Changeset fa649a


Ignore:
Timestamp:
Nov 2, 2009, 12:50:57 PM (15 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
7218f8
Parents:
34e0013
Message:

Small changes.

Location:
src
Files:
8 edited

Legend:

Unmodified
Added
Removed

  • src/boundary.cpp

    r34e0013 rfa649a  
    649649      const double h = x.Norm(); // distance of CoG to triangle
    650650      const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
    651       *out << Verbose(2) << "Area of triangle is " << G << " "
     651      *out << Verbose(2) << "Area of triangle is " << setprecision(10) << G << " "
    652652          << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
    653653          << h << " and the volume is " << PyramidVolume << " "
    … …  
    655655      volume += PyramidVolume;
    656656    }
    657   *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(10)
     657  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(8)
    658658      << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3."
    659659      << endl;
    … …  
    705705void PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol, double ClusterVolume, double celldensity)
    706706{
    707   bool IsAngstroem = NULL;
     707  bool IsAngstroem = true;
    708708  double *GreatestDiameter = NULL;
    709709  Boundaries *BoundaryPoints = NULL;

  • src/builder.cpp

    r34e0013 rfa649a  
    14541454    if (argv[1][0] != '-') {
    14551455      // simply create a new molecule, wherein the config file is loaded and the manipulation takes place
    1456       mol = new molecule(periode);
    1457       mol->ActiveFlag = true;
    1458       molecules->insert(mol);
    1459 
    14601456      cout << Verbose(0) << "Config file given." << endl;
    14611457      test.open(argv[1], ios::in);
    … …  
    14761472        ConfigFileName = argv[1];
    14771473        cout << Verbose(1) << "Specified config file found, parsing ... ";
    1478         switch (configuration.TestSyntax(ConfigFileName, periode, mol)) {
     1474        switch (configuration.TestSyntax(ConfigFileName, periode)) {
    14791475          case 1:
    14801476            cout << "new syntax." << endl;
    1481             configuration.Load(ConfigFileName, BondGraphFileName, periode, mol);
     1477            configuration.Load(ConfigFileName, BondGraphFileName, periode, molecules);
    14821478            configPresent = present;
    14831479            break;
    14841480          case 0:
    14851481            cout << "old syntax." << endl;
    1486             configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, mol);
     1482            configuration.LoadOld(ConfigFileName, BondGraphFileName, periode, molecules);
    14871483            configPresent = present;
    14881484            break;
    … …  
    14941490    } else
    14951491      configPresent = absent;
     1492     // set mol to first active molecule
     1493     if (molecules->ListOfMolecules.size() != 0) {
     1494       for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
     1495         if ((*ListRunner)->ActiveFlag) {
     1496           mol = *ListRunner;
     1497           break;
     1498         }
     1499     }
     1500     if (mol == NULL) {
     1501       mol = new molecule(periode);
     1502       mol->ActiveFlag = true;
     1503       molecules->insert(mol);
     1504     }
     1505
    14961506    // 4. parse again through options, now for those depending on elements db and config presence
    14971507    argptr = 1;

  • src/config.cpp

    r34e0013 rfa649a  
    99#include "element.hpp"
    1010#include "helpers.hpp"
     11#include "lists.hpp"
    1112#include "molecule.hpp"
    1213#include "memoryallocator.hpp"
    … …  
    565566 * \param *filename filename of config file to be tested
    566567 * \param *periode pointer to a periodentafel class with all elements
    567  * \param *mol pointer to molecule containing all atoms of the molecule
    568568 * \return 0 - old syntax, 1 - new syntax, -1 - unknown syntax
    569569 */
    570 int config::TestSyntax(const char * const filename, const periodentafel * const periode, const molecule * const mol) const
     570int config::TestSyntax(const char * const filename, const periodentafel * const periode) const
    571571{
    572572  int test;
    … …  
    833833 * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
    834834 * \param *periode pointer to a periodentafel class with all elements
    835  * \param *mol pointer to molecule containing all atoms of the molecule
    836  */
    837 void config::Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
     835 * \param *&MolList pointer to MoleculeListClass, on return containing all parsed molecules in system
     836 */
     837void config::Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList)
    838838{
     839  molecule *mol = new molecule(periode);
    839840  ifstream *file = new ifstream(filename);
    840841  if (file == NULL) {
    … …  
    10521053  // 3. parse the molecule in
    10531054  LoadMolecule(mol, FileBuffer, periode, FastParsing);
     1055  mol->ActiveFlag = true;
     1056  MolList->insert(mol);
    10541057
    10551058  // 4. dissect the molecule into connected subgraphs
    … …  
    10631066 * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
    10641067 * \param *periode pointer to a periodentafel class with all elements
    1065  * \param *mol pointer to molecule containing all atoms of the molecule
    1066  */
    1067 void config::LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
     1068 * \param *&MolList pointer to MoleculeListClass, on return containing all parsed molecules in system
     1069 */
     1070void config::LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList)
    10681071{
     1072  molecule *mol = new molecule(periode);
    10691073  ifstream *file = new ifstream(filename);
    10701074  if (file == NULL) {
    … …  
    10911095  int verbose = 0;
    10921096
     1097  mol->ActiveFlag = true;
     1098  MolList->insert(mol);
    10931099  /* Namen einlesen */
    10941100

  • src/config.hpp

    r34e0013 rfa649a  
    1010
    1111using namespace std;
     12
     13class MoleculeListClass;
    1214
    1315/*********************************************** includes ***********************************/
    … …  
    134136  ~config();
    135137
    136   int TestSyntax(const char * const filename, const periodentafel * const periode, const molecule * const mol) const;
    137   void Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol);
    138   void LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol);
     138  int TestSyntax(const char * const filename, const periodentafel * const periode) const;
     139  void Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList);
     140  void LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, MoleculeListClass * const &MolList);
    139141  void RetrieveConfigPathAndName(const string filename);
    140142  bool Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const;

  • src/molecule.cpp

    r34e0013 rfa649a  
    2626 * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
    2727 */
    28 molecule::molecule(periodentafel *teil)
     28molecule::molecule(const periodentafel * const teil) : elemente(teil), start(new atom), end(new atom),
     29  first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0),
     30  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.),
     31  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start)
    2932{
    3033  // init atom chain list
    31   start = new atom;
    32   end = new atom;
    3334  start->father = NULL;
    3435  end->father = NULL;
    3536  link(start,end);
    36   InternalPointer = start;
     37
    3738  // init bond chain list
    38   first = new bond(start, end, 1, -1);
    39   last = new bond(start, end, 1, -1);
    4039  link(first,last);
     40
    4141  // other stuff
    42   MDSteps = 0;
    43   last_atom = 0;
    44   elemente = teil;
    45   AtomCount = 0;
    46   BondCount = 0;
    47   NoNonBonds = 0;
    48   NoNonHydrogen = 0;
    49   NoCyclicBonds = 0;
    50   ElementCount = 0;
    5142  for(int i=MAX_ELEMENTS;i--;)
    5243    ElementsInMolecule[i] = 0;
    … …  
    5445  cell_size[1] = cell_size[3] = cell_size[4]= 0.;
    5546  strcpy(name,"none");
    56   IndexNr  = -1;
    57   ActiveFlag = false;
    5847};
    5948
    … …  
    555544};
    556545
    557 /** Remove bond from bond chain list.
     546/** Remove bond from bond chain list and from the both atom::ListOfBonds.
    558547 * \todo Function not implemented yet
    559548 * \param *pointer bond pointer
    … …  
    563552{
    564553  //cerr << Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl;
     554  pointer->leftatom->RegisterBond(pointer);
     555  pointer->rightatom->RegisterBond(pointer);
    565556  removewithoutcheck(pointer);
    566557  return true;

  • src/molecule.hpp

    r34e0013 rfa649a  
    8383  public:
    8484    double cell_size[6];//!< cell size
    85     periodentafel *elemente; //!< periodic table with each element
     85    const periodentafel * const elemente; //!< periodic table with each element
    8686    atom *start;        //!< start of atom list
    8787    atom *end;          //!< end of atom list
    … …  
    9393    int ElementCount;       //!< how many unique elements are therein
    9494    int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
    95     int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
    96     int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
    97     int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
     95    mutable int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
     96    mutable int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
     97    mutable int NoCyclicBonds;  //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
    9898    double BondDistance;  //!< typical bond distance used in CreateAdjacencyList() and furtheron
    9999    bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
    … …  
    102102    int IndexNr;        //!< index of molecule in a MoleculeListClass
    103103
    104   molecule(periodentafel *teil);
     104  molecule(const periodentafel * const teil);
    105105  virtual ~molecule();
    106106
    … …  
    241241  void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
    242242  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
    243   int CorrectBondDegree(ofstream *out);
    244   void OutputBondsList(ofstream *out);
    245   void CyclicBondAnalysis();
    246   void OutputGraphInfoPerAtom(ofstream *out);
    247   void OutputGraphInfoPerBond(ofstream *out);
     243  int CorrectBondDegree(ofstream *out) const;
     244  void OutputBondsList(ofstream *out) const;
     245  void CyclicBondAnalysis() const;
     246  void OutputGraphInfoPerAtom(ofstream *out) const;
     247  void OutputGraphInfoPerBond(ofstream *out) const;
    248248
    249249
    250250  // Graph analysis
    251   MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack);
    252   void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
    253   bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack);
    254   bond * FindNextUnused(atom *vertex);
    255   void SetNextComponentNumber(atom *vertex, int nr);
    256   void InitComponentNumbers();
    257   void ResetAllBondsToUnused();
     251  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack) const;
     252  void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
     253  bool PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
     254  bond * FindNextUnused(atom *vertex) const;
     255  void SetNextComponentNumber(atom *vertex, int nr) const;
     256  void ResetAllBondsToUnused() const;
    258257  int CountCyclicBonds(ofstream *out);
    259258  bool CheckForConnectedSubgraph(ofstream *out, KeySet *Fragment);
    260   string GetColor(enum Shading color);
     259  string GetColor(enum Shading color) const;
    261260  bond * CopyBond(atom *left, atom *right, bond *CopyBond);
    262261
    … …  
    351350
    352351  bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
    353   bool FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
     352  bool FillBondStructureFromReference(ofstream *out, const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
    354353  bool FillRootStackForSubgraphs(ofstream *out, KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
    355354  bool AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);

  • src/molecule_graph.cpp

    r34e0013 rfa649a  
    190190 * \param output stream
    191191 */
    192 void molecule::OutputBondsList(ofstream *out)
     192void molecule::OutputBondsList(ofstream *out) const
    193193{
    194194  *out << Verbose(1) << endl << "From contents of bond chain list:";
    … …  
    210210 * \return number of bonds that could not be corrected
    211211 */
    212 int molecule::CorrectBondDegree(ofstream *out)
     212int molecule::CorrectBondDegree(ofstream *out) const
    213213{
    214214  int No = 0;
    … …  
    265265 * \return string of the flag
    266266 */
    267 string molecule::GetColor(enum Shading color)
     267string molecule::GetColor(enum Shading color) const
    268268{
    269269  switch (color) {
    … …  
    314314 * \param &DFS DFS accounting data
    315315 */
    316 void DepthFirstSearchAnalysis_ProbeAlongUnusedBond(ofstream *out, molecule *mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS)
     316void DepthFirstSearchAnalysis_ProbeAlongUnusedBond(ofstream *out, const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS)
    317317{
    318318  atom *OtherAtom = NULL;
    … …  
    357357 * \param &DFS DFS accounting data
    358358 */
    359 void DepthFirstSearchAnalysis_CheckForaNewComponent(ofstream *out, molecule *mol, atom *&Walker, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
     359void DepthFirstSearchAnalysis_CheckForaNewComponent(ofstream *out, const molecule * const mol, atom *&Walker, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
    360360{
    361361  atom *OtherAtom = NULL;
    … …  
    403403 * \param &DFS DFS accounting data
    404404 */
    405 void DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(ofstream *out, molecule *mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
     405void DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(ofstream *out, const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
    406406{
    407407  atom *OtherAtom = NULL;
    … …  
    467467 * \return list of each disconnected subgraph as an individual molecule class structure
    468468 */
    469 MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack)
     469MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack) const
    470470{
    471471  struct DFSAccounting DFS;
    … …  
    548548/** Scans through all bonds and set bond::Cyclic to true where atom::LowpointNr of both ends is equal: LP criterion.
    549549 */
    550 void molecule::CyclicBondAnalysis()
     550void molecule::CyclicBondAnalysis() const
    551551{
    552552  NoCyclicBonds = 0;
    … …  
    565565 * \param *out output stream
    566566 */
    567 void molecule::OutputGraphInfoPerAtom(ofstream *out)
     567void molecule::OutputGraphInfoPerAtom(ofstream *out) const
    568568{
    569569  *out << Verbose(1) << "Final graph info for each atom is:" << endl;
    … …  
    575575 * \param *out output stream
    576576 */
    577 void molecule::OutputGraphInfoPerBond(ofstream *out)
     577void molecule::OutputGraphInfoPerBond(ofstream *out) const
    578578{
    579579  *out << Verbose(1) << "Final graph info for each bond is:" << endl;
    … …  
    829829 * \param *mol molecule with atoms
    830830 */
    831 void CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(ofstream *out, int *&MinimumRingSize, int &MinRingSize, int &NumCycles, molecule *mol)
     831void CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(ofstream *out, int *&MinimumRingSize, int &MinRingSize, int &NumCycles, const molecule * const mol)
    832832{
    833833  atom *Root = NULL;
    … …  
    864864 * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
    865865 */
    866 void molecule::CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> * BackEdgeStack, int *&MinimumRingSize)
     866void molecule::CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> * BackEdgeStack, int *&MinimumRingSize) const
    867867{
    868868  struct BFSAccounting BFS;
    … …  
    900900
    901901  CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(out, MinimumRingSize, MinRingSize, NumCycles, this);
    902 
    903 }
    904 ;
     902};
    905903
    906904/** Sets the next component number.
    … …  
    909907 * \param nr number to use
    910908 */
    911 void molecule::SetNextComponentNumber(atom *vertex, int nr)
     909void molecule::SetNextComponentNumber(atom *vertex, int nr) const
    912910{
    913911  size_t i = 0;
    … …  
    931929 * \return bond class or NULL
    932930 */
    933 bond * molecule::FindNextUnused(atom *vertex)
     931bond * molecule::FindNextUnused(atom *vertex) const
    934932{
    935933  for (BondList::const_iterator Runner = vertex->ListOfBonds.begin(); Runner != vertex->ListOfBonds.end(); (++Runner))
    … …  
    943941 * \return true - success, false - -failure
    944942 */
    945 void molecule::ResetAllBondsToUnused()
     943void molecule::ResetAllBondsToUnused() const
    946944{
    947945  bond *Binder = first;
    … …  
    11031101 * \return true - everything ok, false - ReferenceStack was empty
    11041102 */
    1105 bool molecule::PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack)
     1103bool molecule::PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const
    11061104{
    11071105  bool status = true;

  • src/moleculelist.cpp

    r34e0013 rfa649a  
    814814 * \return true - success, false - faoilure
    815815 */
    816 bool MoleculeLeafClass::FillBondStructureFromReference(ofstream *out, molecule *reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList)
     816bool MoleculeLeafClass::FillBondStructureFromReference(ofstream *out, const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList)
    817817{
    818818  atom *Walker = NULL;
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