source: src/molecule_graph.cpp@ 435065

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * molecule_graph.cpp
 *
 *  Created on: Oct 5, 2009
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include <stack>

#include "atom.hpp"
#include "bond.hpp"
#include "Graph/BondGraph.hpp"
#include "Box.hpp"
#include "CodePatterns/Assert.hpp"
#include "CodePatterns/Info.hpp"
#include "CodePatterns/Log.hpp"
#include "CodePatterns/Verbose.hpp"
#include "config.hpp"
#include "element.hpp"
#include "Helpers/defs.hpp"
#include "Helpers/fast_functions.hpp"
#include "Helpers/helpers.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "linkedcell.hpp"
#include "molecule.hpp"
#include "PointCloudAdaptor.hpp"
#include "World.hpp"
#include "WorldTime.hpp"

#define MAXBONDS 8

struct BFSAccounting
{
  atom **PredecessorList;
  int *ShortestPathList;
  enum bond::Shading *ColorList;
  std::deque<atom *> *BFSStack;
  std::deque<atom *> *TouchedStack;
  int AtomCount;
  int BondOrder;
  atom *Root;
  bool BackStepping;
  int CurrentGraphNr;
  int ComponentNr;
};

/** Accounting data for Depth First Search.
 */
struct DFSAccounting
{
  std::deque<atom *> *AtomStack;
  std::deque<bond *> *BackEdgeStack;
  int CurrentGraphNr;
  int ComponentNumber;
  atom *Root;
  bool BackStepping;
};

/************************************* Functions for class molecule *********************************/

/** Checks for presence of bonds within atom list.
 * TODO: more sophisticated check for bond structure (e.g. connected subgraph, ...)
 * \return true - bonds present, false - no bonds
 */
bool molecule::hasBondStructure() const
{
  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    if (!ListOfBonds.empty())
      return true;
  }
  return false;
}

/** Prints a list of all bonds to \a *out.
 */
void molecule::OutputBondsList() const
{
  DoLog(1) && (Log() << Verbose(1) << endl << "From contents of bond chain list:");
  for(molecule::const_iterator AtomRunner = molecule::begin(); AtomRunner != molecule::end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner) {
        DoLog(0) && (Log() << Verbose(0) << *(*BondRunner) << "\t" << endl);
      }
  }
  DoLog(0) && (Log() << Verbose(0) << endl);
}
;


/** Counts all cyclic bonds and returns their number.
 * \note Hydrogen bonds can never by cyclic, thus no check for that
 * \return number of cyclic bonds
 */
int molecule::CountCyclicBonds()
{
  NoCyclicBonds = 0;
  int *MinimumRingSize = NULL;
  MoleculeLeafClass *Subgraphs = NULL;
  std::deque<bond *> *BackEdgeStack = NULL;
  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    if ((!ListOfBonds.empty()) && ((*ListOfBonds.begin())->Type == bond::Undetermined)) {
      DoLog(0) && (Log() << Verbose(0) << "No Depth-First-Search analysis performed so far, calling ..." << endl);
      Subgraphs = DepthFirstSearchAnalysis(BackEdgeStack);
      while (Subgraphs->next != NULL) {
        Subgraphs = Subgraphs->next;
        delete (Subgraphs->previous);
      }
      delete (Subgraphs);
      delete[] (MinimumRingSize);
      break;
    }
  }
  for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner)
        if ((*BondRunner)->Cyclic)
          NoCyclicBonds++;
  }
  delete (BackEdgeStack);
  return NoCyclicBonds;
}
;


/** Sets atom::GraphNr and atom::LowpointNr to BFSAccounting::CurrentGraphNr.
 * \param *Walker current node
 * \param &BFS structure with accounting data for BFS
 */
void DepthFirstSearchAnalysis_SetWalkersGraphNr(atom *&Walker, struct DFSAccounting &DFS)
{
  if (!DFS.BackStepping) { // if we don't just return from (8)
    Walker->GraphNr = DFS.CurrentGraphNr;
    Walker->LowpointNr = DFS.CurrentGraphNr;
    DoLog(1) && (Log() << Verbose(1) << "Setting Walker[" << Walker->getName() << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl);
    DFS.AtomStack->push_front(Walker);
    DFS.CurrentGraphNr++;
  }
}
;

/** During DFS goes along unvisited bond and touches other atom.
 * Sets bond::type, if
 *  -# BackEdge: set atom::LowpointNr and push on \a BackEdgeStack
 *  -# TreeEgde: set atom::Ancestor and continue with Walker along this edge
 * Continue until molecule::FindNextUnused() finds no more unused bonds.
 * \param *mol molecule with atoms and finding unused bonds
 * \param *&Binder current edge
 * \param &DFS DFS accounting data
 */
void DepthFirstSearchAnalysis_ProbeAlongUnusedBond(const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS)
{
  atom *OtherAtom = NULL;

  do { // (3) if Walker has no unused egdes, go to (5)
    DFS.BackStepping = false; // reset backstepping flag for (8)
    if (Binder == NULL) // if we don't just return from (11), Binder is already set to next unused
      Binder = mol->FindNextUnused(Walker);
    if (Binder == NULL)
      break;
    DoLog(2) && (Log() << Verbose(2) << "Current Unused Bond is " << *Binder << "." << endl);
    // (4) Mark Binder used, ...
    Binder->MarkUsed(bond::black);
    OtherAtom = Binder->GetOtherAtom(Walker);
    DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->getName() << "." << endl);
    if (OtherAtom->GraphNr != -1) {
      // (4a) ... if "other" atom has been visited (GraphNr != 0), set lowpoint to minimum of both, go to (3)
      Binder->Type = bond::BackEdge;
      DFS.BackEdgeStack->push_front(Binder);
      Walker->LowpointNr = (Walker->LowpointNr < OtherAtom->GraphNr) ? Walker->LowpointNr : OtherAtom->GraphNr;
      DoLog(3) && (Log() << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->getName() << "] to " << Walker->LowpointNr << "." << endl);
    } else {
      // (4b) ... otherwise set OtherAtom as Ancestor of Walker and Walker as OtherAtom, go to (2)
      Binder->Type = bond::TreeEdge;
      OtherAtom->Ancestor = Walker;
      Walker = OtherAtom;
      DoLog(3) && (Log() << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->getName() << "]'s Ancestor is now " << OtherAtom->Ancestor->getName() << ", Walker is OtherAtom " << OtherAtom->getName() << "." << endl);
      break;
    }
    Binder = NULL;
  } while (1); // (3)
}
;

/** Checks whether we have a new component.
 * if atom::LowpointNr of \a *&Walker is greater than atom::GraphNr of its atom::Ancestor, we have a new component.
 * Meaning that if we touch upon a node who suddenly has a smaller atom::LowpointNr than its ancestor, then we
 * have a found a new branch in the graph tree.
 * \param *mol molecule with atoms and finding unused bonds
 * \param *&Walker current node
 * \param &DFS DFS accounting data
 */
void DepthFirstSearchAnalysis_CheckForaNewComponent(const molecule * const mol, atom *&Walker, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
{
  atom *OtherAtom = NULL;

  // (5) if Ancestor of Walker is ...
  DoLog(1) && (Log() << Verbose(1) << "(5) Number of Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "] is " << Walker->Ancestor->GraphNr << "." << endl);

  if (Walker->Ancestor->GraphNr != DFS.Root->GraphNr) {
    // (6)  (Ancestor of Walker is not Root)
    if (Walker->LowpointNr < Walker->Ancestor->GraphNr) {
      // (6a) set Ancestor's Lowpoint number to minimum of of its Ancestor and itself, go to Step(8)
      Walker->Ancestor->LowpointNr = (Walker->Ancestor->LowpointNr < Walker->LowpointNr) ? Walker->Ancestor->LowpointNr : Walker->LowpointNr;
      DoLog(2) && (Log() << Verbose(2) << "(6) Setting Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s Lowpoint to " << Walker->Ancestor->LowpointNr << "." << endl);
    } else {
      // (7) (Ancestor of Walker is a separating vertex, remove all from stack till Walker (including), these and Ancestor form a component
      Walker->Ancestor->SeparationVertex = true;
      DoLog(2) && (Log() << Verbose(2) << "(7) Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s is a separating vertex, creating component." << endl);
      mol->SetNextComponentNumber(Walker->Ancestor, DFS.ComponentNumber);
      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Ancestor's Compont is " << DFS.ComponentNumber << "." << endl);
      mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
      do {
        ASSERT(!DFS.AtomStack->empty(), "DepthFirstSearchAnalysis_CheckForaNewComponent() - DFS.AtomStack is empty!");
        OtherAtom = DFS.AtomStack->front();
        DFS.AtomStack->pop_front();
        LeafWalker->Leaf->AddCopyAtom(OtherAtom);
        mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
        DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
      } while (OtherAtom != Walker);
      DFS.ComponentNumber++;
    }
    // (8) Walker becomes its Ancestor, go to (3)
    DoLog(2) && (Log() << Verbose(2) << "(8) Walker[" << Walker->getName() << "] is now its Ancestor " << Walker->Ancestor->getName() << ", backstepping. " << endl);
    Walker = Walker->Ancestor;
    DFS.BackStepping = true;
  }
}
;

/** Cleans the root stack when we have found a component.
 * If we are not DFSAccounting::BackStepping, then we clear the root stack by putting everything into a
 * component down till we meet DFSAccounting::Root.
 * \param *mol molecule with atoms and finding unused bonds
 * \param *&Walker current node
 * \param *&Binder current edge
 * \param &DFS DFS accounting data
 */
void DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
{
  atom *OtherAtom = NULL;

  if (!DFS.BackStepping) { // coming from (8) want to go to (3)
    // (9) remove all from stack till Walker (including), these and Root form a component
    //DFS.AtomStack->Output(out);
    mol->SetNextComponentNumber(DFS.Root, DFS.ComponentNumber);
    DoLog(3) && (Log() << Verbose(3) << "(9) Root[" << DFS.Root->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
    DoLog(3) && (Log() << Verbose(3) << "(9) Walker[" << Walker->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    do {
      ASSERT(!DFS.AtomStack->empty(), "DepthFirstSearchAnalysis_CleanRootStackDownTillWalker() - DFS.AtomStack is empty!");
      OtherAtom = DFS.AtomStack->front();
      DFS.AtomStack->pop_front();
      LeafWalker->Leaf->AddCopyAtom(OtherAtom);
      mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
      DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    } while (OtherAtom != Walker);
    DFS.ComponentNumber++;

    // (11) Root is separation vertex,  set Walker to Root and go to (4)
    Walker = DFS.Root;
    Binder = mol->FindNextUnused(Walker);
    DoLog(1) && (Log() << Verbose(1) << "(10) Walker is Root[" << DFS.Root->getName() << "], next Unused Bond is " << Binder << "." << endl);
    if (Binder != NULL) { // Root is separation vertex
      DoLog(1) && (Log() << Verbose(1) << "(11) Root is a separation vertex." << endl);
      Walker->SeparationVertex = true;
    }
  }
}
;

/** Initializes DFSAccounting structure.
 * \param &DFS accounting structure to allocate
 * \param *mol molecule with AtomCount, BondCount and all atoms
 */
void DepthFirstSearchAnalysis_Init(struct DFSAccounting &DFS, const molecule * const mol)
{
  DFS.AtomStack = new std::deque<atom *> (mol->getAtomCount());
  DFS.CurrentGraphNr = 0;
  DFS.ComponentNumber = 0;
  DFS.BackStepping = false;
  mol->ResetAllBondsToUnused();
  DFS.BackEdgeStack->clear();
}
;

/** Free's DFSAccounting structure.
 * \param &DFS accounting structure to free
 */
void DepthFirstSearchAnalysis_Finalize(struct DFSAccounting &DFS)
{
  delete (DFS.AtomStack);
  // delete (DFS.BackEdgeStack); // DON'T free, see DepthFirstSearchAnalysis(), is returned as allocated
}
;

void molecule::init_DFS(struct DFSAccounting &DFS) const{
  DepthFirstSearchAnalysis_Init(DFS, this);
  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::resetGraphNr));
  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::InitComponentNr));
}

/** Performs a Depth-First search on this molecule.
 * Marks bonds in molecule as cyclic, bridge, ... and atoms as
 * articulations points, ...
 * We use the algorithm from [Even, Graph Algorithms, p.62].
 * \param *&BackEdgeStack NULL pointer to std::deque<bond *> with all the found back edges, allocated and filled on return
 * \return list of each disconnected subgraph as an individual molecule class structure
 */
MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(std::deque<bond *> *&BackEdgeStack) const
{
  struct DFSAccounting DFS;
  BackEdgeStack = new std::deque<bond *> (getBondCount());
  DFS.BackEdgeStack = BackEdgeStack;
  MoleculeLeafClass *SubGraphs = new MoleculeLeafClass(NULL);
  MoleculeLeafClass *LeafWalker = SubGraphs;
  int OldGraphNr = 0;
  atom *Walker = NULL;
  bond *Binder = NULL;

  if (getAtomCount() == 0)
    return SubGraphs;
  DoLog(0) && (Log() << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl);
  init_DFS(DFS);

  for (molecule::const_iterator iter = begin(); iter != end();) {
    DFS.Root = *iter;
    // (1) mark all edges unused, empty stack, set atom->GraphNr = -1 for all
    DFS.AtomStack->clear();

    // put into new subgraph molecule and add this to list of subgraphs
    LeafWalker = new MoleculeLeafClass(LeafWalker);
    LeafWalker->Leaf = World::getInstance().createMolecule();
    LeafWalker->Leaf->AddCopyAtom(DFS.Root);

    OldGraphNr = DFS.CurrentGraphNr;
    Walker = DFS.Root;
    do { // (10)
      do { // (2) set number and Lowpoint of Atom to i, increase i, push current atom
        DepthFirstSearchAnalysis_SetWalkersGraphNr(Walker, DFS);

        DepthFirstSearchAnalysis_ProbeAlongUnusedBond(this, Walker, Binder, DFS);

        if (Binder == NULL) {
          DoLog(2) && (Log() << Verbose(2) << "No more Unused Bonds." << endl);
          break;
        } else
          Binder = NULL;
      } while (1); // (2)

      // if we came from backstepping, yet there were no more unused bonds, we end up here with no Ancestor, because Walker is Root! Then we are finished!
      if ((Walker == DFS.Root) && (Binder == NULL))
        break;

      DepthFirstSearchAnalysis_CheckForaNewComponent(this, Walker, DFS, LeafWalker);

      DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(this, Walker, Binder, DFS, LeafWalker);

    } while ((DFS.BackStepping) || (Binder != NULL)); // (10) halt only if Root has no unused edges

    // From OldGraphNr to CurrentGraphNr ranges an disconnected subgraph
    DoLog(0) && (Log() << Verbose(0) << "Disconnected subgraph ranges from " << OldGraphNr << " to " << DFS.CurrentGraphNr << "." << endl);
    LeafWalker->Leaf->Output((ofstream *)&(Log() << Verbose(0)));
    DoLog(0) && (Log() << Verbose(0) << endl);

    // step on to next root
    while ((iter != end()) && ((*iter)->GraphNr != -1)) {
      //Log() << Verbose(1) << "Current next subgraph root candidate is " << (*iter)->Name << "." << endl;
      if ((*iter)->GraphNr != -1) // if already discovered, step on
        iter++;
    }
  }
  // set cyclic bond criterium on "same LP" basis
  CyclicBondAnalysis();

  OutputGraphInfoPerAtom();

  OutputGraphInfoPerBond();

  // free all and exit
  DepthFirstSearchAnalysis_Finalize(DFS);
  DoLog(0) && (Log() << Verbose(0) << "End of DepthFirstSearchAnalysis" << endl);
  return SubGraphs;
}
;

/** Scans through all bonds and set bond::Cyclic to true where atom::LowpointNr of both ends is equal: LP criterion.
 */
void molecule::CyclicBondAnalysis() const
{
  NoCyclicBonds = 0;
  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner)
        if ((*BondRunner)->rightatom->LowpointNr == (*BondRunner)->leftatom->LowpointNr) { // cyclic ??
          (*BondRunner)->Cyclic = true;
          NoCyclicBonds++;
        }
  }
}
;

/** Output graph information per atom.
 */
void molecule::OutputGraphInfoPerAtom() const
{
  DoLog(1) && (Log() << Verbose(1) << "Final graph info for each atom is:" << endl);
  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputGraphInfo));
}
;

/** Output graph information per bond.
 */
void molecule::OutputGraphInfoPerBond() const
{
  DoLog(1) && (Log() << Verbose(1) << "Final graph info for each bond is:" << endl);
  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner) {
        const bond *Binder = *BondRunner;
        if (DoLog(2)) {
          ostream &out = (Log() << Verbose(2));
          out << ((Binder->Type == bond::TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
          out << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.";
          Binder->leftatom->OutputComponentNumber(&out);
          out << " ===  ";
          out << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.";
          Binder->rightatom->OutputComponentNumber(&out);
          out << ">." << endl;
        }
        if (Binder->Cyclic) // cyclic ??
          DoLog(3) && (Log() << Verbose(3) << "Lowpoint at each side are equal: CYCLIC!" << endl);
      }
  }
}
;

/** Initialise each vertex as white with no predecessor, empty queue, color Root lightgray.
 * \param &BFS accounting structure
 * \param AtomCount number of entries in the array to allocate
 */
void InitializeBFSAccounting(struct BFSAccounting &BFS, int AtomCount)
{
  BFS.AtomCount = AtomCount;
  BFS.PredecessorList = new atom*[AtomCount];
  BFS.ShortestPathList = new int[AtomCount];
  BFS.ColorList = new enum bond::Shading[AtomCount];
  BFS.BFSStack = new std::deque<atom *> (AtomCount);
  BFS.TouchedStack = new std::deque<atom *> (AtomCount);

  for (int i = AtomCount; i--;) {
    BFS.ShortestPathList[i] = -1;
    BFS.PredecessorList[i] = 0;
    BFS.ColorList[i] = bond::white;
  }
};

/** Free's accounting structure.
 * \param &BFS accounting structure
 */
void FinalizeBFSAccounting(struct BFSAccounting &BFS)
{
  delete[](BFS.PredecessorList);
  delete[](BFS.ShortestPathList);
  delete[](BFS.ColorList);
  delete (BFS.BFSStack);
  delete (BFS.TouchedStack);
  BFS.AtomCount = 0;
};

/** Clean the accounting structure.
 * \param &BFS accounting structure
 */
void CleanBFSAccounting(struct BFSAccounting &BFS)
{
  atom *Walker = NULL;
  while (!BFS.TouchedStack->empty()) {
    Walker = BFS.TouchedStack->front();
    BFS.TouchedStack->pop_front();
    BFS.PredecessorList[Walker->getNr()] = NULL;
    BFS.ShortestPathList[Walker->getNr()] = -1;
    BFS.ColorList[Walker->getNr()] = bond::white;
  }
};

/** Resets shortest path list and BFSStack.
 * \param *&Walker current node, pushed onto BFSAccounting::BFSStack and BFSAccounting::TouchedStack
 * \param &BFS accounting structure
 */
void ResetBFSAccounting(atom *&Walker, struct BFSAccounting &BFS)
{
  BFS.ShortestPathList[Walker->getNr()] = 0;
  BFS.BFSStack->clear(); // start with empty BFS stack
  BFS.BFSStack->push_front(Walker);
  BFS.TouchedStack->push_front(Walker);
};

/** Performs a BFS from \a *Root, trying to find the same node and hence a cycle.
 * \param *&BackEdge the edge from root that we don't want to move along
 * \param &BFS accounting structure
 */
void CyclicStructureAnalysis_CyclicBFSFromRootToRoot(bond *&BackEdge, struct BFSAccounting &BFS)
{
  atom *Walker = NULL;
  atom *OtherAtom = NULL;
  do { // look for Root
    ASSERT(!BFS.BFSStack->empty(), "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - BFS.BFSStack is empty!");
    Walker = BFS.BFSStack->front();
    BFS.BFSStack->pop_front();
    DoLog(2) && (Log() << Verbose(2) << "Current Walker is " << *Walker << ", we look for SP to Root " << *BFS.Root << "." << endl);
    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);
#ifdef ADDHYDROGEN
        if (OtherAtom->getType()->getAtomicNumber() != 1) {
#endif
        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
        if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
          BFS.TouchedStack->push_front(OtherAtom);
          BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
          BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
          BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
          DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
          //if (BFS.ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->nr]) { // Check for maximum distance
          DoLog(3) && (Log() << Verbose(3) << "Putting OtherAtom into queue." << endl);
          BFS.BFSStack->push_front(OtherAtom);
          //}
        } else {
          DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
        }
        if (OtherAtom == BFS.Root)
          break;
#ifdef ADDHYDROGEN
      } else {
        DoLog(2) && (Log() << Verbose(2) << "Skipping hydrogen atom " << *OtherAtom << "." << endl);
        BFS.ColorList[OtherAtom->getNr()] = bond::black;
      }
#endif
      } else {
        DoLog(2) && (Log() << Verbose(2) << "Bond " << *(*Runner) << " not Visiting, is the back edge." << endl);
      }
    }
    BFS.ColorList[Walker->getNr()] = bond::black;
    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    if (OtherAtom == BFS.Root) { // if we have found the root, check whether this cycle wasn't already found beforehand
      // step through predecessor list
      while (OtherAtom != BackEdge->rightatom) {
        if (!OtherAtom->GetTrueFather()->IsCyclic) // if one bond in the loop is not marked as cyclic, we haven't found this cycle yet
          break;
        else
          OtherAtom = BFS.PredecessorList[OtherAtom->getNr()];
      }
      if (OtherAtom == BackEdge->rightatom) { // if each atom in found cycle is cyclic, loop's been found before already
        DoLog(3) && (Log() << Verbose(3) << "This cycle was already found before, skipping and removing seeker from search." << endl);
        do {
          ASSERT(!BFS.TouchedStack->empty(), "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - BFS.TouchedStack is empty!");
          OtherAtom = BFS.TouchedStack->front();
          BFS.TouchedStack->pop_front();
          if (BFS.PredecessorList[OtherAtom->getNr()] == Walker) {
            DoLog(4) && (Log() << Verbose(4) << "Removing " << *OtherAtom << " from lists and stacks." << endl);
            BFS.PredecessorList[OtherAtom->getNr()] = NULL;
            BFS.ShortestPathList[OtherAtom->getNr()] = -1;
            BFS.ColorList[OtherAtom->getNr()] = bond::white;
            // rats ... deque has no find()
            std::deque<atom *>::iterator iter = find(
                BFS.BFSStack->begin(),
                BFS.BFSStack->end(),
                OtherAtom);
            ASSERT(iter != BFS.BFSStack->end(),
                "CyclicStructureAnalysis_CyclicBFSFromRootToRoot() - can't find "+toString(*OtherAtom)+" on stack!");
            BFS.BFSStack->erase(iter);
          }
        } while ((!BFS.TouchedStack->empty()) && (BFS.PredecessorList[OtherAtom->getNr()] == NULL));
        BFS.TouchedStack->push_front(OtherAtom); // last was wrongly popped
        OtherAtom = BackEdge->rightatom; // set to not Root
      } else
        OtherAtom = BFS.Root;
    }
  } while ((!BFS.BFSStack->empty()) && (OtherAtom != BFS.Root) && (OtherAtom != NULL)); // || (ShortestPathList[OtherAtom->getNr()] < MinimumRingSize[Walker->GetTrueFather()->getNr()])));
};

/** Climb back the BFSAccounting::PredecessorList and find cycle members.
 * \param *&OtherAtom
 * \param *&BackEdge denotes the edge we did not want to travel along when doing CyclicBFSFromRootToRoot()
 * \param &BFS accounting structure
 * \param *&MinimumRingSize minimum distance from this node possible without encountering oneself, set on return for each atom
 * \param &MinRingSize global minimum distance from one node without encountering oneself, set on return
 */
void CyclicStructureAnalysis_RetrieveCycleMembers(atom *&OtherAtom, bond *&BackEdge, struct BFSAccounting &BFS, int *&MinimumRingSize, int &MinRingSize)
{
  atom *Walker = NULL;
  int NumCycles = 0;
  int RingSize = -1;

  if (OtherAtom == BFS.Root) {
    // now climb back the predecessor list and thus find the cycle members
    NumCycles++;
    RingSize = 1;
    BFS.Root->GetTrueFather()->IsCyclic = true;
    DoLog(1) && (Log() << Verbose(1) << "Found ring contains: ");
    Walker = BFS.Root;
    while (Walker != BackEdge->rightatom) {
      DoLog(0) && (Log() << Verbose(0) << Walker->getName() << " <-> ");
      Walker = BFS.PredecessorList[Walker->getNr()];
      Walker->GetTrueFather()->IsCyclic = true;
      RingSize++;
    }
    DoLog(0) && (Log() << Verbose(0) << Walker->getName() << "  with a length of " << RingSize << "." << endl << endl);
    // walk through all and set MinimumRingSize
    Walker = BFS.Root;
    MinimumRingSize[Walker->GetTrueFather()->getNr()] = RingSize;
    while (Walker != BackEdge->rightatom) {
      Walker = BFS.PredecessorList[Walker->getNr()];
      if (RingSize < MinimumRingSize[Walker->GetTrueFather()->getNr()])
        MinimumRingSize[Walker->GetTrueFather()->getNr()] = RingSize;
    }
    if ((RingSize < MinRingSize) || (MinRingSize == -1))
      MinRingSize = RingSize;
  } else {
    DoLog(1) && (Log() << Verbose(1) << "No ring containing " << *BFS.Root << " with length equal to or smaller than " << MinimumRingSize[BFS.Root->GetTrueFather()->getNr()] << " found." << endl);
  }
};

/** From a given node performs a BFS to touch the next cycle, for whose nodes \a *&MinimumRingSize is set and set it accordingly.
 * \param *&Root node to look for closest cycle from, i.e. \a *&MinimumRingSize is set for this node
 * \param *&MinimumRingSize minimum distance from this node possible without encountering oneself, set on return for each atom
 * \param AtomCount number of nodes in graph
 */
void CyclicStructureAnalysis_BFSToNextCycle(atom *&Root, atom *&Walker, int *&MinimumRingSize, int AtomCount)
{
  struct BFSAccounting BFS;
  atom *OtherAtom = Walker;

  InitializeBFSAccounting(BFS, AtomCount);

  ResetBFSAccounting(Walker, BFS);
  while (OtherAtom != NULL) { // look for Root
    ASSERT(!BFS.BFSStack->empty(), "CyclicStructureAnalysis_BFSToNextCycle() - BFS.BFSStack is empty!");
    Walker = BFS.BFSStack->front();
    BFS.BFSStack->pop_front();
    //Log() << Verbose(2) << "Current Walker is " << *Walker << ", we look for SP to Root " << *Root << "." << endl;
    const BondList& ListOfBonds = Walker->getListOfBonds();
    for (BondList::const_iterator Runner = ListOfBonds.begin();
        Runner != ListOfBonds.end();
        ++Runner) {
      // "removed (*Runner) != BackEdge) || " from next if, is u
      if ((ListOfBonds.size() == 1)) { // only walk along DFS spanning tree (otherwise we always find SP of 1 being backedge Binder), but terminal hydrogens may be connected via backedge, hence extra check
        OtherAtom = (*Runner)->GetOtherAtom(Walker);
        //Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;
        if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
          BFS.TouchedStack->push_front(OtherAtom);
          BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
          BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
          BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
          //Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl;
          if (OtherAtom->GetTrueFather()->IsCyclic) { // if the other atom is connected to a ring
            MinimumRingSize[Root->GetTrueFather()->getNr()] = BFS.ShortestPathList[OtherAtom->getNr()] + MinimumRingSize[OtherAtom->GetTrueFather()->getNr()];
            OtherAtom = NULL; //break;
            break;
          } else
            BFS.BFSStack->push_front(OtherAtom);
        } else {
          //Log() << Verbose(3) << "Not Adding, has already been visited." << endl;
        }
      } else {
        //Log() << Verbose(3) << "Not Visiting, is a back edge." << endl;
      }
    }
    BFS.ColorList[Walker->getNr()] = bond::black;
    //Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl;
  }
  //CleanAccountingLists(TouchedStack, PredecessorList, ShortestPathList, ColorList);

  FinalizeBFSAccounting(BFS);
}
;

/** All nodes that are not in cycles get assigned a \a *&MinimumRingSizeby BFS to next cycle.
 * \param *&MinimumRingSize array with minimum distance without encountering onself for each atom
 * \param &MinRingSize global minium distance
 * \param &NumCyles number of cycles in graph
 * \param *mol molecule with atoms
 */
void CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(int *&MinimumRingSize, int &MinRingSize, int &NumCycles, const molecule * const mol)
{
  atom *Root = NULL;
  atom *Walker = NULL;
  if (MinRingSize != -1) { // if rings are present
    // go over all atoms
    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
      Root = *iter;

      if (MinimumRingSize[Root->GetTrueFather()->getNr()] == mol->getAtomCount()) { // check whether MinimumRingSize is set, if not BFS to next where it is
        Walker = Root;

        //Log() << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
        CyclicStructureAnalysis_BFSToNextCycle(Root, Walker, MinimumRingSize, mol->getAtomCount());

      }
      DoLog(1) && (Log() << Verbose(1) << "Minimum ring size of " << *Root << " is " << MinimumRingSize[Root->GetTrueFather()->getNr()] << "." << endl);
    }
    DoLog(1) && (Log() << Verbose(1) << "Minimum ring size is " << MinRingSize << ", over " << NumCycles << " cycles total." << endl);
  } else
    DoLog(1) && (Log() << Verbose(1) << "No rings were detected in the molecular structure." << endl);
}
;

/** Analyses the cycles found and returns minimum of all cycle lengths.
 * We begin with a list of Back edges found during DepthFirstSearchAnalysis(). We go through this list - one end is the Root,
 * the other our initial Walker - and do a Breadth First Search for the Root. We mark down each Predecessor and as soon as
 * we have found the Root via BFS, we may climb back the closed cycle via the Predecessors. Thereby we mark atoms and bonds
 * as cyclic and print out the cycles.
 * \param *BackEdgeStack stack with all back edges found during DFS scan. Beware: This stack contains the bonds from the total molecule, not from the subgraph!
 * \param *&MinimumRingSize contains smallest ring size in molecular structure on return or -1 if no rings were found, if set is maximum search distance
 * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
 */
void molecule::CyclicStructureAnalysis(
    std::deque<bond *> * BackEdgeStack,
    int *&MinimumRingSize
    ) const
{
  struct BFSAccounting BFS;
  atom *Walker = NULL;
  atom *OtherAtom = NULL;
  bond *BackEdge = NULL;
  int NumCycles = 0;
  int MinRingSize = -1;

  InitializeBFSAccounting(BFS, getAtomCount());

  //Log() << Verbose(1) << "Back edge list - ";
  //BackEdgeStack->Output(out);

  DoLog(1) && (Log() << Verbose(1) << "Analysing cycles ... " << endl);
  NumCycles = 0;
  while (!BackEdgeStack->empty()) {
    BackEdge = BackEdgeStack->front();
    BackEdgeStack->pop_front();
    // this is the target
    BFS.Root = BackEdge->leftatom;
    // this is the source point
    Walker = BackEdge->rightatom;

    ResetBFSAccounting(Walker, BFS);

    DoLog(1) && (Log() << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl);
    OtherAtom = NULL;
    CyclicStructureAnalysis_CyclicBFSFromRootToRoot(BackEdge, BFS);

    CyclicStructureAnalysis_RetrieveCycleMembers(OtherAtom, BackEdge, BFS, MinimumRingSize, MinRingSize);

    CleanBFSAccounting(BFS);
  }
  FinalizeBFSAccounting(BFS);

  CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(MinimumRingSize, MinRingSize, NumCycles, this);
};

/** Sets the next component number.
 * This is O(N) as the number of bonds per atom is bound.
 * \param *vertex atom whose next atom::*ComponentNr is to be set
 * \param Nr number to use
 */
void molecule::SetNextComponentNumber(atom *vertex, int nr) const
{
  size_t i = 0;
  if (vertex != NULL) {
    const BondList& ListOfBonds = vertex->getListOfBonds();
    for (; i < ListOfBonds.size(); i++) {
      if (vertex->ComponentNr[i] == -1) { // check if not yet used
        vertex->ComponentNr[i] = nr;
        break;
      } else if (vertex->ComponentNr[i] == nr) // if number is already present, don't add another time
        break; // breaking here will not cause error!
    }
    if (i == ListOfBonds.size()) {
      DoeLog(0) && (eLog()<< Verbose(0) << "Error: All Component entries are already occupied!" << endl);
      performCriticalExit();
    }
  } else {
    DoeLog(0) && (eLog()<< Verbose(0) << "Error: Given vertex is NULL!" << endl);
    performCriticalExit();
  }
}
;

/** Returns next unused bond for this atom \a *vertex or NULL of none exists.
 * \param *vertex atom to regard
 * \return bond class or NULL
 */
bond * molecule::FindNextUnused(atom *vertex) const
{
  const BondList& ListOfBonds = vertex->getListOfBonds();
  for (BondList::const_iterator Runner = ListOfBonds.begin();
      Runner != ListOfBonds.end();
      ++Runner)
    if ((*Runner)->IsUsed() == bond::white)
      return ((*Runner));
  return NULL;
}
;

/** Resets bond::Used flag of all bonds in this molecule.
 * \return true - success, false - -failure
 */
void molecule::ResetAllBondsToUnused() const
{
  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
        BondRunner != ListOfBonds.end();
        ++BondRunner)
      if ((*BondRunner)->leftatom == *AtomRunner)
        (*BondRunner)->ResetUsed();
  }
}
;

/** Output a list of flags, stating whether the bond was visited or not.
 * \param *list list to print
 */
void OutputAlreadyVisited(int *list)
{
  DoLog(4) && (Log() << Verbose(4) << "Already Visited Bonds:\t");
  for (int i = 1; i <= list[0]; i++)
    DoLog(0) && (Log() << Verbose(0) << list[i] << "  ");
  DoLog(0) && (Log() << Verbose(0) << endl);
}
;

/** Storing the bond structure of a molecule to file.
 * Simply stores Atom::Nr and then the Atom::Nr of all bond partners per line.
 * \param &filename name of file
 * \param path path to file, defaults to empty
 * \return true - file written successfully, false - writing failed
 */
bool molecule::StoreAdjacencyToFile(std::string filename, std::string path)
{
  ofstream AdjacencyFile;
  string line;
  bool status = true;

  if (path != "")
    line = path + "/" + filename;
  else
    line = filename;
  AdjacencyFile.open(line.c_str(), ios::out);
  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
  if (AdjacencyFile.good()) {
    AdjacencyFile << "m\tn" << endl;
    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
    AdjacencyFile.close();
    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
  } else {
    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    status = false;
  }

  return status;
}
;

/** Storing the bond structure of a molecule to file.
 * Simply stores Atom::Nr and then the Atom::Nr of all bond partners, one per line.
 * \param &filename name of file
 * \param path path to file, defaults to empty
 * \return true - file written successfully, false - writing failed
 */
bool molecule::StoreBondsToFile(std::string filename, std::string path)
{
  ofstream BondFile;
  string line;
  bool status = true;

  if (path != "")
    line = path + "/" + filename;
  else
    line = filename;
  BondFile.open(line.c_str(), ios::out);
  DoLog(1) && (Log() << Verbose(1) << "Saving adjacency list ... " << endl);
  if (BondFile.good()) {
    BondFile << "m\tn" << endl;
    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
    BondFile.close();
    DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
  } else {
    DoLog(1) && (Log() << Verbose(1) << "\t... failed to open file " << line << "." << endl);
    status = false;
  }

  return status;
}
;

bool CheckAdjacencyFileAgainstMolecule_Init(std::string &path, ifstream &File, int *&CurrentBonds)
{
  string filename;
  filename = path + ADJACENCYFILE;
  File.open(filename.c_str(), ios::out);
  DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl);
  if (File.fail())
    return false;

  // allocate storage structure
  CurrentBonds = new int[MAXBONDS]; // contains parsed bonds of current atom
  for(int i=0;i<MAXBONDS;i++)
    CurrentBonds[i] = 0;
  return true;
}
;

void CheckAdjacencyFileAgainstMolecule_Finalize(ifstream &File, int *&CurrentBonds)
{
  File.close();
  File.clear();
  delete[](CurrentBonds);
}
;

void CheckAdjacencyFileAgainstMolecule_CompareBonds(bool &status, int &NonMatchNumber, atom *&Walker, size_t &CurrentBondsOfAtom, int AtomNr, int *&CurrentBonds, atom **ListOfAtoms)
{
  size_t j = 0;
  int id = -1;

  //Log() << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
  const BondList& ListOfBonds = Walker->getListOfBonds();
  if (CurrentBondsOfAtom == ListOfBonds.size()) {
    for (BondList::const_iterator Runner = ListOfBonds.begin();
        Runner != ListOfBonds.end();
        ++Runner) {
      id = (*Runner)->GetOtherAtom(Walker)->getNr();
      j = 0;
      for (; (j < CurrentBondsOfAtom) && (CurrentBonds[j++] != id);)
        ; // check against all parsed bonds
      if (CurrentBonds[j - 1] != id) { // no match ? Then mark in ListOfAtoms
        ListOfAtoms[AtomNr] = NULL;
        NonMatchNumber++;
        status = false;
        DoeLog(2) && (eLog() << Verbose(2) << id << " can not be found in list." << endl);
      } else {
        //Log() << Verbose(0) << "[" << id << "]\t";
      }
    }
    //Log() << Verbose(0) << endl;
  } else {
    DoLog(0) && (Log() << Verbose(0) << "Number of bonds for Atom " << *Walker << " does not match, parsed " << CurrentBondsOfAtom << " against " << ListOfBonds.size() << "." << endl);
    status = false;
  }
}
;

/** Checks contents of adjacency file against bond structure in structure molecule.
 * \param *path path to file
 * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::Nr) to *Atom
 * \return true - structure is equal, false - not equivalence
 */
bool molecule::CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms)
{
  ifstream File;
  bool status = true;
  atom *Walker = NULL;
  int *CurrentBonds = NULL;
  int NonMatchNumber = 0; // will number of atoms with differing bond structure
  size_t CurrentBondsOfAtom = -1;
  const int AtomCount = getAtomCount();

  if (!CheckAdjacencyFileAgainstMolecule_Init(path, File, CurrentBonds)) {
    DoLog(1) && (Log() << Verbose(1) << "Adjacency file not found." << endl);
    return true;
  }

  char buffer[MAXSTRINGSIZE];
  int tmp;
  // Parse the file line by line and count the bonds
  while (!File.eof()) {
    File.getline(buffer, MAXSTRINGSIZE);
    stringstream line;
    line.str(buffer);
    int AtomNr = -1;
    line >> AtomNr;
    CurrentBondsOfAtom = -1; // we count one too far due to line end
    // parse into structure
    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
      Walker = ListOfAtoms[AtomNr];
      while (line >> ws >> tmp) {
        std::cout << "Recognized bond partner " << tmp << std::endl;
        CurrentBonds[++CurrentBondsOfAtom] = tmp;
        ASSERT(CurrentBondsOfAtom < MAXBONDS,
            "molecule::CheckAdjacencyFileAgainstMolecule() - encountered more bonds than allowed: "
            +toString(CurrentBondsOfAtom)+" >= "+toString(MAXBONDS)+"!");
      }
      // compare against present bonds
      CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms);
    } else {
      if (AtomNr != -1)
        DoeLog(2) && (eLog() << Verbose(2) << AtomNr << " is not valid in the range of ids [" << 0 << "," << AtomCount << ")." << endl);
    }
  }
  CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);

  if (status) { // if equal we parse the KeySetFile
    DoLog(1) && (Log() << Verbose(1) << "done: Equal." << endl);
  } else
    DoLog(1) && (Log() << Verbose(1) << "done: Not equal by " << NonMatchNumber << " atoms." << endl);
  return status;
}
;

/** Picks from a global stack with all back edges the ones in the fragment.
 * \param **ListOfLocalAtoms array of father atom::Nr to local atom::Nr (reverse of atom::father)
 * \param *ReferenceStack stack with all the back egdes
 * \param *LocalStack stack to be filled
 * \return true - everything ok, false - ReferenceStack was empty
 */
bool molecule::PickLocalBackEdges(atom **ListOfLocalAtoms, std::deque<bond *> *&ReferenceStack, std::deque<bond *> *&LocalStack) const
{
  bool status = true;
  if (ReferenceStack->empty()) {
    DoLog(1) && (Log() << Verbose(1) << "ReferenceStack is empty!" << endl);
    return false;
  }
  bond *Binder = ReferenceStack->front();
  ReferenceStack->pop_front();
  bond *FirstBond = Binder; // mark the first bond, so that we don't loop through the stack indefinitely
  atom *Walker = NULL, *OtherAtom = NULL;
  ReferenceStack->push_front(Binder);

  do { // go through all bonds and push local ones
    Walker = ListOfLocalAtoms[Binder->leftatom->getNr()]; // get one atom in the reference molecule
    if (Walker != NULL) { // if this Walker exists in the subgraph ...
      const BondList& ListOfBonds = Walker->getListOfBonds();
      for (BondList::const_iterator Runner = ListOfBonds.begin();
          Runner != ListOfBonds.end();
          ++Runner) {
        OtherAtom = (*Runner)->GetOtherAtom(Walker);
        if (OtherAtom == ListOfLocalAtoms[(*Runner)->rightatom->getNr()]) { // found the bond
          LocalStack->push_front((*Runner));
          DoLog(3) && (Log() << Verbose(3) << "Found local edge " << *(*Runner) << "." << endl);
          break;
        }
      }
    }
    ASSERT(!ReferenceStack->empty(), "molecule::PickLocalBackEdges() - ReferenceStack is empty!");
    Binder = ReferenceStack->front(); // loop the stack for next item
    ReferenceStack->pop_front();
    DoLog(3) && (Log() << Verbose(3) << "Current candidate edge " << Binder << "." << endl);
    ReferenceStack->push_front(Binder);
  } while (FirstBond != Binder);

  return status;
}
;

void BreadthFirstSearchAdd_Init(struct BFSAccounting &BFS, atom *&Root, int AtomCount, int BondOrder, atom **AddedAtomList = NULL)
{
  BFS.AtomCount = AtomCount;
  BFS.BondOrder = BondOrder;
  BFS.PredecessorList = new atom*[AtomCount];
  BFS.ShortestPathList = new int[AtomCount];
  BFS.ColorList = new enum bond::Shading[AtomCount];
  BFS.BFSStack = new std::deque<atom *> (AtomCount);

  BFS.Root = Root;
  BFS.BFSStack->clear();
  BFS.BFSStack->push_front(Root);

  // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
  for (int i = AtomCount; i--;) {
    BFS.PredecessorList[i] = NULL;
    BFS.ShortestPathList[i] = -1;
    if ((AddedAtomList != NULL) && (AddedAtomList[i] != NULL)) // mark already present atoms (i.e. Root and maybe others) as visited
      BFS.ColorList[i] = bond::lightgray;
    else
      BFS.ColorList[i] = bond::white;
  }
  //BFS.ShortestPathList[Root->getNr()] = 0; // done by Calloc
}
;

void BreadthFirstSearchAdd_Free(struct BFSAccounting &BFS)
{
  delete[](BFS.PredecessorList);
  delete[](BFS.ShortestPathList);
  delete[](BFS.ColorList);
  delete (BFS.BFSStack);
  BFS.AtomCount = 0;
}
;

void BreadthFirstSearchAdd_UnvisitedNode(molecule *Mol, struct BFSAccounting &BFS, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond, atom **&AddedAtomList, bond **&AddedBondList, bool IsAngstroem)
{
  if (Binder != Bond) // let other atom white if it's via Root bond. In case it's cyclic it has to be reached again (yet Root is from OtherAtom already black, thus no problem)
    BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
  BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
  BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << ((BFS.ColorList[OtherAtom->getNr()] == bond::white) ? "white" : "lightgray") << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
  if ((((BFS.ShortestPathList[OtherAtom->getNr()] < BFS.BondOrder) && (Binder != Bond)))) { // Check for maximum distance
    DoLog(3) && (Log() << Verbose(3));
    if (AddedAtomList[OtherAtom->getNr()] == NULL) { // add if it's not been so far
      AddedAtomList[OtherAtom->getNr()] = Mol->AddCopyAtom(OtherAtom);
      DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
    } else { // this code should actually never come into play (all white atoms are not yet present in BondMolecule, that's why they are white in the first place)
      DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
      if (AddedBondList[Binder->nr] == NULL) {
        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
        DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder->nr]));
      } else
        DoLog(0) && (Log() << Verbose(0) << ", not added Bond ");
    }
    DoLog(0) && (Log() << Verbose(0) << ", putting OtherAtom into queue." << endl);
    BFS.BFSStack->push_front(OtherAtom);
  } else { // out of bond order, then replace
    if ((AddedAtomList[OtherAtom->getNr()] == NULL) && (Binder->Cyclic))
      BFS.ColorList[OtherAtom->getNr()] = bond::white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
    if (Binder == Bond)
      DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is the Root bond");
    else if (BFS.ShortestPathList[OtherAtom->getNr()] >= BFS.BondOrder)
      DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is out of Bond Count of " << BFS.BondOrder);
    if (!Binder->Cyclic)
      DoLog(0) && (Log() << Verbose(0) << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl);
    if (AddedBondList[Binder->nr] == NULL) {
      if ((AddedAtomList[OtherAtom->getNr()] != NULL)) { // .. whether we add or saturate
        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
      } else {
#ifdef ADDHYDROGEN
        if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
        exit(1);
#endif
      }
    }
  }
}
;

void BreadthFirstSearchAdd_VisitedNode(molecule *Mol, struct BFSAccounting &BFS, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond, atom **&AddedAtomList, bond **&AddedBondList, bool IsAngstroem)
{
  DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
  // This has to be a cyclic bond, check whether it's present ...
  if (AddedBondList[Binder->nr] == NULL) {
    if ((Binder != Bond) && (Binder->Cyclic) && (((BFS.ShortestPathList[Walker->getNr()] + 1) < BFS.BondOrder))) {
      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
    } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
#ifdef ADDHYDROGEN
      if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
      exit(1);
#endif
    }
  }
}
;

/** Adds atoms up to \a BondCount distance from \a *Root and notes them down in \a **AddedAtomList.
 * Gray vertices are always enqueued in an std::deque<atom *> FIFO queue, the rest is usual BFS with adding vertices found was
 * white and putting into queue.
 * \param *Mol Molecule class to add atoms to
 * \param **AddedAtomList list with added atom pointers, index is atom father's number
 * \param **AddedBondList list with added bond pointers, index is bond father's number
 * \param *Root root vertex for BFS
 * \param *Bond bond not to look beyond
 * \param BondOrder maximum distance for vertices to add
 * \param IsAngstroem lengths are in angstroem or bohrradii
 */
void molecule::BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem)
{
  struct BFSAccounting BFS;
  atom *Walker = NULL, *OtherAtom = NULL;
  bond *Binder = NULL;

  // add Root if not done yet
  if (AddedAtomList[Root->getNr()] == NULL) // add Root if not yet present
    AddedAtomList[Root->getNr()] = Mol->AddCopyAtom(Root);

  BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, getAtomCount(), AddedAtomList);

  // and go on ... Queue always contains all lightgray vertices
  while (!BFS.BFSStack->empty()) {
    // we have to pop the oldest atom from stack. This keeps the atoms on the stack always of the same ShortestPath distance.
    // e.g. if current atom is 2, push to end of stack are of length 3, but first all of length 2 would be popped. They again
    // append length of 3 (their neighbours). Thus on stack we have always atoms of a certain length n at bottom of stack and
    // followed by n+1 till top of stack.
    Walker = BFS.BFSStack->front(); // pop oldest added
    BFS.BFSStack->pop_front();
    const BondList& ListOfBonds = Walker->getListOfBonds();
    DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->getName() << ", and has " << ListOfBonds.size() << " bonds." << endl);
    for (BondList::const_iterator Runner = ListOfBonds.begin();
        Runner != ListOfBonds.end();
        ++Runner) {
      if ((*Runner) != NULL) { // don't look at bond equal NULL
        Binder = (*Runner);
        OtherAtom = (*Runner)->GetOtherAtom(Walker);
        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
        if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
          BreadthFirstSearchAdd_UnvisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
        } else {
          BreadthFirstSearchAdd_VisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
        }
      }
    }
    BFS.ColorList[Walker->getNr()] = bond::black;
    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
  }
  BreadthFirstSearchAdd_Free(BFS);
}
;

/** Adds a bond as a copy to a given one
 * \param *left leftatom of new bond
 * \param *right rightatom of new bond
 * \param *CopyBond rest of fields in bond are copied from this
 * \return pointer to new bond
 */
bond * molecule::CopyBond(atom *left, atom *right, bond *CopyBond)
{
  bond *Binder = AddBond(left, right, CopyBond->BondDegree);
  Binder->Cyclic = CopyBond->Cyclic;
  Binder->Type = CopyBond->Type;
  return Binder;
}
;

void BuildInducedSubgraph_Init(atom **&ParentList, int AtomCount)
{
  // reset parent list
  ParentList = new atom*[AtomCount];
  for (int i=0;i<AtomCount;i++)
    ParentList[i] = NULL;
  DoLog(3) && (Log() << Verbose(3) << "Resetting ParentList." << endl);
}
;

void BuildInducedSubgraph_FillParentList(const molecule *mol, const molecule *Father, atom **&ParentList)
{
  // fill parent list with sons
  DoLog(3) && (Log() << Verbose(3) << "Filling Parent List." << endl);
  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    ParentList[(*iter)->father->getNr()] = (*iter);
    // Outputting List for debugging
    DoLog(4) && (Log() << Verbose(4) << "Son[" << (*iter)->father->getNr() << "] of " << (*iter)->father << " is " << ParentList[(*iter)->father->getNr()] << "." << endl);
  }
};

void BuildInducedSubgraph_Finalize(atom **&ParentList)
{
  delete[](ParentList);
}
;

bool BuildInducedSubgraph_CreateBondsFromParent(molecule *mol, const molecule *Father, atom **&ParentList)
{
  bool status = true;
  atom *OtherAtom = NULL;
  // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
  DoLog(3) && (Log() << Verbose(3) << "Creating bonds." << endl);
  for (molecule::const_iterator iter = Father->begin(); iter != Father->end(); ++iter) {
    if (ParentList[(*iter)->getNr()] != NULL) {
      if (ParentList[(*iter)->getNr()]->father != (*iter)) {
        status = false;
      } else {
        const BondList& ListOfBonds = (*iter)->getListOfBonds();
        for (BondList::const_iterator Runner = ListOfBonds.begin();
            Runner != ListOfBonds.end();
            ++Runner) {
          OtherAtom = (*Runner)->GetOtherAtom((*iter));
          if (ParentList[OtherAtom->getNr()] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[(*iter)->getNr()]->getName() << " and " << ParentList[OtherAtom->getNr()]->getName() << "." << endl);
            mol->AddBond(ParentList[(*iter)->getNr()], ParentList[OtherAtom->getNr()], (*Runner)->BondDegree);
          }
        }
      }
    }
  }
  return status;
}
;

/** Adds bond structure to this molecule from \a Father molecule.
 * This basically causes this molecule to become an induced subgraph of the \a Father, i.e. for every bond in Father
 * with end points present in this molecule, bond is created in this molecule.
 * Special care was taken to ensure that this is of complexity O(N), where N is the \a Father's molecule::AtomCount.
 * \param *Father father molecule
 * \return true - is induced subgraph, false - there are atoms with fathers not in \a Father
 * \todo not checked, not fully working probably
 */
bool molecule::BuildInducedSubgraph(const molecule *Father){
  bool status = true;
  atom **ParentList = NULL;
  DoLog(2) && (Log() << Verbose(2) << "Begin of BuildInducedSubgraph." << endl);
  BuildInducedSubgraph_Init(ParentList, Father->getAtomCount());
  BuildInducedSubgraph_FillParentList(this, Father, ParentList);
  status = BuildInducedSubgraph_CreateBondsFromParent(this, Father, ParentList);
  BuildInducedSubgraph_Finalize(ParentList);
  DoLog(2) && (Log() << Verbose(2) << "End of BuildInducedSubgraph." << endl);
  return status;
}
;

/** For a given keyset \a *Fragment, checks whether it is connected in the current molecule.
 * \param *Fragment Keyset of fragment's vertices
 * \return true - connected, false - disconnected
 * \note this is O(n^2) for it's just a bug checker not meant for permanent use!
 */
bool molecule::CheckForConnectedSubgraph(KeySet *Fragment)
{
  atom *Walker = NULL, *Walker2 = NULL;
  bool BondStatus = false;
  int size;

  DoLog(1) && (Log() << Verbose(1) << "Begin of CheckForConnectedSubgraph" << endl);
  DoLog(2) && (Log() << Verbose(2) << "Disconnected atom: ");

  // count number of atoms in graph
  size = 0;
  for (KeySet::iterator runner = Fragment->begin(); runner != Fragment->end(); runner++)
    size++;
  if (size > 1)
    for (KeySet::iterator runner = Fragment->begin(); runner != Fragment->end(); runner++) {
      Walker = FindAtom(*runner);
      BondStatus = false;
      for (KeySet::iterator runners = Fragment->begin(); runners != Fragment->end(); runners++) {
        Walker2 = FindAtom(*runners);
        const BondList& ListOfBonds = Walker->getListOfBonds();
        for (BondList::const_iterator Runner = ListOfBonds.begin();
            Runner != ListOfBonds.end();
            ++Runner) {
          if ((*Runner)->GetOtherAtom(Walker) == Walker2) {
            BondStatus = true;
            break;
          }
          if (BondStatus)
            break;
        }
      }
      if (!BondStatus) {
        DoLog(0) && (Log() << Verbose(0) << (*Walker) << endl);
        return false;
      }
    }
  else {
    DoLog(0) && (Log() << Verbose(0) << "none." << endl);
    return true;
  }
  DoLog(0) && (Log() << Verbose(0) << "none." << endl);

  DoLog(1) && (Log() << Verbose(1) << "End of CheckForConnectedSubgraph" << endl);

  return true;
}