Changes in src/analysis_bonds.cpp [68f03d:112b09]

File:

• src/analysis_bonds.cpp (modified) (11 diffs)

src/analysis_bonds.cpp

@@ -5 +5 @@
  *      Author: heber
  */
+
+#include "Helpers/MemDebug.hpp"
 
 #include "analysis_bonds.hpp"
@@ -26 +28 @@
   Mean = 0.;
 
-  atom *Walker = mol->start;
   int AtomCount = 0;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    const int count = Walker->ListOfBonds.size();
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    const int count = (*iter)->ListOfBonds.size();
     if (Max < count)
       Max = count;
@@ -51 +51 @@
  * \param &Max maximum distance on return, 0 if no bond between the two elements
  */
-void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max)
+void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, const element *type1, const element *type2, double &Min, double &Mean, double &Max)
 {
   Min = 2e+6;
@@ -58 +58 @@
 
   int AtomNo = 0;
-  atom *Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    if (Walker->type == type1)
-      for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++)
-        if ((*BondRunner)->GetOtherAtom(Walker)->type == type2) {
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    if ((*iter)->type == type1)
+      for (BondList::const_iterator BondRunner = (*iter)->ListOfBonds.begin(); BondRunner != (*iter)->ListOfBonds.end(); BondRunner++)
+        if ((*BondRunner)->GetOtherAtom((*iter))->type == type2) {
           const double distance = (*BondRunner)->GetDistanceSquared();
           if (Min > distance)
@@ -124 +122 @@
  * \param *InterfaceElement or NULL
  */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
-{
-  atom *Walker = NULL;
-  atom *Runner = NULL;
+int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
+{
   int count = 0;
   int OtherHydrogens = 0;
@@ -133 +129 @@
   bool InterfaceFlag = false;
   bool OtherHydrogenFlag = true;
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); MolRunner++) {
-        Runner = (*MolRunner)->start;
-        while (Runner->next != (*MolRunner)->end) {
-          Runner = Runner->next;
-          if ((Walker->type->Z  == 8) && (Runner->type->Z  == 8)) {
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); ++MolWalker) {
+    molecule::iterator Walker = (*MolWalker)->begin();
+    for(;Walker!=(*MolWalker)->end();++Walker){
+      for (MoleculeList::const_iterator MolRunner = molecules->ListOfMolecules.begin();MolRunner != molecules->ListOfMolecules.end(); ++MolRunner) {
+        molecule::iterator Runner = (*MolRunner)->begin();
+        for(;Runner!=(*MolRunner)->end();++Runner){
+          if (((*Walker)->type->Z  == 8) && ((*Runner)->type->Z  == 8)) {
             // check distance
-            const double distance = Runner->x.DistanceSquared(Walker->x);
+            const double distance = (*Runner)->x.DistanceSquared((*Walker)->x);
             if ((distance > MYEPSILON) && (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE)) { // distance >0 means  different atoms
               // on other atom(Runner) we check for bond to interface element and
@@ -151 +145 @@
               OtherHydrogens = 0;
               InterfaceFlag = (InterfaceElement == NULL);
-              for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
-                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
+              for (BondList::const_iterator BondRunner = (*Runner)->ListOfBonds.begin(); BondRunner != (*Runner)->ListOfBonds.end(); BondRunner++) {
+                atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Runner);
                 // if hydrogen, check angle to be greater(!) than 30 degrees
                 if (OtherAtom->type->Z == 1) {
-                  const double angle = CalculateAngle(&OtherAtom->x, &Runner->x, &Walker->x);
+                  const double angle = CalculateAngle(&OtherAtom->x, &(*Runner)->x, &(*Walker)->x);
                   OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
                   Otherangle += angle;
@@ -176 +170 @@
               if (InterfaceFlag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
-                for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
-                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
+                for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {
+                  atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
                   if (OtherAtom->type->Z == 1) {
                     // check angle
-                    if (CheckHydrogenBridgeBondAngle(Walker, OtherAtom, Runner)) {
-                      DoLog(1) && (Log() << Verbose(1) << Walker->getName() << ", " << OtherAtom->getName() << " and " << Runner->getName() << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &Walker->x, &Runner->x)*(180./M_PI) << "." << endl);
+                    if (CheckHydrogenBridgeBondAngle(*Walker, OtherAtom, *Runner)) {
+                      DoLog(1) && (Log() << Verbose(1) << (*Walker)->getName() << ", " << OtherAtom->getName() << " and " << (*Runner)->getName() << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &(*Walker)->x, &(*Runner)->x)*(180./M_PI) << "." << endl);
                       count++;
                       break;
@@ -205 +199 @@
 int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second)
 {
-  atom *Walker = NULL;
   int count = 0;
 
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      if ((Walker->type == first) || (Walker->type == second)) {  // first element matches
-        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
-          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
-          if (((OtherAtom->type == first) || (OtherAtom->type == second)) && (Walker->nr < OtherAtom->nr)) {
+    molecule::iterator Walker = (*MolWalker)->begin();
+    for(;Walker!=(*MolWalker)->end();++Walker){
+      atom * theAtom = *Walker;
+      if ((theAtom->type == first) || (theAtom->type == second)) {  // first element matches
+        for (BondList::const_iterator BondRunner = theAtom->ListOfBonds.begin(); BondRunner != theAtom->ListOfBonds.end(); BondRunner++) {
+          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
+          if (((OtherAtom->type == first) || (OtherAtom->type == second)) && (theAtom->nr < OtherAtom->nr)) {
             count++;
             DoLog(1) && (Log() << Verbose(1) << first->name << "-" << second->name << " bond found between " << *Walker << " and " << *OtherAtom << "." << endl);
@@ -240 +233 @@
   bool MatchFlag[2];
   bool result = false;
-  atom *Walker = NULL;
   const element * ElementArray[2];
   ElementArray[0] = first;
@@ -246 +238 @@
 
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
-    Walker = (*MolWalker)->start;
-    while (Walker->next != (*MolWalker)->end) {
-      Walker = Walker->next;
-      if (Walker->type == second) {  // first element matches
+    molecule::iterator Walker = (*MolWalker)->begin();
+    for(;Walker!=(*MolWalker)->end();++Walker){
+      atom *theAtom = *Walker;
+      if (theAtom->type == second) {  // first element matches
         for (int i=0;i<2;i++)
           MatchFlag[i] = false;
-        for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {
-          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Walker);
+        for (BondList::const_iterator BondRunner = theAtom->ListOfBonds.begin(); BondRunner != theAtom->ListOfBonds.end(); BondRunner++) {
+          atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
           for (int i=0;i<2;i++)
             if ((!MatchFlag[i]) && (OtherAtom->type == ElementArray[i])) {