diff --git a/modules/io/src/CMakeLists.txt b/modules/io/src/CMakeLists.txt
index 08b65a7a2f2f8509834db7dfcb97a0fdd35d0646..c2a465686698258543707f91b5097e7d5f98ff11 100644
--- a/modules/io/src/CMakeLists.txt
+++ b/modules/io/src/CMakeLists.txt
@@ -13,6 +13,7 @@ io_utils.hh
io_exception.hh
convert.hh
converting_streams.hh
+
formatted_line.hh
)
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index 071be5c11461382803e8a3704bdbd32ba760ed18..6edc7fe430dd928159152bed7ebea0bde53aeb44 100644
--- a/modules/io/src/io_manager.cc
+++ b/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));
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index 05c813456155e14b540e7f00b3848932124db523..cb80b67a9600ed5ec3f98e19a5669dcb4b1f1a1b 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/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
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.cc b/modules/io/src/mol/entity_io_mmcif_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4d4d99777cb45970b113f9c337f428dfce7162ad
--- /dev/null
+++ b/modules/io/src/mol/entity_io_mmcif_handler.cc
@@ -0,0 +1,98 @@
+//------------------------------------------------------------------------------
+// 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
+
+
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.hh b/modules/io/src/mol/entity_io_mmcif_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..2fa262156d4867f665a8fc3f4d5ea8e71877f16f
--- /dev/null
+++ b/modules/io/src/mol/entity_io_mmcif_handler.hh
@@ -0,0 +1,59 @@
+//------------------------------------------------------------------------------
+// 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
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index d8903a9de0baac3dfc3c037c20f449f9cabaa2da..0de35fec5072aff97c421fa8a9de409b8cb2011b 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/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());