Changes in src/moleculelist.cpp [477bb2:244a84]

File:

• src/moleculelist.cpp (modified) (9 diffs)

src/moleculelist.cpp

@@ -4 +4 @@
  *
  */
+
+#include <cstring>
 
 #include "atom.hpp"
@@ -142 +144 @@
 
   // header
-  (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
-  (*out) << "-----------------------------------------------" << endl;
+  Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
+  Log() << Verbose(0) << "-----------------------------------------------" << endl;
   if (ListOfMolecules.size() == 0)
-    (*out) << "\tNone" << endl;
+    Log() << Verbose(0) << "\tNone" << endl;
   else {
     Origin.Zero();
@@ -162 +164 @@
       }
       // output Index, Name, number of atoms, chemical formula
-      (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
+      Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
       Elemental = (*ListRunner)->elemente->end;
       while(Elemental->previous != (*ListRunner)->elemente->start) {
         Elemental = Elemental->previous;
         if (Counts[Elemental->Z] != 0)
-          (*out) << Elemental->symbol << Counts[Elemental->Z];
+          Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
       }
       // Center and size
-      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
+      Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     }
   }
@@ -402 +404 @@
   input.open(line.c_str());
   if (input == NULL) {
-    eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
-    performCriticalExit();
+    Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
     return false;
   }
@@ -740 +741 @@
 /** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
  * \param *out output stream for debugging
- * \param *mol molecule with atoms to dissect
+ * \param *periode periodentafel
  * \param *configuration config with BondGraph
  */
-void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
-{
+void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
+{
+  molecule *mol = new molecule(periode);
+  atom *Walker = NULL;
+  atom *Advancer = NULL;
+  bond *Binder = NULL;
+  bond *Stepper = NULL;
+  // 0. gather all atoms into single molecule
+  for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
+    // shift all atoms to new molecule
+    Advancer = (*MolRunner)->start->next;
+    while (Advancer != (*MolRunner)->end) {
+      Walker = Advancer;
+      Advancer = Advancer->next;
+      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      unlink(Walker);
+      Walker->father = Walker;
+      mol->AddAtom(Walker);    // counting starts at 1
+    }
+    // remove all bonds
+    Stepper = (*MolRunner)->first->next;
+    while (Stepper != (*MolRunner)->last) {
+      Binder = Stepper;
+      Stepper = Stepper->next;
+      delete(Binder);
+    }
+    // remove the molecule
+    delete(*MolRunner);
+    ListOfMolecules.erase(MolRunner);
+  }
+
   // 1. dissect the molecule into connected subgraphs
   configuration->BG->ConstructBondGraph(mol);
@@ -760 +790 @@
   // 4a. create array of molecules to fill
   const int MolCount = Subgraphs->next->Count();
+  char number[MAXSTRINGSIZE];
   molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
   for (int i=0;i<MolCount;i++) {
     molecules[i] = (molecule*) new molecule(mol->elemente);
     molecules[i]->ActiveFlag = true;
+    strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
+    if (MolCount > 1) {
+      sprintf(number, "-%d", i+1);
+      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
+    }
+    cout << "MolName is " << molecules[i]->name << endl;
     insert(molecules[i]);
   }
@@ -771 +808 @@
   int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
-  atom *Walker = NULL;
+  Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -800 +837 @@
     }
   }
-  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintained their ListOfBonds, but we have to remove them from first..last list
-  bond *Binder = mol->first;
+  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
+  Binder = mol->first;
   while (mol->first->next != mol->last) {
     Binder = mol->first->next;
@@ -837 +874 @@
   return AtomNo;
 }
-
-/***********
- * Methods Moved here from the menus
- */
-
-void MoleculeListClass::flipChosen() {
-  int j;
-  Log() << Verbose(0) << "Enter index of molecule: ";
-  cin >> j;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if ((*ListRunner)->IndexNr == j)
-      (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
-}
-
-void MoleculeListClass::createNewMolecule(periodentafel *periode) {
-  molecule *mol = NULL;
-  mol = new molecule(periode);
-  insert(mol);
-};
-
-void MoleculeListClass::loadFromXYZ(periodentafel *periode){
-  molecule *mol = NULL;
-  Vector center;
-  char filename[MAXSTRINGSIZE];
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  mol = new molecule(periode);
-  do {
-    Log() << Verbose(0) << "Enter file name: ";
-    cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-  // center at set box dimensions
-  mol->CenterEdge(&center);
-  mol->cell_size[0] = center.x[0];
-  mol->cell_size[1] = 0;
-  mol->cell_size[2] = center.x[1];
-  mol->cell_size[3] = 0;
-  mol->cell_size[4] = 0;
-  mol->cell_size[5] = center.x[2];
-  insert(mol);
-}
-
-void MoleculeListClass::changeName(){
-  char filename[MAXSTRINGSIZE];
-  molecule *mol = NULL;
-  int nr;
-  do {
-    Log() << Verbose(0) << "Enter index of molecule: ";
-    cin >> nr;
-    mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  Log() << Verbose(0) << "Enter name: ";
-  cin >> filename;
-  strcpy(mol->name, filename);
-}
-
-void MoleculeListClass::setMoleculeFilename() {
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  do {
-    Log() << Verbose(0) << "Enter index of molecule: ";
-    cin >> nr;
-    mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  Log() << Verbose(0) << "Enter name: ";
-  cin >> filename;
-  mol->SetNameFromFilename(filename);
-}
-
-void MoleculeListClass::parseXYZIntoMolecule(){
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  mol = NULL;
-  do {
-   Log() << Verbose(0) << "Enter index of molecule: ";
-   cin >> nr;
-   mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  do {
-   Log() << Verbose(0) << "Enter file name: ";
-   cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-};
-
-void MoleculeListClass::eraseMolecule(){
-  int nr;
-  molecule *mol = NULL;
-  Log() << Verbose(0) << "Enter index of molecule: ";
-  cin >> nr;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if (nr == (*ListRunner)->IndexNr) {
-      mol = *ListRunner;
-      ListOfMolecules.erase(ListRunner);
-      delete(mol);
-      break;
-    }
-};