Changes in src/molecule.cpp [f17e1c:aafd77]

File:

• src/molecule.cpp (modified) (12 diffs)

src/molecule.cpp

@@ -49 +49 @@
 molecule::molecule(const periodentafel * const teil) :
   Observable("molecule"),
-  elemente(teil),  MDSteps(0),  BondCount(0), NoNonHydrogen(0), NoNonBonds(0),
+  elemente(teil),  MDSteps(0),  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0),
   NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
+  formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
 {
 
+  // other stuff
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementsInMolecule[i] = 0;
   strcpy(name,World::getInstance().getDefaultName().c_str());
 };
@@ -97 +101 @@
 }
 
-const Formula &molecule::getFormula(){
-  return formula;
-}
-
-unsigned int molecule::getElementCount(){
-  return formula.getElementCount();
-}
-
-bool molecule::hasElement(const element *element) const{
-  return formula.hasElement(element);
-}
-
-bool molecule::hasElement(atomicNumber_t Z) const{
-  return formula.hasElement(Z);
-}
-
-bool molecule::hasElement(const string &shorthand) const{
-  return formula.hasElement(shorthand);
+const std::string molecule::getFormula(){
+  return *formula;
+}
+
+std::string molecule::calcFormula(){
+  std::map<atomicNumber_t,unsigned int> counts;
+  stringstream sstr;
+  periodentafel *periode = World::getInstance().getPeriode();
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    counts[(*iter)->type->getNumber()]++;
+  }
+  std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
+  for(iter = counts.rbegin(); iter != counts.rend(); ++iter) {
+    atomicNumber_t Z = (*iter).first;
+    sstr << periode->FindElement(Z)->symbol << (*iter).second;
+  }
+  return sstr.str();
 }
 
@@ -207 +210 @@
     pointer->sort = &pointer->nr;
     if (pointer->type != NULL) {
-      formula += pointer->type;
+      if (ElementsInMolecule[pointer->type->Z] == 0)
+        ElementCount++;
+      ElementsInMolecule[pointer->type->Z]++; // increase number of elements
       if (pointer->type->Z != 1)
         NoNonHydrogen++;
@@ -646 +651 @@
 
   // copy values
+  copy->CountElements();
   if (hasBondStructure()) {  // if adjaceny list is present
     copy->BondDistance = BondDistance;
@@ -768 +774 @@
   ASSERT(pointer, "Null pointer passed to molecule::RemoveAtom().");
   OBSERVE;
-  formula-=pointer->type;
+  if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
+    ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
+  } else
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
+    ElementCount--;
   RemoveBonds(pointer);
   erase(pointer);
@@ -782 +793 @@
   if (pointer == NULL)
     return false;
-  formula-=pointer->type;
+  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
+    ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
+  else
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
+    ElementCount--;
   erase(pointer);
   return true;
@@ -855 +871 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+  CountElements();
 
   for (int i=0;i<MAX_ELEMENTS;++i) {
@@ -881 +898 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+  CountElements();
 
   if (output == NULL) {
@@ -922 +940 @@
 bool molecule::Checkout(ofstream * const output)  const
 {
-  return formula.checkOut(output);
+  return elemente->Checkout(output, ElementsInMolecule);
 };
 
@@ -980 +998 @@
 };
 
+/** Brings molecule::ElementCount and molecule::ElementsInMolecule up-to-date.
+ */
+void molecule::CountElements()
+{
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementsInMolecule[i] = 0;
+  ElementCount = 0;
+
+  SetIndexedArrayForEachAtomTo ( ElementsInMolecule, &element::Z, &Increment, 1);
+
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
+};
+
 /** Determines whether two molecules actually contain the same atoms and coordination.
  * \param *out output stream for debugging
@@ -998 +1030 @@
   /// first count both their atoms and elements and update lists thereby ...
   //Log() << Verbose(0) << "Counting atoms, updating list" << endl;
+  CountElements();
+  OtherMolecule->CountElements();
 
   /// ... and compare:
@@ -1007 +1041 @@
     } else Log() << Verbose(4) << "AtomCounts match: " << getAtomCount() << " == " << OtherMolecule->getAtomCount() << endl;
   }
-  /// -# Formula
+  /// -# ElementCount
   if (result) {
-    if (formula != OtherMolecule->formula) {
-      DoLog(4) && (Log() << Verbose(4) << "Formulas don't match: " << formula << " == " << OtherMolecule->formula << endl);
+    if (ElementCount != OtherMolecule->ElementCount) {
+      DoLog(4) && (Log() << Verbose(4) << "ElementCount don't match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl);
       result = false;
-    } else Log() << Verbose(4) << "Formulas match: " << formula << " == " << OtherMolecule->formula << endl;
+    } else Log() << Verbose(4) << "ElementCount match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl;
+  }
+  /// -# ElementsInMolecule
+  if (result) {
+    for (flag=MAX_ELEMENTS;flag--;) {
+      //Log() << Verbose(5) << "Element " <<  flag << ": " << ElementsInMolecule[flag] << " <-> " << OtherMolecule->ElementsInMolecule[flag] << "." << endl;
+      if (ElementsInMolecule[flag] != OtherMolecule->ElementsInMolecule[flag])
+        break;
+    }
+    if (flag < MAX_ELEMENTS) {
+      DoLog(4) && (Log() << Verbose(4) << "ElementsInMolecule don't match." << endl);
+      result = false;
+    } else Log() << Verbose(4) << "ElementsInMolecule match." << endl;
   }
   /// then determine and compare center of gravity for each molecule ...