dsfdsfdf

diff --git a/src/dssptools.cpp b/src/dssptools.cpp
index 5fa605a73674eedb10641d992db759d475d86656..26b6e00174991510535a52413fc7a7a7f065ea27 100644 (file)
--- a/src/dssptools.cpp
+++ b/src/dssptools.cpp
@@ -340,7 +340,6 @@ std::string secondaryStructures::patternSearch(){
 //    analyzeBridgesAndLaddersPatterns();
     analyzeTurnsAndHelicesPatterns();
 //    analyzePPHelicesPatterns();
-    NoChainBreaksBetween(80, 75);
 
 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
@@ -625,30 +624,26 @@ void DsspTool::calculateHBondEnergy(ResInfo& Donor,
     float HbondEnergy{ 0 };
     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 
-   if( !(Donor.is_proline) ){
-       if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
-           && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )  // Kinda ew
+   if( !(Acceptor.is_proline) ){
+       if (Donor.getIndex(backboneAtomTypes::AtomC) && Donor.getIndex(backboneAtomTypes::AtomO)
+           && Acceptor.getIndex(backboneAtomTypes::AtomN) && ( Acceptor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )  // Kinda ew
        {
 
            distanceNO = CalculateAtomicDistances(
-                   Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
+                   Acceptor.getIndex(backboneAtomTypes::AtomN), Donor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
            distanceNC = CalculateAtomicDistances(
-                   Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
+                   Acceptor.getIndex(backboneAtomTypes::AtomN), Donor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 
            if (initParams.addHydrogens){
-               if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
-//                   std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
-//                   std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
-//                   std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
-//                   std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
+               if (Acceptor.prevResi != nullptr && Acceptor.prevResi->getIndex(backboneAtomTypes::AtomC) && Acceptor.prevResi->getIndex(backboneAtomTypes::AtomO)){
                    rvec atomH{};
-                   float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
+                   float prevCODist {CalculateAtomicDistances(Acceptor.prevResi->getIndex(backboneAtomTypes::AtomC), Acceptor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
                    for (int i{XX}; i <= ZZ; ++i){
-                       float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
+                       float prevCO = fr.x[Acceptor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Acceptor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
                        atomH[i] = prevCO / prevCODist;
                    }
-                   distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
-                   distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
+                   distanceHO = CalculateAtomicDistances(atomH, Donor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
+                   distanceHC = CalculateAtomicDistances(atomH, Donor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
                }
                else{
                    distanceHO = distanceNO;
@@ -657,13 +652,13 @@ void DsspTool::calculateHBondEnergy(ResInfo& Donor,
            }
            else {
                distanceHO = CalculateAtomicDistances(
-                       Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
+                       Acceptor.getIndex(backboneAtomTypes::AtomH), Donor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
                distanceHC = CalculateAtomicDistances(
-                       Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
+                       Acceptor.getIndex(backboneAtomTypes::AtomH), Donor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
            }
 
            if (CalculateAtomicDistances(
-                       Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
+                       Acceptor.getIndex(backboneAtomTypes::AtomCA), Donor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
                < minimalCAdistance)
            {
                if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)