feat: read/write SDF from/to string

modules/io/doc/io.rst

@@ -95,6 +95,13 @@ behaviour.
         pdb_str = pdb.read()
         ent = io.PDBStrToEntity(pdb_str, ost.io.profiles['DEFAULT'], True)
 
+.. function:: SDFStrToEntity(sdf_string)
+
+  Load entity from a string in SDF format.
+
+  :param pdb_string: A SDF file as a string.
+
+  :rtype: :class:`~ost.mol.EntityHandle`.
 
 .. class:: ost.io.OMF
 
@@ -267,6 +274,14 @@ file:
 
   :rtype: string.
 
+.. function:: EntityToSDFStr(ent)
+
+  Return entity as a string in SDF format.
+
+  :param entity: The :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+
+  :rtype: string.
+
 .. _seq-io:
 
 Sequences and Alignments

modules/io/pymod/wrap_io.cc

@@ -32,6 +32,7 @@ using namespace boost::python;
 #include <ost/io/mol/entity_io_mae_handler.hh>
 #include <ost/io/mol/entity_io_sdf_handler.hh>
 #include <ost/io/mol/pdb_reader.hh>
+#include <ost/io/mol/sdf_str.hh>
 #include <ost/io/mol/dcd_io.hh>
 #include <ost/io/stereochemical_params_reader.hh>
 using namespace ost;
@@ -65,6 +66,9 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(save_entity_view_ov,
 ost::mol::alg::StereoChemicalProps (*read_props_a)(String filename, bool check) = &ReadStereoChemicalPropsFile;
 ost::mol::alg::StereoChemicalProps (*read_props_b)(bool check) = &ReadStereoChemicalPropsFile;
 
+String (*sdf_str_a)(const mol::EntityHandle&)=&EntityToSDFString;
+String (*sdf_str_b)(const mol::EntityView&)=&EntityToSDFString;
+
 }
 
 void export_pdb_io();
@@ -117,6 +121,11 @@ BOOST_PYTHON_MODULE(_ost_io)
       (arg("sequence"), arg("filename"), arg("format")="auto"));
   def("LoadSDF", &LoadSDF);
 
+  def("EntityToSDFStr", sdf_str_a);
+  def("EntityToSDFStr", sdf_str_b);
+
+  def("SDFStrToEntity", &SDFStringToEntity);
+
   def("LoadCRD", &LoadCRD);
   def("LoadCHARMMTraj_", &LoadCHARMMTraj, (arg("ent"), arg("trj_filename"), 
                                            arg("stride")=1, arg("lazy_load")=false,

modules/io/src/mol/CMakeLists.txt

@@ -20,6 +20,7 @@ star_parser.cc
 mmcif_reader.cc
 mmcif_info.cc
 pdb_str.cc
+sdf_str.cc
 mmcif_str.cc
 stereochemical_params_reader.cc
 omf.cc
@@ -50,6 +51,7 @@ surface_io_handler.hh
 load_surface.hh
 surface_io_msms_handler.hh
 pdb_str.hh
+sdf_str.hh
 mmcif_str.hh
 stereochemical_params_reader.hh
 omf.hh

modules/io/src/mol/sdf_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/sdf_str.hh>
+#include <ost/io/mol/sdf_writer.hh>
+#include <ost/io/mol/sdf_reader.hh>
+
+namespace ost { namespace io {
+
+String EntityToSDFString(const mol::EntityHandle& ent) {
+  std::stringstream stream;
+  SDFWriter writer(stream);
+  writer.Write(ent);
+  return stream.str();
+}
+
+String EntityToSDFString(const mol::EntityView& ent) {
+  std::stringstream stream;
+  SDFWriter writer(stream);
+  writer.Write(ent);
+  return stream.str();
+}
+
+mol::EntityHandle SDFStringToEntity(const String& sdf) {
+  std::stringstream stream(sdf);
+  SDFReader reader(stream);
+  mol::EntityHandle ent = mol::CreateEntity();
+  reader.Import(ent);
+  return ent;
+}
+
+}}

modules/io/src/mol/sdf_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_SDF_STR_HH
+#define OST_IO_SDF_STR_HH
+
+#include <ost/io/module_config.hh>
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/entity_handle.hh>
+
+namespace ost { namespace io {
+
+// Saves an entity to a string in PDB format.
+String DLLEXPORT_OST_IO
+EntityToSDFString(const mol::EntityHandle& ent);
+
+String DLLEXPORT_OST_IO
+EntityToSDFString(const mol::EntityView& ent);
+
+mol::EntityHandle DLLEXPORT_OST_IO
+SDFStringToEntity(const String& pdb);
+
+}}
+
+#endif