source: src/molecule.hpp@ 05a97c

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Last change on this file since 05a97c was c72112, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Repaired GetMAxId() method of molecule
  • Property mode set to 100755
File size: 22.0 KB
Line 
1/** \file molecule.hpp
2 *
3 * Class definitions of atom and molecule, element and periodentafel
4 */
5
6#ifndef MOLECULES_HPP_
7#define MOLECULES_HPP_
8
9using namespace std;
10
11/*********************************************** includes ***********************************/
12
13// GSL headers
14#include <gsl/gsl_eigen.h>
15#include <gsl/gsl_heapsort.h>
16#include <gsl/gsl_linalg.h>
17#include <gsl/gsl_matrix.h>
18#include <gsl/gsl_multimin.h>
19#include <gsl/gsl_vector.h>
20#include <gsl/gsl_randist.h>
21
22//// STL headers
23#include <map>
24#include <set>
25#include <deque>
26#include <list>
27#include <vector>
28
29#include <string>
30
31#include "defs.hpp"
32#include "graph.hpp"
33#include "stackclass.hpp"
34#include "tesselation.hpp"
35#include "Patterns/Observer.hpp"
36#include "Patterns/ObservedIterator.hpp"
37#include "Patterns/Cacheable.hpp"
38
39/****************************************** forward declarations *****************************/
40
41class atom;
42class bond;
43class BondedParticle;
44class BondGraph;
45class element;
46class ForceMatrix;
47class LinkedCell;
48class molecule;
49class MoleculeLeafClass;
50class MoleculeListClass;
51class periodentafel;
52class Vector;
53
54/******************************** Some definitions for easier reading **********************************/
55
56#define MoleculeList list <molecule *>
57#define MoleculeListTest pair <MoleculeList::iterator, bool>
58
59#define DistancePair pair < double, atom* >
60#define DistanceMap multimap < double, atom* >
61#define DistanceTestPair pair < DistanceMap::iterator, bool>
62
63
64/************************************* Class definitions ****************************************/
65
66/** Structure to contain parameters needed for evaluation of constraint potential.
67 */
68struct EvaluatePotential
69{
70 int startstep; //!< start configuration (MDStep in atom::trajectory)
71 int endstep; //!< end configuration (MDStep in atom::trajectory)
72 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
73 DistanceMap **DistanceList; //!< distance list of each atom to each atom
74 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
75 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
76 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
77 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
78 double *PenaltyConstants; //!< penalty constant in front of each term
79};
80
81#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
82enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
83
84
85/** The complete molecule.
86 * Class incorporates number of types
87 */
88class molecule : public PointCloud , public Observable {
89 friend molecule *NewMolecule();
90 friend void DeleteMolecule(molecule *);
91
92 public:
93 typedef std::set<atom*> atomSet;
94 typedef ObservedIterator<atomSet> iterator;
95 typedef atomSet::const_iterator const_iterator;
96
97 double cell_size[6];//!< cell size
98 const periodentafel * const elemente; //!< periodic table with each element
99 // old deprecated atom handling
100 //atom *start; //!< start of atom list
101 //atom *end; //!< end of atom list
102 bond *first; //!< start of bond list
103 bond *last; //!< end of bond list
104 int MDSteps; //!< The number of MD steps in Trajectories
105 //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
106 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
107 int ElementCount; //!< how many unique elements are therein
108 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
109 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
110 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
111 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
112 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
113 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
114 Vector Center; //!< Center of molecule in a global box
115 int IndexNr; //!< index of molecule in a MoleculeListClass
116 char name[MAXSTRINGSIZE]; //!< arbitrary name
117
118 private:
119 Cacheable<string> formula;
120 Cacheable<int> AtomCount;
121 moleculeId_t id;
122 atomSet atoms; //<!set of atoms
123 protected:
124 //void CountAtoms();
125 /**
126 * this iterator type should be used for internal variables, \
127 * since it will not lock
128 */
129 typedef atomSet::iterator internal_iterator;
130
131
132 molecule(const periodentafel * const teil);
133 virtual ~molecule();
134
135
136public:
137 //getter and setter
138 const std::string getName();
139 int getAtomCount() const;
140 int doCountAtoms();
141 moleculeId_t getId();
142 void setId(moleculeId_t);
143 void setName(const std::string);
144 const std::string getFormula();
145 std::string calcFormula();
146
147 iterator begin();
148 const_iterator begin() const;
149 iterator end();
150 const_iterator end() const;
151 bool empty() const;
152 size_t size() const;
153 const_iterator erase( const_iterator loc );
154 const_iterator erase( atom *& key );
155 const_iterator find ( atom *& key ) const;
156 pair<iterator,bool> insert ( atom * const key );
157
158
159 // re-definition of virtual functions from PointCloud
160 const char * const GetName() const;
161 Vector *GetCenter() const ;
162 TesselPoint *GetPoint() const ;
163 int GetMaxId() const;
164 void GoToNext() const ;
165 void GoToFirst() const ;
166 bool IsEmpty() const ;
167 bool IsEnd() const ;
168
169 // templates for allowing global manipulation of all vectors
170 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
171 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
172 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
173 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
174 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
175 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
176 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
177 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v) const;
178
179 // templates for allowing global manipulation of molecule with each atom as single argument
180 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
181 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
182
183 // templates for allowing global copying of molecule with each atom as single argument
184 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
185 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
186
187 // templates for allowing global manipulation of all atoms
188 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
189 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
190 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
191 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
192 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
193 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
194 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V), T t, U u, V v) const;
195 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V) const, T t, U u, V v) const;
196 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W), T t, U u, V v, W w) const;
197 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W) const, T t, U u, V v, W w) const;
198
199 // templates for allowing conditional global copying of molecule with each atom as single argument
200 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
201 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
202 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
203 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
204 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
205 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
206 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
207 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
208 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
209 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
210 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
211 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
212 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
213 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
214 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
215 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
216
217 // templates for allowing global manipulation of an array with one entry per atom
218 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
219 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
220 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
221 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
222 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
223 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
224 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
225 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
226 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
227 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
228 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
229
230 // templates for allowing global manipulation of each atom by entries in an array
231 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
232 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
233
234 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
235 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
236 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
237 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
238
239 /// remove atoms from molecule.
240 bool AddAtom(atom *pointer);
241 bool RemoveAtom(atom *pointer);
242 bool UnlinkAtom(atom *pointer);
243 bool CleanupMolecule();
244
245 /// Add/remove atoms to/from molecule.
246 atom * AddCopyAtom(atom *pointer);
247 bool AddXYZFile(string filename);
248 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
249 bond * AddBond(atom *first, atom *second, int degree = 1);
250 bool RemoveBond(bond *pointer);
251 bool RemoveBonds(atom *BondPartner);
252
253 /// Find atoms.
254 atom * FindAtom(int Nr) const;
255 atom * AskAtom(string text);
256
257 /// Count and change present atoms' coordination.
258 void CountElements();
259 void CalculateOrbitals(class config &configuration);
260 bool CenterInBox();
261 bool BoundInBox();
262 void CenterEdge(Vector *max);
263 void CenterOrigin();
264 void CenterPeriodic();
265 void CenterAtVector(Vector *newcenter);
266 void Translate(const Vector *x);
267 void TranslatePeriodically(const Vector *trans);
268 void Mirror(const Vector *x);
269 void Align(Vector *n);
270 void Scale(const double ** const factor);
271 void DeterminePeriodicCenter(Vector &center);
272 Vector * DetermineCenterOfGravity();
273 Vector * DetermineCenterOfAll() const;
274 void SetNameFromFilename(const char *filename);
275 void SetBoxDimension(Vector *dim);
276 void ScanForPeriodicCorrection();
277 bool VerletForceIntegration(char *file, config &configuration);
278 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
279 void PrincipalAxisSystem(bool DoRotate);
280 double VolumeOfConvexEnvelope(bool IsAngstroem);
281
282 double ConstrainedPotential(struct EvaluatePotential &Params);
283 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
284 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
285 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
286
287 bool CheckBounds(const Vector *x) const;
288 void GetAlignvector(struct lsq_params * par) const;
289
290 /// Initialising routines in fragmentation
291 void CreateAdjacencyListFromDbondFile(ifstream *output);
292 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
293 int CorrectBondDegree() const;
294 void OutputBondsList() const;
295 void CyclicBondAnalysis() const;
296 void OutputGraphInfoPerAtom() const;
297 void OutputGraphInfoPerBond() const;
298
299
300 // Graph analysis
301 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
302 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
303 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
304 bond * FindNextUnused(atom *vertex) const;
305 void SetNextComponentNumber(atom *vertex, int nr) const;
306 void ResetAllBondsToUnused() const;
307 int CountCyclicBonds();
308 bool CheckForConnectedSubgraph(KeySet *Fragment);
309 string GetColor(enum Shading color) const;
310 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
311
312
313 molecule *CopyMolecule();
314 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
315
316 /// Fragment molecule by two different approaches:
317 int FragmentMolecule(int Order, config *configuration);
318 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
319 bool StoreBondsToFile(char *path);
320 bool StoreAdjacencyToFile(char *path);
321 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
322 bool ParseOrderAtSiteFromFile(char *path);
323 bool StoreOrderAtSiteFile(char *path);
324 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
325 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
326 bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
327 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
328 /// -# BOSSANOVA
329 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
330 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
331 bool BuildInducedSubgraph(const molecule *Father);
332 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
333 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
334 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
335 int GuesstimateFragmentCount(int order);
336
337 // Recognize doubly appearing molecules in a list of them
338 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
339 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
340
341 // Output routines.
342 bool Output(ofstream * const output);
343 bool OutputTrajectories(ofstream * const output);
344 void OutputListOfBonds() const;
345 bool OutputXYZ(ofstream * const output) const;
346 bool OutputTrajectoriesXYZ(ofstream * const output);
347 bool Checkout(ofstream * const output) const;
348 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
349
350 // Manipulation routines
351 void flipActiveFlag();
352
353 private:
354 int last_atom; //!< number given to last atom
355 mutable internal_iterator InternalPointer; //!< internal pointer for PointCloud
356};
357
358molecule *NewMolecule();
359void DeleteMolecule(molecule* mol);
360
361#include "molecule_template.hpp"
362
363/** A list of \a molecule classes.
364 */
365class MoleculeListClass : public Observable {
366 public:
367 MoleculeList ListOfMolecules; //!< List of the contained molecules
368 int MaxIndex;
369
370 MoleculeListClass(World *world);
371 ~MoleculeListClass();
372
373 bool AddHydrogenCorrection(char *path);
374 bool StoreForcesFile(char *path, int *SortIndex);
375 void insert(molecule *mol);
376 molecule * ReturnIndex(int index);
377 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
378 int NumberOfActiveMolecules();
379 void Enumerate(ostream *out);
380 void Output(ofstream *out);
381 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
382 int CountAllAtoms() const;
383
384 // Methods moved here from the menus
385 // TODO: more refactoring needed on these methods
386 void flipChosen();
387 void createNewMolecule(periodentafel *periode);
388 void loadFromXYZ(periodentafel *periode);
389 void setMoleculeFilename();
390 void parseXYZIntoMolecule();
391 void eraseMolecule();
392
393
394 // merging of molecules
395 bool SimpleMerge(molecule *mol, molecule *srcmol);
396 bool SimpleAdd(molecule *mol, molecule *srcmol);
397 bool SimpleMultiMerge(molecule *mol, int *src, int N);
398 bool SimpleMultiAdd(molecule *mol, int *src, int N);
399 bool ScatterMerge(molecule *mol, int *src, int N);
400 bool EmbedMerge(molecule *mol, molecule *srcmol);
401
402 private:
403 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
404};
405
406
407/** A leaf for a tree of \a molecule class
408 * Wraps molecules in a tree structure
409 */
410class MoleculeLeafClass {
411 public:
412 molecule *Leaf; //!< molecule of this leaf
413 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
414 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
415 MoleculeLeafClass *previous; //!< Previous leaf on this level
416 MoleculeLeafClass *next; //!< Next leaf on this level
417
418 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
419 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
420 ~MoleculeLeafClass();
421
422 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
423 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
424 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
425 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
426 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
427 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
428 int Count() const;
429};
430
431
432#endif /*MOLECULES_HPP_*/
433
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