.cc
 heuristic_builder.cc

modules/conop/src/chemdict_tool.cc

@@ -29,7 +29,7 @@
 #include <boost/iostreams/filter/gzip.hpp>
 
 
-#include <ost/conop/chemdict_parser.hh>
+#include <ost/io/mol/chemdict_parser.hh>
 
 using namespace ost;
 
@@ -70,7 +70,7 @@ int main(int argc, char const *argv[])
     filtered_istream.push(boost::iostreams::gzip_decompressor());
   }
   filtered_istream.push(istream);  
-  conop::ChemdictParser cdp(filtered_istream, dialect);
+  io::ChemdictParser cdp(filtered_istream, dialect);
   conop::CompoundLibPtr compound_lib;
   if (!strcmp(argv[1], "create")) {
     compound_lib=conop::CompoundLib::Create(argv[3]);

modules/io/src/mol/CMakeLists.txt

@@ -12,12 +12,14 @@ save_entity.cc
 load_entity.cc
 surface_io_msms_handler.cc
 load_surface.cc
+chemdict_parser.cc
 dcd_io.cc
 star_parser.cc
 PARENT_SCOPE
 )
 
 set(OST_IO_MOL_HEADERS
+chemdict_parser.hh
 star_parser.hh
 dcd_io.hh
 entity_io_crd_handler.hh	

modules/conop/src/chemdict_parser.cc → modules/io/src/mol/chemdict_parser.cc

-#include <ost/conop/chemdict_parser.hh>
+#include <ost/io/mol/chemdict_parser.hh>
 
-namespace ost { namespace conop {
+namespace ost { namespace io {
 
+using namespace ost::conop;
+  
 bool ChemdictParser::OnBeginData(const StringRef& data_name) 
 {    
   compound_.reset(new Compound(data_name.str()));
@@ -15,7 +17,7 @@ bool ChemdictParser::OnBeginData(const StringRef& data_name)
   return true; 
 }
 
-bool ChemdictParser::OnBeginLoop(const io::StarLoopDesc& header)
+bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
 { 
   if (header.GetCategory()=="chem_comp_atom") {
     loop_type_=ATOM_SPEC;
@@ -37,7 +39,7 @@ bool ChemdictParser::OnBeginLoop(const io::StarLoopDesc& header)
   return false;
 }
 
-void ChemdictParser::OnDataRow(const io::StarLoopDesc& header, 
+void ChemdictParser::OnDataRow(const StarLoopDesc& header, 
                                const std::vector<StringRef>& columns) 
 {                        
   if (loop_type_==ATOM_SPEC) {
@@ -65,7 +67,7 @@ void ChemdictParser::OnDataRow(const io::StarLoopDesc& header,
   }
 }
 
-void ChemdictParser::OnDataItem(const io::StarDataItem& item)
+void ChemdictParser::OnDataItem(const StarDataItem& item)
 {
   if (item.GetCategory()==StringRef("chem_comp", 9)) {
     if (item.GetName()==StringRef("type", 4)) {

modules/conop/src/chemdict_parser.hh → modules/io/src/mol/chemdict_parser.hh

@@ -28,7 +28,7 @@
 #include <ost/io/mol/star_parser.hh>
 #include <ost/conop/compound_lib.hh>
  
-namespace ost { namespace conop {
+namespace ost { namespace io {
 
 typedef enum {
   ATOM_SPEC,
@@ -36,10 +36,10 @@ typedef enum {
   DONT_KNOW
 } LoopType;
 
-class DLLEXPORT_OST_CONOP ChemdictParser : public io::StarParser {
+class DLLEXPORT_OST_CONOP ChemdictParser : public StarParser {
 public:
-  ChemdictParser(std::istream& stream, Compound::Dialect dialect): 
-    io::StarParser(stream), compound_(new Compound("UNK")), 
+  ChemdictParser(std::istream& stream, conop::Compound::Dialect dialect): 
+    StarParser(stream), compound_(new conop::Compound("UNK")), 
     last_(0), loop_type_(DONT_KNOW), dialect_(dialect)
   {
     this->InitTypeMap();
@@ -47,23 +47,23 @@ public:
 
   virtual bool OnBeginData(const StringRef& data_name);
 
-  virtual bool OnBeginLoop(const io::StarLoopDesc& header);
+  virtual bool OnBeginLoop(const StarLoopDesc& header);
 
-  virtual void OnDataRow(const io::StarLoopDesc& header, 
+  virtual void OnDataRow(const StarLoopDesc& header, 
                          const std::vector<StringRef>& columns);
 
-  virtual void OnDataItem(const io::StarDataItem& item);
+  virtual void OnDataItem(const StarDataItem& item);
 
   virtual void OnEndData();
 
-  void SetCompoundLib(const CompoundLibPtr& lib) 
+  void SetCompoundLib(const conop::CompoundLibPtr& lib) 
   {
     lib_=lib;
   }
 private:
   void InitTypeMap();  
-  CompoundLibPtr                   lib_;
-  CompoundPtr                      compound_;
+  conop::CompoundLibPtr                   lib_;
+  conop::CompoundPtr                      compound_;
   typedef enum {
     ATOM_NAME=0,
     ALT_ATOM_NAME=1,
@@ -82,8 +82,8 @@ private:
   static std::map<String, mol::ChemClass> tm_;  
   std::map<String, int>                   atom_map_;
   LoopType                                loop_type_;  
-  AtomSpec                                atom_;
-  Compound::Dialect                       dialect_;
+  conop::AtomSpec                         atom_;
+  conop::Compound::Dialect                dialect_;
 };