SCHWED-1740: test multi-loop handling for SidechainReconstructor

modelling/src/sidechain_reconstructor.hh

@@ -41,7 +41,7 @@ class SidechainReconstructor {
 public:
 
   SidechainReconstructor(bool keep_sidechains = true,
-                         bool build_disulfids = true, 
+                         bool build_disulfids = true,
                          bool optimize_subrotamers = false,
                          Real remodel_cutoff = 20,
                          Real rigid_frame_cutoff = 0,
@@ -63,8 +63,8 @@ public:
   Reconstruct(uint start_resnum, uint num_residues, uint chain_idx = 0) const;
 
   SidechainReconstructionDataPtr
-  Reconstruct(const std::vector<uint>& start_resnums, 
-              const std::vector<uint>& num_residues, 
+  Reconstruct(const std::vector<uint>& start_resnums,
+              const std::vector<uint>& num_residues,
               const std::vector<uint>& chain_indices) const;
 
   // options as in SidechainEnvListener (only used if no listener there yet!)

modelling/tests/test_sidechain_reconstructor.cc

@@ -42,13 +42,14 @@ SidechainReconstructorPtr GetScRec(const ost::mol::EntityHandle& test_ent) {
   return sc_rec;
 }
 
-void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
-                  uint start_resnum, uint loop_length, uint num_residues) {
-  // reconstruct
-  SidechainReconstructionDataPtr sc_data;
-  sc_data = sc_rec->Reconstruct(start_resnum, loop_length);
+// assume: single chain and res_idx = resnum-1
+void CheckRecData(SidechainReconstructionDataPtr sc_data,
+                  const std::vector<uint>& start_resnums,
+                  const std::vector<uint>& loop_lengths,
+                  uint num_residues) {
   // check all_pos size
   BOOST_CHECK_EQUAL(sc_data->all_pos->GetNumResidues(), num_residues);
+
   // check env_pos consistency
   const uint num_rec_residues = sc_data->env_pos->res_indices.size();
   BOOST_CHECK_EQUAL(sc_data->env_pos->all_pos->GetNumResidues(),
@@ -60,16 +61,32 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
     BOOST_CHECK_EQUAL(sc_data->env_pos->all_pos->GetAA(i),
                       sc_data->all_pos->GetAA(res_idx));
   }
-  // check loop
-  BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), 1u);
-  BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), 1u);
-  BOOST_CHECK_EQUAL(sc_data->loop_lengths[0], loop_length);
-  for (uint i = 0; i < loop_length; ++i) {
+
+  // generate expected data for loops -> set to be ok with flips
+  const uint num_loops = start_resnums.size();
+  std::set<uint> exp_loop_lengths(loop_lengths.begin(), loop_lengths.end());
+  std::set<uint> exp_res_indices;
+  for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
+    for (uint idx = 0; idx < loop_lengths[i_loop]; ++idx) {
+      exp_res_indices.insert(start_resnums[i_loop] + idx - 1);
+    }
+  }
+  // check loops
+  BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), num_loops);
+  BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), num_loops);
+  std::set<uint> sc_loop_lengths(sc_data->loop_lengths.begin(),
+                                 sc_data->loop_lengths.end());
+  BOOST_CHECK(sc_loop_lengths == exp_loop_lengths);
+  std::set<uint> sc_res_indices;
+  for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
     // all loop res. assumed to be contiguous
-    const uint start_idx = sc_data->loop_start_indices[0];
-    const uint res_idx = sc_data->env_pos->res_indices[start_idx + i];
-    BOOST_CHECK(res_idx == start_resnum + i - 1);
+    const uint start_idx = sc_data->loop_start_indices[i_loop];
+    for (uint idx = 0; idx < sc_data->loop_lengths[i_loop]; ++idx) {
+      sc_res_indices.insert(sc_data->env_pos->res_indices[start_idx + idx]);
+    }
   }
+  BOOST_CHECK(sc_res_indices == exp_res_indices);
+
   // check N-ter / C-ter info
   BOOST_CHECK_EQUAL(sc_data->env_pos->res_indices.size(),
                     sc_data->is_n_ter.size());
@@ -82,6 +99,7 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
     BOOST_CHECK(is_nter == sc_data->is_n_ter[i]);
     BOOST_CHECK(is_cter == sc_data->is_c_ter[i]);
   }
+
   // check rotamer_res_indices
   for (uint i = 0; i < sc_data->rotamer_res_indices.size(); ++i) {
     const uint i_res = sc_data->rotamer_res_indices[i];
@@ -89,6 +107,7 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
     const uint res_idx = sc_data->env_pos->res_indices[i_res];
     BOOST_CHECK(!(sc_data->all_pos->IsAllSet(res_idx)));
   }
+
   // check disulfid_bridges
   for (uint i = 0; i < sc_data->disulfid_bridges.size(); ++i) {
     const uint i_res1 = sc_data->disulfid_bridges[i].first;
@@ -102,6 +121,29 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
   }
 }
 
+void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
+                  uint start_resnum, uint loop_length, uint num_residues) {
+  // reconstruct
+  SidechainReconstructionDataPtr sc_data;
+  sc_data = sc_rec->Reconstruct(start_resnum, loop_length);
+  // DEBUG-OUT
+  // std::cout << "SRN: " << start_resnum << ", LL: " << loop_length
+  //           << ", NR: " << num_residues
+  //           << ", RIS: " << sc_data->env_pos->res_indices.size()
+  //           << ", RRIS: " << sc_data->rotamer_res_indices.size()
+  //           << ", DBS: " << sc_data->disulfid_bridges.size() << "\n";
+  // turn into vector for check and to call other one
+  std::vector<uint> start_resnums(1, start_resnum);
+  std::vector<uint> loop_lengths(1, loop_length);
+  // check
+  CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
+  // call other one
+  std::vector<uint> chain_indices(1, 0);
+  sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
+  // check
+  CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
+}
+
 void CheckEmptyLoop(const SidechainReconstructionDataPtr sc_data,
                     uint num_residues) {
   // must all be valid and empty
@@ -145,11 +187,23 @@ BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops) {
   std::vector<uint> chain_indices(1, 0);
   sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
   CheckEmptyLoop(sc_data, num_residues);
+
+  // try three loops (note: overlap resolution is tested with IdxHandler)
+  loop_lengths[0] = 3;
+  start_resnums.push_back(20);
+  start_resnums.push_back(30);
+  loop_lengths.push_back(2);
+  loop_lengths.push_back(1);
+  chain_indices.push_back(0);
+  chain_indices.push_back(0);
+  sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
+  CheckRecData(sc_data, start_resnums, loop_lengths, num_residues);
 }
 
 BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops_crn) {
   // setup crn to test disulfid bridges
   ost::mol::EntityHandle test_ent = LoadTestStructure("data/1crn_sc_test.pdb");
+  // -> sc missing for THR2 & CYS3, 3 disulfid bridges expected...
   uint num_residues = test_ent.GetResidueCount();
   SidechainReconstructorPtr sc_rec = GetScRec(test_ent);