source: src/molecule.hpp@ ce4487

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Last change on this file since ce4487 was ce4487, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Merge branch 'MenuRefactoring' into QT4Refactoring
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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 "types.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#include "Descriptors/MoleculeDescriptor_impl.hpp"
40
41/****************************************** forward declarations *****************************/
42
43class atom;
44class bond;
45class BondedParticle;
46class BondGraph;
47class element;
48class ForceMatrix;
49class LinkedCell;
50class molecule;
51class MoleculeLeafClass;
52class MoleculeListClass;
53class periodentafel;
54class Vector;
55
56/******************************** Some definitions for easier reading **********************************/
57
58#define MoleculeList list <molecule *>
59#define MoleculeListTest pair <MoleculeList::iterator, bool>
60
61#define DistancePair pair < double, atom* >
62#define DistanceMap multimap < double, atom* >
63#define DistanceTestPair pair < DistanceMap::iterator, bool>
64
65
66/************************************* Class definitions ****************************************/
67
68/** Structure to contain parameters needed for evaluation of constraint potential.
69 */
70struct EvaluatePotential
71{
72 int startstep; //!< start configuration (MDStep in atom::trajectory)
73 int endstep; //!< end configuration (MDStep in atom::trajectory)
74 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
75 DistanceMap **DistanceList; //!< distance list of each atom to each atom
76 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
77 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
78 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
79 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
80 double *PenaltyConstants; //!< penalty constant in front of each term
81};
82
83#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
84enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
85
86
87/** The complete molecule.
88 * Class incorporates number of types
89 */
90class molecule : public PointCloud , public Observable {
91 friend molecule *NewMolecule();
92 friend void DeleteMolecule(molecule *);
93
94 public:
95 typedef std::list<atom*> atomSet;
96 typedef std::set<atomId_t> atomIdSet;
97 typedef ObservedIterator<atomSet> iterator;
98 typedef atomSet::const_iterator const_iterator;
99
100 const periodentafel * const elemente; //!< periodic table with each element
101 // old deprecated atom handling
102 //atom *start; //!< start of atom list
103 //atom *end; //!< end of atom list
104 //bond *first; //!< start of bond list
105 //bond *last; //!< end of bond list
106 int MDSteps; //!< The number of MD steps in Trajectories
107 //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
108 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
109 int ElementCount; //!< how many unique elements are therein
110 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
111 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
112 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
113 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
114 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
115 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
116 Vector Center; //!< Center of molecule in a global box
117 int IndexNr; //!< index of molecule in a MoleculeListClass
118 char name[MAXSTRINGSIZE]; //!< arbitrary name
119
120 private:
121 Cacheable<string> formula;
122 Cacheable<int> AtomCount;
123 moleculeId_t id;
124 atomSet atoms; //<!list of atoms
125 atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
126 protected:
127 //void CountAtoms();
128 /**
129 * this iterator type should be used for internal variables, \
130 * since it will not lock
131 */
132 typedef atomSet::iterator internal_iterator;
133
134
135 molecule(const periodentafel * const teil);
136 virtual ~molecule();
137
138
139public:
140 //getter and setter
141 const std::string getName();
142 int getAtomCount() const;
143 int doCountAtoms();
144 moleculeId_t getId();
145 void setId(moleculeId_t);
146 void setName(const std::string);
147 const std::string getFormula();
148 std::string calcFormula();
149
150 iterator begin();
151 const_iterator begin() const;
152 iterator end();
153 const_iterator end() const;
154 bool empty() const;
155 size_t size() const;
156 const_iterator erase( const_iterator loc );
157 const_iterator erase( atom * key );
158 const_iterator find ( atom * key ) const;
159 pair<iterator,bool> insert ( atom * const key );
160 bool containsAtom(atom* key);
161
162
163 // re-definition of virtual functions from PointCloud
164 const char * const GetName() const;
165 Vector *GetCenter() const ;
166 TesselPoint *GetPoint() const ;
167 int GetMaxId() const;
168 void GoToNext() const ;
169 void GoToFirst() const ;
170 bool IsEmpty() const ;
171 bool IsEnd() const ;
172
173 // templates for allowing global manipulation of all vectors
174 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
175 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
176 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
177 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
178 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&), T &t ) const;
179 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&) const, T &t ) const;
180 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
181 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
182 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
183 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;
184
185 // templates for allowing global manipulation of molecule with each atom as single argument
186 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
187 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
188
189 // templates for allowing global copying of molecule with each atom as single argument
190 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
191 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
192
193 // templates for allowing global manipulation of all atoms
194 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
195 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
196 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
197 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
198 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
199 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
200 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;
201 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;
202 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;
203 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;
204
205 // templates for allowing conditional global copying of molecule with each atom as single argument
206 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
207 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
208 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
209 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
210 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
211 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
212 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
213 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
214 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;
215 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;
216 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;
217 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;
218 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;
219 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;
220 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;
221 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;
222
223 // templates for allowing global manipulation of an array with one entry per atom
224 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
225 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
226 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
227 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
228 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
229 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
230 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
231 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
232 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
233 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
234 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
235
236 // templates for allowing global manipulation of each atom by entries in an array
237 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
238 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
239
240 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
241 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
242 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
243 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
244
245 /// remove atoms from molecule.
246 bool AddAtom(atom *pointer);
247 bool RemoveAtom(atom *pointer);
248 bool UnlinkAtom(atom *pointer);
249 bool CleanupMolecule();
250
251 /// Add/remove atoms to/from molecule.
252 atom * AddCopyAtom(atom *pointer);
253 bool AddXYZFile(string filename);
254 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
255 bond * AddBond(atom *first, atom *second, int degree = 1);
256 bool RemoveBond(bond *pointer);
257 bool RemoveBonds(atom *BondPartner);
258 bool hasBondStructure();
259 unsigned int CountBonds() const;
260
261 /// Find atoms.
262 atom * FindAtom(int Nr) const;
263 atom * AskAtom(string text);
264
265 /// Count and change present atoms' coordination.
266 void CountElements();
267 void CalculateOrbitals(class config &configuration);
268 bool CenterInBox();
269 bool BoundInBox();
270 void CenterEdge(Vector *max);
271 void CenterOrigin();
272 void CenterPeriodic();
273 void CenterAtVector(Vector *newcenter);
274 void Translate(const Vector *x);
275 void TranslatePeriodically(const Vector *trans);
276 void Mirror(const Vector *x);
277 void Align(Vector *n);
278 void Scale(const double ** const factor);
279 void DeterminePeriodicCenter(Vector &center);
280 Vector * DetermineCenterOfGravity();
281 Vector * DetermineCenterOfAll() const;
282 Vector * DetermineCenterOfBox() const;
283 void SetNameFromFilename(const char *filename);
284 void SetBoxDimension(Vector *dim);
285 void ScanForPeriodicCorrection();
286 bool VerletForceIntegration(char *file, config &configuration);
287 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
288 void PrincipalAxisSystem(bool DoRotate);
289 double VolumeOfConvexEnvelope(bool IsAngstroem);
290
291 double ConstrainedPotential(struct EvaluatePotential &Params);
292 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
293 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
294 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
295
296 bool CheckBounds(const Vector *x) const;
297 void GetAlignvector(struct lsq_params * par) const;
298
299 /// Initialising routines in fragmentation
300 void CreateAdjacencyListFromDbondFile(ifstream *output);
301 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
302 int CorrectBondDegree() const;
303 void OutputBondsList() const;
304 void CyclicBondAnalysis() const;
305 void OutputGraphInfoPerAtom() const;
306 void OutputGraphInfoPerBond() const;
307
308
309 // Graph analysis
310 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
311 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
312 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
313 bond * FindNextUnused(atom *vertex) const;
314 void SetNextComponentNumber(atom *vertex, int nr) const;
315 void ResetAllBondsToUnused() const;
316 int CountCyclicBonds();
317 bool CheckForConnectedSubgraph(KeySet *Fragment);
318 string GetColor(enum Shading color) const;
319 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
320
321
322 molecule *CopyMolecule();
323 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
324
325 /// Fragment molecule by two different approaches:
326 int FragmentMolecule(int Order, config *configuration);
327 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
328 bool StoreBondsToFile(char *path, char *filename);
329 bool StoreAdjacencyToFile(char *path, char *filename);
330 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
331 bool ParseOrderAtSiteFromFile(char *path);
332 bool StoreOrderAtSiteFile(char *path);
333 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
334 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
335 bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
336 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
337 /// -# BOSSANOVA
338 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
339 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
340 bool BuildInducedSubgraph(const molecule *Father);
341 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
342 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
343 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
344 int GuesstimateFragmentCount(int order);
345
346 // Recognize doubly appearing molecules in a list of them
347 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
348 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
349
350 // Output routines.
351 bool Output(ofstream * const output);
352 bool OutputTrajectories(ofstream * const output);
353 void OutputListOfBonds() const;
354 bool OutputXYZ(ofstream * const output) const;
355 bool OutputTrajectoriesXYZ(ofstream * const output);
356 bool Checkout(ofstream * const output) const;
357 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
358
359 // Manipulation routines
360 void flipActiveFlag();
361
362 private:
363 int last_atom; //!< number given to last atom
364 mutable internal_iterator InternalPointer; //!< internal pointer for PointCloud
365};
366
367molecule *NewMolecule();
368void DeleteMolecule(molecule* mol);
369
370#include "molecule_template.hpp"
371
372/** A list of \a molecule classes.
373 */
374class MoleculeListClass : public Observable {
375 public:
376 MoleculeList ListOfMolecules; //!< List of the contained molecules
377 int MaxIndex;
378
379 MoleculeListClass(World *world);
380 ~MoleculeListClass();
381
382 bool AddHydrogenCorrection(char *path);
383 bool StoreForcesFile(char *path, int *SortIndex);
384 void insert(molecule *mol);
385 void erase(molecule *mol);
386 molecule * ReturnIndex(int index);
387 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
388 int NumberOfActiveMolecules();
389 void Enumerate(ostream *out);
390 void Output(ofstream *out);
391 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
392 int CountAllAtoms() const;
393
394 // Methods moved here from the menus
395 // TODO: more refactoring needed on these methods
396 void flipChosen();
397 void createNewMolecule(periodentafel *periode);
398 void loadFromXYZ(periodentafel *periode);
399 void setMoleculeFilename();
400 void parseXYZIntoMolecule();
401 void eraseMolecule();
402
403
404 // merging of molecules
405 bool SimpleMerge(molecule *mol, molecule *srcmol);
406 bool SimpleAdd(molecule *mol, molecule *srcmol);
407 bool SimpleMultiMerge(molecule *mol, int *src, int N);
408 bool SimpleMultiAdd(molecule *mol, int *src, int N);
409 bool ScatterMerge(molecule *mol, int *src, int N);
410 bool EmbedMerge(molecule *mol, molecule *srcmol);
411
412 private:
413 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
414};
415
416
417/** A leaf for a tree of \a molecule class
418 * Wraps molecules in a tree structure
419 */
420class MoleculeLeafClass {
421 public:
422 molecule *Leaf; //!< molecule of this leaf
423 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
424 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
425 MoleculeLeafClass *previous; //!< Previous leaf on this level
426 MoleculeLeafClass *next; //!< Next leaf on this level
427
428 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
429 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
430 ~MoleculeLeafClass();
431
432 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
433 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
434 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
435 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
436 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
437 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
438 int Count() const;
439};
440
441
442#endif /*MOLECULES_HPP_*/
443
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