add function to read/write PDB directly from/to string

While it has been possible to read/write PDb directly
from/to arbitrary streams, the stream interface is not
exposed to Python yet.

modules/io/pymod/export_pdb_io.cc

@@ -22,6 +22,8 @@ using namespace boost::python;
 #include <ost/io/mol/io_profile.hh>
 #include <ost/io/mol/pdb_reader.hh>
 #include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/pdb_str.hh>
+
 using namespace ost;
 using namespace ost::io;
 
@@ -33,6 +35,9 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(load_PDB_ov, LoadPDB, 1, 2)
 void (PDBWriter::*write_a)(const mol::EntityHandle&)=&PDBWriter::Write;
 void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
 
+String (*pdb_str_a)(const mol::EntityHandle&, const IOProfile&)=&EntityToPDBString;
+String (*pdb_str_b)(const mol::EntityView&, const IOProfile&)=&EntityToPDBString;
+
 void remove_profiles() {
   IOProfileRegistry::RemoveProfiles();
 }
@@ -88,6 +93,12 @@ void export_pdb_io()
                   &PDBWriter::SetWriteMultiModel)
     .def("Write", write_b)    
   ;
+  def("EntityToPDBStr", pdb_str_a,
+      (arg("entity"), arg("profile")=IOProfile()));
+  def("EntityToPDBStr", pdb_str_b,
+      (arg("entity"), arg("profile")=IOProfile()));
+
+  def("PDBStrToEntity", &PDBStringToEntity, (arg("pdb_string"),arg("profile")=IOProfile()));
 
   // we need to make sure there are no pending references to Python objects
   // tied to the IOProfileRegistry singleton. The destructor of 

modules/io/src/mol/CMakeLists.txt

@@ -19,6 +19,7 @@ dcd_io.cc
 star_parser.cc
 mmcif_reader.cc
 mmcif_info.cc
+pdb_str.cc
 PARENT_SCOPE
 )
 
@@ -45,5 +46,6 @@ load_entity.hh
 surface_io_handler.hh
 load_surface.hh
 surface_io_msms_handler.hh
+pdb_str.hh
 PARENT_SCOPE
 )

modules/io/src/mol/pdb_str.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
+//------------------------------------------------------------------------------
+#include <sstream>
+#include <ost/io/mol/pdb_str.hh>
+#include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/pdb_reader.hh>
+
+namespace ost { namespace io {
+
+String EntityToPDBString(const mol::EntityHandle& ent, const IOProfile& profile) {
+  std::stringstream stream;
+  PDBWriter writer(stream, profile);
+  writer.Write(ent);
+  return stream.str();
+}
+
+String EntityToPDBString(const mol::EntityView& ent, const IOProfile& profile) {
+  std::stringstream stream;
+  PDBWriter writer(stream, profile);
+  writer.Write(ent);
+  return stream.str();
+}
+
+mol::EntityHandle PDBStringToEntity(const String& pdb, const IOProfile& profile) {
+  std::stringstream stream(pdb);
+  PDBReader reader(stream, profile);
+  mol::EntityHandle ent = mol::CreateEntity();
+  reader.Import(ent);
+  return ent;
+}
+
+}}

modules/io/src/mol/pdb_str.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_PDB_STR_HH
+#define OST_IO_PDB_STR_HH
+
+#include <ost/io/module_config.hh>
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/io/mol/io_profile.hh>
+
+namespace ost { namespace io {
+
+// Saves an entity to a string in PDB format.
+String DLLEXPORT_OST_IO
+EntityToPDBString(const mol::EntityHandle& ent, const IOProfile& profile=IOProfile());
+
+String DLLEXPORT_OST_IO
+EntityToPDBString(const mol::EntityView& ent, const IOProfile& profile=IOProfile());
+
+mol::EntityHandle DLLEXPORT_OST_IO
+PDBStringToEntity(const String& pdb, const IOProfile& profile=IOProfile());
+
+}}
+
+#endif