source: src/molecule.hpp@ a25aae

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
Last change on this file since a25aae was a25aae, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring
  • Property mode set to 100755
File size: 20.7 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 "graph.hpp"
32#include "stackclass.hpp"
33#include "tesselation.hpp"
34#include "Patterns/Observer.hpp"
35
36/****************************************** forward declarations *****************************/
37
38class atom;
39class bond;
40class BondedParticle;
41class BondGraph;
42class element;
43class ForceMatrix;
44class LinkedCell;
45class molecule;
46class MoleculeLeafClass;
47class MoleculeListClass;
48class periodentafel;
49class Vector;
50
51/******************************** Some definitions for easier reading **********************************/
52
53#define MoleculeList list <molecule *>
54#define MoleculeListTest pair <MoleculeList::iterator, bool>
55
56#define DistancePair pair < double, atom* >
57#define DistanceMap multimap < double, atom* >
58#define DistanceTestPair pair < DistanceMap::iterator, bool>
59
60
61/************************************* Class definitions ****************************************/
62
63/** Structure to contain parameters needed for evaluation of constraint potential.
64 */
65struct EvaluatePotential
66{
67 int startstep; //!< start configuration (MDStep in atom::trajectory)
68 int endstep; //!< end configuration (MDStep in atom::trajectory)
69 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
70 DistanceMap **DistanceList; //!< distance list of each atom to each atom
71 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
72 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
73 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
74 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
75 double *PenaltyConstants; //!< penalty constant in front of each term
76};
77
78#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
79enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
80
81
82/** The complete molecule.
83 * Class incorporates number of types
84 */
85class molecule : public PointCloud , public Observable {
86 public:
87 double cell_size[6];//!< cell size
88 const periodentafel * const elemente; //!< periodic table with each element
89 atom *start; //!< start of atom list
90 atom *end; //!< end of atom list
91 bond *first; //!< start of bond list
92 bond *last; //!< end of bond list
93 int MDSteps; //!< The number of MD steps in Trajectories
94 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
95 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
96 int ElementCount; //!< how many unique elements are therein
97 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
98 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
99 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
100 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
101 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
102 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
103 Vector Center; //!< Center of molecule in a global box
104 int IndexNr; //!< index of molecule in a MoleculeListClass
105 char name[MAXSTRINGSIZE]; //!< arbitrary name
106
107public:
108 molecule(const periodentafel * const teil);
109 virtual ~molecule();
110
111 //getter and setter
112 const std::string getName();
113 void setName(const std::string);
114
115 // re-definition of virtual functions from PointCloud
116 const char * const GetName() const;
117 Vector *GetCenter() const ;
118 TesselPoint *GetPoint() const ;
119 TesselPoint *GetTerminalPoint() const ;
120 int GetMaxId() const;
121 void GoToNext() const ;
122 void GoToPrevious() const ;
123 void GoToFirst() const ;
124 void GoToLast() const ;
125 bool IsEmpty() const ;
126 bool IsEnd() const ;
127
128 // templates for allowing global manipulation of all vectors
129 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
130 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
131 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
132 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
133 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
134 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
135 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
136 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;
137
138 // templates for allowing global manipulation of molecule with each atom as single argument
139 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
140 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
141
142 // templates for allowing global copying of molecule with each atom as single argument
143 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
144 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
145
146 // templates for allowing global manipulation of all atoms
147 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
148 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
149 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
150 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
151 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
152 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
153 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;
154 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;
155 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;
156 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;
157
158 // templates for allowing conditional global copying of molecule with each atom as single argument
159 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
160 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
161 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
162 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
163 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
164 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
165 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
166 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
167 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;
168 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;
169 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;
170 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;
171 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;
172 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;
173 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;
174 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;
175
176 // templates for allowing global manipulation of an array with one entry per atom
177 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
178 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
179 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
180 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
181 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
182 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
183 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
184 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
185 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
186 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
187 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
188
189 // templates for allowing global manipulation of each atom by entries in an array
190 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
191 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
192
193 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
194 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
195 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
196 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
197
198 /// remove atoms from molecule.
199 bool AddAtom(atom *pointer);
200 bool RemoveAtom(atom *pointer);
201 bool UnlinkAtom(atom *pointer);
202 bool CleanupMolecule();
203
204 /// Add/remove atoms to/from molecule.
205 atom * AddCopyAtom(atom *pointer);
206 bool AddXYZFile(string filename);
207 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
208 bond * AddBond(atom *first, atom *second, int degree = 1);
209 bool RemoveBond(bond *pointer);
210 bool RemoveBonds(atom *BondPartner);
211
212 /// Find atoms.
213 atom * FindAtom(int Nr) const;
214 atom * AskAtom(string text);
215
216 /// Count and change present atoms' coordination.
217 void CountAtoms();
218 void CountElements();
219 void CalculateOrbitals(class config &configuration);
220 bool CenterInBox();
221 bool BoundInBox();
222 void CenterEdge(Vector *max);
223 void CenterOrigin();
224 void CenterPeriodic();
225 void CenterAtVector(Vector *newcenter);
226 void Translate(const Vector *x);
227 void TranslatePeriodically(const Vector *trans);
228 void Mirror(const Vector *x);
229 void Align(Vector *n);
230 void Scale(const double ** const factor);
231 void DeterminePeriodicCenter(Vector &center);
232 Vector * DetermineCenterOfGravity();
233 Vector * DetermineCenterOfAll() const;
234 void SetNameFromFilename(const char *filename);
235 void SetBoxDimension(Vector *dim);
236 void ScanForPeriodicCorrection();
237 bool VerletForceIntegration(char *file, config &configuration);
238 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
239 void PrincipalAxisSystem(bool DoRotate);
240 double VolumeOfConvexEnvelope(bool IsAngstroem);
241
242 double ConstrainedPotential(struct EvaluatePotential &Params);
243 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
244 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
245 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
246
247 bool CheckBounds(const Vector *x) const;
248 void GetAlignvector(struct lsq_params * par) const;
249
250 /// Initialising routines in fragmentation
251 void CreateAdjacencyListFromDbondFile(ifstream *output);
252 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
253 int CorrectBondDegree() const;
254 void OutputBondsList() const;
255 void CyclicBondAnalysis() const;
256 void OutputGraphInfoPerAtom() const;
257 void OutputGraphInfoPerBond() const;
258
259
260 // Graph analysis
261 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
262 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
263 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
264 bond * FindNextUnused(atom *vertex) const;
265 void SetNextComponentNumber(atom *vertex, int nr) const;
266 void ResetAllBondsToUnused() const;
267 int CountCyclicBonds();
268 bool CheckForConnectedSubgraph(KeySet *Fragment);
269 string GetColor(enum Shading color) const;
270 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
271
272
273 molecule *CopyMolecule();
274 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
275
276 /// Fragment molecule by two different approaches:
277 int FragmentMolecule(int Order, config *configuration);
278 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
279 bool StoreBondsToFile(char *path);
280 bool StoreAdjacencyToFile(char *path);
281 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
282 bool ParseOrderAtSiteFromFile(char *path);
283 bool StoreOrderAtSiteFile(char *path);
284 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
285 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
286 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
287 /// -# BOSSANOVA
288 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
289 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
290 bool BuildInducedSubgraph(const molecule *Father);
291 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
292 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
293 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
294 int GuesstimateFragmentCount(int order);
295
296 // Recognize doubly appearing molecules in a list of them
297 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
298 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
299
300 // Output routines.
301 bool Output(ofstream * const output);
302 bool OutputTrajectories(ofstream * const output);
303 void OutputListOfBonds() const;
304 bool OutputXYZ(ofstream * const output) const;
305 bool OutputTrajectoriesXYZ(ofstream * const output);
306 bool Checkout(ofstream * const output) const;
307 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
308
309 // Manipulation routines
310 void flipActiveFlag();
311
312 private:
313 int last_atom; //!< number given to last atom
314 mutable atom *InternalPointer; //!< internal pointer for PointCloud
315};
316
317#include "molecule_template.hpp"
318
319/** A list of \a molecule classes.
320 */
321class MoleculeListClass : public Observable {
322 public:
323 MoleculeList ListOfMolecules; //!< List of the contained molecules
324 int MaxIndex;
325
326 MoleculeListClass();
327 ~MoleculeListClass();
328
329 bool AddHydrogenCorrection(char *path);
330 bool StoreForcesFile(char *path, int *SortIndex);
331 void insert(molecule *mol);
332 molecule * ReturnIndex(int index);
333 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
334 int NumberOfActiveMolecules();
335 void Enumerate(ofstream *out);
336 void Output(ofstream *out);
337 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
338 int CountAllAtoms() const;
339
340 // Methods moved here from the menus
341 // TODO: more refactoring needed on these methods
342 void flipChosen();
343 void createNewMolecule(periodentafel *periode);
344 void loadFromXYZ(periodentafel *periode);
345 void setMoleculeFilename();
346 void parseXYZIntoMolecule();
347 void eraseMolecule();
348
349
350 // merging of molecules
351 bool SimpleMerge(molecule *mol, molecule *srcmol);
352 bool SimpleAdd(molecule *mol, molecule *srcmol);
353 bool SimpleMultiMerge(molecule *mol, int *src, int N);
354 bool SimpleMultiAdd(molecule *mol, int *src, int N);
355 bool ScatterMerge(molecule *mol, int *src, int N);
356 bool EmbedMerge(molecule *mol, molecule *srcmol);
357
358 private:
359};
360
361
362/** A leaf for a tree of \a molecule class
363 * Wraps molecules in a tree structure
364 */
365class MoleculeLeafClass {
366 public:
367 molecule *Leaf; //!< molecule of this leaf
368 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
369 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
370 MoleculeLeafClass *previous; //!< Previous leaf on this level
371 MoleculeLeafClass *next; //!< Next leaf on this level
372
373 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
374 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
375 ~MoleculeLeafClass();
376
377 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
378 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
379 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
380 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
381 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
382 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
383 int Count() const;
384};
385
386
387#endif /*MOLECULES_HPP_*/
388
Note: See TracBrowser for help on using the repository browser.