Remove dups in get_backbone_complete_residue_ids()

Making proteins from PDBs involves removing duplicate residues so it
makes sense that get_backbone_complete_residue_ids() should do the same
so that the results tally

Fixes #52

source/uni/file/pdb/pdb.cpp

@@ -34,7 +34,9 @@
 
 #include "biocore/residue_id.hpp"
 #include "chopping/region/region.hpp"
+#include "common/algorithm/contains.hpp"
 #include "common/algorithm/copy_build.hpp"
+#include "common/algorithm/sort_uniq_copy.hpp"
 #include "common/algorithm/transform_build.hpp"
 #include "common/boost_addenda/log/log_to_ostream_guard.hpp"
 #include "common/boost_addenda/range/adaptor/adjacented.hpp"
@@ -59,6 +61,7 @@
 
 #include <fstream>
 #include <iostream>
+#include <set>
 #include <sstream>
 #include <tuple>
 
@@ -434,6 +437,8 @@ coord cath::file::get_residue_ca_coord_of_region_limited_backbone_complete_index
 
 /// \brief Get the list of residues IDs for the backbone-complete residues on first chain of the specified PDB
 ///
+/// \TODO This should probably also remove residues with duplicate residue IDs
+///
 /// \relates pdb
 residue_id_vec cath::file::get_backbone_complete_residue_ids_of_first_chain(const pdb  &arg_pdb,                   ///< The PDB to query
                                                                             const bool &arg_complete_backbone_only ///< Whether to restrict to the backbone-complete residues
@@ -458,15 +463,23 @@ residue_id_vec cath::file::get_backbone_complete_residue_ids_of_first_chain(cons
 
 /// \brief Get the list of residues IDs for the backbone-complete residues on all chains of the specified PDB
 ///
+/// This also remove residues with duplicate residue IDs
+///
 /// \relates pdb
 residue_id_vec cath::file::get_backbone_complete_residue_ids(const pdb &arg_pdb ///< The PDB to query
                                                              ) {
-	return arg_pdb.empty()
-		? residue_id_vec{}
-		: transform_build<residue_id_vec>(
-			arg_pdb | filtered( is_backbone_complete ),
-			[] (const pdb_residue &x) { return x.get_residue_id(); }
-		);
+	residue_id_vec results;
+	vector<residue_id> seen_res_ids;
+	for (const pdb_residue &the_res : arg_pdb) {
+		if ( is_backbone_complete( the_res ) ) {
+			const residue_id the_res_id = the_res.get_residue_id();
+			if ( ! contains( seen_res_ids, the_res_id ) ) {
+				seen_res_ids.push_back( the_res_id );
+				results.push_back( the_res_id );
+			}
+		}
+	}
+	return results;
 }
 
 /// \brief TODOCUMENT

source/uni/file/pdb/pdb_list.cpp

@@ -248,6 +248,8 @@ backbone_complete_indices_vec cath::file::get_backbone_complete_indices(const pd
 
 /// \brief Get the lists of residue IDs for all chains of each of the PDBs in the specified pdb_list
 ///
+/// This also remove residues with duplicate residue IDs
+///
 /// \relates pdb_list
 residue_id_vec_vec cath::file::get_backbone_complete_residue_ids(const pdb_list &arg_pdb_list ///< The PDBs to query
                                                                  ) {
@@ -261,6 +263,8 @@ residue_id_vec_vec cath::file::get_backbone_complete_residue_ids(const pdb_list
 
 /// \brief Get the lists of residue IDs for the first chains of each of the PDBs in the specified pdb_list
 ///
+/// \TODO This should probably also remove residues with duplicate residue IDs
+///
 /// \relates pdb_list
 residue_id_vec_vec cath::file::get_backbone_complete_residue_ids_of_first_chains(const pdb_list &arg_pdb_list ///< The PDBs to query
                                                                                  ) {

source/uni/file/pdb/pdb_test.cpp

@@ -347,6 +347,45 @@ END
 	BOOST_TEST( pdb_file_to_string( read_pdb( pdb_data ) ) == pdb_data );
 }
 
+BOOST_AUTO_TEST_CASE(get_backbone_complete_residue_ids__removes_dupl_res_ids) {
+	ostringstream test_ss;
+	const log_to_ostream_guard the_guard{ test_ss };
+
+	// From 4tsw (as of ~January 2018)
+	//
+	// Ensure that get_backbone_complete_residue_ids() removes duplicate residue_ids
+	// so that it matches the behaviour of making proteins from PDBs.
+	// If necessary, it'd be possible to make both try to handle them but
+	// that will likely require work to fix arising problems and the issue
+	// of duplicated residue is rare and is (mostly? completely?) restricted
+	// to superseded PDBs
+	const string pdb_data = R"(ATOM   2229  N   GLN B 102      31.966  19.126  31.868  1.00 57.91           N  
+ATOM   2230  CA  GLN B 102      32.135  19.286  30.428  1.00 63.27           C  
+ATOM   2231  C   GLN B 102      31.098  20.226  29.827  1.00 65.08           C  
+ATOM   2232  O   GLN B 102      31.295  20.773  28.738  1.00 66.67           O  
+ATOM   2241  N   ARG B 103      30.036  20.481  30.582  1.00 67.41           N  
+ATOM   2242  CA  ARG B 103      28.981  21.363  30.110  1.00 69.06           C  
+ATOM   2243  C   ARG B 103      28.668  22.406  31.174  1.00 68.80           C  
+ATOM   2244  O   ARG B 103      29.483  22.638  32.071  1.00 69.14           O  
+ATOM   2247  N   GLU B 103      27.492  23.017  31.036  1.00 69.00           N  
+ATOM   2248  CA  GLU B 103      26.946  24.055  31.918  1.00 69.65           C  
+ATOM   2249  C   GLU B 103      26.058  24.961  31.066  1.00 71.54           C  
+ATOM   2250  O   GLU B 103      26.334  25.177  29.877  1.00 72.21           O  
+ATOM   2253  N   THR B 105      24.903  25.407  31.312  1.00 71.90           N  
+ATOM   2254  CA  THR B 105      24.124  26.292  30.435  1.00 69.49           C  
+ATOM   2255  C   THR B 105      23.000  27.081  31.135  1.00 67.87           C  
+ATOM   2256  O   THR B 105      22.911  27.101  32.373  1.00 63.94           O  
+TER    2257      THR B 105                                                      
+END   
+)";
+	const residue_id_vec expected = { {
+		make_residue_id( 'B', 102 ),
+		make_residue_id( 'B', 103 ),
+		make_residue_id( 'B', 105 ),
+	} };
+	BOOST_TEST( get_backbone_complete_residue_ids( read_pdb( pdb_data ) ) == expected );
+}
+
 BOOST_AUTO_TEST_CASE(writes_partial_pdb_correctly) {
 	const auto parsed_pdb = read_pdb_file( global_test_constants::EXAMPLE_A_PDB_FILENAME() );