Changes in src/molecule.cpp [7baf4a:f17e1c]

File:

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

src/molecule.cpp

@@ -151 +151 @@
 molecule::const_iterator molecule::erase( const_iterator loc )
 {
-  OBSERVE;
   molecule::const_iterator iter = loc;
   iter--;
@@ -157 +156 @@
   atomIds.erase( atom->getId() );
   atoms.remove( atom );
-  formula-=atom->type;
   atom->removeFromMolecule();
   return iter;
@@ -164 +162 @@
 molecule::const_iterator molecule::erase( atom * key )
 {
-  OBSERVE;
   molecule::const_iterator iter = find(key);
   if (iter != end()){
     atomIds.erase( key->getId() );
     atoms.remove( key );
-    formula-=key->type;
     key->removeFromMolecule();
   }
@@ -187 +183 @@
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
-  OBSERVE;
   pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
     atoms.push_back(key);
-    formula+=key->type;
     return pair<iterator,bool>(molecule::iterator(--end()),res.second);
   } else {
@@ -239 +233 @@
   if (pointer != NULL) {
     atom *walker = pointer->clone();
-    formula += walker->type;
     walker->setName(pointer->getName());
     walker->nr = last_atom++;  // increase number within molecule
@@ -626 +619 @@
 {
   molecule *copy = World::getInstance().createMolecule();
+  atom *LeftAtom = NULL, *RightAtom = NULL;
 
   // copy all atoms
-  for_each(atoms.begin(),atoms.end(),bind1st(mem_fun(&molecule::AddCopyAtom),copy));
+  ActOnCopyWithEachAtom ( &molecule::AddCopyAtom, copy );
 
   // copy all bonds
+  bond *Binder = NULL;
+  bond *NewBond = NULL;
   for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
     for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        bond *Binder = (*BondRunner);
+        Binder = (*BondRunner);
 
         // get the pendant atoms of current bond in the copy molecule
-        atomSet::iterator leftiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->leftatom));
-        atomSet::iterator rightiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->rightatom));
-        ASSERT(leftiter!=atoms.end(),"No original left atom for bondcopy found");
-        ASSERT(leftiter!=atoms.end(),"No original right atom for bondcopy found");
-        atom *LeftAtom = *leftiter;
-        atom *RightAtom = *rightiter;
-
-        bond *NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->leftatom, (const atom **)&LeftAtom );
+        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->rightatom, (const atom **)&RightAtom );
+
+        NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
         NewBond->Cyclic = Binder->Cyclic;
         if (Binder->Cyclic)
@@ -651 +643 @@
       }
   // correct fathers
-  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
+  ActOnAllAtoms( &atom::CorrectFather );
 
   // copy values
@@ -860 +852 @@
  * \param *out output stream
  */
-bool molecule::Output(ostream * const output)
-{
+bool molecule::Output(ofstream * const output)
+{
+  int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+
+  for (int i=0;i<MAX_ELEMENTS;++i) {
+    AtomNo[i] = 0;
+    ElementNo[i] = 0;
+  }
   if (output == NULL) {
     return false;
   } else {
-    int AtomNo[MAX_ELEMENTS];
-    memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
-    enumeration<const element*> elementLookup = formula.enumerateElements();
-    for(map<const element*,unsigned int>::iterator iter=elementLookup.there.begin();
-        iter!=elementLookup.there.end();++iter){
-      cout << "Enumerated element " << *iter->first << " with number " << iter->second << endl;
-    }
     *output << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
-    for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
+    SetIndexedArrayForEachAtomTo ( ElementNo, &element::Z, &AbsoluteValue, 1);
+    int current=1;
+    for (int i=0;i<MAX_ELEMENTS;++i) {
+      if (ElementNo[i] == 1)
+        ElementNo[i] = current++;
+    }
+    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
     return true;
   }
@@ -916 +913 @@
 {
   DoLog(2) && (Log() << Verbose(2) << endl << "From Contents of ListOfBonds, all non-hydrogen atoms:" << endl);
-  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputBondOfAtom));
+  ActOnAllAtoms (&atom::OutputBondOfAtom );
   DoLog(0) && (Log() << Verbose(0) << endl);
 };
@@ -939 +936 @@
     for (int step=0;step<MDSteps;step++) {
       *output << getAtomCount() << "\n\tCreated by molecuilder, step " << step << ", on " << ctime(&now);
-      for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputTrajectoryXYZ,_1,output,step));
+      ActOnAllAtoms( &atom::OutputTrajectoryXYZ, output, step );
     }
     return true;
@@ -956 +953 @@
     now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     *output << getAtomCount() << "\n\tCreated by molecuilder on " << ctime(&now);
-    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputXYZLine),output));
+    ActOnAllAtoms( &atom::OutputXYZLine, output );
     return true;
   } else