added entity io handler for mmcif format

modules/io/src/CMakeLists.txt

@@ -13,6 +13,7 @@ io_utils.hh
 io_exception.hh
 convert.hh
 converting_streams.hh
+
 formatted_line.hh
 )
 

modules/io/src/io_manager.cc

@@ -21,6 +21,7 @@
 #include <ost/io/mol/entity_io_crd_handler.hh>
 #include <ost/io/mol/entity_io_sdf_handler.hh>
 #include <ost/io/mol/entity_io_mae_handler.hh>
+#include <ost/io/mol/entity_io_mmcif_handler.hh>
 #include <ost/io/seq/fasta_io_handler.hh>
 #include <ost/io/seq/pir_io_handler.hh>
 #include <ost/io/seq/promod_io_handler.hh>
@@ -44,6 +45,7 @@ namespace ost { namespace io {
 
 IOManager::IOManager()
 {
+  RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMMCIFHandlerFactory));
   RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOPDBHandlerFactory));
   RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOCRDHandlerFactory));
   RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOSDFHandlerFactory));

modules/io/src/mol/CMakeLists.txt

@@ -5,6 +5,7 @@ pdb_reader.cc
 entity_io_pdb_handler.cc	
 pdb_writer.cc
 entity_io_sdf_handler.cc	
+entity_io_mmcif_handler.cc
 sdf_reader.cc
 sdf_writer.cc
 save_entity.cc
@@ -29,6 +30,7 @@ io_profile.hh
 dcd_io.hh
 entity_io_crd_handler.hh
 entity_io_mae_handler.hh
+entity_io_mmcif_handler.hh
 entity_io_handler.hh
 pdb_reader.hh
 entity_io_pdb_handler.hh

modules/io/src/mol/entity_io_mmcif_handler.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+/*
+  Author: Marco Biasini, Ansgar Philippsen
+ */
+#include <iostream>
+#include <sstream>
+#include <iomanip>
+
+#include <boost/algorithm/string.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/format.hpp>
+#include <boost/lexical_cast.hpp>
+
+#include <ost/log.hh>
+#include <ost/io/io_exception.hh>
+#include "entity_io_mmcif_handler.hh"
+#include <ost/profile.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+namespace ost { namespace io {
+
+using boost::format;
+
+
+bool EntityIOMMCIFHandler::RequiresBuilder() const
+{
+  return true;
+}
+
+
+void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
+                                const boost::filesystem::path& loc) const 
+{
+}
+
+void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent, 
+                                std::istream& stream)
+{
+  MMCifParser reader(stream,ent,  
+                     IOProfileRegistry::Instance().GetDefault());
+  reader.Parse();
+}
+
+void EntityIOMMCIFHandler::Export(const mol::EntityView& ent,
+                                std::ostream& stream) const 
+{
+}
+
+void EntityIOMMCIFHandler::Import(mol::EntityHandle& ent,
+                                const boost::filesystem::path& loc)
+{
+  std::string filename=loc.string();
+  MMCifParser reader(filename, ent,  
+                     IOProfileRegistry::Instance().GetDefault());
+  reader.Parse();
+}
+
+bool EntityIOMMCIFHandler::ProvidesImport(const boost::filesystem::path& loc,
+                                        const String& type)
+{
+  if (type=="auto") {
+    String match_suf_string=loc.string();
+    std::transform(match_suf_string.begin(),match_suf_string.end(),
+                   match_suf_string.begin(),tolower);
+    if(detail::FilenameEndsWith(match_suf_string,".cif") ||
+       detail::FilenameEndsWith(match_suf_string,".cif.gz")){
+      return true;
+    }
+  }
+  return type=="cif";
+}
+
+bool EntityIOMMCIFHandler::ProvidesExport(const boost::filesystem::path& loc,
+                                        const String& type)
+{
+  return false;
+}
+
+
+}} // ns
+
+

modules/io/src/mol/entity_io_mmcif_handler.hh

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_IO_ENTITY_IO_PLUGIN_MMCIF_HH
+#define OST_IO_ENTITY_IO_PLUGIN_MMCIF_HH
+
+#include <vector>
+
+#include <ost/io/mol/entity_io_handler.hh>
+
+namespace ost { namespace io {
+
+
+class DLLEXPORT_OST_IO EntityIOMMCIFHandler: public EntityIOHandler {
+public:
+  virtual void Import(mol::EntityHandle& ent, 
+                      const boost::filesystem::path& loc);
+  
+  virtual void Export(const mol::EntityView& ent, 
+                      const boost::filesystem::path& loc) const;
+                      
+  virtual void Import(mol::EntityHandle& ent, std::istream& stream);
+  
+  virtual void Export(const mol::EntityView& ent, std::ostream& stream) const;
+  
+  static bool ProvidesImport(const boost::filesystem::path& loc, 
+                             const String& format="auto");
+  static bool ProvidesExport(const boost::filesystem::path& loc, 
+                             const String& format="auto");
+  virtual bool RequiresBuilder() const;
+
+  static String GetFormatName() { return String("mmCIF"); }
+  static String GetFormatDescription() { 
+    return String("macromolecular Crystallographic Information File "); 
+  }
+};
+
+
+typedef EntityIOHandlerFactory<EntityIOMMCIFHandler> EntityIOMMCIFHandlerFactory;
+
+
+}} // ns
+
+#endif

modules/io/src/mol/star_parser.cc

@@ -51,6 +51,7 @@ StarParser::StarParser(const String& filename, bool items_as_row):
   items_row_header_(), file_open_(true), items_row_columns_(),
   items_row_values_()
 {
+  items_as_row_=items_as_row;
   if (filename.length() >= 3 &&
       filename.substr(filename.length() - 3) == ".gz") {
     stream_.push(boost::iostreams::gzip_decompressor());