Changes in src/analysis_bonds.cpp [2fe971:bf3817]

File:

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

src/analysis_bonds.cpp

@@ -6 +6 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
@@ -12 +17 @@
 #include "bond.hpp"
 #include "element.hpp"
-#include "info.hpp"
-#include "verbose.hpp"
-#include "log.hpp"
+#include "Helpers/Info.hpp"
+#include "Helpers/Verbose.hpp"
+#include "Helpers/Log.hpp"
 #include "molecule.hpp"
 
@@ -60 +65 @@
   int AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    if ((*iter)->type == type1)
+    if ((*iter)->getType() == type1)
       for (BondList::const_iterator BondRunner = (*iter)->ListOfBonds.begin(); BondRunner != (*iter)->ListOfBonds.end(); BondRunner++)
-        if ((*BondRunner)->GetOtherAtom((*iter))->type == type2) {
+        if ((*BondRunner)->GetOtherAtom((*iter))->getType() == type2) {
           const double distance = (*BondRunner)->GetDistanceSquared();
           if (Min > distance)
@@ -87 +92 @@
  * \return angle between \a *first and \a *second, both relative to origin at \a *origin.
  */
-double CalculateAngle(Vector *first, Vector *central, Vector *second)
+double CalculateAngle(const Vector &first, const Vector &central, const Vector &second)
 {
   Vector OHBond;
   Vector OOBond;
 
-  OHBond = (*first) - (*central);
-  OOBond = (*second) - (*central);
+  OHBond = first - central;
+  OOBond = second - central;
   const double angle = OHBond.Angle(OOBond);
   return angle;
@@ -110 +115 @@
 
   // check angle
-  if (CalculateAngle(&Hydrogen->x, &Oxygen->x, &OtherOxygen->x) < M_PI*(30./180.)) {
+  if (CalculateAngle(Hydrogen->getPosition(), Oxygen->getPosition(), OtherOxygen->getPosition()) < M_PI*(30./180.)) {
     return true;
   } else {
@@ -138 +143 @@
         molecule::iterator Runner = (*MolRunner)->begin();
         for(;Runner!=(*MolRunner)->end();++Runner){
-          if (((*Walker)->type->Z  == 8) && ((*Runner)->type->Z  == 8)) {
+          if (((*Walker)->getType()->Z  == 8) && ((*Runner)->getType()->Z  == 8)) {
             // check distance
-            const double distance = (*Runner)->x.DistanceSquared((*Walker)->x);
+            const double distance = (*Runner)->DistanceSquared(*(*Walker));
             if ((distance > MYEPSILON) && (distance < HBRIDGEDISTANCE*HBRIDGEDISTANCE)) { // distance >0 means  different atoms
               // on other atom(Runner) we check for bond to interface element and
@@ -152 +157 @@
                 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);
+                if (OtherAtom->getType()->Z == 1) {
+                  const double angle = CalculateAngle(OtherAtom->getPosition(), (*Runner)->getPosition(), (*Walker)->getPosition());
                   OtherHydrogenFlag = OtherHydrogenFlag && (angle > M_PI*(30./180.) + MYEPSILON);
                   Otherangle += angle;
                   OtherHydrogens++;
                 }
-                InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
-                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
+                InterfaceFlag = InterfaceFlag || (OtherAtom->getType() == InterfaceElement);
+                Interface2Flag = Interface2Flag || (OtherAtom->getType() == Interface2Element);
               }
               DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
@@ -177 +182 @@
                 for (BondList::const_iterator BondRunner = (*Walker)->ListOfBonds.begin(); BondRunner != (*Walker)->ListOfBonds.end(); BondRunner++) {
                   atom * const OtherAtom = (*BondRunner)->GetOtherAtom(*Walker);
-                  if (OtherAtom->type->Z == 1) {
+                  if (OtherAtom->getType()->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);
+                      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->getPosition(), (*Walker)->getPosition(), (*Runner)->getPosition())*(180./M_PI) << "." << endl);
                       count++;
                       break;
@@ -210 +215 @@
     for(;Walker!=(*MolWalker)->end();++Walker){
       atom * theAtom = *Walker;
-      if ((theAtom->type == first) || (theAtom->type == second)) {  // first element matches
+      if ((theAtom->getType() == first) || (theAtom->getType() == 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)) {
+          if (((OtherAtom->getType() == first) || (OtherAtom->getType() == second)) && (theAtom->nr < OtherAtom->nr)) {
             count++;
             DoLog(1) && (Log() << Verbose(1) << *first << "-" << *second << " bond found between " << *Walker << " and " << *OtherAtom << "." << endl);
@@ -246 +251 @@
     for(;Walker!=(*MolWalker)->end();++Walker){
       atom *theAtom = *Walker;
-      if (theAtom->type == second) {  // first element matches
+      if (theAtom->getType() == second) {  // first element matches
         for (int i=0;i<2;i++)
           MatchFlag[i] = false;
@@ -252 +257 @@
           atom * const OtherAtom = (*BondRunner)->GetOtherAtom(theAtom);
           for (int i=0;i<2;i++)
-            if ((!MatchFlag[i]) && (OtherAtom->type == ElementArray[i])) {
+            if ((!MatchFlag[i]) && (OtherAtom->getType() == ElementArray[i])) {
               MatchFlag[i] = true;
               break;  // each bonding atom can match at most one element we are looking for