SCHWED-1740: resolve overlaps in MmSystemCreator

loop/src/mm_system_creator.cc

 #include <promod3/loop/mm_system_creator.hh>
 
 #include <promod3/loop/hydrogen_constructor.hh>
+#include <promod3/loop/idx_handler.hh>
 #include <promod3/core/message.hh>
 #include <promod3/core/runtime_profiling.hh>
 
@@ -274,6 +275,10 @@ void MmSystemCreator::SetupSystem(const AllAtomPositions& all_pos,
 
   // check data consistency
   const uint num_loops = loop_start_indices.size();
+  if (num_loops != loop_lengths.size()) {
+    throw promod3::Error("Sizes of loop_start_indices and loop_lengths must "
+                         "match in MmSystemCreator::SetupSystem!");
+  }
   for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
     // loop from start_idx to start_idx + loop_lengths[i_loop] - 1
     const uint start_idx = loop_start_indices[i_loop];
@@ -284,11 +289,11 @@ void MmSystemCreator::SetupSystem(const AllAtomPositions& all_pos,
   }
   if (is_n_ter.size() != res_indices.size()) {
     throw promod3::Error("Sizes of res_indices and is_n_ter must match in "
-                         "in MmSystemCreator::SetupSystem!");
+                         "MmSystemCreator::SetupSystem!");
   }
   if (is_c_ter.size() != res_indices.size()) {
     throw promod3::Error("Sizes of res_indices and is_c_ter must match in "
-                         "in MmSystemCreator::SetupSystem!");
+                         "MmSystemCreator::SetupSystem!");
   }
   for (uint i_res = 0; i_res < res_indices.size(); ++i_res) {
     const uint res_idx = res_indices[i_res];
@@ -301,21 +306,25 @@ void MmSystemCreator::SetupSystem(const AllAtomPositions& all_pos,
   for (uint i = 0; i < disulfid_bridges.size(); ++i) {
     if (disulfid_bridges[i].first >= res_indices.size()) {
       throw promod3::Error("Invalid disulfid bridge residue index observed in "
-                           "in MmSystemCreator::SetupSystem!");
+                           "MmSystemCreator::SetupSystem!");
     }
     if (disulfid_bridges[i].second >= res_indices.size()) {
       throw promod3::Error("Invalid disulfid bridge residue index observed in "
-                           "in MmSystemCreator::SetupSystem!");
+                           "MmSystemCreator::SetupSystem!");
     }
   }
 
   // setup internal data (loop_..., is_X_ter_, ff_aa_, first_idx_)
-  num_loop_residues_ = 0;
-  for (uint i_loop = 0; i_loop < num_loops; ++i_loop) {
-    num_loop_residues_ += loop_lengths[i_loop];
-  }
   loop_start_indices_ = loop_start_indices;
   loop_lengths_ = loop_lengths;
+  IdxHandler::ResolveOverlaps(loop_start_indices_, loop_lengths_, true);
+  if (loop_lengths_.empty()) {
+    throw promod3::Error("No valid loops in MmSystemCreator::SetupSystem!");
+  }
+  num_loop_residues_ = 0;
+  for (uint i_loop = 0; i_loop < loop_lengths_.size(); ++i_loop) {
+    num_loop_residues_ += loop_lengths_[i_loop];
+  }
   is_n_ter_ = is_n_ter;
   is_c_ter_ = is_c_ter;
   SetupNextIRes_(res_indices);
@@ -338,7 +347,7 @@ void MmSystemCreator::UpdatePositions(const AllAtomPositions& all_pos,
   // check data consistency
   if (ff_aa_.size() != res_indices.size()) {
     throw promod3::Error("Inconsistent size of res_indices in "
-                         "in MmSystemCreator::SetupSystem!");
+                         "MmSystemCreator::SetupSystem!");
   }
   for (uint i_res = 0; i_res < res_indices.size(); ++i_res) {
     const uint res_idx = res_indices[i_res];