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-              rd0b375b
+              r212c179
 };
-/** Allocates memory for UniqueFragments::BondsPerSPList.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \sa UniqueFragments::FreeSPList()
- */
-void UniqueFragments::InitialiseSPList(int Order)
+{
-  BondsPerSPList.resize(Order);
-  BondsPerSPCount = new int[Order];
-  for (int i=Order;i--;) {
-    BondsPerSPCount[i] = 0;
+  }
-};
-/** Free's memory for for UniqueFragments::BondsPerSPList.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \sa UniqueFragments::InitialiseSPList()
- */
-void UniqueFragments::FreeSPList(int Order)
+{
-  delete[](BondsPerSPCount);
-};
-/** Sets FragmenSearch to initial value.
- * Sets UniqueFragments::BondsPerSPCount to zero (except zero level to 1) and adds initial bond
- * UniqueFragments::Root to UniqueFragments::Root to UniqueFragments::BondsPerSPList
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \sa UniqueFragments::FreeSPList()
- */
-void UniqueFragments::SetSPList(int Order)
+{
-  // prepare root level (SP = 0) and a loop bond denoting Root
-  for (int i=Order;i--;)
-    BondsPerSPCount[i] = 0;
-  BondsPerSPCount[0] = 1;
-  bond *Binder = new bond(Root, Root);
-  BondsPerSPList[0].push_back(Binder);
-};
-/** Cleans bonds from UniqueFragments::BondsPerSPList.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \sa UniqueFragments::InitialiseSPList()
- */
-void UniqueFragments::ResetSPList(int Order)
+{
-  DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
-  for(int i=Order;i--;) {
-    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
-    // delete added bonds
-    for (UniqueFragments::BondsPerSP::iterator iter = BondsPerSPList[i].begin();
-        iter != BondsPerSPList[i].end();
-        ++iter) {
-      delete(*iter);
+    }
-    BondsPerSPList[i].clear();
-    // also start and end node
-    DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
+  }
-};
-/** Fills the Bonds per Shortest Path List and set the vertex labels.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param RestrictedKeySet Restricted vertex set to use in context of molecule
- */
-void UniqueFragments::FillSPListandLabelVertices(int Order, KeySet &RestrictedKeySet)
+{
-  // Actually, we should construct a spanning tree vom the root atom and select all edges therefrom and put them into
-  // according shortest path lists. However, we don't. Rather we fill these lists right away, as they do form a spanning
-  // tree already sorted into various SP levels. That's why we just do loops over the depth (CurrentSP) and breadth
-  // (EdgeinSPLevel) of this tree ...
-  // In another picture, the bonds always contain a direction by rightatom being the one more distant from root and hence
-  // naturally leftatom forming its predecessor, preventing the BFS"seeker" from continuing in the wrong direction.
-  int AtomKeyNr = -1;
-  atom *Walker = NULL;
-  atom *OtherWalker = NULL;
-  atom *Predecessor = NULL;
-  bond *Binder = NULL;
-  int RootKeyNr = Root->GetTrueFather()->getNr();
-  int RemainingWalkers = -1;
-  int SP = -1;
-  DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
-  for (SP = 0; SP < (Order-1); SP++) {
-    DoLog(1) && (Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << BondsPerSPCount[SP] << " item(s)");
-    if (SP > 0) {
-      DoLog(0) && (Log() << Verbose(0) << ", old level closed with " << BondsPerSPCount[SP-1] << " item(s)." << endl);
-      BondsPerSPCount[SP] = 0;
-    } else
-      DoLog(0) && (Log() << Verbose(0) << "." << endl);
-    RemainingWalkers = BondsPerSPCount[SP];
-    for (BondsPerSP::const_iterator CurrentEdge = BondsPerSPList[SP].begin();
-        CurrentEdge != BondsPerSPList[SP].end();
-        ++CurrentEdge) { /// start till end of this SP level's list
-      RemainingWalkers--;
-      Walker = (*CurrentEdge)->rightatom;    // rightatom is always the one more distant
-      Predecessor = (*CurrentEdge)->leftatom;    // ... and leftatom is predecessor
-      AtomKeyNr = Walker->getNr();
-      DoLog(0) && (Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->getNr() << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl);
-      // check for new sp level
-      // go through all its bonds
-      DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
-      const BondList& ListOfBonds = Walker->getListOfBonds();
-      for (BondList::const_iterator Runner = ListOfBonds.begin();
-          Runner != ListOfBonds.end();
-          ++Runner) {
-        OtherWalker = (*Runner)->GetOtherAtom(Walker);
-        if ((RestrictedKeySet.find(OtherWalker->getNr()) != RestrictedKeySet.end())
-  #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->getAtomicNumber() != 1)
-  #endif
-                                                              ) {  // skip hydrogens and restrict to fragment
-          DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->getNr() << " in bond " << *(*Runner) << "." << endl);
-          // set the label if not set (and push on root stack as well)
-          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->getNr() > RootKeyNr)) { // only pass through those with label bigger than Root's
-            // add the bond in between to the SP list
-            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
-            BondsPerSPList[SP+1].push_back(Binder);
-            BondsPerSPCount[SP+1]++;
-            DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << BondsPerSPCount[SP+1] << " item(s)." << endl);
-          } else {
-            if (OtherWalker != Predecessor)
-              DoLog(3) && (Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->getNr() << " is smaller than that of Root " << RootKeyNr << "." << endl);
-            else
-              DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
+          }
-        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
+      }
+    }
+  }
-};
-/** prints the Bonds per Shortest Path list in UniqueFragments.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- */
-void UniqueFragments::OutputSPList(int Order)
+{
-  DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
-  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
-    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
-    for (UniqueFragments::BondsPerSP::const_iterator Binder = BondsPerSPList[i].begin();
-        Binder != BondsPerSPList[i].end();
-        ++Binder) {
-      DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
+    }
+  }
-};
-/** Simply counts all bonds in all UniqueFragments::BondsPerSPList lists.
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- */
-int UniqueFragments::CountNumbersInBondsList(int Order)
+{
-  int SP = -1;  // the Root <-> Root edge must be subtracted!
-  for(int i=Order;i--;) { // sum up all found edges
-    for (UniqueFragments::BondsPerSP::const_iterator Binder = BondsPerSPList[i].begin();
-        Binder != BondsPerSPList[i].end();
-        ++Binder) {
-      SP++;
+    }
+  }
-  return SP;
-};
 /** Initialization for UniqueFragments.
+ *
 …
  * @return const ref to root atom.
  */
 const atom *UniqueFragments::getRoot() const
+atom * const UniqueFragments::getRoot() const
+{
   return Root;
 …
   Root=_root;
+}
+/** Sets initial values before PowerSetGenerator uses this class.
+ *
+ * @param _TEFactor total energy factor
+ * @param _Leaflet current graph to work on
+ * @param _Root root atom
+ */
+void UniqueFragments::PrepareForPowersetGeneration(double _TEFactor, Graph *_Leaflet, atom *_Root)
+{
+  TEFactor = _TEFactor;
+  Leaflet = _Leaflet;
+  Root = _Root;
+}

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Changeset 212c179 for src/Fragmentation/UniqueFragments.cpp

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src/Fragmentation/UniqueFragments.cpp

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