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diff --git a/src/dssptools.cpp b/src/dssptools.cpp
index 75546a33614867be94947ba48e720a95698bf3f5..280f46cb10cee73beec9e230a1c79906c31eac32 100644 (file)
--- a/src/dssptools.cpp
+++ b/src/dssptools.cpp
@@ -256,11 +256,11 @@ void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
         std::size_t stride {static_cast<std::size_t>(i) + 3};
         for(std::size_t j {0}; j + static_cast<std::size_t>(i) < SecondaryStructuresStatusMap.size(); ++j){
 //            std::cout << "Testing " << j << " and " << j + stride << std::endl;
-            if ( hasHBondBetween(j, j + (static_cast<std::size_t>(i))) && NoChainBreaksBetween(j, j + stride) ){
+            if ( hasHBondBetween(j, j + stride) && NoChainBreaksBetween(j, j + stride) ){
 //                std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
-                SecondaryStructuresStatusMap[j + static_cast<std::size_t>(i)].setStatus(HelixPositions::End, i);
+                SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 
-                for (std::size_t k {1}; k < (static_cast<std::size_t>(i)); ++k){
+                for (std::size_t k {1}; k < stride; ++k){
                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
                     }
@@ -724,7 +724,7 @@ float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trx
 {
    gmx::RVec r{ 0, 0, 0 };
    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
-   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
+//   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 }
 
@@ -733,7 +733,7 @@ float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_tr
 {
    gmx::RVec r{ 0, 0, 0 };
    pbc_dx(pbc, A, fr.x[B], r.as_vec());
-   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
+//   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 }