Changes in src/Legacy/oldmenu.cpp [112b09:42a101]

File:

• src/Legacy/oldmenu.cpp (modified) (14 diffs)

src/Legacy/oldmenu.cpp

@@ -6 +6 @@
  *
  */
-
-#include "Helpers/MemDebug.hpp"
 
 #include "Legacy/oldmenu.hpp"
@@ -38 +36 @@
 #include "Menu/DisplayMenuItem.hpp"
 #include "Menu/SubMenuItem.hpp"
-#include "Actions/MapOfActions.hpp"
 #include "Actions/MethodAction.hpp"
 #include "Actions/ErrorAction.hpp"
@@ -427 +424 @@
 void oldmenu::RemoveAtoms(molecule *mol)
 {
-  atom *second;
+  atom *first, *second;
   int axis;
   double tmp1, tmp2;
@@ -450 +447 @@
       break;
     case 'b':
-      {
-        second = mol->AskAtom("Enter number of atom as reference point: ");
-        Log() << Verbose(0) << "Enter radius: ";
-        cin >> tmp1;
-        molecule::iterator runner;
-        for (molecule::iterator iter = mol->begin(); iter != mol->end(); ) {
-          runner = iter++;
-          if ((*runner)->x.DistanceSquared((*runner)->x) > tmp1*tmp1) // distance to first above radius ...
-            mol->RemoveAtom((*runner));
-        }
+      second = mol->AskAtom("Enter number of atom as reference point: ");
+      Log() << Verbose(0) << "Enter radius: ";
+      cin >> tmp1;
+      first = mol->start;
+      second = first->next;
+      while(second != mol->end) {
+        first = second;
+        second = first->next;
+        if (first->x.DistanceSquared(second->x) > tmp1*tmp1) // distance to first above radius ...
+          mol->RemoveAtom(first);
       }
       break;
@@ -469 +466 @@
       Log() << Verbose(0) << "Upper boundary: ";
       cin >> tmp2;
-      molecule::iterator runner;
-      for (molecule::iterator iter = mol->begin(); iter != mol->end(); ) {
-        runner = iter++;
-        if (((*runner)->x[axis] < tmp1) || ((*runner)->x[axis] > tmp2)) {// out of boundary ...
-          //Log() << Verbose(0) << "Atom " << *(*runner) << " with " << (*runner)->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
-          mol->RemoveAtom((*runner));
+      first = mol->start;
+      second = first->next;
+      while(second != mol->end) {
+        first = second;
+        second = first->next;
+        if ((first->x[axis] < tmp1) || (first->x[axis] > tmp2)) {// out of boundary ...
+          //Log() << Verbose(0) << "Atom " << *first << " with " << first->x.x[axis] << " on axis " << axis << " is out of bounds [" << tmp1 << "," << tmp2 << "]." << endl;
+          mol->RemoveAtom(first);
         }
       }
@@ -517 +516 @@
         min[i] = 0.;
 
-      for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-        Z = (*iter)->type->Z;
+      second = mol->start;
+      while ((second->next != mol->end)) {
+        second = second->next; // advance
+        Z = second->type->Z;
         tmp1 = 0.;
-        if (first != (*iter)) {
-          x = first->x - (*iter)->x;
+        if (first != second) {
+          x = first->x - second->x;
           tmp1 = x.Norm();
         }
         if ((tmp1 != 0.) && ((min[Z] == 0.) || (tmp1 < min[Z]))) min[Z] = tmp1;
-        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << ((*iter)->nr << ": " << tmp1 << " a.u." << endl;
+        //Log() << Verbose(0) << "Bond length between Atom " << first->nr << " and " << second->nr << ": " << tmp1 << " a.u." << endl;
       }
       for (int i=MAX_ELEMENTS;i--;)
@@ -608 +609 @@
   Log() << Verbose(0) << "What's the desired bond order: ";
   cin >> Order1;
-  if (mol->hasBondStructure()) {
+  if (mol->first->next != mol->last) {  // there are bonds
     start = clock();
     mol->FragmentMolecule(Order1, configuration);
@@ -754 +755 @@
     Log() << Verbose(0) << "State the factor: ";
     cin >> faktor;
-    if (mol->getAtomCount() != 0) {  // if there is more than none
-      count = mol->getAtomCount();  // is changed becausing of adding, thus has to be stored away beforehand
+
+    mol->CountAtoms(); // recount atoms
+    if (mol->AtomCount != 0) {  // if there is more than none
+      count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
       Elements = new const element *[count];
       vectors = new Vector *[count];
       j = 0;
-      for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-        Elements[j] = (*iter)->type;
-        vectors[j] = &(*iter)->x;
+      first = mol->start;
+      while (first->next != mol->end) { // make a list of all atoms with coordinates and element
+        first = first->next;
+        Elements[j] = first->type;
+        vectors[j] = &first->x;
         j++;
       }
@@ -778 +783 @@
         }
       }
-      if (mol->hasBondStructure())
+      if (mol->first->next != mol->last) // if connect matrix is present already, redo it
         mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
       // free memory
@@ -904 +909 @@
   molecule *srcmol = NULL, *destmol = NULL;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  dialog->queryMolecule("molecule-by-id",&destmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
-  dialog->queryMolecule("molecule-by-id",&srcmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
+  dialog->queryMolecule("Enter index of destination molecule: ",&destmol, molecules);
+  dialog->queryMolecule("Enter index of source molecule to add from: ",&srcmol, molecules);
   if(dialog->display()) {
     molecules->SimpleAdd(srcmol, destmol);
@@ -918 +923 @@
   molecule *srcmol = NULL, *destmol = NULL;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  dialog->queryMolecule("molecule-by-id",&destmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
-  dialog->queryMolecule("molecule-by-id",&srcmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
+  dialog->queryMolecule("Enter index of matrix molecule (the variable one): ",&srcmol,molecules);
+  dialog->queryMolecule("Enter index of molecule to merge into (the fixed one): ",&destmol,molecules);
   if(dialog->display()) {
     molecules->EmbedMerge(destmol, srcmol);
@@ -1020 +1025 @@
     return;
   }
+  atom *Walker = mol->start;
 
   // generate some KeySets
   Log() << Verbose(0) << "Generating KeySets." << endl;
-  KeySet TestSets[mol->getAtomCount()+1];
+  KeySet TestSets[mol->AtomCount+1];
   i=1;
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+  while (Walker->next != mol->end) {
+    Walker = Walker->next;
     for (int j=0;j<i;j++) {
-      TestSets[j].insert((*iter)->nr);
+      TestSets[j].insert(Walker->nr);
     }
     i++;
@@ -1033 +1040 @@
   Log() << Verbose(0) << "Testing insertion of already present item in KeySets." << endl;
   KeySetTestPair test;
-  molecule::const_iterator iter = mol->begin();
-  if (iter != mol->end()) {
-    test = TestSets[mol->getAtomCount()-1].insert((*iter)->nr);
-    if (test.second) {
-      Log() << Verbose(1) << "Insertion worked?!" << endl;
-    } else {
-      Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
-    }
+  test = TestSets[mol->AtomCount-1].insert(Walker->nr);
+  if (test.second) {
+    Log() << Verbose(1) << "Insertion worked?!" << endl;
   } else {
-    eLog() << Verbose(1) << "No atoms to test double insertion." << endl;
-  }
+    Log() << Verbose(1) << "Insertion rejected: Present object is " << (*test.first) << "." << endl;
+  }
+  TestSets[mol->AtomCount].insert(mol->end->previous->nr);
+  TestSets[mol->AtomCount].insert(mol->end->previous->previous->previous->nr);
 
   // constructing Graph structure
@@ -1051 +1055 @@
   // insert KeySets into Subgraphs
   Log() << Verbose(0) << "Inserting KeySets into Subgraph class." << endl;
-  for (int j=0;j<mol->getAtomCount();j++) {
+  for (int j=0;j<mol->AtomCount;j++) {
     Subgraphs.insert(GraphPair (TestSets[j],pair<int, double>(counter++, 1.)));
   }
   Log() << Verbose(0) << "Testing insertion of already present item in Subgraph." << endl;
   GraphTestPair test2;
-  test2 = Subgraphs.insert(GraphPair (TestSets[mol->getAtomCount()],pair<int, double>(counter++, 1.)));
+  test2 = Subgraphs.insert(GraphPair (TestSets[mol->AtomCount],pair<int, double>(counter++, 1.)));
   if (test2.second) {
     Log() << Verbose(1) << "Insertion worked?!" << endl;