--- branches/new_design/OOPSE-2.0/src/primitives/Molecule.cpp	2004/11/01 20:15:58	1692
+++ branches/new_design/OOPSE-2.0/src/primitives/Molecule.cpp	2004/11/01 22:52:57	1695
@@ -30,56 +30,60 @@
  * @version 1.0
  */ 
 
-#include "primitives/Molecule.hpp"
 #include <algorithm>
+#include <set>
 
+#include "primitives/Molecule.hpp"
+#include "utils/MemoryUtils.hpp"
+
 namespace oopse {
 
 Molecule::~Molecule() {
 
-    deleteVectorOfPointer(atoms_);
-    deleteVectorOfPointer(bonds_);
-    deleteVectorOfPointer(bends_);
-    deleteVectorOfPointer(torsions_);
-    deleteVectorOfPointer(rigidbodies_);
-    deleteVectorOfPointer(cutoffGroups_);
+    MemoryUtils::deleteVectorOfPointer(atoms_);
+    MemoryUtils::deleteVectorOfPointer(bonds_);
+    MemoryUtils::deleteVectorOfPointer(bends_);
+    MemoryUtils::deleteVectorOfPointer(torsions_);
+    MemoryUtils::deleteVectorOfPointer(rigidBodies_);
+    MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
 
+    //integrableObjects_ don't own the objects
     integrableObjects_.clear();
     
 }
 
 void Molecule::addAtom(Atom* atom) {
-    if (atoms_.find(atom) == atoms_.end()) {
+    if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
         atoms_.push_back(atom);
     }
 }
 
 void Molecule::addBond(Bond* bond) {
-    if (bonds_.find(bond) == bonds_.end()) {
+    if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
         bonds_.push_back(bond);
     }
 }
 
 void Molecule::addBend(Bend* bend) {
-    if (bends_.find(bend) == bends_.end()) {
+    if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
         bends_.push_back(bend);
     }
 }
 
 void Molecule::addTorsion(Torsion* torsion) {
-    if (torsions_.find(torsion) == torsions_.end()) {
+    if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
         torsions_.push_back(torsion);
     }
 }
 
 void Molecule::addRigidBody(RigidBody *rb) {
-    if (rigidBodies_.find(bond) == bonds_.end()) {
+    if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
         rigidBodies_.push_back(rb);
     }
 }
 
 void Molecule::addCutoffGroup(CutoffGroup* cp) {
-    if (cutoffGroups_.find(bond) == bonds_.end()) {
+    if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
         cutoffGroups_.push_back(cp);
     }
 
@@ -92,11 +96,11 @@ void Molecule::complete() {
 
     std::set<Atom*> rigidAtoms;
     RigidBody* rb;
-    std::vector<RigidBody*> rbIter;
+    std::vector<RigidBody*>::iterator rbIter;
 
     
     for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
-        rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter());
+        rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
     }
 
     //find all free atoms (which do not belong to rigid bodies)  
@@ -190,10 +194,10 @@ void Molecule::calcForces() {
     Bond* bond;
     Bend* bend;
     Torsion* torsion;
-    std::vector<RigidBody*> rbIter;
-    std::vector<Bond*> bondIter;;
-    std::vector<Bend*> bendIter;
-    std::vector<Torsion*> torsionIter;
+    std::vector<RigidBody*>::iterator rbIter;
+    std::vector<Bond*>::iterator bondIter;;
+    std::vector<Bend*>::iterator bendIter;
+    std::vector<Torsion*>::iterator torsionIter;
 
     for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
         rb->updateAtoms();
@@ -219,9 +223,9 @@ double Molecule::getPotential() {
     Bend* bend;
     Torsion* torsion;
     //std::vector<RigidBody*> rbIter;
-    std::vector<Bond*> bondIter;;
-    std::vector<Bend*> bendIter;
-    std::vector<Torsion*> torsionIter;
+    std::vector<Bond*>::iterator bondIter;;
+    std::vector<Bend*>::iterator bendIter;
+    std::vector<Torsion*>::iterator torsionIter;
 
     double potential = 0;
     
@@ -262,12 +266,12 @@ void Molecule::moveCom(const Vetor3d& delta) {
     return com;
 }
 
-void Molecule::moveCom(const Vetor3d& delta) {
+void Molecule::moveCom(const Vector3d& delta) {
     StuntDouble* sd;
     std::vector<StuntDouble*>::iterator i;
     
     for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
-        s->setPos(sd->getPos() + delta);
+        sd->setPos(sd->getPos() + delta);
     }
 
 }
@@ -290,7 +294,7 @@ std::ostream& operator <<(std::ostream& o, const Molec
     return velCom;
 }
 
-std::ostream& operator <<(std::ostream& o, const Molecule& mol) {
+std::ostream& operator <<(std::ostream& o, Molecule& mol) {
     o << std::endl;
     o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
     o << mol.getNAtoms() << " atoms" << std::endl;