Changes in src/molecule.cpp [2ba827:24a5e0]

File:

• src/molecule.cpp (modified) (10 diffs)

src/molecule.cpp

@@ -8 +8 @@
 #include <boost/bind.hpp>
 
+#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -30 +31 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(const periodentafel * const teil) : elemente(teil), start(new atom), end(new atom), 
+molecule::molecule(const periodentafel * const teil) : elemente(teil), start(World::get()->createAtom()), end(World::get()->createAtom()),
   first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0), 
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
-  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start),
-  formula(this,boost::bind(&molecule::calcFormula,this))
+  ActiveFlag(false), IndexNr(-1),
+  formula(this,boost::bind(&molecule::calcFormula,this)),
+  last_atom(0),
+  InternalPointer(start)
 {
   // init atom chain list
@@ -52 +55 @@
 };
 
+molecule *NewMolecule(){
+  return new molecule(World::get()->getPeriode());
+}
+
 /** Destructor of class molecule.
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
@@ -60 +67 @@
   delete(first);
   delete(last);
-  delete(end);
-  delete(start);
-};
-
+  end->getWorld()->destroyAtom(end);
+  start->getWorld()->destroyAtom(start);
+};
+
+
+void DeleteMolecule(molecule *mol){
+  delete mol;
+}
 
 // getter and setter
@@ -73 +84 @@
   OBSERVE;
   strncpy(name,_name.c_str(),MAXSTRINGSIZE);
+}
+
+moleculeId_t molecule::getId(){
+  return id;
+}
+
+void molecule::setId(moleculeId_t _id){
+  id =_id;
 }
 
@@ -135 +154 @@
   OBSERVE;
   if (pointer != NULL) {
-    atom *walker = new atom(pointer);
+    atom *walker = pointer->clone();
     walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
     strcpy (walker->Name, pointer->Name);
@@ -242 +261 @@
   switch(TopBond->BondDegree) {
     case 1:
-      FirstOtherAtom = new atom();    // new atom
+      FirstOtherAtom = World::get()->createAtom();    // new atom
       FirstOtherAtom->type = elemente->FindElement(1);  // element is Hydrogen
       FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
@@ -299 +318 @@
 
       // create the two Hydrogens ...
-      FirstOtherAtom = new atom();
-      SecondOtherAtom = new atom();
+      FirstOtherAtom = World::get()->createAtom();
+      SecondOtherAtom = World::get()->createAtom();
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
@@ -354 +373 @@
     case 3:
       // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
-      FirstOtherAtom = new atom();
-      SecondOtherAtom = new atom();
-      ThirdOtherAtom = new atom();
+      FirstOtherAtom = World::get()->createAtom();
+      SecondOtherAtom = World::get()->createAtom();
+      ThirdOtherAtom = World::get()->createAtom();
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
@@ -475 +494 @@
     MDSteps++;
   for(i=0;i<NumberOfAtoms;i++){
-    Walker = new atom;
+    Walker = World::get()->createAtom();
     getline(xyzfile,line,'\n');
     istringstream *item = new istringstream(line);