Changes in src/moleculelist.cpp [244a84:482373]

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -4 +4 @@
  *
  */
-
-#include <cstring>
 
 #include "atom.hpp"
@@ -741 +739 @@
 /** 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 *periode periodentafel
+ * \param *mol molecule with atoms to dissect
  * \param *configuration config with BondGraph
  */
-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);
-  }
-
+void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
+{
   // 1. dissect the molecule into connected subgraphs
   configuration->BG->ConstructBondGraph(mol);
@@ -790 +759 @@
   // 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]);
   }
@@ -808 +770 @@
   int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
-  Walker = NULL;
+  atom *Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -837 +799 @@
     }
   }
-  // 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;
+  // 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;
   while (mol->first->next != mol->last) {
     Binder = mol->first->next;