From: Горелов Сергей Васильевич <gorelov_sv@pnpi.nrcki.ru>
Date: Mon, 3 Oct 2022 10:37:16 +0000 (+0300)
Subject: Пробую поменять тюрны
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=d2f254ef68c850c8f9c098021a67a28400ee32e2;p=alexxy%2Fgromacs-dssp.git

Пробую поменять тюрны
---

diff --git a/src/dssptools.cpp b/src/dssptools.cpp
index d50c630..2e261ee 100644
--- a/src/dssptools.cpp
+++ b/src/dssptools.cpp
@@ -402,7 +402,7 @@ void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
                 for (std::size_t k {1}; k < stride; ++k){
                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
-                        SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
+//                        SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
                     }
                 }
 
@@ -451,20 +451,20 @@ void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 
     /* Не знаю зач они в дссп так сделали, этож полное говно */
 
-//    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
-//        if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
-//            bool isTurn = false;
-//            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
-//                std::size_t stride {static_cast<std::size_t>(j) + 3};
-//                for(std::size_t k {1}; k < stride and !isTurn; ++k){
-//                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
-//                }
-//            }
-//            if (isTurn){
-//                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
-//            }
-//        }
-//    }
+    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
+        if (static_cast<int>(SecondaryStructuresStatusMap[i].getStatus()) <= static_cast<int>(secondaryStructureTypes::Turn)){
+            bool isTurn = false;
+            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
+                std::size_t stride {static_cast<std::size_t>(j) + 3};
+                for(std::size_t k {1}; k < stride and !isTurn; ++k){
+                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
+                }
+            }
+            if (isTurn){
+                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
+            }
+        }
+    }
 
 }
 
@@ -771,27 +771,27 @@ float DsspTool::CalculateDihedralAngle(const int &A, const int &B, const int &C,
         y[i] = (z[j] * x[k]) - (z[k] * x[j]);
     }
 
-    std::cout << "v12 = " << v12[0] << ", " << v12[1] << ", " << v12[2] << std::endl;
-    std::cout << "v43 = " << v43[0] << ", " << v43[1] << ", " << v43[2] << std::endl;
-    std::cout << "z = " << z[0] << ", " << z[1] << ", " << z[2] << std::endl;
-    std::cout << "p = " << p[0] << ", " << p[1] << ", " << p[2] << std::endl;
-    std::cout << "x = " << x[0] << ", " << x[1] << ", " << x[2] << std::endl;
-    std::cout << "y = " << y[0] << ", " << y[1] << ", " << y[2] << std::endl;
+//    std::cout << "v12 = " << v12[0] << ", " << v12[1] << ", " << v12[2] << std::endl;
+//    std::cout << "v43 = " << v43[0] << ", " << v43[1] << ", " << v43[2] << std::endl;
+//    std::cout << "z = " << z[0] << ", " << z[1] << ", " << z[2] << std::endl;
+//    std::cout << "p = " << p[0] << ", " << p[1] << ", " << p[2] << std::endl;
+//    std::cout << "x = " << x[0] << ", " << x[1] << ", " << x[2] << std::endl;
+//    std::cout << "y = " << y[0] << ", " << y[1] << ", " << y[2] << std::endl;
 
     u = (x[XX] * x[XX]) + (x[YY] * x[YY]) + (x[ZZ] * x[ZZ]);
     v = (y[XX] * y[XX]) + (y[YY] * y[YY]) + (y[ZZ] * y[ZZ]);
 
-    std::cout << "u = " << u << std::endl;
-    std::cout << "v = " << v << std::endl;
+//    std::cout << "u = " << u << std::endl;
+//    std::cout << "v = " << v << std::endl;
 
     if (u > 0 and v > 0){
         u = ((p[XX] * x[XX]) + (p[YY] * x[YY]) + (p[ZZ] * x[ZZ])) / std::sqrt(u);
         v = ((p[XX] * y[XX]) + (p[YY] * y[YY]) + (p[ZZ] * y[ZZ])) / std::sqrt(v);
-        std::cout << "new u = " << u << std::endl;
-        std::cout << "new v = " << v << std::endl;
+//        std::cout << "new u = " << u << std::endl;
+//        std::cout << "new v = " << v << std::endl;
         if (u != 0 or v != 0){
             result = std::atan2(v, u) * gmx::c_rad2Deg;
-            std::cout << "result = " << result << std::endl;
+//            std::cout << "result = " << result << std::endl;
         }
     }
     return result;
@@ -810,7 +810,7 @@ void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
 //    psi.resize(IndexMap.size(), 360);
 
     for (std::size_t i = 1; i + 1 < IndexMap.size(); ++i){ // TODO add index verifictaion (check if those atom indexes exist)
-        std::cout << "For resi " << i << " :" << std::endl;
+//        std::cout << "For resi " << i << " :" << std::endl;
         phi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i - 1].getIndex(backboneAtomTypes::AtomC)),
                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
@@ -824,8 +824,8 @@ void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
                                         fr,
                                         pbc);
 //        std::cout << "For " << i << " phi = " << phi[i] << ", psi = " << psi[i] << std::endl;
-        std::cout << "phi[" << i << "] = " << phi[i] << std::endl;
-        std::cout << "psi[" << i << "] = " << psi[i] << std::endl;
+//        std::cout << "phi[" << i << "] = " << phi[i] << std::endl;
+//        std::cout << "psi[" << i << "] = " << psi[i] << std::endl;
     }
 
     for (std::size_t i = 1; i + 3 < IndexMap.size(); ++i){