source: src/molecules.cpp@ b0a0c3

/** \file molecules.cpp
 * 
 * Functions for the class molecule.
 * 
 */

#include "molecules.hpp"

/************************************* Other Functions *************************************/

/** Determines sum of squared distances of \a X to all \a **vectors.
 * \param *x reference vector
 * \param *params
 * \return sum of square distances
 */
double LSQ (const gsl_vector * x, void * params)
{
  double sum = 0.;
  struct LSQ_params *par = (struct LSQ_params *)params;
  vector **vectors = par->vectors;
  int num = par->num;

  for (int i=0;i<num;i++) {
    for(int j=0;j<NDIM;j++)
      sum += (gsl_vector_get(x,j) - (vectors[i])->x[j])*(gsl_vector_get(x,j) - (vectors[i])->x[j]);
  }
  
  return sum;
};

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

/** Constructor of class molecule.
 * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
 */
molecule::molecule(periodentafel *teil) 
{ 
  // init atom chain list
  start = new atom; 
  end = new atom;
  start->father = NULL; 
  end->father = NULL;
  link(start,end);
  // init bond chain list
  first = new bond(start, end, 1, -1);
  last = new bond(start, end, 1, -1);
  link(first,last);
  // other stuff 
  last_atom = 0; 
  elemente = teil;
  AtomCount = 0;
  BondCount = 0;
  NoNonBonds = 0;
        NoNonHydrogen = 0;
  NoCyclicBonds = 0;
  ListOfBondsPerAtom = NULL;
  NumberOfBondsPerAtom = NULL;
  ElementCount = 0;
  for(int i=0;i<MAX_ELEMENTS;i++)
    ElementsInMolecule[i] = 0;
  cell_size[0] = cell_size[2] = cell_size[5]= 20.;
  cell_size[1] = cell_size[3] = cell_size[4]= 0.;
};

/** Destructor of class molecule.
 * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
 */
molecule::~molecule() 
{
  if (ListOfBondsPerAtom != NULL)
    for(int i=0;i<AtomCount;i++)
      Free((void **)&ListOfBondsPerAtom[i], "molecule::~molecule: ListOfBondsPerAtom[i]");
  Free((void **)&ListOfBondsPerAtom, "molecule::~molecule: ListOfBondsPerAtom");
  Free((void **)&NumberOfBondsPerAtom, "molecule::~molecule: NumberOfBondsPerAtom");
  CleanupMolecule();
  delete(first);
  delete(last);
  delete(end);
  delete(start); 
};

/** Adds given atom \a *pointer from molecule list.
 * Increases molecule::last_atom and gives last number to added atom and names it according to its element::abbrev and molecule::AtomCount 
 * \param *pointer allocated and set atom
 * \return true - succeeded, false - atom not found in list
 */
bool molecule::AddAtom(atom *pointer)
{ 
  if (pointer != NULL) {
    pointer->sort = &pointer->nr; 
    pointer->nr = last_atom++;  // increase number within molecule
    AtomCount++;
    if (pointer->type != NULL) {
      if (ElementsInMolecule[pointer->type->Z] == 0)
        ElementCount++;
      ElementsInMolecule[pointer->type->Z]++; // increase number of elements
      if (pointer->type->Z != 1)
        NoNonHydrogen++;
      if (pointer->Name == NULL) {
        Free((void **)&pointer->Name, "molecule::AddAtom: *pointer->Name");
        pointer->Name = (char *) Malloc(sizeof(char)*6, "molecule::AddAtom: *pointer->Name");
        sprintf(pointer->Name, "%2s%02d", pointer->type->symbol, pointer->nr+1);
      }
    }
    return add(pointer, end);
  } else
    return false; 
};

/** Adds a copy of the given atom \a *pointer from molecule list.
 * Increases molecule::last_atom and gives last number to added atom.
 * \param *pointer allocated and set atom
 * \return true - succeeded, false - atom not found in list
 */
atom * molecule::AddCopyAtom(atom *pointer)
{ 
  if (pointer != NULL) {
        atom *walker = new atom();
        walker->type = pointer->type;   // copy element of atom
        walker->x.CopyVector(&pointer->x); // copy coordination
    walker->v.CopyVector(&pointer->v); // copy velocity
    walker->FixedIon = pointer->FixedIon;
    walker->sort = &walker->nr; 
    walker->nr = last_atom++;  // increase number within molecule
    walker->father = pointer; //->GetTrueFather();
    walker->Name = (char *) Malloc(sizeof(char)*strlen(pointer->Name)+1, "molecule::AddCopyAtom: *Name");
    strcpy (walker->Name, pointer->Name);
    add(walker, end);
    if ((pointer->type != NULL) && (pointer->type->Z != 1))
      NoNonHydrogen++;
    AtomCount++;
    return walker;
  } else
    return NULL; 
};

/** Adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
 * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
 * a different scheme when adding \a *replacement atom for the given one.
 * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
 * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
 *    *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalVector().
 *    The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
 *    replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
 *    element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
 *    hydrogens forming this angle with *origin.
 * -# Triple Bond: The idea is to set up a tetraoid (C1-H1-H2-H3) (however the lengths \f$b\f$ of the sides of the base
 *    triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
 *    determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
 *    We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
 *    \f[ h = l \cdot \cos{\left (\frac{\alpha}{2} \right )} \qquad b = 2l \cdot \sin{\left (\frac{\alpha}{2} \right)} \quad \rightarrow \quad d = l \cdot \sqrt{\cos^2{\left (\frac{\alpha}{2} \right)}-\frac{1}{3}\cdot\sin^2{\left (\frac{\alpha}{2}\right )}}
 *    \f]
 *    vector::GetNormalVector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalVector creates
 *    the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
 *    The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
 *    the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
 *    \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2} 
 *    \f]
 *    as the coordination of all three atoms in the coordinate system of these three vectors: 
 *    \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
 * 
 * \param *out output stream for debugging
 * \param *Bond pointer to bond between \a *origin and \a *replacement 
 * \param *TopOrigin son of \a *origin of upper level molecule (the atom added to this molecule as a copy of \a *origin) 
 * \param *origin pointer to atom which acts as the origin for scaling the added hydrogen to correct bond length
 * \param *replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
 * \param **BondList list of bonds \a *replacement has (necessary to determine plane for double and triple bonds)
 * \param NumBond  number of bonds in \a **BondList
 * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
 * \return number of atoms added, if < bond::BondDegree then something went wrong
 * \todo double and triple bonds splitting (always use the tetraeder angle!)
 */
bool molecule::AddHydrogenReplacementAtom(ofstream *out, bond *TopBond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bond **BondList, int NumBond, bool IsAngstroem)
{
  double bondlength;  // bond length of the bond to be replaced/cut
  double bondangle;  // bond angle of the bond to be replaced/cut
  double BondRescale;   // rescale value for the hydrogen bond length
  bool AllWentWell = true;    // flag gathering the boolean return value of molecule::AddAtom and other functions, as return value on exit
  bond *FirstBond = NULL, *SecondBond = NULL; // Other bonds in double bond case to determine "other" plane
  atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
  int i;  // loop variable
  double b,l,d,f,g, alpha, factors[NDIM];    // hold temporary values in triple bond case for coordination determination
  vector OrthoVector1, OrthoVector2;  // temporary vectors in coordination construction
  vector InBondVector;    // vector in direction of *Bond
  bond *Binder = NULL;
  double *matrix;

        *out << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
  // create vector in direction of bond
  InBondVector.CopyVector(&TopReplacement->x);
  InBondVector.SubtractVector(&TopOrigin->x);
  bondlength = InBondVector.Norm();
   
   // is greater than typical bond distance? Then we have to correct periodically
   // the problem is not the H being out of the box, but InBondVector have the wrong direction
   // due to TopReplacement or Origin being on the wrong side! 
  if (bondlength > BondDistance) { 
    *out << Verbose(4) << "InBondVector is: ";
    InBondVector.Output(out);
    *out << endl;
    OrthoVector1.Zero();
    for (int i=0;i<NDIM;i++) {
      l = TopReplacement->x.x[i] - TopOrigin->x.x[i];
      if (fabs(l) > BondDistance) { // is component greater than bond distance
        OrthoVector1.x[i] = (l < 0) ? -1. : +1.;
      } // (signs are correct, was tested!)
    }
    matrix = ReturnFullMatrixforSymmetric(cell_size);
    OrthoVector1.MatrixMultiplication(matrix);
    InBondVector.SubtractVector(&OrthoVector1); // subtract just the additional translation
    Free((void **)&matrix, "molecule::AddHydrogenReplacementAtom: *matrix");
    bondlength = InBondVector.Norm();
    *out << Verbose(4) << "Corrected InBondVector is now: ";
    InBondVector.Output(out);
    *out << endl;
  } // periodic correction finished
  
  InBondVector.Normalize();
  // get typical bond length and store as scale factor for later
  BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
  if (BondRescale == -1) {
    cerr << Verbose(3) << "WARNING: There is no typical bond distance for bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
    BondRescale = bondlength; 
  } else {
    if (!IsAngstroem)
      BondRescale /= (1.*AtomicLengthToAngstroem);
  }

  // discern single, double and triple bonds
  switch(TopBond->BondDegree) {
    case 1:
      FirstOtherAtom = new atom();    // new atom
      FirstOtherAtom->type = elemente->FindElement(1);  // element is Hydrogen
      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
      if (TopReplacement->type->Z == 1) { // neither rescale nor replace if it's already hydrogen
        FirstOtherAtom->father = TopReplacement;
        BondRescale = bondlength;
      } else {
        FirstOtherAtom->father = NULL;  // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
      }
      InBondVector.Scale(&BondRescale);   // rescale the distance vector to Hydrogen bond length
      FirstOtherAtom->x.CopyVector(&TopOrigin->x); // set coordination to origin ...
      FirstOtherAtom->x.AddVector(&InBondVector);  // ... and add distance vector to replacement atom
      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
      FirstOtherAtom->x.Output(out);
      *out << endl;
      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      break;
    case 2:
      // determine two other bonds (warning if there are more than two other) plus valence sanity check
      for (i=0;i<NumBond;i++) {
        if (BondList[i] != TopBond) {
          if (FirstBond == NULL) {
            FirstBond = BondList[i];
            FirstOtherAtom = BondList[i]->GetOtherAtom(TopOrigin);
          } else if (SecondBond == NULL) {
            SecondBond = BondList[i];
            SecondOtherAtom = BondList[i]->GetOtherAtom(TopOrigin);
          } else {
            *out << Verbose(3) << "WARNING: Detected more than four bonds for atom " << TopOrigin->Name;
          }
        }
      }
      if (SecondOtherAtom == NULL) {  // then we have an atom with valence four, but only 3 bonds: one to replace and one which is TopBond (third is FirstBond)
        SecondBond = TopBond;
        SecondOtherAtom = TopReplacement;
      }
      if (FirstOtherAtom != NULL) { // then we just have this double bond and the plane does not matter at all
        *out << Verbose(3) << "Regarding the double bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") to be constructed: Taking " << FirstOtherAtom->Name << " and " << SecondOtherAtom->Name << " along with " << TopOrigin->Name << " to determine orthogonal plane." << endl;
        
        // determine the plane of these two with the *origin
        AllWentWell = AllWentWell && OrthoVector1.MakeNormalVector(&TopOrigin->x, &FirstOtherAtom->x, &SecondOtherAtom->x);
      } else {
        OrthoVector1.GetOneNormalVector(&InBondVector);
      }
      //*out << Verbose(3)<< "Orthovector1: ";
      //OrthoVector1.Output(out);
      //*out << endl;
      // orthogonal vector and bond vector between origin and replacement form the new plane
      OrthoVector1.MakeNormalVector(&InBondVector);
      OrthoVector1.Normalize();
      //*out << Verbose(3) << "ReScaleCheck: " << OrthoVector1.Norm() << " and " << InBondVector.Norm() << "." << endl;
      
      // create the two Hydrogens ...
      FirstOtherAtom = new atom();
      SecondOtherAtom = new atom();
      FirstOtherAtom->type = elemente->FindElement(1);
      SecondOtherAtom->type = elemente->FindElement(1);
      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
      FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
      SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
      bondangle = TopOrigin->type->HBondAngle[1];
      if (bondangle == -1) {
        *out << Verbose(3) << "WARNING: There is no typical bond angle for bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl;
        bondangle = 0;
      }
      bondangle *= M_PI/180./2.;
//      *out << Verbose(3) << "ReScaleCheck: InBondVector ";
//      InBondVector.Output(out);
//      *out << endl;
//      *out << Verbose(3) << "ReScaleCheck: Orthovector ";
//      OrthoVector1.Output(out);
//      *out << endl;
      *out << Verbose(3) << "Half the bond angle is " << bondangle << ", sin and cos of it: " << sin(bondangle) << ", " << cos(bondangle) << endl;
      FirstOtherAtom->x.Zero();
      SecondOtherAtom->x.Zero();
      for(i=0;i<NDIM;i++) { // rotate by half the bond angle in both directions (InBondVector is bondangle = 0 direction)
        FirstOtherAtom->x.x[i] = InBondVector.x[i] * cos(bondangle) + OrthoVector1.x[i] * (sin(bondangle));
        SecondOtherAtom->x.x[i] = InBondVector.x[i] * cos(bondangle) + OrthoVector1.x[i] * (-sin(bondangle));
      }
      FirstOtherAtom->x.Scale(&BondRescale);  // rescale by correct BondDistance 
      SecondOtherAtom->x.Scale(&BondRescale);
      //*out << Verbose(3) << "ReScaleCheck: " << FirstOtherAtom->x.Norm() << " and " << SecondOtherAtom->x.Norm() << "." << endl;
      for(i=0;i<NDIM;i++) { // and make relative to origin atom
        FirstOtherAtom->x.x[i] += TopOrigin->x.x[i]; 
        SecondOtherAtom->x.x[i] += TopOrigin->x.x[i];
      }
      // ... and add to molecule
      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
      AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
      FirstOtherAtom->x.Output(out);
      *out << endl;
      *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
      SecondOtherAtom->x.Output(out);
      *out << endl;
      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      break;
    case 3:
      // take the "usual" tetraoidal angle and add the three Hydrogen in direction of the bond (height of the tetraoid)
      FirstOtherAtom = new atom();
      SecondOtherAtom = new atom();
      ThirdOtherAtom = new atom();
      FirstOtherAtom->type = elemente->FindElement(1);
      SecondOtherAtom->type = elemente->FindElement(1);
      ThirdOtherAtom->type = elemente->FindElement(1);
      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
      ThirdOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
      ThirdOtherAtom->FixedIon = TopReplacement->FixedIon;
      FirstOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
      SecondOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
      ThirdOtherAtom->father = NULL;  //  we are just an added hydrogen with no father

      // we need to vectors orthonormal the InBondVector
      AllWentWell = AllWentWell && OrthoVector1.GetOneNormalVector(&InBondVector);
      *out << Verbose(3) << "Orthovector1: ";
      OrthoVector1.Output(out);
      *out << endl;
      AllWentWell = AllWentWell && OrthoVector2.MakeNormalVector(&InBondVector, &OrthoVector1);
      *out << Verbose(3) << "Orthovector2: "; 
      OrthoVector2.Output(out);
      *out << endl;
      
      // create correct coordination for the three atoms
      alpha = (TopOrigin->type->HBondAngle[2])/180.*M_PI/2.;  // retrieve triple bond angle from database
      l = BondRescale;        // desired bond length
      b = 2.*l*sin(alpha);    // base length of isosceles triangle
      d = l*sqrt(cos(alpha)*cos(alpha) - sin(alpha)*sin(alpha)/3.);   // length for InBondvector
      f = b/sqrt(3.);   // length for OrthVector1
      g = b/2.;         // length for OrthVector2
      *out << Verbose(3) << "Bond length and half-angle: " << l << ", " << alpha << "\t (b,d,f,g) = " << b << ", " << d << ", " << f << ", " << g << ", " << endl;
      *out << Verbose(3) << "The three Bond lengths: " << sqrt(d*d+f*f) << ", " << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << ", "  << sqrt(d*d+(-0.5*f)*(-0.5*f)+g*g) << endl;
      factors[0] = d;
      factors[1] = f;
      factors[2] = 0.; 
      FirstOtherAtom->x.LinearCombinationOfVectors(&InBondVector, &OrthoVector1, &OrthoVector2, factors);
      factors[1] = -0.5*f;
      factors[2] = g; 
      SecondOtherAtom->x.LinearCombinationOfVectors(&InBondVector, &OrthoVector1, &OrthoVector2, factors);
      factors[2] = -g; 
      ThirdOtherAtom->x.LinearCombinationOfVectors(&InBondVector, &OrthoVector1, &OrthoVector2, factors);

      // rescale each to correct BondDistance
//      FirstOtherAtom->x.Scale(&BondRescale);
//      SecondOtherAtom->x.Scale(&BondRescale);
//      ThirdOtherAtom->x.Scale(&BondRescale);

      // and relative to *origin atom
      FirstOtherAtom->x.AddVector(&TopOrigin->x);
      SecondOtherAtom->x.AddVector(&TopOrigin->x);
      ThirdOtherAtom->x.AddVector(&TopOrigin->x);

      // ... and add to molecule
      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
      AllWentWell = AllWentWell && AddAtom(SecondOtherAtom);
      AllWentWell = AllWentWell && AddAtom(ThirdOtherAtom);
      *out << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
      FirstOtherAtom->x.Output(out);
      *out << endl;
      *out << Verbose(4) << "Added " << *SecondOtherAtom << " at: ";
      SecondOtherAtom->x.Output(out);
      *out << endl;
      *out << Verbose(4) << "Added " << *ThirdOtherAtom << " at: ";
      ThirdOtherAtom->x.Output(out);
      *out << endl;
      Binder = AddBond(BottomOrigin, FirstOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      Binder = AddBond(BottomOrigin, SecondOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      Binder = AddBond(BottomOrigin, ThirdOtherAtom, 1);
      Binder->Cyclic = false;
      Binder->Type = TreeEdge;
      break;
    default:
      cerr << "ERROR: BondDegree does not state single, double or triple bond!" << endl;
      AllWentWell = false;
      break;
  }

        *out << Verbose(3) << "End of AddHydrogenReplacementAtom." << endl;
  return AllWentWell;
};

/** Adds given atom \a *pointer from molecule list.
 * Increases molecule::last_atom and gives last number to added atom.
 * \param filename name and path of xyz file
 * \return true - succeeded, false - file not found
 */
bool molecule::AddXYZFile(string filename)
{ 
  istringstream *input = NULL;
  int NumberOfAtoms = 0; // atom number in xyz read
  int i, j; // loop variables
  atom *first = NULL;  // pointer to added atom
  char shorthand[3];  // shorthand for atom name
  ifstream xyzfile;   // xyz file
  string line;    // currently parsed line
  double x[3];    // atom coordinates
  
  xyzfile.open(filename.c_str());
  if (!xyzfile)
    return false;

  getline(xyzfile,line,'\n'); // Read numer of atoms in file
  input = new istringstream(line);
  *input >> NumberOfAtoms;
  cout << Verbose(0) << "Parsing " << NumberOfAtoms << " atoms in file." << endl; 
  getline(xyzfile,line,'\n'); // Read comment
  cout << Verbose(1) << "Comment: " << line << endl;

  for(i=0;i<NumberOfAtoms;i++){
    first = new atom;
    getline(xyzfile,line,'\n');
    istringstream *item = new istringstream(line);
    //istringstream input(line);
    cout << Verbose(1) << "Reading: " << line << endl;
    *item >> shorthand;
    *item >> x[0];
    *item >> x[1];
    *item >> x[2];
    first->type = elemente->FindElement(shorthand);
    if (first->type == NULL) {
      cerr << "Could not parse the element at line: '" << line << "', setting to H.";
      first->type = elemente->FindElement(1);
    }
    for(j=0;j<NDIM;j++)
      first->x.x[j] = x[j];
     AddAtom(first);  // add to molecule
    delete(item);
  }
  xyzfile.close();
  delete(input);
  return true; 
};

/** Creates a copy of this molecule.
 * \return copy of molecule
 */
molecule *molecule::CopyMolecule()
{
  molecule *copy = new molecule(elemente);
  atom *CurrentAtom = NULL;
  atom *LeftAtom = NULL, *RightAtom = NULL;
  atom *Walker = NULL;
  
  // copy all atoms
  Walker = start;
  while(Walker->next != end) {
    Walker = Walker->next;
    CurrentAtom = copy->AddCopyAtom(Walker);
  }
  
  // copy all bonds
  bond *Binder = first;
  bond *NewBond = NULL;
  while(Binder->next != last) {
    Binder = Binder->next;
    // get the pendant atoms of current bond in the copy molecule
    LeftAtom = copy->start;
    while (LeftAtom->next != copy->end) {
      LeftAtom = LeftAtom->next;
      if (LeftAtom->father == Binder->leftatom)
        break;
    }
    RightAtom = copy->start;
    while (RightAtom->next != copy->end) {
      RightAtom = RightAtom->next;
      if (RightAtom->father == Binder->rightatom)
        break;
    }
    NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
    NewBond->Cyclic = Binder->Cyclic;
    if (Binder->Cyclic)
      copy->NoCyclicBonds++;
    NewBond->Type = Binder->Type;
  }  
  // correct fathers
  Walker = copy->start;
  while(Walker->next != copy->end) {
    Walker = Walker->next;
    if (Walker->father->father == Walker->father)   // same atom in copy's father points to itself
      Walker->father = Walker;  // set father to itself (copy of a whole molecule)
    else
     Walker->father = Walker->father->father;  // set father to original's father
  }
  // copy values
  copy->CountAtoms((ofstream *)&cout);
  copy->CountElements();
  if (first->next != last) {  // if adjaceny list is present
    copy->BondDistance = BondDistance;
    copy->CreateListOfBondsPerAtom((ofstream *)&cout);
  }
  
  return copy;
};

/** Adds a bond to a the molecule specified by two atoms, \a *first and \a *second.
 * Also updates molecule::BondCount and molecule::NoNonBonds.
 * \param *first first atom in bond
 * \param *second atom in bond
 * \return pointer to bond or NULL on failure
 */
bond * molecule::AddBond(atom *atom1, atom *atom2, int degree=1)
{
  bond *Binder = NULL;
  if ((atom1 != NULL) && (FindAtom(atom1->nr) != NULL) && (atom2 != NULL) && (FindAtom(atom2->nr) != NULL)) {
    Binder = new bond(atom1, atom2, degree, BondCount++);
    if ((atom1->type != NULL) && (atom1->type->Z != 1) && (atom2->type != NULL) && (atom2->type->Z != 1))
      NoNonBonds++;
    add(Binder, last);
  } else {
    cerr << Verbose(1) << "ERROR: Could not add bond between " << atom1->Name << " and " << atom2->Name << " as one or both are not present in the molecule." << endl;
  }
  return Binder;
};

/** Remove bond from bond chain list.
 * \todo Function not implemented yet 
 * \param *pointer bond pointer
 * \return true - bound found and removed, false - bond not found/removed
 */
bool molecule::RemoveBond(bond *pointer)
{
  //cerr << Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl;
  removewithoutcheck(pointer);
  return true;
};

/** Remove every bond from bond chain list that atom \a *BondPartner is a constituent of.
 * \todo Function not implemented yet 
 * \param *BondPartner atom to be removed
 * \return true - bounds found and removed, false - bonds not found/removed
 */
bool molecule::RemoveBonds(atom *BondPartner)
{
  cerr << Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl;
  return false;
};

/** Sets the molecule::cell_size to the components of \a *dim (rectangular box)
 * \param *dim vector class
 */
void molecule::SetBoxDimension(vector *dim)
{
  cell_size[0] = dim->x[0];
  cell_size[1] = 0.;
  cell_size[2] = dim->x[1];
  cell_size[3] = 0.;
  cell_size[4] = 0.;
  cell_size[5] = dim->x[2];
};

/** Centers the edge of the atoms at (0,0,0).
 * \param *out output stream for debugging
 * \param *max coordinates of other edge, specifying box dimensions.
 */
void molecule::CenterEdge(ofstream *out, vector *max)
{
  vector *min = new vector;
  
  *out << Verbose(3) << "Begin of CenterEdge." << endl;
  atom *ptr = start->next;  // start at first in list
  if (ptr != end) {   //list not empty?
    for (int i=0;i<NDIM;i++) {
      max->x[i] = ptr->x.x[i];
      min->x[i] = ptr->x.x[i];
    }
    while (ptr->next != end) {  // continue with second if present
      ptr = ptr->next;
      //ptr->Output(1,1,out);
      for (int i=0;i<NDIM;i++) {
        max->x[i] = (max->x[i] < ptr->x.x[i]) ? ptr->x.x[i] : max->x[i];
        min->x[i] = (min->x[i] > ptr->x.x[i]) ? ptr->x.x[i] : min->x[i];
      }
    }
    *out << Verbose(4) << "Maximum is "; 
    max->Output(out);
    *out << ", Minimum is ";
    min->Output(out);
    *out << endl;
    
    for (int i=0;i<NDIM;i++) {
      min->x[i] *= -1.;
      max->x[i] += min->x[i];
    } 
    Translate(min);
  } 
  delete(min);
  *out << Verbose(3) << "End of CenterEdge." << endl;
}; 

/** Centers the center of the atoms at (0,0,0).
 * \param *out output stream for debugging
 * \param *center return vector for translation vector
 */
void molecule::CenterOrigin(ofstream *out, vector *center)
{
  int Num = 0;
  atom *ptr = start->next;  // start at first in list
 
  for(int i=0;i<NDIM;i++) // zero center vector
    center->x[i] = 0.;
    
  if (ptr != end) {   //list not empty?
    while (ptr->next != end) {  // continue with second if present
      ptr = ptr->next;
      Num++;
      center->AddVector(&ptr->x);       
    }
    center->Scale(-1./Num); // divide through total number (and sign for direction)
    Translate(center);
  }
}; 

/** Centers the center of gravity of the atoms at (0,0,0).
 * \param *out output stream for debugging
 * \param *center return vector for translation vector
 */
void molecule::CenterGravity(ofstream *out, vector *center)
{
  double Num = 0;
  atom *ptr = start->next;  // start at first in list
  vector tmp;
  
  for(int i=0;i<NDIM;i++) // zero center vector
    center->x[i] = 0.;
    
  if (ptr != end) {   //list not empty?
    while (ptr->next != end) {  // continue with second if present
      ptr = ptr->next;
      Num += ptr->type->mass;
      tmp.CopyVector(&ptr->x);
      tmp.Scale(ptr->type->mass);  // scale by mass
      center->AddVector(&tmp);       
    }
    center->Scale(-1./Num); // divide through total mass (and sign for direction)
    Translate(center);
  }
}; 

/** Scales all atoms by \a *factor.
 * \param *factor pointer to scaling factor
 */
void molecule::Scale(double **factor)
{
  atom *ptr = start;

  while (ptr->next != end) {
    ptr = ptr->next;
    ptr->x.Scale(factor);
  }      
};

/** Translate all atoms by given vector. 
 * \param trans[] translation vector.
 */
void molecule::Translate(const vector *trans)
{
  atom *ptr = start;

  while (ptr->next != end) {
    ptr = ptr->next;
    ptr->x.Translate(trans);
  }      
};

/** Mirrors all atoms against a given plane. 
 * \param n[] normal vector of mirror plane.
 */
void molecule::Mirror(const vector *n)
{
  atom *ptr = start;

  while (ptr->next != end) {
    ptr = ptr->next;
    ptr->x.Mirror(n);
  }      
};

/** Determines center of gravity (yet not considering atom masses).
 * \param CenterOfGravity reference to return vector
 */
void molecule::DetermineCenterOfGravity(vector &CenterOfGravity)
{
  atom *Walker = start;
  bond *Binder = NULL;
  double *matrix = ReturnFullMatrixforSymmetric(cell_size);
  double tmp;
  bool flag;
  vector TestVector, TranslationVector;
  
  do {
    CenterOfGravity.Zero();
    flag = true;
    while (Walker->next != end) {
      Walker = Walker->next;
#ifdef ADDHYDROGEN
      if (Walker->type->Z != 1) {
#endif
        TestVector.CopyVector(&Walker->x);
        TestVector.InverseMatrixMultiplication(matrix);
        TranslationVector.Zero();
        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr]; i++) {
          Binder = ListOfBondsPerAtom[Walker->nr][i];
          if (Walker->nr < Binder->GetOtherAtom(Walker)->nr) // otherwise we shift one to, the other fro and gain nothing
            for (int j=0;j<NDIM;j++) {
              tmp = Walker->x.x[j] - Binder->GetOtherAtom(Walker)->x.x[j]; 
              if ((fabs(tmp)) > BondDistance) {
                flag = false;
                cout << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *Binder << " has to be shifted due to " << tmp << "." << endl;
                if (tmp > 0)
                  TranslationVector.x[j] -= 1.;
                else
                  TranslationVector.x[j] += 1.;
              }
            }
        }
        TestVector.AddVector(&TranslationVector);
        TestVector.MatrixMultiplication(matrix);
        CenterOfGravity.AddVector(&TestVector);
        cout << Verbose(1) << "Vector is: ";
        TestVector.Output((ofstream *)&cout);
        cout << endl;     
#ifdef ADDHYDROGEN
        // now also change all hydrogens
        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr]; i++) {
          Binder = ListOfBondsPerAtom[Walker->nr][i];
          if (Binder->GetOtherAtom(Walker)->type->Z == 1) {
            TestVector.CopyVector(&Binder->GetOtherAtom(Walker)->x);
            TestVector.InverseMatrixMultiplication(matrix);
            TestVector.AddVector(&TranslationVector);
            TestVector.MatrixMultiplication(matrix);
            CenterOfGravity.AddVector(&TestVector);
            cout << Verbose(1) << "Hydrogen Vector is: ";
            TestVector.Output((ofstream *)&cout);
            cout << endl;     
          }
        }
      }
#endif
    }
  } while (!flag);
  Free((void **)&matrix, "molecule::DetermineCenterOfGravity: *matrix");
  CenterOfGravity.Scale(1./(double)AtomCount);
};

/** Align all atoms in such a manner that given vector \a *n is along z axis. 
 * \param n[] alignment vector.
 */
void molecule::Align(vector *n)
{
  atom *ptr = start;
  double alpha, tmp;
  vector z_axis;
  z_axis.x[0] = 0.;
  z_axis.x[1] = 0.;
  z_axis.x[2] = 1.;

  // rotate on z-x plane
  cout << Verbose(0) << "Begin of Aligning all atoms." << endl;
  alpha = atan(-n->x[0]/n->x[2]);
  cout << Verbose(1) << "Z-X-angle: " << alpha << " ... ";
  while (ptr->next != end) {
    ptr = ptr->next;
    tmp = ptr->x.x[0];
    ptr->x.x[0] =  cos(alpha) * tmp + sin(alpha) * ptr->x.x[2]; 
    ptr->x.x[2] = -sin(alpha) * tmp + cos(alpha) * ptr->x.x[2];
  }      
  // rotate n vector
  tmp = n->x[0];
  n->x[0] =  cos(alpha) * tmp +  sin(alpha) * n->x[2];
  n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
  cout << Verbose(1) << "alignment vector after first rotation: ";
  n->Output((ofstream *)&cout);
  cout << endl;
  
  // rotate on z-y plane
  ptr = start;
  alpha = atan(-n->x[1]/n->x[2]);
  cout << Verbose(1) << "Z-Y-angle: " << alpha << " ... ";
  while (ptr->next != end) {
    ptr = ptr->next;
    tmp = ptr->x.x[1];
    ptr->x.x[1] =  cos(alpha) * tmp + sin(alpha) * ptr->x.x[2]; 
    ptr->x.x[2] = -sin(alpha) * tmp + cos(alpha) * ptr->x.x[2];
  }      
  // rotate n vector (for consistency check)
  tmp = n->x[1];
  n->x[1] =  cos(alpha) * tmp +  sin(alpha) * n->x[2];
  n->x[2] = -sin(alpha) * tmp +  cos(alpha) * n->x[2];
  
  cout << Verbose(1) << "alignment vector after second rotation: ";
  n->Output((ofstream *)&cout);
  cout << Verbose(1) << endl;
  cout << Verbose(0) << "End of Aligning all atoms." << endl;
};

/** Removes atom from molecule list.
 * \param *pointer atom to be removed
 * \return true - succeeded, false - atom not found in list
 */
bool molecule::RemoveAtom(atom *pointer)  
{ 
  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
    ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
  else
    cerr << "ERROR: Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl; 
  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
    ElementCount--;
  return remove(pointer, start, end);
};

/** Removes every atom from molecule list.
 * \return true - succeeded, false - atom not found in list
 */
bool molecule::CleanupMolecule() 
{ 
  return (cleanup(start,end) && cleanup(first,last)); 
};

/** Finds an atom specified by its continuous number.
 * \param Nr number of atom withim molecule
 * \return pointer to atom or NULL
 */
atom * molecule::FindAtom(int Nr)  const{
  atom * walker = find(&Nr, start,end);
  if (walker != NULL) {
    //cout << Verbose(0) << "Found Atom Nr. " << walker->nr << endl;
    return walker;
  } else {
    cout << Verbose(0) << "Atom not found in list." << endl;
    return NULL;  
  }
};

/** Asks for atom number, and checks whether in list.
 * \param *text question before entering
 */
atom * molecule::AskAtom(char *text)
{
  int No;
  atom *ion = NULL;
  do {
    //cout << Verbose(0) << "============Atom list==========================" << endl;
    //mol->Output((ofstream *)&cout);
    //cout << Verbose(0) << "===============================================" << endl;
    cout << Verbose(0) << text;
    cin >> No;
    ion = this->FindAtom(No);
  } while (ion == NULL);
  return ion;
};

/** Checks if given coordinates are within cell volume.
 * \param *x array of coordinates
 * \return true - is within, false - out of cell
 */
bool molecule::CheckBounds(const vector *x) const
{
  bool result = true;
  int j =-1;
  for (int i=0;i<3;i++) {
    j += i+1;
    result = result && ((x->x[i] >= 0) && (x->x[i] < cell_size[j]));
  }
  //return result;
  return true; /// probably not gonna use the check no more
};

/** Calculates sum over least square distance to line hidden in \a *x.
 * \param *x offset and direction vector
 * \param *params pointer to lsq_params structure
 * \return \f$ sum_i^N | y_i - (a + t_i b)|^2\f$
 */
double LeastSquareDistance (const gsl_vector * x, void * params)
{
  double res = 0, t;
  vector a,b,c,d;
  struct lsq_params *par = (struct lsq_params *)params;
  atom *ptr = par->mol->start;
  
  // initialize vectors
  a.x[0] = gsl_vector_get(x,0);
  a.x[1] = gsl_vector_get(x,1);
  a.x[2] = gsl_vector_get(x,2);
  b.x[0] = gsl_vector_get(x,3);
  b.x[1] = gsl_vector_get(x,4);
  b.x[2] = gsl_vector_get(x,5);
  // go through all atoms
  while (ptr != par->mol->end) {
    ptr = ptr->next;
    if (ptr->type == ((struct lsq_params *)params)->type) { // for specific type
      c.CopyVector(&ptr->x);  // copy vector to temporary one
      c.SubtractVector(&a);   // subtract offset vector
      t = c.ScalarProduct(&b);           // get direction parameter
      d.CopyVector(&b);       // and create vector
      d.Scale(&t);
      c.SubtractVector(&d);   // ... yielding distance vector
      res += d.ScalarProduct((const vector *)&d);        // add squared distance
    }
  }
  return res;
};

/** By minimizing the least square distance gains alignment vector.
 * \bug this is not yet working properly it seems
 */
void molecule::GetAlignVector(struct lsq_params * par) const
{
    int np = 6;
    
   const gsl_multimin_fminimizer_type *T =
     gsl_multimin_fminimizer_nmsimplex;
   gsl_multimin_fminimizer *s = NULL;
   gsl_vector *ss;
   gsl_multimin_function minex_func;
 
   size_t iter = 0, i;
   int status;
   double size;
 
   /* Initial vertex size vector */
   ss = gsl_vector_alloc (np);
 
   /* Set all step sizes to 1 */
   gsl_vector_set_all (ss, 1.0);
 
   /* Starting point */
   par->x = gsl_vector_alloc (np);
   par->mol = this;
 
   gsl_vector_set (par->x, 0, 0.0);  // offset
   gsl_vector_set (par->x, 1, 0.0);
   gsl_vector_set (par->x, 2, 0.0);
   gsl_vector_set (par->x, 3, 0.0);  // direction
   gsl_vector_set (par->x, 4, 0.0);
   gsl_vector_set (par->x, 5, 1.0);
 
   /* Initialize method and iterate */
   minex_func.f = &LeastSquareDistance;
   minex_func.n = np;
   minex_func.params = (void *)par;
 
   s = gsl_multimin_fminimizer_alloc (T, np);
   gsl_multimin_fminimizer_set (s, &minex_func, par->x, ss);
 
   do
     {
       iter++;
       status = gsl_multimin_fminimizer_iterate(s);
 
       if (status)
         break;
 
       size = gsl_multimin_fminimizer_size (s);
       status = gsl_multimin_test_size (size, 1e-2);
 
       if (status == GSL_SUCCESS)
         {
           printf ("converged to minimum at\n");
         }
 
       printf ("%5d ", (int)iter);
       for (i = 0; i < (size_t)np; i++)
         {
           printf ("%10.3e ", gsl_vector_get (s->x, i));
         }
       printf ("f() = %7.3f size = %.3f\n", s->fval, size);
     }
   while (status == GSL_CONTINUE && iter < 100);
 
  for (i=0;i<(size_t)np;i++)
    gsl_vector_set(par->x, i, gsl_vector_get(s->x, i));
   //gsl_vector_free(par->x);
   gsl_vector_free(ss);
   gsl_multimin_fminimizer_free (s);
};

/** Prints molecule to *out.
 * \param *out output stream
 */
bool molecule::Output(ofstream *out)
{
  element *runner = elemente->start;
  atom *walker = NULL;
  int ElementNo, AtomNo;
  CountElements();
  
  if (out == NULL) {
    return false;
  } else {
    *out << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
    ElementNo = 0;
    while (runner->next != elemente->end) { // go through every element
                runner = runner->next;
      if (ElementsInMolecule[runner->Z]) { // if this element got atoms
        ElementNo++;
        AtomNo = 0;
        walker = start;
        while (walker->next != end) { // go through every atom of this element
          walker = walker->next;
          if (walker->type == runner) { // if this atom fits to element
            AtomNo++;
            walker->Output(ElementNo, AtomNo, out);
          }
        }
      }
    }
    return true;
  }
};

/** Output of element before the actual coordination list.
 * \param *out stream pointer
 */
bool molecule::Checkout(ofstream *out)  const
{
        return elemente->Checkout(out, ElementsInMolecule);
};

/** Prints molecule to *out as xyz file.
 * \param *out output stream
 */
bool molecule::OutputXYZ(ofstream *out) const
{
  atom *walker = NULL;
  int No = 0;
  time_t now;
  
  now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
  walker = start;
  while (walker->next != end) { // go through every atom and count
    walker = walker->next;
    No++;
  }
  if (out != NULL) {
    *out << No << "\n\tCreated by molecuilder on " << ctime(&now);
    walker = start;
    while (walker->next != end) { // go through every atom of this element
      walker = walker->next;
      walker->OutputXYZLine(out);
    }
    return true;
  } else
    return false;
};

/** Brings molecule::AtomCount and atom::*Name up-to-date.
 * \param *out output stream for debugging
 */
void molecule::CountAtoms(ofstream *out)
{
        int i = 0;
        atom *Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    i++;
  }
  if ((AtomCount == 0) || (i != AtomCount)) {
    *out << Verbose(3) << "Mismatch in AtomCount " << AtomCount << " and recounted number " << i << ", renaming all." << endl;
        AtomCount = i;

    // count NonHydrogen atoms and give each atom a unique name
    if (AtomCount != 0) {
            i=0;
            NoNonHydrogen = 0;
      Walker = start;
            while (Walker->next != end) {
              Walker = Walker->next;
              Walker->nr = i;   // update number in molecule (for easier referencing in FragmentMolecule lateron)
              if (Walker->type->Z != 1) // count non-hydrogen atoms whilst at it
                NoNonHydrogen++; 
              Free((void **)&Walker->Name, "molecule::CountAtoms: *walker->Name");
              Walker->Name = (char *) Malloc(sizeof(char)*6, "molecule::CountAtoms: *walker->Name");
              sprintf(Walker->Name, "%2s%02d", Walker->type->symbol, Walker->nr+1);
        *out << "Naming atom nr. " << Walker->nr << " " << Walker->Name << "." << endl;
              i++;
            }
    } else
        *out << Verbose(3) << "AtomCount is still " << AtomCount << ", thus counting nothing." << endl; 
  }
};

/** Brings molecule::ElementCount and molecule::ElementsInMolecule up-to-date.
 */
void molecule::CountElements()
{
        int i = 0;
  for(i=0;i<MAX_ELEMENTS;i++)
        ElementsInMolecule[i] = 0;
        ElementCount = 0;
        
  atom *walker = start;
  while (walker->next != end) {
    walker = walker->next;
    ElementsInMolecule[walker->type->Z]++;
    i++;
  }
  for(i=0;i<MAX_ELEMENTS;i++)
        ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
};

/** Counts all cyclic bonds and returns their number.
 * \note Hydrogen bonds can never by cyclic, thus no check for that
 * \param *out output stream for debugging
 * \return number opf cyclic bonds
 */
int molecule::CountCyclicBonds(ofstream *out)
{
  int No = 0;
  int MinimumRingSize;
  MoleculeLeafClass *Subgraphs = NULL;
  bond *Binder = first;
  if ((Binder->next != last) && (Binder->next->Type == Undetermined)) {
    *out << Verbose(0) << "No Depth-First-Search analysis performed so far, calling ..." << endl;
    Subgraphs = DepthFirstSearchAnalysis(out, false, MinimumRingSize);
    while (Subgraphs->next != NULL) {
      Subgraphs = Subgraphs->next;
      delete(Subgraphs->previous);
    }
    delete(Subgraphs);
  }
  while(Binder->next != last) {
    Binder = Binder->next;
    if (Binder->Cyclic)
      No++;    
  }
  return No;
};

/** Returns Shading as a char string.
 * \param color the Shading
 * \return string of the flag
 */
char * molecule::GetColor(enum Shading color)
{
  switch(color) {
    case white:
      return "white";
      break;
    case lightgray:
      return "lightgray";
      break;
    case darkgray:
      return "darkgray";
      break;
    case black:
      return "black";
      break;
    default:
      return "uncolored";
      break;
  };
};


/** Counts necessary number of valence electrons and returns number and SpinType.
 * \param configuration containing everything
 */
void molecule::CalculateOrbitals(class config &configuration)
{
  configuration.MaxPsiDouble = configuration.PsiMaxNoDown = configuration.PsiMaxNoUp = configuration.PsiType = 0;
  for(int i=0;i<MAX_ELEMENTS;i++) {
    if (ElementsInMolecule[i] != 0) {
      //cout << "CalculateOrbitals: " << elemente->FindElement(i)->name << " has a valence of " << (int)elemente->FindElement(i)->Valence << " and there are " << ElementsInMolecule[i] << " of it." << endl;
      configuration.MaxPsiDouble += ElementsInMolecule[i]*((int)elemente->FindElement(i)->Valence);
    }
  }
  configuration.PsiMaxNoDown = configuration.MaxPsiDouble/2 + (configuration.MaxPsiDouble % 2);
  configuration.PsiMaxNoUp = configuration.MaxPsiDouble/2;
  configuration.MaxPsiDouble /= 2;
  configuration.PsiType = (configuration.PsiMaxNoDown == configuration.PsiMaxNoUp) ? 0 : 1;
  if ((configuration.PsiType == 1) && (configuration.ProcPEPsi < 2)) {
    configuration.ProcPEGamma /= 2;
    configuration.ProcPEPsi *= 2;
  } else {
    configuration.ProcPEGamma *= configuration.ProcPEPsi;
    configuration.ProcPEPsi = 1;
  }
  configuration.InitMaxMinStopStep = configuration.MaxMinStopStep = configuration.MaxPsiDouble;
};

/** Creates an adjacency list of the molecule.
 * Generally, we use the CSD approach to bond recognition, that is the the distance
 * between two atoms A and B must be within [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with
 * a threshold t = 0.4 Angstroem. 
 * To make it O(N log N) the function uses the linked-cell technique as follows:
 * The procedure is step-wise:
 *  -# Remove every bond in list
 *  -# Count the atoms in the molecule with CountAtoms()
 *  -# partition cell into smaller linked cells of size \a bonddistance
 *  -# put each atom into its corresponding cell
 *  -# go through every cell, check the atoms therein against all possible bond partners in the 27 adjacent cells, add bond if true
 *  -# create the list of bonds via CreateListOfBondsPerAtom()
 *  -# correct the bond degree iteratively (single->double->triple bond)
 *  -# finally print the bond list to \a *out if desired
 * \param *out out stream for printing the matrix, NULL if no output
 * \param bonddistance length of linked cells (i.e. maximum minimal length checked)
 */
void molecule::CreateAdjacencyList(ofstream *out, double bonddistance)
{
  atom *Walker = NULL, *OtherWalker = NULL;
  int No, NoBonds;
  bond *Binder = NULL;
  int NumberCells, divisor[NDIM], n[NDIM], N[NDIM], index, Index, j;
  molecule **CellList;
  double distance, MinDistance, MaxDistance;
  double *matrix = ReturnFullMatrixforSymmetric(cell_size);
  vector x;
 
  BondDistance = bonddistance;
  *out << Verbose(0) << "Begin of CreateAdjacencyList." << endl;
  // remove every bond from the list
  if ((first->next != last) && (last->previous != first)) {  // there are bonds present
    cleanup(first,last);
  }
        
  // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
  CountAtoms(out);
  *out << Verbose(1) << "AtomCount " << AtomCount << "." << endl;

  if (AtomCount != 0) {
    // 1. find divisor for each axis, such that a sphere with radius of at least bonddistance can be placed into each cell
    j=-1;
    for (int i=0;i<NDIM;i++) {
      j += i+1;
      divisor[i] = (int)floor(cell_size[j]/bonddistance); // take smaller value such that size of linked cell is at least bonddistance
      *out << Verbose(1) << "divisor[" << i << "]  = " << divisor[i] << "." << endl;
    }
    // 2a. allocate memory for the cell list
    NumberCells = divisor[0]*divisor[1]*divisor[2];
    *out << Verbose(1) << "Allocating " << NumberCells << " cells." << endl;
    CellList = (molecule **) Malloc(sizeof(molecule *)*NumberCells, "molecule::CreateAdjacencyList - ** CellList");
    for (int i=0;i<NumberCells;i++)
      CellList[i] = NULL;
  
    // 2b. put all atoms into its corresponding list
    Walker = start;
    while(Walker->next != end) {
      Walker = Walker->next;
      //*out << Verbose(1) << "Current atom is " << *Walker << " with coordinates ";
      //Walker->x.Output(out);
      //*out << "." << endl;
      // compute the cell by the atom's coordinates
      j=-1;
      for (int i=0;i<NDIM;i++) {
        j += i+1;
        x.CopyVector(&(Walker->x));
        x.KeepPeriodic(out, matrix);
        n[i] = (int)floor(x.x[i]/cell_size[j]*(double)divisor[i]);
      }
      index = n[2] + (n[1] + n[0] * divisor[1]) * divisor[2];
      *out << Verbose(1) << "Atom " << *Walker << " goes into cell number [" << n[0] << "," << n[1] << "," << n[2] << "] = " << index << "." << endl;
      // add copy atom to this cell
      if (CellList[index] == NULL)  // allocate molecule if not done
        CellList[index] = new molecule(elemente);
      OtherWalker = CellList[index]->AddCopyAtom(Walker); // add a copy of walker to this atom, father will be walker for later reference 
      //*out << Verbose(1) << "Copy Atom is " << *OtherWalker << "." << endl; 
    }
    //for (int i=0;i<NumberCells;i++)
      //*out << Verbose(1) << "Cell number " << i << ": " << CellList[i] << "." << endl;
      
    // 3a. go through every cell
    for (N[0]=0;N[0]<divisor[0];N[0]++)
      for (N[1]=0;N[1]<divisor[1];N[1]++)
        for (N[2]=0;N[2]<divisor[2];N[2]++) {
          Index = N[2] + (N[1] + N[0] * divisor[1]) * divisor[2];
          if (CellList[Index] != NULL) { // if there atoms in this cell
            //*out << Verbose(1) << "Current cell is " << Index << "." << endl;
            // 3b. for every atom therein
            Walker = CellList[Index]->start;
            while (Walker->next != CellList[Index]->end) {  // go through every atom
              Walker = Walker->next;
              //*out << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
              // 3c. check for possible bond between each atom in this and every one in the 27 cells 
              for (n[0]=-1;n[0]<=1;n[0]++)
                for (n[1]=-1;n[1]<=1;n[1]++)
                  for (n[2]=-1;n[2]<=1;n[2]++) {
                     // compute the index of this comparison cell and make it periodic
                    index = ((N[2]+n[2]+divisor[2])%divisor[2]) + (((N[1]+n[1]+divisor[1])%divisor[1]) + ((N[0]+n[0]+divisor[0])%divisor[0]) * divisor[1]) * divisor[2];
                    //*out << Verbose(1) << "Number of comparison cell is " << index << "." << endl;
                    if (CellList[index] != NULL) {  // if there are any atoms in this cell
                      OtherWalker = CellList[index]->start;
                      while(OtherWalker->next != CellList[index]->end) {  // go through every atom in this cell
                        OtherWalker = OtherWalker->next;
                        //*out << Verbose(0) << "Current comparison atom is " << *OtherWalker << "." << endl;
                        /// \todo periodic check is missing here!
                        //*out << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistance(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                        MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;  
                        MaxDistance = MinDistance + BONDTHRESHOLD;
                        MinDistance -= BONDTHRESHOLD;
                        distance =   OtherWalker->x.PeriodicDistance(&(Walker->x), cell_size);
                        if ((OtherWalker->father->nr > Walker->father->nr) && (distance <= MaxDistance*MaxDistance) && (distance >= MinDistance*MinDistance)) { // create bond if distance is smaller
                          *out << Verbose(0) << "Adding Bond between " << *Walker << " and " << *OtherWalker << "." << endl;
                          AddBond(Walker->father, OtherWalker->father, 1);  // also increases molecule::BondCount
                        } else {
                          //*out << Verbose(1) << "Not Adding: Wrong label order or distance too great." << endl;
                        }
                      }
                    }
                  }
            }
          }
        }
    // 4. free the cell again
    for (int i=0;i<NumberCells;i++)
      if (CellList[i] != NULL) {
        delete(CellList[i]);
      }
    Free((void **)&CellList, "molecule::CreateAdjacencyList - ** CellList"); 
  
    // create the adjacency list per atom
    CreateListOfBondsPerAtom(out);
                
    // correct Bond degree of each bond by checking of updated(!) sum of bond degree for an atom match its valence count
    // bond degrres are correctled iteratively by one, so that 2-2 instead of 1-3 or 3-1 corrections are favoured: We want
    // a rather symmetric distribution of higher bond degrees
                if (BondCount != 0) {
      NoCyclicBonds = 0;
                  *out << Verbose(1) << "correct Bond degree of each bond" << endl;
                  do {
                    No = 0; // No acts as breakup flag (if 1 we still continue)
        Walker = start;
        while (Walker->next != end) { // go through every atom
          Walker = Walker->next;
          for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) { // go through each of its bond partners
            OtherWalker = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
                  // count valence of first partner (updated!), might have changed during last bond partner
                  NoBonds = 0;
            for(j=0;j<NumberOfBondsPerAtom[Walker->nr];j++)
              NoBonds += ListOfBondsPerAtom[Walker->nr][j]->BondDegree;
                  *out << Verbose(3) << "Walker: " << (int)Walker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
                  if ((int)(Walker->type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check NoBonds of other atom
                    // count valence of second partner
              NoBonds = 0;
              for(j=0;j<NumberOfBondsPerAtom[OtherWalker->nr];j++)
                NoBonds += ListOfBondsPerAtom[OtherWalker->nr][j]->BondDegree;
              *out << Verbose(3) << "OtherWalker: " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
                    if ((int)(OtherWalker->type->NoValenceOrbitals) > NoBonds) // increase bond degree by one
                ListOfBondsPerAtom[Walker->nr][i]->BondDegree++;
                  }
          }
                    }
                  } while (No);
                
                } else
                        *out << Verbose(1) << "BondCount is " << BondCount << ", no bonds between any of the " << AtomCount << " atoms." << endl;
          *out << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << bonddistance << "." << endl;
                
          // output bonds for debugging (if bond chain list was correctly installed)
          *out << Verbose(1) << endl << "From contents of bond chain list:";
    Binder = first;
    while(Binder->next != last) {
      Binder = Binder->next;
                        *out << *Binder << "\t" << endl;
    }
    *out << endl;
  } else
        *out << Verbose(1) << "AtomCount is " << AtomCount << ", thus no bonds, no connections!." << endl; 
  *out << Verbose(0) << "End of CreateAdjacencyList." << endl;
  Free((void **)&matrix, "molecule::CreateAdjacencyList: *matrix");
};

/** 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 *out output stream for debugging
 * \param ReturnStack true - return pointer to atom stack of separable components, false - return NULL
 * \param MinimumRingSize contains smallest ring size in molecular structure on return or -1 if no rings were found
 * \return list of each disconnected subgraph as an individual molecule class structure
 */
MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, bool ReturnStack, int &MinimumRingSize)
{
  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
  MoleculeLeafClass *SubGraphs = new MoleculeLeafClass(NULL);
  MoleculeLeafClass *LeafWalker = SubGraphs;
  int CurrentGraphNr = 0, OldGraphNr;
  int CyclicBonds;
  int ComponentNumber = 0;
  atom *Walker = NULL, *OtherAtom = NULL, *Root = start->next;
  bond *Binder = NULL;
  bool BackStepping = false;
  
  *out << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl;
  
  ResetAllBondsToUnused();
  ResetAllAtomNumbers();
  InitComponentNumbers();
  while (Root != end) { // if there any atoms at all
    // (1) mark all edges unused, empty stack, set atom->GraphNr = 0 for all
    AtomStack->ClearStack();

    // put into new subgraph molecule and add this to list of subgraphs
    LeafWalker = new MoleculeLeafClass(LeafWalker);
    LeafWalker->Leaf = new molecule(elemente);
    LeafWalker->Leaf->AddCopyAtom(Root);
    
    OldGraphNr = CurrentGraphNr;
    Walker = Root;
    do { // (10)
      do { // (2) set number and Lowpoint of Atom to i, increase i, push current atom
        if (!BackStepping) { // if we don't just return from (8)
          Walker->GraphNr = CurrentGraphNr;
          Walker->LowpointNr = CurrentGraphNr;
          *out << Verbose(1) << "Setting Walker[" << Walker->Name << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl;
          AtomStack->Push(Walker);
          CurrentGraphNr++;
        }      
        do { // (3) if Walker has no unused egdes, go to (5)
          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 = FindNextUnused(Walker);
          if (Binder == NULL)
            break;
          *out << Verbose(2) << "Current Unused Bond is " << *Binder << "." << endl;
          // (4) Mark Binder used, ...
          Binder->MarkUsed(black);
          OtherAtom = Binder->GetOtherAtom(Walker);
          *out << Verbose(2) << "(4) OtherAtom is " << OtherAtom->Name << "." << 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 = BackEdge;
            Walker->LowpointNr = ( Walker->LowpointNr < OtherAtom->GraphNr ) ? Walker->LowpointNr : OtherAtom->GraphNr;
            *out << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->Name << "] to " << Walker->LowpointNr << "." << endl;
          } else {
            // (4b) ... otherwise set OtherAtom as Ancestor of Walker and Walker as OtherAtom, go to (2)
            Binder->Type = TreeEdge;
            OtherAtom->Ancestor = Walker;
            Walker = OtherAtom;
            *out << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->Name << "]'s Ancestor is now " << OtherAtom->Ancestor->Name << ", Walker is OtherAtom " << OtherAtom->Name << "." << endl;
            break;
          }
          Binder = NULL;
        } while (1);  // (3)
        if (Binder == NULL) {
          *out << 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 == Root) && (Binder == NULL))
        break;
        
      // (5) if Ancestor of Walker is ... 
      *out << Verbose(1) << "(5) Number of Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "] is " << Walker->Ancestor->GraphNr << "." << endl;
      if (Walker->Ancestor->GraphNr != 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;
          *out << Verbose(2) << "(6) Setting Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'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;
          *out << Verbose(2) << "(7) Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'s is a separating vertex, creating component." << endl;
          SetNextComponentNumber(Walker->Ancestor, ComponentNumber);
          *out << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Ancestor's Compont is " << ComponentNumber << "." << endl;
          SetNextComponentNumber(Walker, ComponentNumber);
          *out << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Compont is " << ComponentNumber << "." << endl;
          do {
            OtherAtom = AtomStack->PopLast();
            LeafWalker->Leaf->AddCopyAtom(OtherAtom);
            SetNextComponentNumber(OtherAtom, ComponentNumber);
            *out << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << ComponentNumber << "." << endl;
          } while (OtherAtom != Walker);
          ComponentNumber++;
        }
        // (8) Walker becomes its Ancestor, go to (3)
        *out << Verbose(2) << "(8) Walker[" << Walker->Name << "] is now its Ancestor " << Walker->Ancestor->Name << ", backstepping. " << endl;
        Walker = Walker->Ancestor;
        BackStepping = true;
      }
      if (!BackStepping) {  // coming from (8) want to go to (3)
        // (9) remove all from stack till Walker (including), these and Root form a component
        AtomStack->Output(out);
        SetNextComponentNumber(Root, ComponentNumber);
        *out << Verbose(3) << "(9) Root[" << Root->Name << "]'s Component is " << ComponentNumber << "." << endl;
        SetNextComponentNumber(Walker, ComponentNumber);
        *out << Verbose(3) << "(9) Walker[" << Walker->Name << "]'s Component is " << ComponentNumber << "." << endl;
        do {
          OtherAtom = AtomStack->PopLast();
          LeafWalker->Leaf->AddCopyAtom(OtherAtom);
          SetNextComponentNumber(OtherAtom, ComponentNumber);
          *out << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << ComponentNumber << "." << endl;
        } while (OtherAtom != Walker);
        ComponentNumber++;
    
        // (11) Root is separation vertex,  set Walker to Root and go to (4)
        Walker = Root;
        Binder = FindNextUnused(Walker);
        *out << Verbose(1) << "(10) Walker is Root[" << Root->Name << "], next Unused Bond is " << Binder << "." << endl;
        if (Binder != NULL) { // Root is separation vertex
          *out << Verbose(1) << "(11) Root is a separation vertex." << endl;
          Walker->SeparationVertex = true;
        }
      }
    } while ((BackStepping) || (Binder != NULL)); // (10) halt only if Root has no unused edges

    // From OldGraphNr to CurrentGraphNr ranges an disconnected subgraph
    *out << Verbose(0) << "Disconnected subgraph ranges from " << OldGraphNr << " to " << CurrentGraphNr << "." << endl;    
    LeafWalker->Leaf->Output(out);
    *out << endl;
    
    // step on to next root
    while ((Root != end) && (Root->GraphNr != -1)) {
      //*out << Verbose(1) << "Current next subgraph root candidate is " << Root->Name << "." << endl;
      if (Root->GraphNr != -1) // if already discovered, step on
        Root = Root->next; 
    }
  }
  // set cyclic bond criterium on "same LP" basis
  Binder = first;
  while(Binder->next != last) {
    Binder = Binder->next;
    if (Binder->rightatom->LowpointNr == Binder->leftatom->LowpointNr) { // cyclic ??
      Binder->Cyclic = true;
      NoCyclicBonds++;
    }
  }

  // correct cyclic bonds that are not included in "same LP" argument
  Binder = first;
  while (Binder->next != last) {
    Binder = Binder->next;
    Walker = Binder->leftatom;
    OtherAtom = Binder->rightatom;
    // now check whether both have a cyclic bond in their list
    CyclicBonds = 0;   // counts cyclic bonds;
    for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
      if ((CyclicBonds == 0) && (ListOfBondsPerAtom[Walker->nr][i]->Cyclic))
        CyclicBonds = 1;  
    for(int i=0;i<NumberOfBondsPerAtom[OtherAtom->nr];i++)
      if ((CyclicBonds == 1) && (ListOfBondsPerAtom[OtherAtom->nr][i]->Cyclic))
        CyclicBonds = 2;  
    Binder->Cyclic = (Binder->Cyclic) || (CyclicBonds == 2); // set the Cyclic criterium either or ... 
  }
  
  // further analysis of the found cycles (print rings, get minimum cycle length)
  CyclicStructureAnalysis(out, MinimumRingSize);
  *out << Verbose(1) << "Final graph info for each atom is:" << endl;
  Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    *out << Verbose(2) << "Atom " << Walker->Name << " is " << ((Walker->SeparationVertex) ? "a" : "not a") << " separation vertex, components are ";
    OutputComponentNumber(out, Walker);
    *out << " with Lowpoint " << Walker->LowpointNr << " and Graph Nr. " << Walker->GraphNr << "." << endl;
  }
  
  *out << Verbose(1) << "Final graph info for each bond is:" << endl;
  Binder = first;
  while(Binder->next != last) {
    Binder = Binder->next;
    *out << Verbose(2) << ((Binder->Type == TreeEdge) ? "TreeEdge " : "BackEdge ") << *Binder << ": <";
    *out << ((Binder->leftatom->SeparationVertex) ? "SP," : "") << "L" << Binder->leftatom->LowpointNr << " G" << Binder->leftatom->GraphNr << " Comp.";
    OutputComponentNumber(out, Binder->leftatom);
    *out << " ===  ";
    *out << ((Binder->rightatom->SeparationVertex) ? "SP," : "") << "L" << Binder->rightatom->LowpointNr << " G" << Binder->rightatom->GraphNr << " Comp.";
    OutputComponentNumber(out, Binder->rightatom);
    *out << ">." << endl; 
    if (Binder->Cyclic) // cyclic ??
      *out << Verbose(3) << "Lowpoint at each side are equal: CYCLIC!" << endl;
  }

  // further analysis of the found cycles (print rings, get minimum cycle length)
  CyclicStructureAnalysis(out, MinimumRingSize);
  
  // free all and exit
  delete(AtomStack);
  *out << Verbose(0) << "End of DepthFirstSearchAnalysis" << endl;
  return SubGraphs;
};

/** Analyses the cycles found and returns minimum of all cycle lengths.
 * \param *out output stream for debugging
 * \param MinimumRingSize contains smallest ring size in molecular structure on return or -1 if no rings were found
 * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
 */
void molecule::CyclicStructureAnalysis(ofstream *out, int &MinimumRingSize)
{
  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
  int LP;
  atom *Walker = NULL, *OtherAtom = NULL, *Root = NULL, *Runner = NULL;
  bond *Binder = NULL;
  int RingSize, NumCycles;

  // go through every atom
  AtomStack->ClearStack();
  int *NoCyclicBondsPerAtom = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CyclicStructureAnalysis: *NoCyclicBondsPerAtom");
  Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    NoCyclicBondsPerAtom[Walker->nr] = 0;
    // check whether it's connected to cyclic bonds and count per atom
    // 0 means not part of a cycle, 2 means in a cycle, 3 or more means interconnection site of cycles
    for (int i=0;i<NumberOfBondsPerAtom[Walker->nr]; i++) {
      Binder = ListOfBondsPerAtom[Walker->nr][i];
      NoCyclicBondsPerAtom[Walker->nr] += (int) Binder->Cyclic;
      if (NoCyclicBondsPerAtom[Walker->nr] == 3)  //push all intersections
        AtomStack->Push(Walker);
    }
  }
  *out << Verbose(1) << "NoCyclicBondsPerAtom: ";
  for(int i=0;i<AtomCount;i++) {
    *out << NoCyclicBondsPerAtom[i] << " ";
  }
  *out << endl;
  *out << Verbose(1) << "Analysing cycles ... " << endl;
  MinimumRingSize = -1;
  NumCycles = 0;
  while (!AtomStack->IsEmpty()) {
    Walker = AtomStack->PopFirst();
    if (NoCyclicBondsPerAtom[Walker->nr] > 1) {
      NoCyclicBondsPerAtom[Walker->nr]--; // remove one for being intersection
      RingSize = 0;
      *out << Verbose(2) << "Current intersection is " << *Walker << ", expect to find " << NoCyclicBondsPerAtom[Walker->nr] << " cycles." << endl;
      for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
        Binder = ListOfBondsPerAtom[Walker->nr][i];
        OtherAtom = Binder->GetOtherAtom(Walker);
        // note down the LowPoint number of this cycle
        if (NoCyclicBondsPerAtom[OtherAtom->nr] > 1) {
          LP = OtherAtom->LowpointNr;
          NoCyclicBondsPerAtom[Walker->nr]--; // walker is start of cycle
          if (LP != Walker->LowpointNr)
            *out << Verbose(2) << "Tributary cycle: ... <-> " << Walker->Name;
          else 
            *out << Verbose(2) << "Main cycle: ... <-> " << Walker->Name;
          Root = Walker;  // root acts as predecessor marker so that we don't step back accidentally
          RingSize = 1;
          do {
            for(int j=0;j<NumberOfBondsPerAtom[OtherAtom->nr];j++) {  // search among its bonds for next in cycle (same lowpoint nr)
              Runner = ListOfBondsPerAtom[OtherAtom->nr][j]->GetOtherAtom(OtherAtom);
              if (((Runner->LowpointNr == LP) || (Runner->LowpointNr == Walker->LowpointNr)) && (Runner != Root)) {
                // first check is to stay in the cycle
                // middle check is allow for getting back into main cycle briefly from tributary cycle (just one step, then while further down stops)
                // last check is not step back
                *out << " <-> " << OtherAtom->Name;
                NoCyclicBondsPerAtom[OtherAtom->nr]--;
                Root = OtherAtom;
                OtherAtom = Runner;
                NoCyclicBondsPerAtom[Root->nr]--;
                RingSize++;
                break;
              }
            }
          } while ((OtherAtom->LowpointNr == LP) && (Walker != OtherAtom) && (Root->LowpointNr == OtherAtom->LowpointNr));
          // now check if the LP is different from Walker's, as then there is one more bond to follow
          if (LP != Walker->LowpointNr) {
            // find last bond to home base
            for(int j=0;j<NumberOfBondsPerAtom[OtherAtom->nr];j++)
              if (ListOfBondsPerAtom[OtherAtom->nr][j]->GetOtherAtom(OtherAtom) == Root) {
                *out << " <-> " << OtherAtom->Name;
                RingSize++;
                NoCyclicBondsPerAtom[OtherAtom->nr]--;
              }
          } else {
            // we have made the complete cycle
          }
          *out << " <-> ... with cycle length of " << RingSize << "." << endl;
          NumCycles++;
          if ((RingSize < MinimumRingSize) || (MinimumRingSize == -1))
            MinimumRingSize = RingSize;
        }
      }
    }
  }

  // print NoCyclicBondsPerAtom to visually check of all are zero
  *out << Verbose(1) << "NoCyclicBondsPerAtom: ";
  for(int i=0;i<AtomCount;i++) {
    if (NoCyclicBondsPerAtom[i] > 0)
      cerr << "There was an error in  molecule::CyclicStructureAnalysis!" << endl;
    *out << NoCyclicBondsPerAtom[i] << " ";
  }
  *out << endl;

  if (MinimumRingSize != -1)
    *out << Verbose(1) << "Minimum ring size is " << MinimumRingSize << ", over " << NumCycles << " cycles total." << endl;
  else
    *out << Verbose(1) << "No rings were detected in the molecular structure." << endl;

  Free((void **)&NoCyclicBondsPerAtom, "molecule::CyclicStructureAnalysis: *NoCyclicBondsPerAtom");
  delete(AtomStack);
};

/** 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)
{
  int i=0;
  if (vertex != NULL) {
    for(;i<NumberOfBondsPerAtom[vertex->nr];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 == NumberOfBondsPerAtom[vertex->nr])
      cerr << "Error: All Component entries are already occupied!" << endl;
  } else
      cerr << "Error: Given vertex is NULL!" << endl;
};

/** Output a list of flags, stating whether the bond was visited or not.
 * \param *out output stream for debugging
 */
void molecule::OutputComponentNumber(ofstream *out, atom *vertex)
{
  for(int i=0;i<NumberOfBondsPerAtom[vertex->nr];i++) 
    *out << vertex->ComponentNr[i] << "  ";
};

/** Allocates memory for all atom::*ComponentNr in this molecule and sets each entry to -1.
 */
void molecule::InitComponentNumbers()
{
  atom *Walker = start;
  while(Walker->next != end) {
    Walker = Walker->next;
    if (Walker->ComponentNr != NULL)
      Free((void **)&Walker->ComponentNr, "molecule::InitComponentNumbers: **Walker->ComponentNr");
    Walker->ComponentNr = (int *) Malloc(sizeof(int)*NumberOfBondsPerAtom[Walker->nr], "molecule::InitComponentNumbers: *Walker->ComponentNr");
    for (int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
      Walker->ComponentNr[i] = -1;
  }
};

/** 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)
{
  for(int i=0;i<NumberOfBondsPerAtom[vertex->nr];i++)
    if (ListOfBondsPerAtom[vertex->nr][i]->IsUsed() == white)
      return(ListOfBondsPerAtom[vertex->nr][i]);
  return NULL;
};

/** Resets bond::Used flag of all bonds in this molecule.
 * \return true - success, false - -failure
 */
void molecule::ResetAllBondsToUnused()
{
  bond *Binder = first;
  while (Binder->next != last) {
    Binder = Binder->next;
    Binder->ResetUsed();
  }
};

/** Resets atom::nr to -1 of all atoms in this molecule.
 */
void molecule::ResetAllAtomNumbers()
{
  atom *Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    Walker->GraphNr  = -1;
  }
};

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

/** Estimates by educated guessing (using upper limit) the expected number of fragments.
 * The upper limit is
 * \f[
 *  n = N \cdot C^k
 * \f]
 * where \f$C=2^c\f$ and c is the maximum bond degree over N number of atoms.
 * \param *out output stream for debugging
 * \param order bond order k
 * \return number n of fragments
 */
int molecule::GuesstimateFragmentCount(ofstream *out, int order)
{
  int c = 0;
  int FragmentCount; 
  // get maximum bond degree
  atom *Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    c = (NumberOfBondsPerAtom[Walker->nr] > c) ? NumberOfBondsPerAtom[Walker->nr] : c;
  }
  FragmentCount = NoNonHydrogen*(1 << (c*order));
  *out << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl;
  return FragmentCount;
};  

/** Scans a single line for number and puts them into \a KeySet.
 * \param *out output stream for debugging
 * \param *buffer buffer to scan
 * \param &CurrentSet filled KeySet on return 
 * \return true - at least one valid atom id parsed, false - CurrentSet is empty
 */
bool molecule::ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet)
{
  stringstream line;
  int AtomNr;
  int status = 0;
  
  line.str(buffer);
  while (!line.eof()) {
    line >> AtomNr;
    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
      CurrentSet.insert(AtomNr);
      status++;
    } // else it's "-1" or else and thus must not be added
  }
  return (status != 0);
};

/** Parses the KeySet file and fills \a *FragmentList from the known molecule structure.
 * \param *out output stream for debugging
 * \param *path path to file
 * \param **ListOfAtoms allocated (molecule::AtomCount) and filled lookup table for ids (Atom::nr) to *Atom
 * \param *FragmentList NULL, filled on return
 * \param IsAngstroem whether we have Ansgtroem or bohrradius
 * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
 */
bool molecule::ParseKeySetFile(ofstream *out, char *path, atom **ListOfAtoms, MoleculeListClass *&FragmentList, bool IsAngstroem)
{
  bool status = true;
  ifstream KeySetFile;
  stringstream line;
  char *filename = (char *) Malloc(sizeof(char)*255, "molecule::ParseKeySetFile - filename");
  
  if (FragmentList != NULL) { // check list pointer
    cerr << "Error: FragmentList was not NULL as supposed to be, already atoms present therein?" << endl;
    return false;
  }
  cout << Verbose(1) << "Parsing the KeySet file ... ";
  // open file and read
  sprintf(filename, "%s/%s%s", path, "BondFragment", "KeySets.dat");
  KeySetFile.open(filename);
  if (KeySetFile != NULL) {
    // each line represents a new fragment
    int NumberOfFragments = 0;
    char *buffer = (char *) Malloc(sizeof(char)*255, "molecule::ParseKeySetFile - *buffer");
    // 1. scan through file to know number of fragments
    while (!KeySetFile.eof()) {
      KeySetFile.getline(buffer, 255);
      if (strlen(buffer) > 0) // there is at least on possible number on the parsed line
        NumberOfFragments++;
    }
    // 2. allocate the MoleculeListClass accordingly
    FragmentList = new MoleculeListClass(NumberOfFragments, AtomCount);
    // 3. Clear File, go to beginning and parse again, now adding found ids to each keyset and converting into molecules
    KeySetFile.clear();
    KeySetFile.seekg(ios::beg);
    NumberOfFragments = 0;
    while ((!KeySetFile.eof()) && (FragmentList->NumberOfMolecules > NumberOfFragments)) {
      KeySetFile.getline(buffer, 255);
      KeySet CurrentSet;
      if ((strlen(buffer) > 0) && (ScanBufferIntoKeySet(out, buffer, CurrentSet)))  // if at least one valid atom was added, write config
        FragmentList->ListOfMolecules[NumberOfFragments++] = StoreFragmentFromKeySet(out, CurrentSet, IsAngstroem);
    }
    // 4. Free and done
    Free((void **)&buffer, "molecule::ParseKeySetFile - *buffer");
    cout << "done." << endl;
  } else {
    cout << "File not found." << endl;
    status = false;
  }
  Free((void **)&filename, "molecule::ParseKeySetFile - filename");

  return status;
};

/** 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 *out output stream for debugging
 * \param *path path to file
 * \return true - file written successfully, false - writing failed
 */
bool molecule::StoreAdjacencyToFile(ofstream *out, char *path)
{
  ofstream AdjacencyFile;
  atom *Walker = NULL;
  char *filename = (char *) Malloc(sizeof(char)*255, "molecule::StoreAdjacencyToFile - filename");
  bool status = true;

  sprintf(filename, "%s/%s%s", path, "BondFragment", "Adjacency.dat");
  AdjacencyFile.open(filename);
  cout << Verbose(1) << "Saving adjacency list ... ";
  if (AdjacencyFile != NULL) {
    Walker = start;
    while(Walker->next != end) {
      Walker = Walker->next;
      AdjacencyFile << Walker->nr << "\t";
      for (int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
        AdjacencyFile << ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker)->nr << "\t";
      AdjacencyFile << endl;
    }
    AdjacencyFile.close();
    cout << "done." << endl;
  } else {
    cout << "failed." << endl;
    status = false;
  }
  Free((void **)&filename, "molecule::StoreAdjacencyToFile - filename");
  
  return status;
};

/** Checks contents of adjacency file against bond structure in structure molecule.
 * \param *out output stream for debugging
 * \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(ofstream *out, char *path, atom **ListOfAtoms)
{
  char *filename = (char *) Malloc(sizeof(char)*255, "molecule::CheckAdjacencyFileAgainstMolecule - filename");
  ifstream File;
  bool status = true;
  
  sprintf(filename, "%s/%s%s", path, "BondFragment", "Adjacency.dat");
  File.open(filename);
  *out << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ...";
  if (File != NULL) {
    // allocate storage structure
    int NonMatchNumber = 0;   // will number of atoms with differing bond structure
    int *CurrentBonds = (int *) Malloc(sizeof(int)*8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
    int CurrentBondsOfAtom;
    // Parse the file line by line and count the bonds
    while (!File.eof()) {
      File.getline(filename, 255);
      stringstream line;
      line.str(filename);
      int AtomNr = -1;
      line >> AtomNr;
      CurrentBondsOfAtom = -1; // we count one too far due to line end
      // parse into structure
      if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
        while (!line.eof())
          line >> CurrentBonds[ ++CurrentBondsOfAtom ];
        // compare against present bonds
        //cout << Verbose(2) << "Walker is " << *Walker << ", bond partners: ";
        if (CurrentBondsOfAtom == NumberOfBondsPerAtom[AtomNr]) {
          for(int i=0;i<NumberOfBondsPerAtom[AtomNr];i++) {
            int id = ListOfBondsPerAtom[AtomNr][i]->GetOtherAtom(ListOfAtoms[AtomNr])->nr;
            int 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;
              //out << "[" << id << "]\t";
            } else {
              //out << id << "\t";
            }
          }
          //out << endl;
        } else {
          *out << "Number of bonds for Atom " << *ListOfAtoms[AtomNr] << " does not match, parsed " << CurrentBondsOfAtom << " against " << NumberOfBondsPerAtom[AtomNr] << "." << endl;
          status = false;
        }
      }
    }
    File.close();
    File.clear();
    if (status) { // if equal we parse the KeySetFile
      *out << " done: Equal." << endl;
      status = true;
    } else
      *out << " done: Not equal by " << NonMatchNumber << " atoms." << endl;
    Free((void **)&CurrentBonds, "molecule::CheckAdjacencyFileAgainstMolecule - **CurrentBonds");
  } else {
    *out << " Adjacency file not found." << endl;
    status = false;
  }
  Free((void **)&filename, "molecule::CheckAdjacencyFileAgainstMolecule - filename");
  
  return status;
};

/** Performs a many-body bond order analysis for a given bond order.
 * Writes for each fragment a config file.
 * \param *out output stream for debugging
 * \param BottomUpOrder up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
 * \param TopDownOrder up to how many neighbouring bonds a fragment contains in BondOrderScheme::TopDown scheme
 * \param Scheme which BondOrderScheme to use for the fragmentation
 * \param *configuration configuration for writing config files for each fragment
 * \param CutCyclic whether to add cut cyclic bond or to saturate
 */
void molecule::FragmentMolecule(ofstream *out, int BottomUpOrder, int TopDownOrder, enum BondOrderScheme Scheme, config *configuration, enum CutCyclicBond CutCyclic)
{
        MoleculeListClass **BondFragments = NULL;
  MoleculeListClass *FragmentList = NULL;
  atom *Walker = NULL;
  int *SortIndex = NULL;
  element *runner = NULL;
  int AtomNo;
  int MinimumRingSize;
  int TotalFragmentCounter = 0;
  int FragmentCounter = 0;
  MoleculeLeafClass *MolecularWalker = NULL;
  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
  fstream File;
  bool status = true;

  cout << endl;
#ifdef ADDHYDROGEN
  cout << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
#else
  cout << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
#endif

  // fill the adjacency list
  CreateListOfBondsPerAtom(out);

  // === compare it with adjacency file ===
  atom **ListOfAtoms = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::FragmentMolecule - **ListOfAtoms");
  Walker = start;
  while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron 
    Walker = Walker->next;
    if ((Walker->nr >= 0) && (Walker->nr < AtomCount)) {
      ListOfAtoms[Walker->nr] = Walker;
    } else
      break;
  }
  if (Walker->next != end) {  // everything went alright
    *out << " range of nuclear ids exceeded [0, AtomCount)." << endl;
    status = false;
  }
  if (CheckAdjacencyFileAgainstMolecule(out, configuration->GetDefaultPath(), ListOfAtoms)) {  // NULL entries in ListOfAtoms contain NonMatches
    status = ParseKeySetFile(out, configuration->GetDefaultPath(), ListOfAtoms, FragmentList, configuration->GetIsAngstroem());
  }
  Free((void **)&ListOfAtoms, "molecule::FragmentMolecule - **ListOfAtoms");

  // =================================== Begin of FRAGMENTATION ===============================
  if (!status) {
    // === store Adjacency file ===
    StoreAdjacencyToFile(out, configuration->GetDefaultPath());

    // === first perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs ===
    Subgraphs = DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);
    MolecularWalker = Subgraphs;
    // fill the bond structure of the individually stored subgraphs
    while (MolecularWalker->next != NULL) {
      MolecularWalker = MolecularWalker->next;
      cout << Verbose(1) << "Creating adjacency list for subgraph " << MolecularWalker << "." << endl;
      MolecularWalker->Leaf->CreateAdjacencyList((ofstream *)&cout, BondDistance);
      MolecularWalker->Leaf->CreateListOfBondsPerAtom((ofstream *)&cout);
    }
    
    // === fragment all subgraphs ===
    if ((MinimumRingSize != -1) && ((BottomUpOrder >= MinimumRingSize) || (TopDownOrder >= MinimumRingSize))) {
      cout << Verbose(0) << "Bond order greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
    } else {
      FragmentCounter = 0;
      MolecularWalker = Subgraphs;
      // count subgraphs
      while (MolecularWalker->next != NULL) {
        MolecularWalker = MolecularWalker->next;
        FragmentCounter++;
      }
      BondFragments = (MoleculeListClass **) Malloc(sizeof(MoleculeListClass *)*FragmentCounter, "molecule::FragmentMolecule - **BondFragments");
      // fill the bond fragment list
      FragmentCounter = 0;
      MolecularWalker = Subgraphs;
      while (MolecularWalker->next != NULL) {
        MolecularWalker = MolecularWalker->next;
        cout << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
        if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
            // output ListOfBondsPerAtom for debugging
          *out << Verbose(0) << endl << "From Contents of ListOfBondsPerAtom, all non-hydrogen atoms:" << endl;
          Walker = MolecularWalker->Leaf->start;
          while (Walker->next != MolecularWalker->Leaf->end) {
            Walker = Walker->next; 
  #ifdef ADDHYDROGEN
            if (Walker->type->Z != 1) {   // regard only non-hydrogen
  #endif
              *out << Verbose(0) << "Atom " << Walker->Name << " has Bonds: "<<endl;
              for(int j=0;j<MolecularWalker->Leaf->NumberOfBondsPerAtom[Walker->nr];j++) {
                *out << Verbose(1) << *(MolecularWalker->Leaf->ListOfBondsPerAtom)[Walker->nr][j] << endl;
              }
  #ifdef ADDHYDROGEN
            }
  #endif
          }
          *out << endl;
        
          *out << Verbose(0) << endl << " ========== BOND ENERGY ========================= " << endl;
          *out << Verbose(0) << "Begin of bond fragmentation." << endl;
          BondFragments[FragmentCounter] = NULL;
          if (Scheme == ANOVA) {
            BondFragments[FragmentCounter] = MolecularWalker->Leaf->FragmentBOSSANOVA(out,BottomUpOrder,configuration);
          }  
          if ((Scheme == BottomUp) || (Scheme == Combined)) { // get overlapping subgraphs
            BondFragments[FragmentCounter] = FragmentList = MolecularWalker->Leaf->FragmentBottomUp(out, BottomUpOrder, configuration, CutCyclic);
          }
          if (Scheme == TopDown) { // initialise top level with whole molecule
            *out << Verbose(2) << "Initial memory allocating and initialising for whole molecule." << endl;
            FragmentList = new MoleculeListClass(1, MolecularWalker->Leaf->AtomCount);
            FragmentList->ListOfMolecules[0] = MolecularWalker->Leaf->CopyMolecule();
            FragmentList->TEList[0] = 1.;
          }
          if ((Scheme == Combined) || (Scheme == TopDown)) {
            *out << Verbose(1) << "Calling TopDown." << endl;
            BondFragments[FragmentCounter] = FragmentList->FragmentTopDown(out, TopDownOrder, BondDistance, configuration, CutCyclic);
            // remove this molecule from list again and free wrapper list
            delete(FragmentList);
            FragmentList = NULL;
          }
        } else {
          cout << Verbose(0) << "Connection matrix has not yet been generated!" << endl;
        }
        TotalFragmentCounter += BondFragments[FragmentCounter]->NumberOfMolecules;
        FragmentCounter++;  // next fragment list
      }
    }
  
    // === combine bond fragments list into a single one ===
    FragmentList = new MoleculeListClass(TotalFragmentCounter, AtomCount);
    TotalFragmentCounter = 0;
    for (int i=0;i<FragmentCounter;i++) {
      for(int j=0;j<BondFragments[i]->NumberOfMolecules;j++) {
        FragmentList->ListOfMolecules[TotalFragmentCounter] =  BondFragments[i]->ListOfMolecules[j];
        BondFragments[i]->ListOfMolecules[j] = NULL;
        FragmentList->TEList[TotalFragmentCounter++] = BondFragments[i]->TEList[j];
      }
      delete(BondFragments[i]);
    }
    Free((void **)&BondFragments, "molecule::FragmentMolecule - **BondFragments");
  } else
    cout << Verbose(0) << "Using fragments reconstructed from the KeySetFile." << endl;
  // ==================================== End of FRAGMENTATION ================================
  
  // === Save fragments' configuration to disk ===
  if (FragmentList != NULL) {
    // create a SortIndex to map from BFS labels to the sequence in which the atoms are given in the config file
    SortIndex = (int *) Malloc(sizeof(int)*AtomCount, "molecule::FragmentMolecule: *SortIndex");
    for(int i=0;i<AtomCount;i++)
      SortIndex[i] = -1;
    runner = elemente->start;
    AtomNo = 0;
    while (runner->next != elemente->end) { // go through every element
      runner = runner->next;
      if (ElementsInMolecule[runner->Z]) { // if this element got atoms
        Walker = start;
        while (Walker->next != end) { // go through every atom of this element
          Walker = Walker->next;
          if (Walker->type->Z == runner->Z) // if this atom fits to element
            SortIndex[Walker->nr] = AtomNo++;
        }
      }
    }
    *out << Verbose(1) << "Writing " << FragmentList->NumberOfMolecules << " possible bond fragmentation configs" << endl;
    if (FragmentList->OutputConfigForListOfFragments("BondFragment", configuration, SortIndex))
      *out << Verbose(1) << "All configs written." << endl;
    else
      *out << Verbose(1) << "Some configs' writing failed." << endl;
    Free((void **)&SortIndex, "molecule::FragmentMolecule: *SortIndex"); 
    
    // restore orbital and Stop values
    CalculateOrbitals(*configuration);
    
    // free memory for bond part
    *out << Verbose(1) << "Freeing bond memory" << endl;
    delete(FragmentList); // remove bond molecule from memory
    FragmentList = NULL;
  } else
    *out << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
  // free subgraph memory again
  if (Subgraphs != NULL) {
    while (Subgraphs->next != NULL) {
      Subgraphs = Subgraphs->next;
      delete(Subgraphs->previous);
    }
    delete(Subgraphs);
  }

  *out << Verbose(0) << "End of bond fragmentation." << endl;
};

/** Creates an 2d array of pointer with an entry for each atom and each bond it has.
 * Updates molecule::ListOfBondsPerAtom, molecule::NumberOfBondsPerAtom by parsing through
 * bond chain list, using molecule::AtomCount and molecule::BondCount.
 * Allocates memory, fills the array and exits
 * \param *out output stream for debugging
 */
void molecule::CreateListOfBondsPerAtom(ofstream *out)
{
  bond *Binder = NULL;
  atom *Walker = NULL;
  int TotalDegree;
  *out << Verbose(1) << "Begin of Creating ListOfBondsPerAtom: AtomCount = " << AtomCount << "\tBondCount = " << BondCount << "\tNoNonBonds = " << NoNonBonds << "." << endl;

  // re-allocate memory
  *out << Verbose(2) << "(Re-)Allocating memory." << endl;
  if (ListOfBondsPerAtom != NULL) {
    for(int i=0;i<AtomCount;i++)
      Free((void **)&ListOfBondsPerAtom[i], "molecule::CreateListOfBondsPerAtom: ListOfBondsPerAtom[i]");
    Free((void **)&ListOfBondsPerAtom, "molecule::CreateListOfBondsPerAtom: ListOfBondsPerAtom");
  }
  if (NumberOfBondsPerAtom != NULL)
    Free((void **)&NumberOfBondsPerAtom, "molecule::CreateListOfBondsPerAtom: NumberOfBondsPerAtom");
  ListOfBondsPerAtom = (bond ***) Malloc(sizeof(bond **)*AtomCount, "molecule::CreateListOfBondsPerAtom: ***ListOfBondsPerAtom");
  NumberOfBondsPerAtom = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfBondsPerAtom: *NumberOfBondsPerAtom");

  // reset bond counts per atom
  for(int i=0;i<AtomCount;i++)
    NumberOfBondsPerAtom[i] = 0;
  // count bonds per atom
  Binder = first;
  while (Binder->next != last) {
    Binder = Binder->next;
    NumberOfBondsPerAtom[Binder->leftatom->nr]++;
    NumberOfBondsPerAtom[Binder->rightatom->nr]++;
  }
  // allocate list of bonds per atom
  for(int i=0;i<AtomCount;i++)
    ListOfBondsPerAtom[i] = (bond **) Malloc(sizeof(bond *)*NumberOfBondsPerAtom[i], "molecule::CreateListOfBondsPerAtom: **ListOfBondsPerAtom[]");
  // clear the list again, now each NumberOfBondsPerAtom marks current free field
  for(int i=0;i<AtomCount;i++)
    NumberOfBondsPerAtom[i] = 0;
  // fill the list
  Binder = first;
  while (Binder->next != last) {
    Binder = Binder->next;
    ListOfBondsPerAtom[Binder->leftatom->nr][NumberOfBondsPerAtom[Binder->leftatom->nr]++] = Binder;
    ListOfBondsPerAtom[Binder->rightatom->nr][NumberOfBondsPerAtom[Binder->rightatom->nr]++] = Binder;
  }

  // output list for debugging
  *out << Verbose(3) << "ListOfBondsPerAtom for each atom:" << endl;
  Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next; 
    *out << Verbose(4) << "Atom " << Walker->Name << " with " << NumberOfBondsPerAtom[Walker->nr] << " bonds: ";
    TotalDegree = 0;
    for (int j=0;j<NumberOfBondsPerAtom[Walker->nr];j++) {
      *out << *ListOfBondsPerAtom[Walker->nr][j] << "\t";
      TotalDegree += ListOfBondsPerAtom[Walker->nr][j]->BondDegree;
    }
    *out << " -- TotalDegree: " << TotalDegree << endl;
  }      
  *out << Verbose(1) << "End of Creating ListOfBondsPerAtom." << endl << endl;
};

/** Splits up a molecule into atomic, non-hydrogen, hydrogen-saturated fragments.
 * \param *out output stream for debugging
 * \param NumberOfTopAtoms number to initialise second parameter of MoleculeListClass with
 * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
 * \param factor additional factor TE and forces factors are multiplied with
 * \param CutCyclic whether to add cut cyclic bond or to saturate
 * \return MoleculelistClass of pointer to each atomic fragment.
 */
MoleculeListClass * molecule::GetAtomicFragments(ofstream *out, int NumberOfTopAtoms, bool IsAngstroem, double factor, enum CutCyclicBond CutCyclic)
{
  atom *TopAtom = NULL, *BottomAtom = NULL; // Top = this, Bottom = AtomicFragment->ListOfMolecules[No]
  atom *Walker = NULL;
  MoleculeListClass *AtomicFragments = NULL;
  atom **AtomList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::GetAtomicFragments: **AtomList");
  for (int i=0;i<AtomCount;i++)
    AtomList[i] = NULL;
  bond **BondList = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::GetAtomicFragments: **AtomList");
  for (int i=0;i<BondCount;i++)
    BondList[i] = NULL;
  int No = 0, Cyclic;

  *out << Verbose(0) << "Begin of GetAtomicFragments." << endl;

  *out << Verbose(1) << "Atoms in Molecule: ";
  Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    *out << Walker << "\t";
  } 
  *out << endl;
#ifdef ADDHYDROGEN
  if (NoNonHydrogen != 0) {
    AtomicFragments = new MoleculeListClass(NoNonHydrogen, NumberOfTopAtoms);
  } else {
    *out << Verbose(1) << "NoNonHydrogen is " << NoNonHydrogen << ", can't allocated MoleculeListClass." << endl;
#else
  if (AtomCount != 0) {
    AtomicFragments = new MoleculeListClass(AtomCount, NumberOfTopAtoms);
  } else {
    *out << Verbose(1) << "AtomCount is " << AtomCount << ", can't allocated MoleculeListClass." << endl;
#endif
    return (AtomicFragments);
  }
  
  TopAtom = start;
  while (TopAtom->next != end) {
    TopAtom = TopAtom->next;
  //for(int i=0;i<AtomCount;i++) {
#ifdef ADDHYDROGEN
    if (TopAtom->type->Z != 1) {   // regard only non-hydrogen
#endif
      //TopAtom = AtomsInMolecule[i];
      *out << Verbose(1) << "Current non-Hydrogen Atom: " << TopAtom->Name << endl;

      // go through all bonds to check if cyclic
      Cyclic = 0;
      for(int i=0;i<NumberOfBondsPerAtom[TopAtom->nr];i++)
        Cyclic += (ListOfBondsPerAtom[TopAtom->nr][i]->Cyclic) ? 1 : 0;

#ifdef ADDHYDROGEN
      if (No > NoNonHydrogen) {
#else
      if (No > AtomCount) {
#endif
        *out << Verbose(1) << "Access on created AtomicFragmentsListOfMolecules[" << No << "] beyond NumberOfMolecules " << AtomicFragments->NumberOfMolecules << "." << endl;
        break;
      }
      if (AtomList[TopAtom->nr] == NULL) {
        // create new molecule
        AtomicFragments->ListOfMolecules[No] = new molecule(elemente); // allocate memory
        AtomicFragments->TEList[No] = factor;
        AtomicFragments->ListOfMolecules[No]->BondDistance = BondDistance;
        
        // add central atom
        BottomAtom = AtomicFragments->ListOfMolecules[No]->AddCopyAtom(TopAtom); // add this central atom to molecule
        AtomList[TopAtom->nr] = BottomAtom; // mark down in list

        // create fragment          
        *out << Verbose(1) << "New fragment around atom: " << TopAtom->Name << endl;
        BreadthFirstSearchAdd(out,AtomicFragments->ListOfMolecules[No], AtomList, BondList, TopAtom, NULL, 0, IsAngstroem, (Cyclic == 0) ? SaturateBond : CutCyclic);
        AtomicFragments->ListOfMolecules[No]->CountAtoms(out);
        // actually we now have to reset both arrays to NULL again, but BFS is overkill anyway for getting the atomic fragments
        // thus we do it in O(1) and avoid the O(n) which would make this routine O(N^2)!  
        AtomList[TopAtom->nr] = NULL;  // remove this fragment's central atom again from the list
        
        *out << Verbose(1) << "Atoms in Fragment " << TopAtom->nr << ": ";
        Walker = AtomicFragments->ListOfMolecules[No]->start;
        while (Walker->next != AtomicFragments->ListOfMolecules[No]->end) {
          Walker = Walker->next; 
        //for(int k=0;k<AtomicFragments->ListOfMolecules[No]->AtomCount;k++)
          *out << Walker << "(" << Walker->father << ")\t";
        }
        *out << endl;
        No++;
      }
#ifdef ADDHYDROGEN
    } else
      *out << Verbose(1) << "Current Hydrogen Atom: " << TopAtom->Name << endl;
#endif
  }

  // output of full list before reduction
  if (AtomicFragments != NULL) {
    *out << "AtomicFragments: ";
    AtomicFragments->Output(out);
    *out << endl;
  } else 
    *out << Verbose(1) << "AtomicFragments is zero on return, splitting failed." << endl;

  // Reducing the atomic fragments
  if (AtomicFragments != NULL) {
    // check whether there are equal fragments by GetMappingToUniqueFragments
    AtomicFragments->ReduceToUniqueList(out, &cell_size[0], BondDistance);
  } else
    *out << Verbose(1) << "AtomicFragments is zero, reducing failed." << endl;
  Free((void **)&BondList, "molecule::GetAtomicFragments: **BondList");
  Free((void **)&AtomList, "molecule::GetAtomicFragments: **AtomList");
  *out << Verbose(0) << "End of GetAtomicFragments." << endl;
  return (AtomicFragments);
};

/** Splits up the bond in a molecule into a left and a right fragment.
 * \param *out output stream for debugging
 * \param *Bond bond to broken up into getting allocated ...
 * \param *LeftFragment ... left fragment molecule ... (ptr to the memory cell wherein the adress for the Fragment is to be stored)
 * \param *RightFragment ... and right fragment molecule to be returned.(ptr to the memory cell wherein the adress for the Fragment is to be stored)
 * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
 * \param CutCyclic whether to add cut cyclic bond or not
 * \sa FragmentTopDown()
 */
void molecule::FragmentMoleculeByBond(ofstream *out, bond *Bond, molecule **LeftFragment, molecule **RightFragment, bool IsAngstroem, enum CutCyclicBond CutCyclic)
{
  *out << Verbose(0) << "Begin of FragmentMoleculeByBond." << endl; 
#ifdef ADDHYDROGEN
  if ((Bond->leftatom->type->Z != 1) && (Bond->rightatom->type->Z != 1)) { // if both bond partners aren't hydrogen ...
#endif    
    *out << Verbose(1) << "Current Non-Hydrogen Bond: " << Bond->leftatom->Name << " and " << Bond->rightatom->Name << endl;
    *LeftFragment = new molecule(elemente);
    *RightFragment = new molecule(elemente);
    // initialise marker list for all atoms
    atom **AddedAtomListLeft = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::FragmentMoleculeByBond: **AddedAtomListLeft");
    atom **AddedAtomListRight = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::FragmentMoleculeByBond: **AddedAtomListRight");
    for (int i=0;i<AtomCount;i++) {
      AddedAtomListLeft[i] = NULL;
      AddedAtomListRight[i] = NULL;
    }
    bond **AddedBondListLeft = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::FragmentMoleculeByBond: **AddedBondListLeft");
    bond **AddedBondListRight = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::FragmentMoleculeByBond: **AddedBondListRight");
    for (int i=0;i<BondCount;i++) {
      AddedBondListLeft[i] = NULL;
      AddedBondListRight[i] = NULL;
    }
  
    // tag and add all atoms that have to be included
    *out << Verbose(1) << "Adding BFS-wise on left hand side with Bond Order " << NoNonBonds-1 << "." << endl;
    AddedAtomListLeft[Bond->leftatom->nr] = (*LeftFragment)->AddCopyAtom(Bond->leftatom);
    BreadthFirstSearchAdd(out, *LeftFragment, AddedAtomListLeft, AddedBondListLeft, Bond->leftatom, Bond, 
#ifdef ADDHYDROGEN
    NoNonBonds
#else
    BondCount
#endif    
                                                                                                            , IsAngstroem, CutCyclic);
    *out << Verbose(1) << "Adding BFS-wise on right hand side with Bond Order " << NoNonBonds-1 << "." << endl;
    AddedAtomListRight[Bond->rightatom->nr] = (*RightFragment)->AddCopyAtom(Bond->rightatom);
    BreadthFirstSearchAdd(out, *RightFragment, AddedAtomListRight, AddedBondListRight, Bond->rightatom, Bond, 
#ifdef ADDHYDROGEN
    NoNonBonds
#else
    BondCount
#endif    
                                                                                                            , IsAngstroem, CutCyclic);  
 
    // count atoms
    (*LeftFragment)->CountAtoms(out);
    (*RightFragment)->CountAtoms(out);
    // free all and exit
    Free((void **)&AddedAtomListLeft, "molecule::FragmentMoleculeByBond: **AddedAtomListLeft");
    Free((void **)&AddedAtomListRight, "molecule::FragmentMoleculeByBond: **AddedAtomListRight");
    Free((void **)&AddedBondListLeft, "molecule::FragmentMoleculeByBond: **AddedBondListLeft");
    Free((void **)&AddedBondListRight, "molecule::FragmentMoleculeByBond: **AddedBondListRight");
#ifdef ADDHYDROGEN
  }
#endif
  *out << Verbose(0) << "End of FragmentMoleculeByBond." << endl;
};

/** Returns the given \a **FragmentList filled with molecules around each bond including up to \a BondDegree neighbours.
 * \param *out output stream for debugging
 * \param BondOrder neighbours on each side to be ...
 * \param IsAngstroem whether atomic coordination is in Angstroem (true) or atomic length/bohrradous (false)
 * \param CutCyclic whether to add cut cyclic bond or to saturate
 * \sa FragmentBottomUp(), molecule::AddBondOrdertoMolecule()
 */
MoleculeListClass * molecule::GetEachBondFragmentOfOrder(ofstream *out, int BondOrder, bool IsAngstroem, enum CutCyclicBond CutCyclic)
{
  /// Allocate memory for Bond list and go through each bond and fragment molecule up to bond order and fill the list to be returned.
  MoleculeListClass *FragmentList = NULL;
  atom **AddedAtomList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::GetBondFragmentOfOrder: **AddedAtomList");
  bond **AddedBondList = (bond **) Malloc(sizeof(bond *)*BondCount, "molecule::GetBondFragmentOfOrder: **AddedBondList");
  bond *Binder = NULL;

  *out << Verbose(0) << "Begin of GetEachBondFragmentOfOrder." << endl;
#ifdef ADDHYDROGEN
  if (NoNonBonds != 0) {
    FragmentList = new MoleculeListClass(NoNonBonds, AtomCount);
  } else {
    *out << Verbose(1) << "NoNonBonds is " << NoNonBonds << ", can't allocate list." << endl;
#else
  if (BondCount != 0) {
    FragmentList = new MoleculeListClass(BondCount, AtomCount);
  } else {
    *out << Verbose(1) << "BondCount is " << BondCount << ", can't allocate list." << endl;
#endif
  }
  int No = 0;
  Binder = first;
  while (Binder->next != last) { // get each bond, NULL is returned if it is a H-H bond
    Binder = Binder->next;
#ifdef ADDHYDROGEN
    if ((Binder->leftatom->type->Z != 1) && (Binder->rightatom->type->Z != 1))  // if both bond partners aren't hydrogen ...
#endif
      if ((CutCyclic == SaturateBond) || (!Binder->Cyclic)) {
        *out << Verbose(1) << "Getting Fragment for Non-Hydrogen Bond: " << Binder->leftatom->Name << " and " << Binder->rightatom->Name << endl;
        FragmentList->ListOfMolecules[No] = new molecule(elemente);
        // initialise marker list for all atoms
        for (int i=0;i<AtomCount;i++)
          AddedAtomList[i] = NULL;
        for (int i=0;i<BondCount;i++)
          AddedBondList[i] = NULL;
      
        // add root bond as first bond (this is needed later on fragmenting)
        *out << Verbose(1) << "Adding Root Bond " << *Binder << " and its atom." << endl;
        AddedAtomList[Binder->leftatom->nr] = FragmentList->ListOfMolecules[No]->AddCopyAtom(Binder->leftatom);
        AddedAtomList[Binder->rightatom->nr] = FragmentList->ListOfMolecules[No]->AddCopyAtom(Binder->rightatom);
        AddedBondList[Binder->nr] = FragmentList->ListOfMolecules[No]->AddBond(AddedAtomList[Binder->leftatom->nr], AddedAtomList[Binder->rightatom->nr], Binder->BondDegree);
    
        // tag and add all atoms that have to be included
        *out << Verbose(1) << "Adding BFS-wise on left hand side." << endl;
        BreadthFirstSearchAdd(out, FragmentList->ListOfMolecules[No], AddedAtomList, AddedBondList, Binder->leftatom, NULL, BondOrder, IsAngstroem, CutCyclic);  
        *out << Verbose(1) << "Adding BFS-wise on right hand side." << endl;
        BreadthFirstSearchAdd(out, FragmentList->ListOfMolecules[No], AddedAtomList, AddedBondList, Binder->rightatom, NULL, BondOrder, IsAngstroem, CutCyclic);  
        
        // count atoms
        FragmentList->ListOfMolecules[No]->CountAtoms(out);
        FragmentList->TEList[No] = 1.;
        *out << Verbose(1) << "GetBondFragmentOfOrder: " << Binder->nr << "th Fragment: " << FragmentList->ListOfMolecules[No] << "." << endl;
        No++;
      }
  }
  // free all lists
  Free((void **)&AddedAtomList, "molecule::GetBondFragmentOfOrder: **AddedAtomList");
  Free((void **)&AddedBondList, "molecule::GetBondFragmentOfOrder: **AddedBondList");
  // output and exit
  FragmentList->Output(out);
  *out << Verbose(0) << "End of GetEachBondFragmentOfOrder." << endl;
  return (FragmentList);
}; 

/** Adds atoms up to \a BondCount distance from \a *Root and notes them down in \a **AddedAtomList.
 * Gray vertices are always enqueued in an AtomStackClass FIFO queue, the rest is usual BFS with adding vertices found was
 * white and putting into queue. 
 * \param *out output stream for debugging
 * \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
 * \param CutCyclic whether to cut cyclic bonds (means saturate on need with hydrogen) or to always add
 */  
void molecule::BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem, enum CutCyclicBond CutCyclic)
{
  atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::BreadthFirstSearchAdd: **PredecessorList");
  int *ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::BreadthFirstSearchAdd: *ShortestPathList");
  enum Shading *ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::BreadthFirstSearchAdd: *ColorList");
  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
  atom *Walker = NULL, *OtherAtom = NULL;
  bond *Binder = NULL;

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

  // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
  for (int i=0;i<AtomCount;i++) {
    PredecessorList[i] = NULL;
    ShortestPathList[i] = -1;
    if (AddedAtomList[i] != NULL) // mark already present atoms (i.e. Root and maybe others) as visited
      ColorList[i] = lightgray;
    else
      ColorList[i] = white;
  }
  ShortestPathList[Root->nr] = 0;
  
  // and go on ... Queue always contains all lightgray vertices
  while (!AtomStack->IsEmpty()) {
    // 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 = AtomStack->PopFirst(); // pop oldest added
    *out << Verbose(1) << "Current Walker is: " << Walker->Name << ", and has " << NumberOfBondsPerAtom[Walker->nr] << " bonds." << endl; 
    for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
      Binder = ListOfBondsPerAtom[Walker->nr][i];
      if (Binder != NULL) { // don't look at bond equal NULL
        OtherAtom = Binder->GetOtherAtom(Walker);
        *out << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *Binder << "." << endl;
        if (ColorList[OtherAtom->nr] == white) {
          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) 
            ColorList[OtherAtom->nr] = lightgray;
          PredecessorList[OtherAtom->nr] = Walker;  // Walker is the predecessor
          ShortestPathList[OtherAtom->nr] = ShortestPathList[Walker->nr]+1;
          *out << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " " << ((ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->Name << " and its Shortest Path is " << ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl; 
          if ((((ShortestPathList[OtherAtom->nr] < BondOrder) && (Binder != Bond)) || (Binder->Cyclic && (CutCyclic == KeepBond))) ) { // Check for maximum distance
            *out << Verbose(3);
            if (AddedAtomList[OtherAtom->nr] == NULL) { // add if it's not been so far
              AddedAtomList[OtherAtom->nr] = Mol->AddCopyAtom(OtherAtom);
              *out << "Added OtherAtom " << OtherAtom->Name;
              AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
              AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
              AddedBondList[Binder->nr]->Type = Binder->Type;
              *out << " 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)
              *out << "Not adding OtherAtom " << OtherAtom->Name;
              if (AddedBondList[Binder->nr] == NULL) {
                AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
                AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
                AddedBondList[Binder->nr]->Type = Binder->Type;
                *out << ", added Bond " << *(AddedBondList[Binder->nr]);
              } else
                *out << ", not added Bond ";
            }
            *out << ", putting OtherAtom into queue." << endl;
            AtomStack->Push(OtherAtom);
          } else { // out of bond order, then replace
            if ((AddedAtomList[OtherAtom->nr] == NULL) && (Binder->Cyclic))
              ColorList[OtherAtom->nr] = white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
            if (Binder == Bond)
              *out << Verbose(3) << "Not Queueing, is the Root bond";
            else if (ShortestPathList[OtherAtom->nr] >= BondOrder)
              *out << Verbose(3) << "Not Queueing, is out of Bond Count of " << BondOrder;
            if ((Binder->Cyclic && (CutCyclic != KeepBond)))
              *out << ", is part of a cyclic bond yet we don't keep them, saturating bond with Hydrogen." << endl;
            if (!Binder->Cyclic)
              *out << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl;
            if (AddedBondList[Binder->nr] == NULL) {
              if ((AddedAtomList[OtherAtom->nr] != NULL) && (CutCyclic == KeepBond)) { // .. whether we add or saturate
                AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
                AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
                AddedBondList[Binder->nr]->Type = Binder->Type;
              } else {
#ifdef ADDHYDROGEN
                Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem);
#endif
              }
            }
          }
        } else {
          *out << 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) && (((ShortestPathList[Walker->nr]+1) < BondOrder) || (CutCyclic == KeepBond))) { 
              AddedBondList[Binder->nr] = Mol->AddBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder->BondDegree);
              AddedBondList[Binder->nr]->Cyclic = Binder->Cyclic;
              AddedBondList[Binder->nr]->Type = Binder->Type;
            } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
#ifdef ADDHYDROGEN
              Mol->AddHydrogenReplacementAtom(out, Binder, AddedAtomList[Walker->nr], Walker, OtherAtom, ListOfBondsPerAtom[Walker->nr], NumberOfBondsPerAtom[Walker->nr], IsAngstroem);
#endif
            }
          }
        }
      }
    }
    ColorList[Walker->nr] = black;
    *out << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl; 
  }
  Free((void **)&PredecessorList, "molecule::BreadthFirstSearchAdd: **PredecessorList");
  Free((void **)&ShortestPathList, "molecule::BreadthFirstSearchAdd: **ShortestPathList");
  Free((void **)&ColorList, "molecule::BreadthFirstSearchAdd: **ColorList");
  delete(AtomStack);
};

/** 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 *out output stream for debugging
 * \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(ofstream *out, const molecule *Father)
{
  atom *Walker = NULL, *OtherAtom = NULL;
  bool status = true;
  atom **ParentList = (atom **) Malloc(sizeof(atom *)*Father->AtomCount, "molecule::BuildInducedSubgraph: **ParentList");

  *out << Verbose(2) << "Begin of BuildInducedSubgraph." << endl;
  
  // reset parent list
  *out << Verbose(3) << "Resetting ParentList." << endl;
  for (int i=0;i<Father->AtomCount;i++)
    ParentList[i] = NULL;
  
  // fill parent list with sons
  *out << Verbose(3) << "Filling Parent List." << endl;
  Walker = start;
  while (Walker->next != end) {
    Walker = Walker->next;
    ParentList[Walker->father->nr] = Walker;
    // Outputting List for debugging
    *out << Verbose(4) << "Son["<< Walker->father->nr <<"] of " << Walker->father <<  " is " << ParentList[Walker->father->nr] << "." << endl;
  }

  // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
  *out << Verbose(3) << "Creating bonds." << endl;
  Walker = Father->start;
  while (Walker->next != Father->end) {
    Walker = Walker->next;
    if (ParentList[Walker->nr] != NULL) {
      if (ParentList[Walker->nr]->father != Walker) {
        status = false;
      } else {
        for (int i=0;i<Father->NumberOfBondsPerAtom[Walker->nr];i++) {
          OtherAtom = Father->ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
          if (ParentList[OtherAtom->nr] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
            *out << Verbose(4) << "Endpoints of Bond " << Father->ListOfBondsPerAtom[Walker->nr][i] << " are both present: " << ParentList[Walker->nr]->Name << " and " << ParentList[OtherAtom->nr]->Name << "." << endl;
            AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], Father->ListOfBondsPerAtom[Walker->nr][i]->BondDegree);
          }
        }
      }
    }
  }

  Free((void **)&ParentList, "molecule::BuildInducedSubgraph: **ParentList");
  *out << Verbose(2) << "End of BuildInducedSubgraph." << endl;
  return status;
};


/** Looks through a AtomStackClass and returns the likeliest removal candiate.
 * \param *out output stream for debugging messages
 * \param *&Leaf KeySet to look through
 * \param *&ShortestPathList list of the shortest path to decide which atom to suggest as removal candidate in the end
 * \param index of the atom suggested for removal 
 */
int molecule::LookForRemovalCandidate(ofstream *&out, KeySet *&Leaf, int *&ShortestPathList)
{
  atom *Runner = NULL;
  int SP, Removal;
  
  *out << Verbose(2) << "Looking for removal candidate." << endl;
  SP = -1; //0;  // not -1, so that Root is never removed
  Removal = -1;
  for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
    Runner = FindAtom((*runner));
    if (Runner->type->Z != 1) { // skip all those added hydrogens when re-filling snake stack
      if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
        SP = ShortestPathList[(*runner)];
        Removal = (*runner);
      }
    }
  }
  return Removal;
};

/** Stores a fragment from \a KeySet into \a molecule.
 * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
 * molecule and adds missing hydrogen where bonds were cut. 
 * \param *out output stream for debugging messages
 * \param &Leaflet pointer to KeySet structure 
 * \param IsAngstroem whether we have Ansgtroem or bohrradius
 * \return pointer to constructed molecule
 */
molecule * molecule::StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem)
{
  atom *Runner = NULL, *FatherOfRunner = NULL, *OtherFather = NULL;
  atom **SonList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::StoreFragmentFromStack: **SonList");
  molecule *Leaf = new molecule(elemente);
  
  *out << Verbose(1) << "Begin of StoreFragmentFromKeyset." << endl;
  
  Leaf->BondDistance = BondDistance;
  for(int i=0;i<NDIM*2;i++)
    Leaf->cell_size[i] = cell_size[i]; 

  // initialise SonList (indicates when we need to replace a bond with hydrogen instead)
  for(int i=0;i<AtomCount;i++)
    SonList[i] = NULL;

  // first create the minimal set of atoms from the KeySet
  for(KeySet::iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
    FatherOfRunner =  FindAtom((*runner));
    SonList[FatherOfRunner->nr] = Leaf->AddCopyAtom(FatherOfRunner);
  }
  
  // create the bonds between all: Make it an induced subgraph and add hydrogen
  *out << Verbose(2) << "Creating bonds from father graph (i.e. induced subgraph creation)." << endl;
  Runner = Leaf->start;
  while (Runner->next != Leaf->end) {
    Runner = Runner->next;
    FatherOfRunner = Runner->father;
    if (SonList[FatherOfRunner->nr] != NULL)  {  // check if this, our father, is present in list
      // create all bonds
      for (int i=0;i<NumberOfBondsPerAtom[FatherOfRunner->nr];i++) { // go through every bond of father 
        OtherFather = ListOfBondsPerAtom[FatherOfRunner->nr][i]->GetOtherAtom(FatherOfRunner);
        *out << Verbose(2) << "Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->nr] << " is bound to " << *OtherFather;
        if (SonList[OtherFather->nr] != NULL) {
          *out << ", whose son is " << *SonList[OtherFather->nr] << "." << endl; 
          if (OtherFather->nr > FatherOfRunner->nr) { // add bond (nr check is for adding only one of both variants: ab, ba)
            *out << Verbose(3) << "Adding Bond: " << Leaf->AddBond(Runner, SonList[OtherFather->nr], ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree) << "." << endl;
            //NumBonds[Runner->nr]++;
          } else { 
            *out << Verbose(3) << "Not adding bond, labels in wrong order." << endl;
          }
        } else {
          *out << ", who has no son in this fragment molecule." << endl; 
#ifdef ADDHYDROGEN
          *out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
          Leaf->AddHydrogenReplacementAtom(out, ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, ListOfBondsPerAtom[FatherOfRunner->nr],NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem);
#endif
          //NumBonds[Runner->nr] += ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree;
        }
      }
    } else {
      *out << Verbose(0) << "ERROR: Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
    }
#ifdef ADDHYDROGEN
    while ((Runner->next != Leaf->end) && (Runner->next->type->Z == 1)) // skip added hydrogen
      Runner = Runner->next;
#endif       
  }
  Leaf->CreateListOfBondsPerAtom(out);
  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
  Free((void **)&SonList, "molecule::StoreFragmentFromStack: **SonList");
  *out << Verbose(1) << "End of StoreFragmentFromKeyset." << endl;
  return Leaf;
};

/** Creates \a MoleculeListClass of all unique fragments of the \a molecule containing \a Order atoms or vertices.
 * The picture to have in mind is that of a DFS "snake" of a certain length \a Order, i.e. as in the infamous
 * computer game, that winds through the connected graph representing the molecule. Color (white,
 * lightgray, darkgray, black) indicates whether a vertex has been discovered so far or not. Labels will help in
 * creating only unique fragments and not additional ones with vertices simply in different sequence.
 * The Predecessor is always the one that came before in discovering, needed on backstepping. And
 * finally, the ShortestPath is needed for removing vertices from the snake stack during the back-
 * stepping.
 * \param *out output stream for debugging
 * \param Order number of atoms in each fragment
 * \param *configuration configuration for writing config files for each fragment
 * \return List of all unique fragments with \a Order atoms
 */
/*
MoleculeListClass * molecule::CreateListOfUniqueFragmentsOfOrder(ofstream *out, int Order, config *configuration)
{
  atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
  int *ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
  int *Labels = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
  enum Shading *ColorVertexList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ColorList");
  enum Shading *ColorEdgeList = (enum Shading *) Malloc(sizeof(enum Shading)*BondCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ColorBondList");
  AtomStackClass *RootStack = new AtomStackClass(AtomCount);
  AtomStackClass *TouchedStack = new AtomStackClass((int)pow(4,Order)+2); // number of atoms reached from one with maximal 4 bonds plus Root itself
  AtomStackClass *SnakeStack = new AtomStackClass(Order+1); // equal to Order is not possible, as then the AtomStackClass cannot discern between full and empty stack!
  MoleculeLeafClass *Leaflet = NULL, *TempLeaf = NULL; 
  MoleculeListClass *FragmentList = NULL;
  atom *Walker = NULL, *OtherAtom = NULL, *Root = NULL, *Removal = NULL;
  bond *Binder = NULL;
  int RunningIndex = 0, FragmentCounter = 0;

  *out << Verbose(1) << "Begin of CreateListOfUniqueFragmentsOfOrder." << endl;

  // reset parent list
  *out << Verbose(3) << "Resetting labels, parent, predecessor, color and shortest path lists." << endl;
  for (int i=0;i<AtomCount;i++) { // reset all atom labels
    // initialise each vertex as white with no predecessor, empty queue, color lightgray, not labelled, no sons
                Labels[i] = -1;
    SonList[i] = NULL;
    PredecessorList[i] = NULL;
    ColorVertexList[i] = white;
    ShortestPathList[i] = -1;
  }
  for (int i=0;i<BondCount;i++)
    ColorEdgeList[i] = white;
        RootStack->ClearStack();        // clearstack and push first atom if exists
  TouchedStack->ClearStack();
  Walker = start->next;
  while ((Walker != end)
#ifdef ADDHYDROGEN
   && (Walker->type->Z == 1)
#endif
                        ) { // search for first non-hydrogen atom
    *out << Verbose(4) << "Current Root candidate is " << Walker->Name << "." << endl;
    Walker = Walker->next;
  }
  if (Walker != end)
    RootStack->Push(Walker);
  else
    *out << Verbose(0) << "ERROR: Could not find an appropriate Root atom!" << endl;
  *out << Verbose(3) << "Root " << Walker->Name << " is on AtomStack, beginning loop through all vertices ..." << endl;

  ///// OUTER LOOP ////////////
  while (!RootStack->IsEmpty()) {
        // get new root vertex from atom stack
        Root = RootStack->PopFirst();
    ShortestPathList[Root->nr] = 0;
    if (Labels[Root->nr] == -1)
      Labels[Root->nr] = RunningIndex++; // prevent it from getting again on AtomStack
    PredecessorList[Root->nr] = Root;
    TouchedStack->Push(Root);
    *out << Verbose(0) << "Root for this loop is: " << Root->Name << ".\n";

                // clear snake stack
          SnakeStack->ClearStack();
    //SnakeStack->TestImplementation(out, start->next);    

    ///// INNER LOOP ////////////
    // Problems:
    // - what about cyclic bonds?
    Walker = Root;
        do {
      *out << Verbose(1) << "Current Walker is: " << Walker->Name;
      // initial setting of the new Walker: label, color, shortest path and put on stacks
                if (Labels[Walker->nr] == -1)   {       // give atom a unique, monotonely increasing number
                        Labels[Walker->nr] = RunningIndex++;
        RootStack->Push(Walker);
      }
      *out << ", has label " << Labels[Walker->nr];
                if ((ColorVertexList[Walker->nr] == white) || ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white))) {     // color it if newly discovered and push on stacks (and if within reach!)
        if ((Binder != NULL) && (ColorEdgeList[Binder->nr] == white)) {
          // Binder ought to be set still from last neighbour search
          *out << ", coloring bond " << *Binder << " black";
          ColorEdgeList[Binder->nr] = black; // mark this bond as used
        }
        if (ShortestPathList[Walker->nr] == -1) {
          ShortestPathList[Walker->nr] = ShortestPathList[PredecessorList[Walker->nr]->nr]+1; 
          TouchedStack->Push(Walker); // mark every atom for lists cleanup later, whose shortest path has been changed
        }
        if ((ShortestPathList[Walker->nr] < Order) && (ColorVertexList[Walker->nr] != darkgray)) {  // if not already on snake stack
          SnakeStack->Push(Walker);
          ColorVertexList[Walker->nr] = darkgray; // mark as dark gray of on snake stack
        }
                }
      *out << ", SP of " << ShortestPathList[Walker->nr]  << " and its color is " << GetColor(ColorVertexList[Walker->nr]) << "." << endl;

      // then check the stack for a newly stumbled upon fragment
                if (SnakeStack->ItemCount() == Order) { // is stack full?
        // store the fragment if it is one and get a removal candidate
        Removal = StoreFragmentFromStack(out, Root, Walker, Leaflet, SnakeStack, ShortestPathList, SonList, Labels, &FragmentCounter, configuration);
        // remove the candidate if one was found
        if (Removal != NULL) {
          *out << Verbose(2) << "Removing item " << Removal->Name << " with SP of " << ShortestPathList[Removal->nr] << " from snake stack." << endl;
          SnakeStack->RemoveItem(Removal);
          ColorVertexList[Removal->nr] = lightgray; // return back to not on snake stack but explored marking
          if (Walker == Removal) { // if the current atom is to be removed, we also have to take a step back
            Walker = PredecessorList[Removal->nr];
            *out << Verbose(2) << "Stepping back to " << Walker->Name << "." << endl;
          }
        }
                } else
        Removal = NULL;

      // finally, look for a white neighbour as the next Walker
      Binder = NULL;
      if ((Removal == NULL) || (Walker != PredecessorList[Removal->nr])) {  // don't look, if a new walker has been set above
        *out << Verbose(2) << "Snake has currently " << SnakeStack->ItemCount() << " item(s)." << endl;
                        OtherAtom = NULL; // this is actually not needed, every atom has at least one neighbour
        if (ShortestPathList[Walker->nr] < Order) {
                        for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {
            Binder = ListOfBondsPerAtom[Walker->nr][i];
            *out << Verbose(2) << "Current bond is " << *Binder << ": ";
                                OtherAtom = Binder->GetOtherAtom(Walker);
            if ((Labels[OtherAtom->nr] != -1) && (Labels[OtherAtom->nr] < Labels[Root->nr])) { // we don't step up to labels bigger than us
              *out << "Label " << Labels[OtherAtom->nr] << " is smaller than Root's " << Labels[Root->nr] << "." << endl; 
              //ColorVertexList[OtherAtom->nr] = lightgray;    // mark as explored
            } else { // otherwise check its colour and element
                                if (
#ifdef ADDHYDROGEN
              (OtherAtom->type->Z != 1) && 
#endif
                    (ColorEdgeList[Binder->nr] == white)) {  // skip hydrogen, look for unexplored vertices
                *out << "Moving along " << GetColor(ColorEdgeList[Binder->nr]) << " bond " << Binder << " to " << ((ColorVertexList[OtherAtom->nr] == white) ? "unexplored" : "explored") << " item: " << OtherAtom->Name << "." << endl;
                // i find it currently rather sensible to always set the predecessor in order to find one's way back
                //if (PredecessorList[OtherAtom->nr] == NULL) {
                PredecessorList[OtherAtom->nr] = Walker;
                *out << Verbose(3) << "Setting Predecessor of " << OtherAtom->Name << " to " << PredecessorList[OtherAtom->nr]->Name << "." << endl;
                //} else {
                //  *out << Verbose(3) << "Predecessor of " << OtherAtom->Name << " is " << PredecessorList[OtherAtom->nr]->Name << "." << endl;
                //} 
                Walker = OtherAtom;
                break;
              } else {
                if (OtherAtom->type->Z == 1) 
                  *out << "Links to a hydrogen atom." << endl;
                else                 
                  *out << "Bond has not white but " << GetColor(ColorEdgeList[Binder->nr]) << " color." << endl;
              }
            }
                        }
        } else {  // means we have stepped beyond the horizon: Return!
          Walker = PredecessorList[Walker->nr];
          OtherAtom = Walker;
          *out << Verbose(3) << "We have gone too far, stepping back to " << Walker->Name << "." << endl;
        }
                        if (Walker != OtherAtom) {      // if no white neighbours anymore, color it black 
          *out << Verbose(2) << "Coloring " << Walker->Name << " black." << endl;
                                ColorVertexList[Walker->nr] = black;
                                Walker = PredecessorList[Walker->nr];
                        }
      }
        } while ((Walker != Root) || (ColorVertexList[Root->nr] != black));
    *out << Verbose(2) << "Inner Looping is finished." << endl;    

    // if we reset all AtomCount atoms, we have again technically O(N^2) ...
    *out << Verbose(2) << "Resetting lists." << endl;
    Walker = NULL;
    Binder = NULL;
    while (!TouchedStack->IsEmpty()) {
      Walker = TouchedStack->PopLast();
      *out << Verbose(3) << "Re-initialising entries of " << *Walker << "." << endl;
      for(int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++)
        ColorEdgeList[ListOfBondsPerAtom[Walker->nr][i]->nr] = white;
      PredecessorList[Walker->nr] = NULL;
      ColorVertexList[Walker->nr] = white;
      ShortestPathList[Walker->nr] = -1;
    }
  }
  *out << Verbose(1) << "Outer Looping over all vertices is done." << endl; 

  // copy together
  *out << Verbose(1) << "Copying all fragments into MoleculeList structure." << endl; 
  FragmentList = new MoleculeListClass(FragmentCounter, AtomCount);
  RunningIndex = 0;
  while ((Leaflet != NULL) && (RunningIndex < FragmentCounter))  {
    FragmentList->ListOfMolecules[RunningIndex++] = Leaflet->Leaf;
    Leaflet->Leaf = NULL; // prevent molecule from being removed
    TempLeaf = Leaflet;
    Leaflet = Leaflet->previous;
    delete(TempLeaf);
  };

  // free memory and exit
  Free((void **)&PredecessorList, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
  Free((void **)&ShortestPathList, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
  Free((void **)&Labels, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
  Free((void **)&ColorVertexList, "molecule::CreateListOfUniqueFragmentsOfOrder: *ColorList");
  delete(RootStack);
  delete(TouchedStack);
  delete(SnakeStack);

  *out << Verbose(1) << "End of CreateListOfUniqueFragmentsOfOrder." << endl;
  return FragmentList;
};
*/

/** Structure containing all values in power set combination generation.
 */
struct UniqueFragments {
  config *configuration;
  atom *Root;
  Graph *Leaflet;
  KeySet *FragmentSet;
  int ANOVAOrder;
  int FragmentCounter;
  int CurrentIndex;
  int *Labels;
  int *ShortestPathList;
  bool **UsedList;
  bond **BondsPerSPList;
  double TEFactor;
  int *BondsPerSPCount;
};

/** From a given set of Bond sorted by Shortest Path distance, create all possible fragments of size \a SetDimension.
 * This basically involves recursion to create all power set combinations.
 * \param *out output stream for debugging
 * \param FragmentSearch UniqueFragments structure with all values needed
 * \param RootDistance current shortest path level, whose set of edges is represented by **BondsSet
 * \param SetDimension Number of possible bonds on this level (i.e. size of the array BondsSet[])
 * \param SubOrder remaining number of allowed vertices to add
 */
void molecule::SPFragmentGenerator(ofstream *out, struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder)
{
  atom *OtherWalker = NULL;
  int verbosity = 0; //FragmentSearch->ANOVAOrder-SubOrder;
  int NumCombinations;
  bool bit;
  int bits, TouchedIndex, SubSetDimension, SP;
  int Removal;
  int *TouchedList = (int *) Malloc(sizeof(int)*(SubOrder+1), "molecule::SPFragmentGenerator: *TouchedList");
  bond *Binder = NULL;
  bond **BondsList = NULL;

  NumCombinations = 1 << SetDimension;
  
  // Hier muessen von 1 bis NumberOfBondsPerAtom[Walker->nr] alle Kombinationen
  // von Endstuecken (aus den Bonds) hinzugefÃŒgt werden und fÃŒr verbleibende ANOVAOrder
  // rekursiv GraphCrawler in der nÀchsten Ebene aufgerufen werden
  
  *out << Verbose(1+verbosity) << "Begin of SPFragmentGenerator." << endl;
  *out << Verbose(1+verbosity) << "We are " << RootDistance << " away from Root, which is " << *FragmentSearch->Root << ", SubOrder is " << SubOrder << ", SetDimension is " << SetDimension << " and this means " <<  NumCombinations-1 << " combination(s)." << endl;

  // initialised touched list (stores added atoms on this level) 
  *out << Verbose(1+verbosity) << "Clearing touched list." << endl;
  for (TouchedIndex=0;TouchedIndex<=SubOrder;TouchedIndex++)  // empty touched list
    TouchedList[TouchedIndex] = -1;
  TouchedIndex = 0;
  
  // create every possible combination of the endpieces
  *out << Verbose(1+verbosity) << "Going through all combinations of the power set." << endl;
  for (int i=1;i<NumCombinations;i++) {  // sweep through all power set combinations (skip empty set!)
    // count the set bit of i
    bits = 0;
    for (int j=0;j<SetDimension;j++)
      bits += (i & (1 << j)) >> j;
      
    *out << Verbose(1+verbosity) << "Current set is " << Binary(i | (1 << SetDimension)) << ", number of bits is " << bits << "." << endl;
    if (bits <= SubOrder) { // if not greater than additional atoms allowed on stack, continue
      // --1-- add this set of the power set of bond partners to the snake stack
      for (int j=0;j<SetDimension;j++) {  // pull out every bit by shifting
        bit = ((i & (1 << j)) != 0);  // mask the bit for the j-th bond
        if (bit) {  // if bit is set, we add this bond partner
                OtherWalker = BondsSet[j]->rightatom;   // rightatom is always the one more distant, i.e. the one to add 
          //*out << Verbose(1+verbosity) << "Current Bond is " << ListOfBondsPerAtom[Walker->nr][i] << ", checking on " << *OtherWalker << "." << endl;
          //if ((!FragmentSearch->UsedList[OtherWalker->nr][i]) && (FragmentSearch->Labels[OtherWalker->nr] > FragmentSearch->Labels[FragmentSearch->Root->nr])) { 
            //*out << Verbose(2+verbosity) << "Not used so far, label " << FragmentSearch->Labels[OtherWalker->nr] << " is bigger than Root's " << FragmentSearch->Labels[FragmentSearch->Root->nr] << "." << endl;
          *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << "." << endl;
          TouchedList[TouchedIndex++] = OtherWalker->nr;  // note as added
          FragmentSearch->FragmentSet->insert( FragmentSearch->FragmentSet->end(), OtherWalker->nr);
            //FragmentSearch->UsedList[OtherWalker->nr][i] = true;
          //}
        } else {
          *out << Verbose(2+verbosity) << "Not adding." << endl;
        }
      }
      
      if (bits < SubOrder) {
        *out << Verbose(1+verbosity) << "There's still some space left on stack: " << (SubOrder - bits) << "." << endl;
        // --2-- look at all added end pieces of this combination, construct bond subsets and sweep through a power set of these by recursion
        SP = RootDistance+1;    // this is the next level
        // first count the members in the subset
        SubSetDimension = 0;
        Binder = FragmentSearch->BondsPerSPList[2*SP];          // start node for this level
        while (Binder->next != FragmentSearch->BondsPerSPList[2*SP+1]) {                // compare to end node of this level
          Binder = Binder->next;
          for (int k=0;k<TouchedIndex;k++) {
            if (Binder->Contains(TouchedList[k]))   // if we added this very endpiece
              SubSetDimension++;
          }
        }
        // then allocate and fill the list
        BondsList = (bond **) Malloc(sizeof(bond *)*SubSetDimension, "molecule::SPFragmentGenerator: **BondsList");
        SubSetDimension = 0;
        Binder = FragmentSearch->BondsPerSPList[2*SP];
        while (Binder->next != FragmentSearch->BondsPerSPList[2*SP+1]) {
          Binder = Binder->next;
          for (int k=0;k<TouchedIndex;k++) {
            if (Binder->leftatom->nr == TouchedList[k])   // leftatom is always the close one
              BondsList[SubSetDimension++] = Binder;
          }
        }
        *out << Verbose(2+verbosity) << "Calling subset generator " << SP << " away from root " << *FragmentSearch->Root << " with sub set dimension " << SubSetDimension << "." << endl;
        SPFragmentGenerator(out, FragmentSearch, SP, BondsList, SubSetDimension, SubOrder-bits);  
        Free((void **)&BondsList, "molecule::SPFragmentGenerator: **BondsList");
      } else {
        // --2-- otherwise store the complete fragment
        *out << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
        // store fragment as a KeySet
        *out << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], indices are: ";
        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++) {
          *out << (*runner)+1 << " "; 
        }
        InsertFragmentIntoGraph(out, FragmentSearch);
        Removal = LookForRemovalCandidate(out, FragmentSearch->FragmentSet, FragmentSearch->ShortestPathList);
        //Removal = StoreFragmentFromStack(out, FragmentSearch->Root, FragmentSearch->Leaflet, FragmentSearch->FragmentStack, FragmentSearch->ShortestPathList,FragmentSearch->Labels, &FragmentSearch->FragmentCounter, FragmentSearch->configuration);
      }
      
      // --3-- remove all added items in this level from snake stack
      *out << Verbose(1+verbosity) << "Removing all items that were added on this SP level " << RootDistance << "." << endl;
      for(int j=0;j<TouchedIndex;j++) {
        Removal = TouchedList[j];
        *out << Verbose(2+verbosity) << "Removing item nr. " << Removal+1 << " from snake stack." << endl;
        FragmentSearch->FragmentSet->erase(Removal);
        TouchedList[j] = -1;
      }
      TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
    } else {
      *out << Verbose(2+verbosity) << "More atoms to add for this set (" << bits << ") than space left on stack " << SubOrder << ", skipping this set." << endl;
    }
  }
  Free((void **)&TouchedList, "molecule::SPFragmentGenerator: *TouchedList");  
  *out << Verbose(1+verbosity) << "End of SPFragmentGenerator " << RootDistance << " away from Root " << *FragmentSearch->Root << " and SubOrder is " << SubOrder << "." << endl;
};

/** Creates a list of all unique fragments of certain vertex size from a given graph \a Fragment in the context of \a this molecule.
 * Note that we may use the fact that the atoms are SP-ordered on the atomstack. I.e. when popping always the last, we first get all
 * with SP of 2, then those with SP of 3, then those with SP of 4 and so on.
 * \param *out output stream for debugging
 * \param Order number of vertices
 * \param *ListOfGraph Graph structure to insert found fragments into
 * \param Fragment Restricted vertex set to use in context of molecule
 * \param TEFactor TEFactor to store in graphlist in the end
 * \param *configuration configuration needed for IsAngstroem
 * \return number of inserted fragments
 * \note ShortestPathList in FragmentSearch structure is probably due to NumberOfAtomsSPLevel and SP not needed anymore
 */
int molecule::CreateListOfUniqueFragmentsOfOrder(ofstream *out, int Order, Graph *ListOfGraph, KeySet Fragment, double TEFactor, config *configuration) 
{
  int SP, UniqueIndex, RootKeyNr, AtomKeyNr;
  int *NumberOfAtomsSPLevel = (int *) Malloc(sizeof(int)*Order, "molecule::CreateListOfUniqueFragmentsOfOrder: *SPLevelCount");
  atom *Walker = NULL, *OtherWalker = NULL;
  bond *Binder = NULL;
  bond **BondsList = NULL;
  KeyStack RootStack;
  KeyStack AtomStack;
  atom **PredecessorList = (atom **) Malloc(sizeof(atom *)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
  KeySet::iterator runner;

  // initialise the fragments structure
  struct UniqueFragments FragmentSearch;
  FragmentSearch.BondsPerSPList = (bond **) Malloc(sizeof(bond *)*Order*2, "molecule::CreateListOfUniqueFragmentsOfOrder: ***BondsPerSPList");
  FragmentSearch.BondsPerSPCount = (int *) Malloc(sizeof(int)*Order, "molecule::CreateListOfUniqueFragmentsOfOrder: *BondsPerSPCount");
  FragmentSearch.ShortestPathList = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
  FragmentSearch.Labels = (int *) Malloc(sizeof(int)*AtomCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
  FragmentSearch.FragmentCounter = 0;
  FragmentSearch.FragmentSet = new KeySet;
  FragmentSearch.configuration = configuration;
  FragmentSearch.TEFactor = TEFactor;
  FragmentSearch.Leaflet = ListOfGraph;      // set to insertion graph
  for (int i=0;i<AtomCount;i++) {
    FragmentSearch.Labels[i] = -1;
    FragmentSearch.ShortestPathList[i] = -1;
    PredecessorList[i] = NULL;
  }
  for (int i=0;i<Order;i++) {
    FragmentSearch.BondsPerSPList[2*i] = new bond();    // start node
    FragmentSearch.BondsPerSPList[2*i+1] = new bond();  // end node
    FragmentSearch.BondsPerSPList[2*i]->next = FragmentSearch.BondsPerSPList[2*i+1];     // intertwine these two 
    FragmentSearch.BondsPerSPList[2*i+1]->previous = FragmentSearch.BondsPerSPList[2*i];
    FragmentSearch.BondsPerSPCount[i] = 0;
  }  
  
  *out << endl;
  *out << Verbose(0) << "Begin of CreateListOfUniqueFragmentsOfOrder with order " << Order << "." << endl;

  RootStack.clear();  
  // find first root candidates  
  runner = Fragment.begin();
  Walker = NULL;
  while ((Walker == NULL) && (runner != Fragment.end())) { // search for first non-hydrogen atom
    Walker = FindAtom((*runner));
    *out << Verbose(4) << "Current Root candidate is " << Walker->Name << "." << endl;
#ifdef ADDHYDROGEN
    if (Walker->type->Z == 1) // skip hydrogen
      Walker = NULL;
#endif
    runner++;
  }
  if (Walker != NULL)
    RootStack.push_back(Walker->nr);
  else
    *out << Verbose(0) << "ERROR: Could not find an appropriate Root atom!" << endl;
  
  UniqueIndex = 0;
  while (!RootStack.empty()) {
    // Get Root and prepare
    RootKeyNr = RootStack.front();
    RootStack.pop_front();
    FragmentSearch.Root = FindAtom(RootKeyNr);
    if (FragmentSearch.Labels[RootKeyNr] == -1)
      FragmentSearch.Labels[RootKeyNr] = UniqueIndex++;
    FragmentSearch.ShortestPathList[RootKeyNr] = 0;
    // prepare the atom stack counters (number of atoms with certain SP on stack)
    for (int i=0;i<Order;i++)
      NumberOfAtomsSPLevel[i] = 0;
    NumberOfAtomsSPLevel[0] = 1;  // for root
    SP = -1;
    *out << endl;
    *out << Verbose(0) << "Starting BFS analysis with current Root: " << *FragmentSearch.Root << "." << endl;
    // push as first on atom stack and goooo ...
    AtomStack.clear();  
    AtomStack.push_back(RootKeyNr);
    *out << Verbose(0) << "Cleared AtomStack and pushed root as first item onto it." << endl;
    // do a BFS search to fill the SP lists and label the found vertices
    while (!AtomStack.empty()) {
      // pop next atom
      AtomKeyNr = AtomStack.front();
      AtomStack.pop_front();
      if (SP != -1)
        NumberOfAtomsSPLevel[SP]--;
      if ((SP == -1) || (NumberOfAtomsSPLevel[SP] == -1)) {
      ////if (SP < FragmentSearch.ShortestPathList[AtomKeyNr]) { // bfs has reached new SP level, hence allocate for new list
        SP++;
        NumberOfAtomsSPLevel[SP]--; // carry over "-1" to next level
        ////SP = FragmentSearch.ShortestPathList[AtomKeyNr];
        *out << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with 0 item(s)";
        if (SP > 0)
          *out << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
        else
          *out << "." << endl;
        FragmentSearch.BondsPerSPCount[SP] = 0;
      } else {
        *out << Verbose(1) << "Still " << NumberOfAtomsSPLevel[SP]+1 << " on this SP (" << SP << ") level, currently having " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
      }
      Walker = FindAtom(AtomKeyNr);
      *out << Verbose(0) << "Current Walker is: " << *Walker << " with label " << FragmentSearch.Labels[AtomKeyNr] << " and SP of " << SP << "." << endl;
      // check for new sp level
      // go through all its bonds
      *out << Verbose(1) << "Going through all bonds of Walker." << endl;
      for (int i=0;i<NumberOfBondsPerAtom[AtomKeyNr];i++) {
        Binder = ListOfBondsPerAtom[AtomKeyNr][i];
        OtherWalker = Binder->GetOtherAtom(Walker);
        if ((Fragment.find(OtherWalker->nr) != Fragment.end())
#ifdef ADDHYDROGEN
         && (OtherWalker->type->Z != 1)
#endif
                                                              ) {  // skip hydrogens and restrict to fragment
          *out << Verbose(2) << "Current partner is " << *OtherWalker << " in bond " << *Binder << "." << endl;
          // set the label if not set (and push on root stack as well)
          if (FragmentSearch.Labels[OtherWalker->nr] == -1) {
            RootStack.push_back(OtherWalker->nr);
            FragmentSearch.Labels[OtherWalker->nr] = UniqueIndex++;
            *out << Verbose(3) << "Set label to " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
          } else {
            *out << Verbose(3) << "Label is already " << FragmentSearch.Labels[OtherWalker->nr] << "." << endl;
          }
          if ((OtherWalker != PredecessorList[AtomKeyNr]) && (FragmentSearch.Labels[OtherWalker->nr] > FragmentSearch.Labels[RootKeyNr])) { // only pass through those with label bigger than Root's
            // set shortest path if not set or longer
            //if ((FragmentSearch.ShortestPathList[OtherWalker->nr] == -1) || (FragmentSearch.ShortestPathList[OtherWalker->nr] > FragmentSearch.ShortestPathList[AtomKeyNr]))  {
              FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
              *out << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
            //} else {
            //  *out << Verbose(3) << "Shortest Path is already " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
            //}
            if (FragmentSearch.ShortestPathList[OtherWalker->nr] < Order) { // only pass through those within reach of Order
              // push for exploration on stack (only if the SP of OtherWalker is longer than of Walker! (otherwise it has been added already!)
              if (FragmentSearch.ShortestPathList[OtherWalker->nr] > SP) {
                if (FragmentSearch.ShortestPathList[OtherWalker->nr] < (Order-1)) {
                  *out << Verbose(3) << "Putting on atom stack for further exploration." << endl;
                  PredecessorList[OtherWalker->nr] = Walker;    // note down the one further up the exploration tree
                  AtomStack.push_back(OtherWalker->nr);
                  NumberOfAtomsSPLevel[FragmentSearch.ShortestPathList[OtherWalker->nr]]++;
                } else {
                  *out << Verbose(3) << "Not putting on atom stack, is at end of reach." << endl;
                }
                // 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
                add(Binder, FragmentSearch.BondsPerSPList[2*SP+1]);
                FragmentSearch.BondsPerSPCount[SP]++;
                *out << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP] << " item(s)." << endl;
              } else {
                *out << Verbose(3) << "Not putting on atom stack, nor adding bond, as " << *OtherWalker << "'s SP is shorter than Walker's." << endl;
              }
            } else {
              *out << Verbose(3) << "Not continuing, as " << *OtherWalker << " is out of reach of order " << Order << "." << endl;
            }
          } else {
            *out << Verbose(3) << "Not passing on, as label of " << *OtherWalker << " " << FragmentSearch.Labels[OtherWalker->nr] << " is smaller than that of Root " << FragmentSearch.Labels[RootKeyNr] << " or this is my predecessor." << endl;
          }
        } else {
          *out << Verbose(2) << "Is not in the Fragment or skipping hydrogen " << *OtherWalker << "." << endl;
        }
      }
    }
    // reset predecessor list
    for(int i=0;i<Order;i++) {
      Binder = FragmentSearch.BondsPerSPList[2*i];
      *out << Verbose(1) << "Current SP level is " << i << "." << endl;
      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
        Binder = Binder->next;
        PredecessorList[Binder->rightatom->nr] = NULL;  // By construction "OtherAtom" is always Bond::rightatom!
      } 
    }
    *out << endl;
    *out << Verbose(0) << "Printing all found lists." << endl;
    // outputting all list for debugging
    for(int i=0;i<Order;i++) {
      Binder = FragmentSearch.BondsPerSPList[2*i];
      *out << Verbose(1) << "Current SP level is " << i << "." << endl;
      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
        Binder = Binder->next;
        *out << Verbose(2) << *Binder << endl;
      } 
    }
    
    // creating fragments with the found edge sets
    SP = 0;
    for(int i=0;i<Order;i++) { // sum up all found edges
      Binder = FragmentSearch.BondsPerSPList[2*i];
      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
        Binder = Binder->next;
        SP ++; 
      }
    }
    *out << Verbose(0) << "Total number of edges is " << SP << "." << endl;
    if (SP >= (Order-1)) {
      // start with root (push on fragment stack)
      *out << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << "." << endl;
      FragmentSearch.FragmentSet->clear();  
      FragmentSearch.FragmentSet->insert(FragmentSearch.Root->nr);
      
      if (FragmentSearch.FragmentSet->size() == (unsigned int) Order) {
        *out << Verbose(0) << "Enough items on stack already for a fragment!" << endl;
        // store fragment as a KeySet
        *out << Verbose(2) << "Found a new fragment[" << FragmentSearch.FragmentCounter << "], indices are: ";
        for(KeySet::iterator runner = FragmentSearch.FragmentSet->begin(); runner != FragmentSearch.FragmentSet->end(); runner++) {
          *out << (*runner)+1 << " "; 
        }
        *out << endl;
        InsertFragmentIntoGraph(out, &FragmentSearch);
        //StoreFragmentFromStack(out, FragmentSearch.Root, FragmentSearch.Leaflet, FragmentSearch.FragmentStack, FragmentSearch.ShortestPathList,FragmentSearch.Labels, &FragmentSearch.FragmentCounter, FragmentSearch.configuration);
      } else {
        *out << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
        // prepare the subset and call the generator
        BondsList = (bond **) Malloc(sizeof(bond *)*FragmentSearch.BondsPerSPCount[0], "molecule::CreateListOfUniqueFragmentsOfOrder: **BondsList");
        Binder = FragmentSearch.BondsPerSPList[0];
        for(int i=0;i<FragmentSearch.BondsPerSPCount[0];i++) {
          Binder = Binder->next;
          BondsList[i] = Binder;
        }
        SPFragmentGenerator(out, &FragmentSearch, 0, BondsList, FragmentSearch.BondsPerSPCount[0], Order-1);  
        Free((void **)&BondsList, "molecule::CreateListOfUniqueFragmentsOfOrder: **BondsList");
      }
    } else {
      *out << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
    }
    
    // remove root from stack
    *out << Verbose(0) << "Removing root again from stack." << endl;
    FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);    

    // free'ing the bonds lists
    *out << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
    for(int i=0;i<Order;i++) {
      *out << Verbose(1) << "Current SP level is " << i << ": ";
      Binder = FragmentSearch.BondsPerSPList[2*i];
      while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
        Binder = Binder->next;
        FragmentSearch.ShortestPathList[Binder->leftatom->nr] = -1;
        FragmentSearch.ShortestPathList[Binder->rightatom->nr] = -1;
      }
      // delete added bonds
      cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
      // also start and end node
      *out << "cleaned." << endl;
    }
  }
  
  // free allocated memory
  Free((void **)&NumberOfAtomsSPLevel, "molecule::CreateListOfUniqueFragmentsOfOrder: *SPLevelCount");
  Free((void **)&PredecessorList, "molecule::CreateListOfUniqueFragmentsOfOrder: **PredecessorList");
  for(int i=0;i<Order;i++) { // delete start and end of each list
    delete(FragmentSearch.BondsPerSPList[2*i]);
    delete(FragmentSearch.BondsPerSPList[2*i+1]);
  }
  Free((void **)&FragmentSearch.BondsPerSPList, "molecule::CreateListOfUniqueFragmentsOfOrder: ***BondsPerSPList");
  Free((void **)&FragmentSearch.BondsPerSPCount, "molecule::CreateListOfUniqueFragmentsOfOrder: *BondsPerSPCount");
  Free((void **)&FragmentSearch.ShortestPathList, "molecule::CreateListOfUniqueFragmentsOfOrder: *ShortestPathList");
  Free((void **)&FragmentSearch.Labels, "molecule::CreateListOfUniqueFragmentsOfOrder: *Labels");
  delete(FragmentSearch.FragmentSet);
  
//  // gather all the leaves together
//  *out << Verbose(0) << "Copying all fragments into MoleculeList structure." << endl; 
//  FragmentList = new Graph;
//  UniqueIndex = 0;
//  while ((FragmentSearch.Leaflet != NULL) && (UniqueIndex < FragmentSearch.FragmentCounter))  {
//    FragmentList->insert();
//    FragmentList->ListOfMolecules[UniqueIndex++] = FragmentSearch.Leaflet->Leaf;
//    FragmentSearch.Leaflet->Leaf = NULL; // prevent molecule from being removed
//    TempLeaf = FragmentSearch.Leaflet;
//    FragmentSearch.Leaflet = FragmentSearch.Leaflet->previous;
//    delete(TempLeaf);
//  };

  // return list  
  *out << Verbose(0) << "End of CreateListOfUniqueFragmentsOfOrder." << endl;
  return FragmentSearch.FragmentCounter;
};

/** Corrects the nuclei position if the fragment was created over the cell borders.
 * Scans all bonds, checks the distance, if greater than typical, we have a candidate for the correction.
 * We remove the bond whereafter the graph probably separates. Then, we translate the one component periodically
 * and re-add the bond. Looping on the distance check.
 * \param *out ofstream for debugging messages
 */
void molecule::ScanForPeriodicCorrection(ofstream *out)
{
  bond *Binder = NULL;
  bond *OtherBinder = NULL;
  atom *Walker = NULL;
  atom *OtherWalker = NULL;
  double *matrix = ReturnFullMatrixforSymmetric(cell_size);
  enum Shading *ColorList = NULL;
  double tmp;
  vector TranslationVector;
  //AtomStackClass *CompStack = NULL;
  AtomStackClass *AtomStack = new AtomStackClass(AtomCount);
  bool flag = true;

  *out << Verbose(1) << "Begin of ScanForPeriodicCorrection." << endl;

  ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
  while (flag) {
    // remove bonds that are beyond bonddistance
    for(int i=0;i<NDIM;i++)
      TranslationVector.x[i] = 0.; 
    // scan all bonds
    Binder = first;
    flag = false;
    while ((!flag) && (Binder->next != last)) {
      Binder = Binder->next;
      for (int i=0;i<NDIM;i++) {
        tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]);
        //*out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
        if (tmp > BondDistance) {
          OtherBinder = Binder->next; // note down binding partner for later re-insertion
          unlink(Binder);   // unlink bond
          *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
          flag = true;
          break;
        }
      }
    }
    if (flag) {
      // create translation vector from their periodically modified distance
      for (int i=0;i<NDIM;i++) {
        tmp = Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i];
        if (fabs(tmp) > BondDistance)
          TranslationVector.x[i] = (tmp < 0) ? +1. : -1.;
      }
      TranslationVector.MatrixMultiplication(matrix);
      //*out << "Translation vector is ";
      //TranslationVector.Output(out);
      //*out << endl;
      // apply to all atoms of first component via BFS
      for (int i=0;i<AtomCount;i++)
        ColorList[i] = white;
      AtomStack->Push(Binder->leftatom);
      while (!AtomStack->IsEmpty()) {
        Walker = AtomStack->PopFirst();
        //*out << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
        ColorList[Walker->nr] = black;    // mark as explored
        Walker->x.AddVector(&TranslationVector); // translate
        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {  // go through all binding partners
          if (ListOfBondsPerAtom[Walker->nr][i] != Binder) {
            OtherWalker = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
            if (ColorList[OtherWalker->nr] == white) {
              AtomStack->Push(OtherWalker); // push if yet unexplored
            }
          }
        }
      }
      // re-add bond    
      link(Binder, OtherBinder);
    } else {
      *out << Verbose(2) << "No corrections for this fragment." << endl;
    }
    //delete(CompStack);
  }

  // free allocated space from ReturnFullMatrixforSymmetric()
  delete(AtomStack);
  Free((void **)&ColorList, "molecule::ScanForPeriodicCorrection: *ColorList");
  Free((void **)&matrix, "molecule::ScanForPeriodicCorrection: *matrix");
  *out << Verbose(1) << "End of ScanForPeriodicCorrection." << endl;
};

/** Blows the 6-dimensional \a cell_size array up to a full NDIM by NDIM matrix.
 * \param *symm 6-dim array of unique symmetric matrix components
 * \return allocated NDIM*NDIM array with the symmetric matrix
 */
double * molecule::ReturnFullMatrixforSymmetric(double *symm)
{
  double *matrix = (double *) Malloc(sizeof(double)*NDIM*NDIM, "molecule::ReturnFullMatrixforSymmetric: *matrix");
  matrix[0] = symm[0];
  matrix[1] = symm[1];
  matrix[2] = symm[3];
  matrix[3] = symm[1];
  matrix[4] = symm[2];
  matrix[5] = symm[4];
  matrix[6] = symm[3];
  matrix[7] = symm[4];
  matrix[8] = symm[5];
  return matrix;
};

bool KeyCompare::operator() (const KeySet SubgraphA, const KeySet SubgraphB) const
{
  //cout << "my check is used." << endl;
  if (SubgraphA.size() < SubgraphB.size()) {
    return true;
  } else {
    if (SubgraphA.size() > SubgraphB.size()) {
      return false;
    } else {
      KeySet::iterator IteratorA = SubgraphA.begin();
      KeySet::iterator IteratorB = SubgraphB.begin();
      while ((IteratorA != SubgraphA.end()) && (IteratorB != SubgraphB.end())) {
        if ((*IteratorA) <  (*IteratorB))
          return true;
        else if ((*IteratorA) > (*IteratorB)) {
            return false;
          } // else, go on to next index
        IteratorA++;
        IteratorB++;
      } // end of while loop
    }// end of check in case of equal sizes 
  }
  return false; // if we reach this point, they are equal
};

//bool operator < (KeySet SubgraphA, KeySet SubgraphB)
//{
//  return KeyCompare(SubgraphA, SubgraphB);
//};

/** Checking whether KeySet is not already present in Graph, if so just adds factor.
 * \param *out output stream for debugging
 * \param &set KeySet to insert
 * \param &graph Graph to insert into
 * \param *counter pointer to unique fragment count
 * \param factor energy factor for the fragment
 */
inline void InsertFragmentIntoGraph(ofstream *out, struct UniqueFragments *Fragment)
{
  GraphTestPair testGraphInsert;

  testGraphInsert = Fragment->Leaflet->insert(GraphPair (*Fragment->FragmentSet,pair<int,double>(Fragment->FragmentCounter,Fragment->TEFactor)));  // store fragment number and current factor
  if (testGraphInsert.second) {
    *out << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " successfully inserted." << endl;
    Fragment->FragmentCounter++;
  } else {
    *out << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first << endl;
    ((*(testGraphInsert.first)).second).second += Fragment->TEFactor;
    *out << Verbose(2) << "New factor is " << ((*(testGraphInsert.first)).second).second << "." << endl;
  }
};
//void inline InsertIntoGraph(ofstream *out, KeyStack &stack, Graph &graph, int *counter, double factor)
//{
//  // copy stack contents to set and call overloaded function again
//  KeySet set;
//  for(KeyStack::iterator runner = stack.begin(); runner != stack.begin(); runner++)
//    set.insert((*runner));
//  InsertIntoGraph(out, set, graph, counter, factor);
//};

/** Inserts each KeySet in \a graph2 into \a graph1.
 * \param *out output stream for debugging
 * \param graph1 first (dest) graph
 * \param graph2 second (source) graph
 */
inline void InsertGraphIntoGraph(ofstream *out, Graph &graph1, Graph &graph2, int *counter)
{
  GraphTestPair testGraphInsert;

  for(Graph::iterator runner = graph2.begin(); runner != graph2.end(); runner++) {
    testGraphInsert = graph1.insert(GraphPair ((*runner).first,pair<int,double>((*counter)++,((*runner).second).second)));  // store fragment number and current factor
    if (testGraphInsert.second) {
      *out << Verbose(2) << "KeySet " << (*counter)-1 << " successfully inserted." << endl;
    } else {
      *out << Verbose(2) << "KeySet " << (*counter)-1 << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first << endl;
      ((*(testGraphInsert.first)).second).second += (*runner).second.second;
      *out << Verbose(2) << "New factor is " << (*(testGraphInsert.first)).second.second << "." << endl;
    }
  }
};


/** Creates truncated BOSSANOVA expansion up to order \a k.
 * \param *out output stream for debugging
 * \param ANOVAOrder ANOVA expansion is truncated above this order
 * \param *configuration configuration for writing config files for each fragment
 * \return pointer to MoleculeListClass with all the fragments or NULL if something went wrong.
 */
MoleculeListClass * molecule::FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration)
{
  Graph *FragmentList = NULL, ***FragmentLowerOrdersList = NULL;
  MoleculeListClass *FragmentMoleculeList = NULL;
  int Order, NumLevels, NumMolecules, TotalNumMolecules = 0, *NumMoleculesOfOrder = NULL;
  int counter = 0;
  
  *out << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;

  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
  // with all needed lower orders that are subtracted, the other dimension is the BondOrder (i.e. from 1 to 5)
  NumMoleculesOfOrder = (int *) Malloc(sizeof(int)*ANOVAOrder, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
  FragmentLowerOrdersList = (Graph ***) Malloc(sizeof(Graph **)*ANOVAOrder, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");

  // Construct the complete KeySet
  atom *Walker = start;
  KeySet CompleteMolecule;
  while (Walker->next != end) {
    Walker = Walker->next;
    CompleteMolecule.insert(Walker->nr);
  } 

  for (int BondOrder=1;BondOrder<=ANOVAOrder;BondOrder++) {
    // this can easily be seen: if Order is 5, then the number of levels for each lower order is the total sum of the number of levels above, as
    // each has to be split up. E.g. for the second level we have one from 5th, one from 4th, two from 3th (which in turn is one from 5th, one from 4th),
    // hence we have overall four 2th order levels for splitting. This also allows for putting all into a single array (FragmentLowerOrdersList[])
    // with the order along the cells as this: 5433222211111111 for BondOrder 5 needing 16=pow(2,5-1) cells (only we use bit-shifting which is faster)
    NumLevels = 1 << (BondOrder-1); // (int)pow(2,BondOrder-1);
    *out << Verbose(0) << "BondOrder is (" << BondOrder << "/" << ANOVAOrder << ") and NumLevels is " << NumLevels << "." << endl;
  
    // allocate memory for all lower level orders in this 1D-array of ptrs
    FragmentLowerOrdersList[BondOrder-1] = (Graph **) Malloc(sizeof(Graph *)*NumLevels, "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
  
    // create top order where nothing is reduced
    *out << Verbose(0) << "==============================================================================================================" << endl;
    *out << Verbose(0) << "Creating list of unique fragments of Bond Order " << BondOrder << " itself." << endl;
    // Create list of Graphs of current Bond Order (i.e. F_{ij})
    FragmentLowerOrdersList[BondOrder-1][0] =  new Graph;
    NumMoleculesOfOrder[BondOrder-1] = CreateListOfUniqueFragmentsOfOrder(out, BondOrder, FragmentLowerOrdersList[BondOrder-1][0], CompleteMolecule, 1., configuration);
    *out << Verbose(1) << "Number of resulting molecules is: " << NumMoleculesOfOrder[BondOrder-1] << "." << endl;
    NumMolecules = 0;
    
    // create lower order fragments
    *out << Verbose(0) << "Creating list of unique fragments of lower Bond Order terms to be subtracted." << endl;
    Order = BondOrder;
    for (int source=0;source<(NumLevels >> 1);source++) { // 1-terms don't need any more splitting, that's why only half is gone through (shift again)

      // step down to next order at (virtual) boundary of powers of 2 in array
      while (source >= (1 << (BondOrder-Order))) // (int)pow(2,BondOrder-Order))    
        Order--;
      *out << Verbose(0) << "Current Order is: " << Order << "." << endl;
      for (int SubOrder=Order;SubOrder>1;SubOrder--) {
        int dest = source + (1 << (BondOrder-SubOrder));
        *out << Verbose(0) << "--------------------------------------------------------------------------------------------------------------" << endl;
        *out << Verbose(0) << "Current SubOrder is: " << SubOrder-1 << " with source " << source << " to destination " << dest << "." << endl;
  
        // every molecule is split into a list of again (Order - 1) molecules, while counting all molecules
        //*out << Verbose(1) << "Splitting the " << (*FragmentLowerOrdersList[BondOrder-1][source]).size() << " molecules of the " << source << "th cell in the array." << endl;
        //NumMolecules = 0;
        FragmentLowerOrdersList[BondOrder-1][dest] = new Graph;
        for(Graph::iterator runner = (*FragmentLowerOrdersList[BondOrder-1][source]).begin();runner != (*FragmentLowerOrdersList[BondOrder-1][source]).end(); runner++) {
          NumMolecules += CreateListOfUniqueFragmentsOfOrder(out,SubOrder-1, FragmentLowerOrdersList[BondOrder-1][dest], (*runner).first, -(*runner).second.second, configuration);
        }
        *out << Verbose(1) << "Number of resulting molecules is: " << NumMolecules << "." << endl;
      }
    }
    // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current BondOrder
    //NumMoleculesOfOrder[BondOrder-1] = NumMolecules;
    TotalNumMolecules += NumMoleculesOfOrder[BondOrder-1];
    *out << Verbose(1) << "Number of resulting molecules for Order " << BondOrder << " is: " << NumMoleculesOfOrder[BondOrder-1] << "." << endl;    
  }
  *out << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
  // now, FragmentLowerOrdersList is complete, it looks - for BondOrder 5 - as this (number is the ANOVA Order of the terms therein) 
  // 5433222211111111
  // 43221111
  // 3211
  // 21
  // 1
  // Subsequently, we combine same orders into a single list (FragmentByOrderList) and reduce these by order

  *out << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl;
  FragmentList = new Graph;
  for (int BondOrder=1;BondOrder<=ANOVAOrder;BondOrder++) {
    NumLevels = 1 << (BondOrder-1);
    for(int i=0;i<NumLevels;i++) {
      InsertGraphIntoGraph(out, *FragmentList, (*FragmentLowerOrdersList[BondOrder-1][i]), &counter);
      delete(FragmentLowerOrdersList[BondOrder-1][i]);
    }
    Free((void **)&FragmentLowerOrdersList[BondOrder-1], "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
  }
  Free((void **)&FragmentLowerOrdersList, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
  Free((void **)&NumMoleculesOfOrder, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
  // allocate memory for the pointer array and transmorph graphs into full molecular fragments
  FragmentMoleculeList = new MoleculeListClass(TotalNumMolecules, AtomCount);
  int k=0;
  for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++) {
    KeySet test = (*runner).first;
    FragmentMoleculeList->ListOfMolecules[k] = StoreFragmentFromKeySet(out, test, configuration);
    FragmentMoleculeList->TEList[k] = ((*runner).second).second;
    k++;
  }
  
  *out << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
  delete(FragmentList); 
  return FragmentMoleculeList;
};

/** Fragments a molecule, taking \a BondDegree neighbours into accent.
 * First of all, we have to split up the molecule into bonds ranging out till \a BondDegree.
 * These fragments serve in the following as the basis the calculate the bond energy of the bond
 * they originated from. Thus, they are split up in a left and a right part, each calculated for
 * the total energy, including the fragment as a whole and then we get: 
 * E(fragment) - E(left) - E(right) = E(bond)
 * The splitting up is done via Breadth-First-Search, \sa BreadthFirstSearchAdd().
 * \param *out output stream for debugging
 * \param BondOrder up to how many neighbouring bonds a fragment contains
 * \param *configuration configuration for writing config files for each fragment
 * \param CutCyclic whether to add cut cyclic bond or to saturate
 * \return pointer to MoleculeListClass with all the fragments or NULL if something went wrong.
 */
MoleculeListClass * molecule::FragmentBottomUp(ofstream *out, int BondOrder, config *configuration, enum CutCyclicBond CutCyclic)
{
  int Num;
  MoleculeListClass *FragmentList =  NULL, **FragmentsList = NULL;
  bond *Bond = NULL;

  *out << Verbose(0) << "Begin of FragmentBottomUp." << endl; 
  FragmentsList = (MoleculeListClass **) Malloc(sizeof(MoleculeListClass *)*2, "molecule::FragmentBottomUp: **FragmentsList");
  *out << Verbose(0) << "Getting Atomic fragments." << endl;
  FragmentsList[0] = GetAtomicFragments(out, AtomCount, configuration->GetIsAngstroem(), 1., CutCyclic);

  // create the fragments including each one bond of the original molecule and up to \a BondDegree neighbours
  *out << Verbose(0) << "Getting " << 
#ifdef ADDHYDROGEN  
  NoNonBonds 
#else
  BondCount
#endif
                                        << " Bond fragments." << endl;
  FragmentList = GetEachBondFragmentOfOrder(out, BondOrder, configuration->GetIsAngstroem(), CutCyclic);

  // check whether there are equal fragments by ReduceToUniqueOnes
  FragmentList->ReduceToUniqueList(out, &cell_size[0], BondDistance);

        *out << Verbose(0) << "Begin of Separating " << FragmentList->NumberOfMolecules << " Fragments into Bond pieces." << endl;
        // as we have the list, we have to take each fragment split it relative to its originating
        // bond into left and right and store these in a new list
  *out << Verbose(2) << endl << "Allocating MoleculeListClass" << endl; 
  FragmentsList[1] =  new MoleculeListClass(3*FragmentList->NumberOfMolecules, AtomCount); // for each molecule the whole and its left and right part 
  *out << Verbose(2) << "Creating TEList." << endl; 
  // and create TE summation for these bond energy approximations (bond = whole - left - right)
  for(int i=0;i<FragmentList->NumberOfMolecules;i++) {
    // make up factors to regain total energy of whole molecule
    FragmentsList[1]->TEList[3*i] = FragmentList->TEList[i];       // bond energy is 1 * whole 
    FragmentsList[1]->TEList[3*i+1] = -FragmentList->TEList[i];    // - 1. * left part
    FragmentsList[1]->TEList[3*i+2] = -FragmentList->TEList[i];    // - 1. * right part

    // shift the pointer on whole molecule to new list in order to avoid that this molecule is deleted on deconstructing FragmentList
    FragmentsList[1]->ListOfMolecules[3*i] = FragmentList->ListOfMolecules[i]; 
    *out << Verbose(2) << "shifting whole fragment pointer for fragment " << FragmentList->ListOfMolecules[i] << " -> " <<  FragmentsList[1]->ListOfMolecules[3*i] << "." << endl;
    // create bond matrix and count bonds
    *out << Verbose(2) << "Updating bond list for fragment " << i << " [" << FragmentList << "]: " << FragmentList->ListOfMolecules[i] << endl; 
    // create list of bonds per atom for this fragment (atoms were counted above)
    FragmentsList[1]->ListOfMolecules[3*i]->CreateListOfBondsPerAtom(out);
     
    *out << Verbose(0) << "Getting left & right fragments for fragment " << i << "." << endl;
    // the bond around which the fragment has been setup is always the first by construction (bond partners are first added atoms)
    Bond = FragmentsList[1]->ListOfMolecules[3*i]->first->next; // is the bond between atom 0 and another in the middle
    FragmentsList[1]->ListOfMolecules[3*i]->FragmentMoleculeByBond(out, Bond, &(FragmentsList[1]->ListOfMolecules[3*i+1]), &(FragmentsList[1]->ListOfMolecules[3*i+2]), configuration->GetIsAngstroem(), CutCyclic);
    if ((FragmentsList[1]->ListOfMolecules[3*i+1] == NULL) || (FragmentsList[1]->ListOfMolecules[3*i+2] == NULL)) {
      *out << Verbose(2) << "Left and/or Right Fragment is NULL!" << endl;
    } else {
      *out << Verbose(3) << "Left Fragment is " <<  FragmentsList[1]->ListOfMolecules[3*i+1] << ": " << endl;
      FragmentsList[1]->ListOfMolecules[3*i+1]->Output(out);
      *out << Verbose(3) << "Right Fragment is " <<  FragmentsList[1]->ListOfMolecules[3*i+2] << ": " << endl;
      FragmentsList[1]->ListOfMolecules[3*i+2]->Output(out);
      *out << endl;
    }
    // remove in old list, so that memory for this molecule is not free'd on final delete of this list
    FragmentList->ListOfMolecules[i] = NULL;
  }
        *out << Verbose(0) << "End of Separating Fragments into Bond pieces." << endl;
  delete(FragmentList);
  FragmentList = NULL;

  // combine atomic and bond list
  FragmentList = new MoleculeListClass(FragmentsList[0]->NumberOfMolecules + FragmentsList[1]->NumberOfMolecules, AtomCount);
  Num = 0;
  for(int i=0;i<2;i++) {
    for(int j=0;j<FragmentsList[i]->NumberOfMolecules;j++) {
      // transfer molecule
      FragmentList->ListOfMolecules[Num] = FragmentsList[i]->ListOfMolecules[j];
      FragmentsList[i]->ListOfMolecules[j] = NULL;
      // transfer TE factor
      FragmentList->TEList[Num] = FragmentsList[i]->TEList[j];
      Num++;
    }
    delete(FragmentsList[i]);
    FragmentsList[i] = NULL;
  }
  *out << Verbose(2) << "Memory cleanup and return with filled list." << endl; 
  Free((void **)&FragmentsList, "molecule::FragmentBottomUp: **FragmentsList");

  // reducing list
  FragmentList->ReduceToUniqueList(out, &cell_size[0], BondDistance);
        
        // write configs for all fragements (are written in FragmentMolecule)
  // free FragmentList
  *out << Verbose(0) << "End of FragmentBottomUp." << endl; 
  return FragmentList;
};


/** Comparision function for GSL heapsort on distances in two molecules.
 * \param *a
 * \param *b
 * \return <0, \a *a less than \a *b, ==0 if equal, >0 \a *a greater than \a *b
 */
int CompareDoubles (const void * a, const void * b)
{
  if (*(double *)a > *(double *)b)
    return -1;
  else if (*(double *)a < *(double *)b)
    return 1;
  else
    return 0;
};

/** Determines whether two molecules actually contain the same atoms and coordination.
 * \param *out output stream for debugging
 * \param *OtherMolecule the molecule to compare this one to
 * \param threshold upper limit of difference when comparing the coordination.
 * \return NULL - not equal, otherwise an allocated (molecule::AtomCount) permutation map of the atom numbers (which corresponds to which)
 */
int * molecule::IsEqualToWithinThreshold(ofstream *out, molecule *OtherMolecule, double threshold)
{
  int flag;
  double *Distances = NULL, *OtherDistances = NULL;
  vector CenterOfGravity, OtherCenterOfGravity;
  size_t *PermMap = NULL, *OtherPermMap = NULL;
  int *PermutationMap = NULL;
  atom *Walker = NULL;
  bool result = true; // status of comparison
  
  *out << Verbose(3) << "Begin of IsEqualToWithinThreshold." << endl; 
  /// first count both their atoms and elements and update lists thereby ...
  //*out << Verbose(0) << "Counting atoms, updating list" << endl;
  CountAtoms(out);
  OtherMolecule->CountAtoms(out);
  CountElements();
  OtherMolecule->CountElements();

  /// ... and compare:
  /// -# AtomCount
  if (result) {
    if (AtomCount != OtherMolecule->AtomCount) {
      *out << Verbose(4) << "AtomCounts don't match: " << AtomCount << " == " << OtherMolecule->AtomCount << endl;
      result = false;
    } else *out << Verbose(4) << "AtomCounts match: " << AtomCount << " == " << OtherMolecule->AtomCount << endl;
  }
  /// -# ElementCount
  if (result) {
    if (ElementCount != OtherMolecule->ElementCount) {
      *out << Verbose(4) << "ElementCount don't match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl;
      result = false;
    } else *out << Verbose(4) << "ElementCount match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl;
  }
  /// -# ElementsInMolecule
  if (result) {
    for (flag=0;flag<MAX_ELEMENTS;flag++) {
      //*out << Verbose(5) << "Element " <<  flag << ": " << ElementsInMolecule[flag] << " <-> " << OtherMolecule->ElementsInMolecule[flag] << "." << endl;
      if (ElementsInMolecule[flag] != OtherMolecule->ElementsInMolecule[flag])
        break;
    }
    if (flag < MAX_ELEMENTS) {
      *out << Verbose(4) << "ElementsInMolecule don't match." << endl;
      result = false;
    } else *out << Verbose(4) << "ElementsInMolecule match." << endl;
  }
  /// then determine and compare center of gravity for each molecule ...
  if (result) {
    *out << Verbose(5) << "Calculating Centers of Gravity" << endl;
    DetermineCenterOfGravity(CenterOfGravity);
    OtherMolecule->DetermineCenterOfGravity(OtherCenterOfGravity);
    *out << Verbose(5) << "Center of Gravity: ";
    CenterOfGravity.Output(out);
    *out << endl << Verbose(5) << "Other Center of Gravity: ";
    OtherCenterOfGravity.Output(out);
    *out << endl;
    if (CenterOfGravity.Distance(&OtherCenterOfGravity) > threshold) {
      *out << Verbose(4) << "Centers of gravity don't match." << endl;
      result = false;  
    }
  }
  
  /// ... then make a list with the euclidian distance to this center for each atom of both molecules
  if (result) {
    *out << Verbose(5) << "Calculating distances" << endl;
    Distances = (double *) Malloc(sizeof(double)*AtomCount, "molecule::IsEqualToWithinThreshold: Distances");
    OtherDistances = (double *) Malloc(sizeof(double)*AtomCount, "molecule::IsEqualToWithinThreshold: OtherDistances");
    Walker = start;
    while (Walker->next != end) {
      Walker = Walker->next;
    //for (i=0;i<AtomCount;i++) {
      Distances[Walker->nr] = CenterOfGravity.Distance(&Walker->x);
    }
    Walker = OtherMolecule->start;
    while (Walker->next != OtherMolecule->end) {
      Walker = Walker->next;
      OtherDistances[Walker->nr] = OtherCenterOfGravity.Distance(&Walker->x);
    }
  
    /// ... sort each list (using heapsort (o(N log N)) from GSL)
    *out << Verbose(5) << "Sorting distances" << endl;
    PermMap = (size_t *) Malloc(sizeof(size_t)*AtomCount, "molecule::IsEqualToWithinThreshold: *PermMap");
    OtherPermMap = (size_t *) Malloc(sizeof(size_t)*AtomCount, "molecule::IsEqualToWithinThreshold: *OtherPermMap");
    gsl_heapsort_index (PermMap, Distances, AtomCount, sizeof(double), CompareDoubles);
    gsl_heapsort_index (OtherPermMap, OtherDistances, AtomCount, sizeof(double), CompareDoubles);
    PermutationMap = (int *) Malloc(sizeof(int)*AtomCount, "molecule::IsEqualToWithinThreshold: *PermutationMap");
    *out << Verbose(5) << "Combining Permutation Maps" << endl;
    for(int i=0;i<AtomCount;i++)
      PermutationMap[PermMap[i]] = (int) OtherPermMap[i];
    
    /// ... and compare them step by step, whether the difference is individiually(!) below \a threshold for all
    *out << Verbose(4) << "Comparing distances" << endl;
    flag = 0;
    for (int i=0;i<AtomCount;i++) {
      *out << Verbose(5) << "Distances: |" << Distances[PermMap[i]] << " - " << OtherDistances[OtherPermMap[i]] << "| = " << fabs(Distances[PermMap[i]] - OtherDistances[OtherPermMap[i]]) << " ?<? " <<  threshold << endl;
      if (fabs(Distances[PermMap[i]] - OtherDistances[OtherPermMap[i]]) > threshold)
        flag = 1;
    }
    Free((void **)&PermMap, "molecule::IsEqualToWithinThreshold: *PermMap");
    Free((void **)&OtherPermMap, "molecule::IsEqualToWithinThreshold: *OtherPermMap");
      
    /// free memory
    Free((void **)&Distances, "molecule::IsEqualToWithinThreshold: Distances");
    Free((void **)&OtherDistances, "molecule::IsEqualToWithinThreshold: OtherDistances");
    if (flag) { // if not equal
      Free((void **)&PermutationMap, "molecule::IsEqualToWithinThreshold: *PermutationMap");
      result = false;
    }
  } 
  /// return pointer to map if all distances were below \a threshold
  *out << Verbose(3) << "End of IsEqualToWithinThreshold." << endl;
  if (result) {
    *out << Verbose(3) << "Result: Equal." << endl;
    return PermutationMap;
  } else {
    *out << Verbose(3) << "Result: Not equal." << endl;
    return NULL;
  } 
};

/** Returns an index map for two father-son-molecules.
 * The map tells which atom in this molecule corresponds to which one in the other molecul with their fathers.
 * \param *out output stream for debugging
 * \param *OtherMolecule corresponding molecule with fathers
 * \return allocated map of size molecule::AtomCount with map
 * \todo make this with a good sort O(n), not O(n^2)
 */
int * molecule::GetFatherSonAtomicMap(ofstream *out, molecule *OtherMolecule)
{
  atom *Walker = NULL, *OtherWalker = NULL;
  *out << Verbose(3) << "Begin of GetFatherAtomicMap." << endl;
  int *AtomicMap = (int *) Malloc(sizeof(int)*AtomCount, "molecule::GetAtomicMap: *AtomicMap");  //Calloc
  for (int i=0;i<AtomCount;i++)
    AtomicMap[i] = -1;
  if (OtherMolecule == this) {  // same molecule
    for (int i=0;i<AtomCount;i++) // no need as -1 means already that there is trivial correspondence
      AtomicMap[i] = i;
    *out << Verbose(4) << "Map is trivial." << endl;
  } else {
    *out << Verbose(4) << "Map is ";
    Walker = start;
    while (Walker->next != end) {
      Walker = Walker->next;
      if (Walker->father == NULL) {
        AtomicMap[Walker->nr] = -2;
      } else {
        OtherWalker = OtherMolecule->start;
        while (OtherWalker->next != OtherMolecule->end) {
          OtherWalker = OtherWalker->next;
      //for (int i=0;i<AtomCount;i++) { // search atom
        //for (int j=0;j<OtherMolecule->AtomCount;j++) {
          //*out << Verbose(4) << "Comparing father " << Walker->father << " with the other one " << OtherWalker->father << "." << endl;
          if (Walker->father == OtherWalker)
            AtomicMap[Walker->nr] = OtherWalker->nr;
        }
      }
      *out << AtomicMap[Walker->nr] << "\t";
    }
    *out << endl;
  }
  *out << Verbose(3) << "End of GetFatherAtomicMap." << endl;
  return AtomicMap;
};