Add+test basic superposition_context JSON-writing

source/superposition/superposition_context.cpp

@@ -20,11 +20,17 @@
 
 #include "superposition_context.h"
 
+#include <boost/log/trivial.hpp>
+#include <boost/property_tree/json_parser.hpp>
+#include <boost/property_tree/ptree_fwd.hpp>
+#include <boost/range/algorithm_ext/for_each.hpp>
+
 #include "alignment/alignment_context.h"
 #include "exception/invalid_argument_exception.h"
 #include "file/pdb/pdb.h"
 #include "file/pdb/pdb_atom.h"
 #include "file/pdb/pdb_residue.h"
+#include "superposition/io/superposition_io.h"
 
 using namespace cath;
 using namespace cath::align;
@@ -33,6 +39,11 @@ using namespace cath::file;
 using namespace cath::sup;
 using namespace std;
 
+using boost::log::trivial::severity_level;
+using boost::property_tree::json_parser::write_json;
+using boost::property_tree::ptree;
+using boost::range::for_each;
+
 /// \brief TODOCUMENT
 superposition_context::superposition_context(const pdb_list      &arg_pdbs,         ///< TODOCUMENT
                                              const str_vec       &arg_names,        ///< TODOCUMENT
@@ -99,3 +110,66 @@ alignment_context cath::sup::make_alignment_context(const superposition_context
 		arg_superposition_context.get_alignment_cref()
 	);
 }
+
+/// \brief TODOCUMENT
+///
+/// At present, this stores the names and the superposition but does nothing
+/// with the alignment or the PDBs
+///
+/// \relates superposition_context
+void cath::sup::save_to_ptree(ptree                       &arg_ptree,      ///< TODOCUMENT
+                              const superposition_context &arg_sup_context ///< TODOCUMENT
+                              ) {
+	if ( arg_sup_context.has_alignment() ) {
+		BOOST_LOG_TRIVIAL( warning ) << "Whilst converting a superposition_context to JSON, its alignment will be ignored because that is not currently supported";
+	}
+
+	/// \todo DRY
+	const auto transformations_key = string( "transformations" );
+	const auto supn_ptree          = make_ptree_of( arg_sup_context.get_superposition_cref() );
+	const auto trans_ptrees        = supn_ptree.get_child( transformations_key );
+
+	const auto entries_key = "entries";
+	arg_ptree.put_child( entries_key, ptree{} );
+	auto &entries_ptree = arg_ptree.get_child( entries_key );
+
+	for_each(
+		arg_sup_context.get_names_cref(),
+		trans_ptrees,
+		[&] (const string &name, const pair<string, ptree> &trans_ptree) {
+			ptree entry_ptree;
+			entry_ptree.put      ( "name",           name               );
+			entry_ptree.put_child( "transformation", trans_ptree.second );
+			entries_ptree.push_back( make_pair( "", entry_ptree ) );
+		}
+	);
+}
+
+/// \brief TODOCUMENT
+///
+/// At present, this stores the names and the superposition but does nothing
+/// with the alignment or the PDBs
+///
+/// \relates superposition_context
+ptree cath::sup::make_ptree_of(const superposition_context &arg_sup_context ///< TODOCUMENT
+                               ) {
+	ptree new_ptree;
+	save_to_ptree( new_ptree, arg_sup_context );
+	return new_ptree;
+}
+
+/// \brief Create a JSON string to represent the specified superposition
+///
+/// At present, this stores the names and the superposition but does nothing
+/// with the alignment or the PDBs
+///
+/// \relates superposition_context
+string cath::sup::to_json_string(const superposition_context &arg_sup_context, ///< The superposition_context to represent in the JSON string
+                                 const bool                  &arg_pretty_print ///< Whether to use whitespace (including line breaks) in the JSON to make it more human-readable
+                                 ) {
+	ostringstream json_ss;
+	ptree temp_ptree;
+	save_to_ptree( temp_ptree, arg_sup_context );
+	write_json( json_ss, temp_ptree, arg_pretty_print );
+	return json_ss.str();
+}

source/superposition/superposition_context.h

@@ -65,6 +65,14 @@ namespace cath {
 		};
 
 		align::alignment_context make_alignment_context(const superposition_context &);
+
+		void save_to_ptree(boost::property_tree::ptree &,
+		                   const superposition_context &);
+
+		boost::property_tree::ptree make_ptree_of(const superposition_context &);
+
+		std::string to_json_string(const superposition_context &,
+		                           const bool &arg_pretty_print = true);
 	}
 }
 

source/superposition/superposition_context_test.cpp

@@ -20,23 +20,57 @@
 
 #include <boost/test/auto_unit_test.hpp>
 
+#include "file/pdb/pdb.h"
+#include "file/pdb/pdb_atom.h"
+#include "file/pdb/pdb_list.h"
+#include "file/pdb/pdb_residue.h"
+#include "structure/geometry/coord_list.h"
+#include "superposition/superposition_context.h"
+
+using namespace cath::file;
+using namespace cath::geom;
+using namespace cath::sup;
+
 namespace cath {
 	namespace test {
 
 		/// \brief The superposition_context_test_suite_fixture to assist in testing superposition_context
 		struct superposition_context_test_suite_fixture {
 		protected:
 			~superposition_context_test_suite_fixture() noexcept = default;
+
+			coord_list coord_list_1{ { coord{  1.0,  0.0,  0.0 }, coord{  2.0,   0.0,   0.0 } } };
+			coord_list coord_list_2{ { coord{  0.0, -1.0,  0.0 }, coord{  0.0,  -2.0,   0.0 } } };
+			superposition the_sup = create_pairwise_superposition( coord_list_1, coord_list_2 );
+			superposition_context the_sup_con{
+				pdb_list{ pdb_vec{ 2, pdb{} } },
+				str_vec { "name_a", "name_b" },
+				the_sup
+			};
 		};
 
 	}
 }
 
 BOOST_FIXTURE_TEST_SUITE(superposition_context_test_suite, cath::test::superposition_context_test_suite_fixture)
 
-/// \brief TODOCUMENT
-BOOST_AUTO_TEST_CASE(basic) {
-	BOOST_CHECK( true );
+BOOST_AUTO_TEST_CASE(to_json_string_works_for_example_sup_con) {
+	BOOST_CHECK_EQUAL(
+		to_json_string( the_sup_con, false ),
+		R"({"entries":[{"name":"name_a","transformation":{"translation":)"
+		R"({"x":"0","y":"0","z":"0"},)"
+		R"("rotation":)"
+		R"([["1","0","0"],)"
+		R"(["0","1","0"],)"
+		R"(["0","0","1"])"
+		R"(]}},{"name":"name_b","transformation":{"translation":)"
+		R"({"x":"0","y":"0","z":"0"},)"
+		R"("rotation":)"
+		R"([["0","-1","0"],)"
+		R"(["0","0","-1"],)"
+		R"(["1","0","0"])"
+		R"(]}}]})" "\n"
+	);
 }
 
 BOOST_AUTO_TEST_SUITE_END()