Changes in / [4c9101:fc3aff]

Files:

• configure.ac (modified) (1 diff)
• src/Graph/CyclicStructureAnalysis.cpp (modified) (8 diffs)
• src/Graph/CyclicStructureAnalysis.hpp (modified) (1 diff)
• src/UIElements/Views/Qt4/QDebugStream.hpp (modified) (4 diffs)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at (modified) (1 diff)
• tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at (modified) (1 diff)

configure.ac

@@ -158 +158 @@
           AC_DEFINE(LOG_OBSERVER,1, ["Use observer log."])
           AC_DEFINE(HAVE_DEBUG,2, ["Use debug setting to compile code."])
-          dnl AC_DEFINE(QT_DEBUG,, ["Enable Qt debug messages."])
+          AC_DEFINE(QT_DEBUG,, ["Enable Qt debug messages."])
           have_debug="full"
         ],[
           AC_DEFINE(NDEBUG,1, ["Don't compile in debugging code."])
           AC_DEFINE(HAVE_DEBUG,0, ["Use debug setting to compile code."])
-          AC_DEFINE(QT_NO_DEBUG_OUTPUT,, ["Disable Qt debug messages."])
+          AC_DEFINE(QT_NO_DEBUG,, ["Disable Qt debug messages."])
           have_debug="no"
         ])

src/Graph/CyclicStructureAnalysis.cpp

@@ -103 +103 @@
 }
 
-/** Performs a BFS from \a *Root, trying to find the same node and hence all cycles.
- *
- * We exclude the back edge, hence the direct way is prohibited. But as it is a back edge,
- * there must be at least one more way to \a *Root. This leads us to all cycles for this
- * back edge.
- *
+/** Performs a BFS from \a *Root, trying to find the same node and hence a cycle.
  * \param OtherAtom pointing to Root on return indicating found cycle
  * \param *&BackEdge the edge from root that we don't want to move along
- * \param MinRingSize set to minimum over all cycles encountered
- */
-void CyclicStructureAnalysis::findAllCyclesforBackEdge(
-    atom *&OtherAtom,
-    bond::ptr &BackEdge,
-    int &MinRingSize)
-{
-  size_t MaximumHorizon = (size_t)-1; // will overflow to largest number
+ */
+void CyclicStructureAnalysis::CyclicBFSFromRootToRoot(atom *&OtherAtom, bond::ptr &BackEdge)
+{
   atom *Walker = NULL;
   do { // look for Root
@@ -125 +115 @@
     BFSStack.pop_back();
     LOG(2, "INFO: Current Walker is " << *Walker << ", we look for SP to Root " << *Root << ".");
-
-    // check all edges/bonds from current Walker
-    if (MaximumHorizon >=  (size_t)ShortestPathList[Walker->getNr()]) {
-      const BondList& ListOfBonds = Walker->getListOfBonds();
-      for (BondList::const_iterator Runner = ListOfBonds.begin();
-          Runner != ListOfBonds.end();
-          ++Runner) {
-        if ((*Runner) != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
-          OtherAtom = (*Runner)->GetOtherAtom(Walker);
-          if ((treatment == IncludeHydrogen) || (OtherAtom->getType()->getAtomicNumber() != 1)) {
-            LOG(2, "INFO: Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << ".");
-            if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
-              // we discovered a new node/atom
-              TouchedStack.push_front(OtherAtom);
-              ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
-              PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
-              ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
-              LOG(2, "INFO: Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long.");
-              //if (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()]) { // Check for maximum distance
-              LOG(3, "ACCEPT: Putting OtherAtom " << OtherAtom->getName() << " into queue.");
-              BFSStack.push_front(OtherAtom);
-              //}
-            } else {
-              LOG(3, "REJECT: Not Adding, has already been visited.");
+    const BondList& ListOfBonds = Walker->getListOfBonds();
+    for (BondList::const_iterator Runner = ListOfBonds.begin();
+        Runner != ListOfBonds.end();
+        ++Runner) {
+      if ((*Runner) != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
+        OtherAtom = (*Runner)->GetOtherAtom(Walker);
+        if ((treatment == IncludeHydrogen) || (OtherAtom->getType()->getAtomicNumber() != 1)) {
+          LOG(2, "INFO: Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << ".");
+          if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {
+            TouchedStack.push_front(OtherAtom);
+            ColorList[OtherAtom->getNr()] = GraphEdge::lightgray;
+            PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
+            ShortestPathList[OtherAtom->getNr()] = ShortestPathList[Walker->getNr()] + 1;
+            LOG(2, "INFO: Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long.");
+            //if (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()]) { // Check for maximum distance
+            LOG(3, "ACCEPT: Putting OtherAtom " << OtherAtom->getName() << " into queue.");
+            BFSStack.push_front(OtherAtom);
+            //}
+          } else {
+            LOG(3, "REJECT: Not Adding, has already been visited.");
+          }
+          if (OtherAtom == Root)
+            break;
+        } else {
+          LOG(2, "INFO: Skipping hydrogen atom " << *OtherAtom << ".");
+          ColorList[OtherAtom->getNr()] = GraphEdge::black;
+        }
+      } else {
+        LOG(2, "REJECT: Bond " << *(*Runner) << " not Visiting, is the back edge.");
+      }
+    }
+    ColorList[Walker->getNr()] = GraphEdge::black;
+    LOG(1, "INFO: Coloring Walker " << Walker->getName() << " " << GraphEdge::getColorName(ColorList[Walker->getNr()]) << ".");
+    if (OtherAtom == Root) { // if we have found the root, check whether this cycle wasn't already found beforehand
+      // step through predecessor list
+      LOG(4, "DEBUG: Checking whether all predecessors are already marked cyclic ...");
+      while (OtherAtom != BackEdge->rightatom) {  // Note that leftatom is Root itself
+        if (!OtherAtom->GetTrueFather()->IsCyclic) { // if one bond in the loop is not marked as cyclic, we haven't found this cycle yet
+          LOG(4, "\tDEBUG: OtherAtom " << *OtherAtom << " is not cyclic, breaking.");
+          break;
+        } else
+          OtherAtom = PredecessorList[OtherAtom->getNr()];
+      }
+      LOG(4, "DEBUG: Checking done.");
+      // if each atom in found cycle is cyclic, loop's been found before already
+      if (OtherAtom == BackEdge->rightatom) { // loop got round completely
+        LOG(3, "INFO: All bonds are marked cyclic already, checking allcycles whether cycle is already present.");
+        const cycle_t currentcycle = extractCurrentCycle(BackEdge);
+        const cycles_t::const_iterator iter =
+            std::find(allcycles.begin(), allcycles.end(), currentcycle);
+        if (iter == allcycles.end()) { // not found
+          OtherAtom = Root;
+          LOG(2, "INFO: Cycle is not present.");
+          LOG(2, "INFO: We have reached Root " << *OtherAtom << " and may extract the cycle.");
+        } else {
+          LOG(2, "INFO: Cycle is already present.");
+          do {
+            ASSERT(!TouchedStack.empty(), "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - TouchedStack is empty!");
+            OtherAtom = TouchedStack.front();
+            TouchedStack.pop_front();
+            if (PredecessorList[OtherAtom->getNr()] == Walker) {
+              LOG(4, "INFO: Removing " << *OtherAtom << " from lists and stacks.");
+              PredecessorList[OtherAtom->getNr()] = NULL;
+              ShortestPathList[OtherAtom->getNr()] = -1;
+              ColorList[OtherAtom->getNr()] = GraphEdge::white;
+              // rats ... deque has no find()
+              std::deque<atom *>::iterator iter = find(
+                  BFSStack.begin(),
+                  BFSStack.end(),
+                  OtherAtom);
+              ASSERT(iter != BFSStack.end(),
+                  "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - can't find "+toString(*OtherAtom)+" on stack!");
+              BFSStack.erase(iter);
             }
-            if (OtherAtom == Root)
-              break;
-          } else {
-            LOG(2, "INFO: Skipping hydrogen atom " << *OtherAtom << ".");
-            ColorList[OtherAtom->getNr()] = GraphEdge::black;
-          }
-        } else {
-          LOG(2, "REJECT: Bond " << *(*Runner) << " not Visiting, is the back edge.");
+          } while ((!TouchedStack.empty()) && (PredecessorList[OtherAtom->getNr()] == NULL));
+          TouchedStack.push_front(OtherAtom); // last was wrongly popped
+          OtherAtom = BackEdge->rightatom; // set to not Root
         }
+      } else {
+        OtherAtom = Root;
+        LOG(2, "INFO: We have reached Root " << *OtherAtom << " and may extract the cycle.");
       }
-      ColorList[Walker->getNr()] = GraphEdge::black;
-      LOG(1, "INFO: Coloring Walker " << Walker->getName() << " " << GraphEdge::getColorName(ColorList[Walker->getNr()]) << ".");
-    } else {
-      LOG(1, "INFO: Skipping bonds for " << Walker->getName() << " as it resides on the horizon.");
-    }
-
-    // have we closed the cycle, i.e. stumbled upon Root by another mean than
-    // the back edge?
-    if (OtherAtom == Root) {
-      // check whether this cycle wasn't already found beforehand by stepping
-      // through predecessor list
-      int RingSize = RetrieveCycleMembers(OtherAtom, BackEdge, MinRingSize);
-      MaximumHorizon = std::min( MaximumHorizon, (size_t)RingSize );
-      LOG(2, "INFO: Maximum horizon is set to " << MaximumHorizon);
-
-      // remove last step and prepare for a possible yet another path to Root
-      do {
-        ASSERT(!TouchedStack.empty(), "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - TouchedStack is empty!");
-        OtherAtom = TouchedStack.front();
-        TouchedStack.pop_front();
-        if (PredecessorList[OtherAtom->getNr()] == Walker) {
-          LOG(4, "INFO: Removing " << *OtherAtom << " from lists and stacks.");
-          PredecessorList[OtherAtom->getNr()] = NULL;
-          ShortestPathList[OtherAtom->getNr()] = -1;
-          ColorList[OtherAtom->getNr()] = GraphEdge::white;
-          // rats ... deque has no find()
-          std::deque<atom *>::iterator iter = find(
-              BFSStack.begin(),
-              BFSStack.end(),
-              OtherAtom);
-          ASSERT(iter != BFSStack.end(),
-              "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - can't find "+toString(*OtherAtom)+" on stack!");
-          BFSStack.erase(iter);
-        }
-      } while ((!TouchedStack.empty()) && (PredecessorList[OtherAtom->getNr()] == NULL));
-      TouchedStack.push_front(OtherAtom); // last was wrongly popped
-      OtherAtom = BackEdge->rightatom; // set to not Root
     }
   } while ((!BFSStack.empty()) && (OtherAtom != Root) && (OtherAtom != NULL)); // || (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()])));
@@ -233 +233 @@
  * \param &BFS accounting structure
  * \param &MinRingSize global minimum distance from one node without encountering oneself, set on return
- * \return size of found cycle, -1 - nothing found, something went wrong
- */
-int CyclicStructureAnalysis::RetrieveCycleMembers(
+ * \param &NumCyles number of cycles in graph
+ */
+void CyclicStructureAnalysis::RetrieveCycleMembers(
     atom *&OtherAtom,
     bond::ptr &BackEdge,
-    int &MinRingSize)
-{
+    int &MinRingSize,
+    int &NumCycles)
+{
+  atom *Walker = NULL;
   int RingSize = -1;
-  bool newcycle = false;
 
   if (OtherAtom == Root) {
     // now climb back the predecessor list and thus find the cycle members
+    NumCycles++;
     Root->GetTrueFather()->IsCyclic = true;
 
+    // exctract cycle
     {
-      // check whether cycle is present already
-      atom *Walker = Root;
-      LOG(4, "DEBUG: Checking whether all predecessors are already marked cyclic ...");
-      while (Walker != BackEdge->rightatom) {  // Note that leftatom is Root itself
-        if (!Walker->GetTrueFather()->IsCyclic) { // if one bond in the loop is not marked as cyclic, we haven't found this cycle yet
-          LOG(4, "\tDEBUG: Walker " << *Walker << " is not cyclic, breaking.");
-          break;
-        } else
-          Walker = PredecessorList[Walker->getNr()];
-      }
-      LOG(4, "DEBUG: Checking done.");
-
-      // if each atom in found cycle is cyclic, loop's been found before already
-
-      // exctract cycle
-      {
-        const cycle_t currentcycle = extractCurrentCycle(BackEdge);
-        if (Walker != BackEdge->rightatom) { // loop got round completely
-          allcycles.push_back(currentcycle);
-          newcycle = true;
-        } else {
-          LOG(3, "INFO: All bonds are marked cyclic already, checking allcycles whether cycle is already present.");
-          const cycles_t::const_iterator iter =
-              std::find(allcycles.begin(), allcycles.end(), currentcycle);
-          if (iter == allcycles.end()) { // not found
-            allcycles.push_back(currentcycle);
-            newcycle = true;
-          }
-        }
-        RingSize = currentcycle.size();
-        if (newcycle) {
-          LOG(0, "INFO: " << "Found ring contains: " << currentcycle << "  with a length of " << RingSize);
-        } else {
-          LOG(1, "INFO: cycle " << currentcycle << " is already present.");
-        }
-      }
-    }
-
-    if (newcycle) {
-      // walk through all and set MinimumRingSize
-      atom *Walker = Root;
+      allcycles.push_back(extractCurrentCycle(BackEdge));
+      CyclicStructureAnalysis::cycle_t &lastcycle = allcycles.back();
+      RingSize = lastcycle.size();
+      LOG(0, "INFO: " << "Found ring contains: " << lastcycle << "  with a length of " << RingSize);
+    }
+
+    // walk through all and set MinimumRingSize
+    Walker = Root;
+    if ((MinimumRingSize.count(Walker->GetTrueFather()->getNr()) == 0)
+        || (RingSize < MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
+      MinimumRingSize[Walker->GetTrueFather()->getNr()] = RingSize;
+    } else {
+      LOG(3, "INFO: Not setting MinimumRingSize of "<< *(Walker->GetTrueFather())
+          << " to " << RingSize << " which is already set to "
+          << MinimumRingSize[Walker->GetTrueFather()->getNr()] << ".");
+    }
+    while (Walker != BackEdge->rightatom) { // note that Root is leftatom
+      Walker = PredecessorList[Walker->getNr()];
       if ((MinimumRingSize.count(Walker->GetTrueFather()->getNr()) == 0)
-          || (RingSize < MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
+          || (RingSize < MinimumRingSize[Walker->GetTrueFather()->getNr()]))
         MinimumRingSize[Walker->GetTrueFather()->getNr()] = RingSize;
-      } else {
-        LOG(3, "INFO: Not setting MinimumRingSize of "<< *(Walker->GetTrueFather())
-            << " to " << RingSize << " which is already set to "
-            << MinimumRingSize[Walker->GetTrueFather()->getNr()] << ".");
-      }
-      while (Walker != BackEdge->rightatom) { // note that Root is leftatom
-        Walker = PredecessorList[Walker->getNr()];
-        if ((MinimumRingSize.count(Walker->GetTrueFather()->getNr()) == 0)
-            || (RingSize < MinimumRingSize[Walker->GetTrueFather()->getNr()]))
-          MinimumRingSize[Walker->GetTrueFather()->getNr()] = RingSize;
-      }
-      if ((RingSize < MinRingSize) || (MinRingSize == -1))
-        MinRingSize = RingSize;
-    }
+    }
+    if ((RingSize < MinRingSize) || (MinRingSize == -1))
+      MinRingSize = RingSize;
   } else {
     LOG(1, "INFO: No ring containing " << *Root << " with length equal to or smaller than " << MinimumRingSize[Root->GetTrueFather()->getNr()] << " found.");
   }
-  return RingSize;
 }
 
@@ -390 +358 @@
  * \param *&MinimumRingSize array with minimum distance without encountering oneself for each atom
  * \param MinRingSize global minium distance
- */
-void CyclicStructureAnalysis::AssignRingSizetoNonCycleMembers(const int MinRingSize)
+ * \param NumCyles number of cycles in graph
+ */
+void CyclicStructureAnalysis::AssignRingSizetoNonCycleMembers(const int MinRingSize, const int NumCycles)
 {
   atom *Walker = NULL;
@@ -411 +380 @@
       LOG(1, "INFO: Minimum ring size of " << *Walker << " is " << MinimumRingSize[Walker->GetTrueFather()->getNr()] << ".");
     }
-    LOG(1, "INFO: Minimum ring size is " << MinRingSize << ", over " << allcycles.size() << " cycle(s) total.");
+    LOG(1, "INFO: Minimum ring size is " << MinRingSize << ", over " << NumCycles << " cycle(s) total.");
   } else
     LOG(1, "INFO: No rings were detected in the molecular structure.");
@@ -430 +399 @@
   atom *OtherAtom = NULL;
   bond::ptr BackEdge;
+  int NumCycles = 0;
   int MinRingSize = -1;
 
@@ -445 +415 @@
 
   LOG(1, "STATUS: Analysing cycles ... ");
+  NumCycles = 0;
   while (!BackEdgeStack->empty()) {
     BackEdge = BackEdgeStack->front();
@@ -457 +428 @@
     LOG(1, "---------------------------------------------------------------------------------------------------------");
     OtherAtom = NULL;
-    // find all cycles for current BackEdge
-    findAllCyclesforBackEdge(OtherAtom, BackEdge, MinRingSize);
+    // go to next cycle via BFS
+    CyclicBFSFromRootToRoot(OtherAtom, BackEdge);
+    // get all member nodes of this cycle
+    RetrieveCycleMembers(OtherAtom, BackEdge, MinRingSize, NumCycles);
 
     CleanAllTouched();
   }
-  AssignRingSizetoNonCycleMembers(MinRingSize);
+  AssignRingSizetoNonCycleMembers(MinRingSize, NumCycles);
 }
 

src/Graph/CyclicStructureAnalysis.hpp

@@ -58 +58 @@
   void InitializeToRoot(atom *&Walker);
   // performing tasks
-  void findAllCyclesforBackEdge(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize);
-  int RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize);
+  void CyclicBFSFromRootToRoot(atom *&OtherAtom, bond::ptr &BackEdge);
+  void RetrieveCycleMembers(atom *&OtherAtom, bond::ptr &BackEdge, int &MinRingSize, int &NumCycles);
   cycle_t extractCurrentCycle(bond::ptr &BackEdge);
   void BFSToNextCycle(atom *Walker);
-  void AssignRingSizetoNonCycleMembers(const int MinRingSize);
+  void AssignRingSizetoNonCycleMembers(const int MinRingSize, const int NumCycles);
   // output
   void OutputAlreadyVisited(int *list);

src/UIElements/Views/Qt4/QDebugStream.hpp

@@ -15 +15 @@
 
 #include <QTextEdit>
-#include <QDebug>
 
 #include <ostream>
@@ -42 +41 @@
   {
     // output anything that is left
-    if (!m_string.empty()) {
+    if (!m_string.empty())
       log_window->append(m_string.c_str());
-      qDebug() << m_string.c_str();
-    }
 
     m_stream.rdbuf(m_old_buf);
@@ -55 +52 @@
     if (v == '\n') {
       log_window->append(m_string.c_str());
-      qDebug() << m_string.c_str();
       m_string.erase(m_string.begin(), m_string.end());
     } else
@@ -73 +69 @@
         std::string tmp(m_string.begin(), m_string.begin() + pos);
         log_window->append(tmp.c_str());
-        qDebug() << tmp.c_str();
         m_string.erase(m_string.begin(), m_string.begin() + pos + 1);
       }

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at

@@ -33 +33 @@
 AT_CHECK([chmod u+w $file], 0)
 
-AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
 AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
 AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])