source: src/molecule.hpp@ 112f90

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 Candidate_v1.7.0 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 112f90 was f17e1c, checked in by Tillmann Crueger <crueger@…>, 15 years ago

Made the molecule::getFormula() method return an acutal formula object
  • 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
9/*********************************************** includes ***********************************/
10
11#ifdef HAVE_CONFIG_H
12#include <config.h>
13#endif
14
15//// STL headers
16#include <map>
17#include <set>
18#include <deque>
19#include <list>
20#include <vector>
21
22#include <string>
23
24#include "types.hpp"
25#include "graph.hpp"
26#include "tesselation.hpp"
27#include "Patterns/Observer.hpp"
28#include "Patterns/ObservedIterator.hpp"
29#include "Patterns/Cacheable.hpp"
30#include "Formula.hpp"
31
32#include "Descriptors/MoleculeDescriptor_impl.hpp"
33
34/****************************************** forward declarations *****************************/
35
36class atom;
37class bond;
38class BondedParticle;
39class BondGraph;
40class element;
41class ForceMatrix;
42class LinkedCell;
43class molecule;
44class MoleculeLeafClass;
45class MoleculeListClass;
46class periodentafel;
47class Vector;
48class Shape;
49template <class> class StackClass;
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/** The complete molecule.
79 * Class incorporates number of types
80 */
81class molecule : public PointCloud , public Observable {
82 friend molecule *NewMolecule();
83 friend void DeleteMolecule(molecule *);
84
85 public:
86 typedef std::list<atom*> atomSet;
87 typedef std::set<atomId_t> atomIdSet;
88 typedef ObservedIterator<atomSet> iterator;
89 typedef atomSet::const_iterator const_iterator;
90
91 const periodentafel * const elemente; //!< periodic table with each element
92 // old deprecated atom handling
93 //atom *start; //!< start of atom list
94 //atom *end; //!< end of atom list
95 //bond *first; //!< start of bond list
96 //bond *last; //!< end of bond list
97 int MDSteps; //!< The number of MD steps in Trajectories
98 //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
99 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
100 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
101 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
102 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
103 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
104 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
105 Vector Center; //!< Center of molecule in a global box
106 int IndexNr; //!< index of molecule in a MoleculeListClass
107 char name[MAXSTRINGSIZE]; //!< arbitrary name
108
109 private:
110 Formula formula;
111 Cacheable<int> AtomCount;
112 moleculeId_t id;
113 atomSet atoms; //<!list of atoms
114 atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
115 protected:
116 //void CountAtoms();
117 /**
118 * this iterator type should be used for internal variables, \
119 * since it will not lock
120 */
121 typedef atomSet::iterator internal_iterator;
122
123
124 molecule(const periodentafel * const teil);
125 virtual ~molecule();
126
127
128public:
129 //getter and setter
130 const std::string getName();
131 int getAtomCount() const;
132 int doCountAtoms();
133 moleculeId_t getId();
134 void setId(moleculeId_t);
135 void setName(const std::string);
136 const Formula &getFormula();
137 unsigned int getElementCount();
138 bool hasElement(const element*) const;
139 bool hasElement(atomicNumber_t) const;
140 bool hasElement(const std::string&) const;
141
142
143 iterator begin();
144 const_iterator begin() const;
145 iterator end();
146 const_iterator end() const;
147 bool empty() const;
148 size_t size() const;
149 const_iterator erase( const_iterator loc );
150 const_iterator erase( atom * key );
151 const_iterator find ( atom * key ) const;
152 pair<iterator,bool> insert ( atom * const key );
153 bool containsAtom(atom* key);
154
155
156 // re-definition of virtual functions from PointCloud
157 const char * const GetName() const;
158 Vector *GetCenter() const ;
159 TesselPoint *GetPoint() const ;
160 int GetMaxId() const;
161 void GoToNext() const ;
162 void GoToFirst() const ;
163 bool IsEmpty() const ;
164 bool IsEnd() const ;
165
166 // templates for allowing global manipulation of all vectors
167 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
168 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
169 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
170 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
171 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&), T &t ) const;
172 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&) const, T &t ) const;
173 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
174 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
175 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
176 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;
177
178 // templates for allowing global manipulation of molecule with each atom as single argument
179 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
180 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
181
182 // templates for allowing global copying of molecule with each atom as single argument
183 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
184 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
185
186 // templates for allowing global manipulation of all atoms
187 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
188 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
189 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
190 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
191 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
192 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
193 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;
194 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;
195 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;
196 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;
197
198 // templates for allowing conditional global copying of molecule with each atom as single argument
199 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
200 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
201 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
202 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
203 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
204 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
205 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
206 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
207 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;
208 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;
209 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;
210 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;
211 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;
212 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;
213 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;
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) const, T t, U u, V v ) const;
215
216 // templates for allowing global manipulation of an array with one entry per atom
217 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
218 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
219 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), 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 element::* index, void (*Setor)(T *, T *)) const;
222 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), 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, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
225 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
226 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
227 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
228
229 // templates for allowing global manipulation of each atom by entries in an array
230 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
231 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
232
233 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
234 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
235 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
236 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
237
238 /// remove atoms from molecule.
239 bool AddAtom(atom *pointer);
240 bool RemoveAtom(atom *pointer);
241 bool UnlinkAtom(atom *pointer);
242 bool CleanupMolecule();
243
244 /// Add/remove atoms to/from molecule.
245 atom * AddCopyAtom(atom *pointer);
246 bool AddXYZFile(string filename);
247 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
248 bond * AddBond(atom *first, atom *second, int degree = 1);
249 bool RemoveBond(bond *pointer);
250 bool RemoveBonds(atom *BondPartner);
251 bool hasBondStructure();
252 unsigned int CountBonds() const;
253
254 /// Find atoms.
255 atom * FindAtom(int Nr) const;
256 atom * AskAtom(string text);
257
258 /// Count and change present atoms' coordination.
259 bool CenterInBox();
260 bool BoundInBox();
261 void CenterEdge(Vector *max);
262 void CenterOrigin();
263 void CenterPeriodic();
264 void CenterAtVector(Vector *newcenter);
265 void Translate(const Vector *x);
266 void TranslatePeriodically(const Vector *trans);
267 void Mirror(const Vector *x);
268 void Align(Vector *n);
269 void Scale(const double ** const factor);
270 void DeterminePeriodicCenter(Vector &center);
271 Vector * DetermineCenterOfGravity();
272 Vector * DetermineCenterOfAll() const;
273 Vector * DetermineCenterOfBox() const;
274 void SetNameFromFilename(const char *filename);
275 void SetBoxDimension(Vector *dim);
276 void ScanForPeriodicCorrection();
277 bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
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, std::string &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 Shape&) const;
315
316 /// Fragment molecule by two different approaches:
317 int FragmentMolecule(int Order, std::string &prefix);
318 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
319 bool StoreBondsToFile(std::string &filename, std::string path = "");
320 bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
321 bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
322 bool ParseOrderAtSiteFromFile(std::string &path);
323 bool StoreOrderAtSiteFile(std::string &path);
324 bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &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(std::string &path);
374 bool StoreForcesFile(std::string &path, int *SortIndex);
375 void insert(molecule *mol);
376 void erase(molecule *mol);
377 molecule * ReturnIndex(int index);
378 bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
379 int NumberOfActiveMolecules();
380 void Enumerate(ostream *out);
381 void Output(ofstream *out);
382 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
383 int CountAllAtoms() const;
384
385 // Methods moved here from the menus
386 // TODO: more refactoring needed on these methods
387 void flipChosen();
388 void createNewMolecule(periodentafel *periode);
389 void loadFromXYZ(periodentafel *periode);
390 void setMoleculeFilename();
391 void parseXYZIntoMolecule();
392 void eraseMolecule();
393
394
395 // merging of molecules
396 bool SimpleMerge(molecule *mol, molecule *srcmol);
397 bool SimpleAdd(molecule *mol, molecule *srcmol);
398 bool SimpleMultiMerge(molecule *mol, int *src, int N);
399 bool SimpleMultiAdd(molecule *mol, int *src, int N);
400 bool ScatterMerge(molecule *mol, int *src, int N);
401 bool EmbedMerge(molecule *mol, molecule *srcmol);
402
403 private:
404 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
405};
406
407
408/** A leaf for a tree of \a molecule class
409 * Wraps molecules in a tree structure
410 */
411class MoleculeLeafClass {
412 public:
413 molecule *Leaf; //!< molecule of this leaf
414 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
415 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
416 MoleculeLeafClass *previous; //!< Previous leaf on this level
417 MoleculeLeafClass *next; //!< Next leaf on this level
418
419 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
420 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
421 ~MoleculeLeafClass();
422
423 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
424 bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
425 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
426 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
427 bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList);
428 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
429 int Count() const;
430};
431
432
433#endif /*MOLECULES_HPP_*/
434
Note: See TracBrowser for help on using the repository browser.