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

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