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-              r5034e1
+              rd2943b
 };
+/** Clears the touched list
+ * \param *out output stream for debugging
+ * \param verbosity verbosity level
+ * \param *&TouchedList touched list
+ * \param SubOrder current suborder
+ * \param TouchedIndex currently touched
+ */
+void SPFragmentGenerator_ClearingTouched(ofstream *out, int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex)
+{
+  *out << Verbose(1+verbosity) << "Clearing touched list." << endl;
+  for (TouchedIndex=SubOrder+1;TouchedIndex--;)  // empty touched list
+    TouchedList[TouchedIndex] = -1;
+  TouchedIndex = 0;
+}
+/** Adds the current combination of the power set to the snake stack.
+ * \param *out output stream for debugging
+ * \param verbosity verbosity level
+ * \param CurrentCombination
+ * \param SetDimension maximum number of bits in power set
+ * \param *FragmentSet snake stack to remove from
+ * \param *&TouchedList touched list
+ * \param TouchedIndex currently touched
+ * \return number of set bits
+ */
+int AddPowersetToSnakeStack(ofstream *out, int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, bond **BondsSet, int *&TouchedList, int &TouchedIndex)
+{
+  atom *OtherWalker = NULL;
+  bool bit = false;
+  KeySetTestPair TestKeySetInsert;
+  int Added = 0;
+  for (int j=0;j<SetDimension;j++) {  // pull out every bit by shifting
+    bit = ((CurrentCombination & (1 << j)) != 0);  // mask the bit for the j-th bond
+    if (bit) {  // if bit is set, we add this bond partner
+      OtherWalker = BondsSet[j]->rightatom;  // rightatom is always the one more distant, i.e. the one to add
+      //*out << Verbose(1+verbosity) << "Current Bond is " << ListOfBondsPerAtom[Walker->nr][CurrentCombination] << ", checking on " << *OtherWalker << "." << endl;
+      *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->nr << "." << endl;
+      TestKeySetInsert = FragmentSet->insert(OtherWalker->nr);
+      if (TestKeySetInsert.second) {
+        TouchedList[TouchedIndex++] = OtherWalker->nr;  // note as added
+        Added++;
+      } else {
+        *out << Verbose(2+verbosity) << "This was item was already present in the keyset." << endl;
+      }
+    } else {
+      *out << Verbose(2+verbosity) << "Not adding." << endl;
+    }
+  }
+  return Added;
+};
+/** Counts the number of elements in a power set.
+ * \param *SetFirst
+ * \param *SetLast
+ * \param *&TouchedList touched list
+ * \param TouchedIndex currently touched
+ * \return number of elements
+ */
+int CountSetMembers(bond *SetFirst, bond *SetLast, int *&TouchedList, int TouchedIndex)
+{
+  int SetDimension = 0;
+  bond *Binder = SetFirst;    // start node for this level
+  while (Binder->next != SetLast) {    // compare to end node of this level
+    Binder = Binder->next;
+    for (int k=TouchedIndex;k--;) {
+      if (Binder->Contains(TouchedList[k]))   // if we added this very endpiece
+        SetDimension++;
+    }
+  }
+  return SetDimension;
+};
+/** Counts the number of elements in a power set.
+ * \param *BondsList bonds list to fill
+ * \param *SetFirst
+ * \param *SetLast
+ * \param *&TouchedList touched list
+ * \param TouchedIndex currently touched
+ * \return number of elements
+ */
+int FillBondsList(bond **BondsList, bond *SetFirst, bond *SetLast, int *&TouchedList, int TouchedIndex)
+{
+  int SetDimension = 0;
+  bond *Binder = SetFirst;    // start node for this level
+  while (Binder->next != SetLast) {    // compare to end node of this level
+    Binder = Binder->next;
+    for (int k=0;k<TouchedIndex;k++) {
+      if (Binder->leftatom->nr == TouchedList[k])   // leftatom is always the close one
+        BondsList[SetDimension++] = Binder;
+    }
+  }
+  return SetDimension;
+};
+/** Remove all items that were added on this SP level.
+ * \param *out output stream for debugging
+ * \param verbosity verbosity level
+ * \param *FragmentSet snake stack to remove from
+ * \param *&TouchedList touched list
+ * \param TouchedIndex currently touched
+ */
+void RemoveAllTouchedFromSnakeStack(ofstream *out, int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex)
+{
+  int Removal = 0;
+  for(int j=0;j<TouchedIndex;j++) {
+    Removal = TouchedList[j];
+    *out << Verbose(2+verbosity) << "Removing item nr. " << Removal << " from snake stack." << endl;
+    FragmentSet->erase(Removal);
+    TouchedList[j] = -1;
+  }
+  *out << Verbose(2) << "Remaining local nr.s on snake stack are: ";
+  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
+    *out << (*runner) << " ";
+  *out << endl;
+  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
+};
 /** From a given set of Bond sorted by Shortest Path distance, create all possible fragments of size \a SetDimension.
  * -# loops over every possible combination (2^dimension of edge set)
 …
 void molecule::SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder)
+{
-  atom *OtherWalker = NULL;
   int verbosity = 0; //FragmentSearch->ANOVAOrder-SubOrder;
   int NumCombinations;
-  bool bit;
   int bits, TouchedIndex, SubSetDimension, SP, Added;
-  int Removal;
   int SpaceLeft;
   int *TouchedList = Malloc<int>(SubOrder + 1, "molecule::SPFragmentGenerator: *TouchedList");
-  bond *Binder = NULL;
   bond **BondsList = NULL;
   KeySetTestPair TestKeySetInsert;
 …
   // initialised touched list (stores added atoms on this level)
+  *out << Verbose(1+verbosity) << "Clearing touched list." << endl;
+  for (TouchedIndex=SubOrder+1;TouchedIndex--;)  // empty touched list
+    TouchedList[TouchedIndex] = -1;
+  TouchedIndex = 0;
+  SPFragmentGenerator_ClearingTouched(out, verbosity, TouchedList, SubOrder, TouchedIndex);
   // create every possible combination of the endpieces
 …
     if (bits <= SubOrder) { // if not greater than additional atoms allowed on stack, continue
       // --1-- add this set of the power set of bond partners to the snake stack
+      Added = 0;
+      for (int j=0;j<SetDimension;j++) {  // pull out every bit by shifting
+        bit = ((i & (1 << j)) != 0);  // mask the bit for the j-th bond
+        if (bit) {  // if bit is set, we add this bond partner
+          OtherWalker = BondsSet[j]->rightatom;  // rightatom is always the one more distant, i.e. the one to add
+          //*out << Verbose(1+verbosity) << "Current Bond is " << ListOfBondsPerAtom[Walker->nr][i] << ", checking on " << *OtherWalker << "." << endl;
+          *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->nr << "." << endl;
+          TestKeySetInsert = FragmentSearch->FragmentSet->insert(OtherWalker->nr);
+          if (TestKeySetInsert.second) {
+            TouchedList[TouchedIndex++] = OtherWalker->nr;  // note as added
+            Added++;
+          } else {
+            *out << Verbose(2+verbosity) << "This was item was already present in the keyset." << endl;
+          }
+            //FragmentSearch->UsedList[OtherWalker->nr][i] = true;
+          //}
+        } else {
+          *out << Verbose(2+verbosity) << "Not adding." << endl;
+        }
+      }
+      Added = AddPowersetToSnakeStack(out, verbosity, i, SetDimension, FragmentSearch->FragmentSet, BondsSet, TouchedList, TouchedIndex);
       SpaceLeft = SubOrder - Added ;// SubOrder - bits; // due to item's maybe being already present, this does not work anymore
 …
           // --2-- look at all added end pieces of this combination, construct bond subsets and sweep through a power set of these by recursion
           SP = RootDistance+1;  // this is the next level
           // first count the members in the subset
+          SubSetDimension = 0;
+          Binder = FragmentSearch->BondsPerSPList[2*SP];    // start node for this level
+          while (Binder->next != FragmentSearch->BondsPerSPList[2*SP+1]) {    // compare to end node of this level
+            Binder = Binder->next;
+            for (int k=TouchedIndex;k--;) {
+              if (Binder->Contains(TouchedList[k]))   // if we added this very endpiece
+                SubSetDimension++;
+            }
+          }
+          SubSetDimension = CountSetMembers(FragmentSearch->BondsPerSPList[2*SP], FragmentSearch->BondsPerSPList[2*SP+1], TouchedList, TouchedIndex);
           // then allocate and fill the list
           BondsList = Malloc<bond*>(SubSetDimension, "molecule::SPFragmentGenerator: **BondsList");
+          SubSetDimension = 0;
+          Binder = FragmentSearch->BondsPerSPList[2*SP];
+          while (Binder->next != FragmentSearch->BondsPerSPList[2*SP+1]) {
+            Binder = Binder->next;
+            for (int k=0;k<TouchedIndex;k++) {
+              if (Binder->leftatom->nr == TouchedList[k])   // leftatom is always the close one
+                BondsList[SubSetDimension++] = Binder;
+            }
+          }
+          SubSetDimension = FillBondsList(BondsList, FragmentSearch->BondsPerSPList[2*SP], FragmentSearch->BondsPerSPList[2*SP+1], TouchedList, TouchedIndex);
+          // then iterate
           *out << Verbose(2+verbosity) << "Calling subset generator " << SP << " away from root " << *FragmentSearch->Root << " with sub set dimension " << SubSetDimension << "." << endl;
           SPFragmentGenerator(out, FragmentSearch, SP, BondsList, SubSetDimension, SubOrder-bits);
           Free(&BondsList);
+        }
 …
           //*out << Verbose(0) << "ERROR: The found fragment is not a connected subgraph!" << endl;
         InsertFragmentIntoGraph(out, FragmentSearch);
-        //Removal = LookForRemovalCandidate(out, FragmentSearch->FragmentSet, FragmentSearch->ShortestPathList);
-        //Removal = StoreFragmentFromStack(out, FragmentSearch->Root, FragmentSearch->Leaflet, FragmentSearch->FragmentStack, FragmentSearch->ShortestPathList, &FragmentSearch->FragmentCounter, FragmentSearch->configuration);
+      }
       // --3-- remove all added items in this level from snake stack
       *out << Verbose(1+verbosity) << "Removing all items that were added on this SP level " << RootDistance << "." << endl;
+      for(int j=0;j<TouchedIndex;j++) {
+        Removal = TouchedList[j];
+        *out << Verbose(2+verbosity) << "Removing item nr. " << Removal << " from snake stack." << endl;
+        FragmentSearch->FragmentSet->erase(Removal);
+        TouchedList[j] = -1;
+      }
+      *out << Verbose(2) << "Remaining local nr.s on snake stack are: ";
+      for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
+        *out << (*runner) << " ";
+      *out << endl;
+      TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
+      RemoveAllTouchedFromSnakeStack(out, verbosity, FragmentSearch->FragmentSet, TouchedList, TouchedIndex);
     } else {
       *out << Verbose(2+verbosity) << "More atoms to add for this set (" << bits << ") than space left on stack " << SubOrder << ", skipping this set." << endl;

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Changeset d2943b for src

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src/molecule_fragmentation.cpp

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