Load mmcif from strings

modules/io/pymod/export_mmcif_io.cc

@@ -26,6 +26,7 @@ using namespace boost::python;
 #include <ost/io/mol/io_profile.hh>
 #include <ost/io/mol/mmcif_reader.hh>
 #include <ost/io/mol/mmcif_info.hh>
+#include <ost/io/mmcif_str.hh>
 using namespace ost;
 using namespace ost::io;
 using namespace ost::mol;
@@ -44,6 +45,16 @@ boost::python::list WrapGetNames(MMCifInfo *p){
   return VecToList<String>(names);
 }
 
+boost::python::tuple WrapMMCifStringToEntity(const String& mmcif,
+                                             const IOProfile& profile=IOProfile(),
+                                             bool process=false) {
+  std::tuple<mol::EntityHandle, MMCifInfo, ost::seq::SequenceList> res =
+  MMCifStringToEntity(mmcif, profile, process);
+  return boost::python::make_tuple(std::get<0>(res),
+                                   std::get<1>(res),
+                                   std::get<2>(res));
+}
+
 void export_mmcif_io()
 {
   class_<MMCifReader, boost::noncopyable>("MMCifReader", init<const String&, EntityHandle&, const IOProfile&>())
@@ -436,4 +447,8 @@ void export_mmcif_io()
                   &MMCifInfo::SetObsoleteInfo)
     .add_property("revisions", &MMCifInfo::GetRevisions)
  ;
+
+  def("MMCifStrToEntity", &WrapMMCifStringToEntity, (arg("pdb_string"),
+                                                     arg("profile")=IOProfile(),
+                                                     arg("process")=false));
 }

modules/io/src/mol/CMakeLists.txt

@@ -20,6 +20,7 @@ star_parser.cc
 mmcif_reader.cc
 mmcif_info.cc
 pdb_str.cc
+mmcif_str.cc
 stereochemical_params_reader.cc
 omf.cc
 PARENT_SCOPE
@@ -49,6 +50,7 @@ surface_io_handler.hh
 load_surface.hh
 surface_io_msms_handler.hh
 pdb_str.hh
+mmcif_str.hh
 stereochemical_params_reader.hh
 omf.hh
 PARENT_SCOPE

modules/io/src/mol/mmcif_str.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2020 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/mmcif_str.hh>
+#include <ost/io/mol/mmcif_reader.hh>
+
+namespace ost { namespace io {
+
+std::tuple<mol::EntityHandle, MMCifInfo, ost::seq::SequenceList>
+MMCifStringToEntity(const String& mmcif, const IOProfile& profile, bool process) {
+  std::stringstream stream(mmcif);
+  mol::EntityHandle ent = mol::CreateEntity();
+  MMCifReader reader(stream, ent, profile);
+  reader.SetReadSeqRes(true);
+  reader.Parse();
+  if(profile.processor && process) {
+    profile.processor->Process(ent);
+  }
+  return std::make_tuple(ent, reader.GetInfo(), reader.GetSeqRes());
+}
+
+}}

modules/io/src/mol/mmcif_str.hh

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2020 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_MMCIF_STR_HH
+#define OST_IO_MMCIF_STR_HH
+
+#include <ost/io/module_config.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/io/mmcif_reader.hh>
+#include <ost/io/mol/io_profile.hh>
+
+namespace ost { namespace io {
+
+std::tuple<mol::EntityHandle, MMCifInfo, ost::seq::SequenceList> DLLEXPORT_OST_IO
+MMCifStringToEntity(const String& mmcif, const IOProfile& profile, bool process);
+
+}}
+
+#endif