source: src/molecule.hpp@ ae959a

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Last change on this file since ae959a was a7a087, checked in by Frederik Heber <heber@…>, 15 years ago

new function World::changeMoleculeId().

  • copied from changeAtomId()
  • needed for undoing changes to the set of molecules in the World.
  • Property mode set to 100755
File size: 20.4 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 "PointCloud.hpp"
27#include "Patterns/Observer.hpp"
28#include "Patterns/ObservedIterator.hpp"
29#include "Patterns/Cacheable.hpp"
30#include "Formula.hpp"
31#include "AtomSet.hpp"
32
33#include "Descriptors/MoleculeDescriptor_impl.hpp"
34
35/****************************************** forward declarations *****************************/
36
37class atom;
38class bond;
39class BondedParticle;
40class BondGraph;
41class element;
42class ForceMatrix;
43class LinkedCell;
44class molecule;
45class MoleculeLeafClass;
46class MoleculeListClass;
47class periodentafel;
48class Vector;
49class Shape;
50template <class> class StackClass;
51
52/******************************** Some definitions for easier reading **********************************/
53
54#define MoleculeList list <molecule *>
55#define MoleculeListTest pair <MoleculeList::iterator, bool>
56
57#define DistancePair pair < double, atom* >
58#define DistanceMap multimap < double, atom* >
59#define DistanceTestPair pair < DistanceMap::iterator, bool>
60
61
62/************************************* Class definitions ****************************************/
63
64/** Structure to contain parameters needed for evaluation of constraint potential.
65 */
66struct EvaluatePotential
67{
68 int startstep; //!< start configuration (MDStep in atom::trajectory)
69 int endstep; //!< end configuration (MDStep in atom::trajectory)
70 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
71 DistanceMap **DistanceList; //!< distance list of each atom to each atom
72 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
73 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
74 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
75 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
76 double *PenaltyConstants; //!< penalty constant in front of each term
77};
78
79/** The complete molecule.
80 * Class incorporates number of types
81 */
82class molecule : public PointCloud , public Observable {
83 friend molecule *NewMolecule();
84 friend void DeleteMolecule(molecule *);
85
86 public:
87 typedef ATOMSET(std::list) atomSet;
88 typedef std::set<atomId_t> atomIdSet;
89 typedef ObservedIterator<atomSet> iterator;
90 typedef atomSet::const_iterator const_iterator;
91
92 const periodentafel * const elemente; //!< periodic table with each element
93 // old deprecated atom handling
94 //atom *start; //!< start of atom list
95 //atom *end; //!< end of atom list
96 //bond *first; //!< start of bond list
97 //bond *last; //!< end of bond list
98 int MDSteps; //!< The number of MD steps in Trajectories
99 //int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
100 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
101 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
102 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
103 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
104 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
105 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
106 //Vector Center; //!< Center of molecule in a global box
107 int IndexNr; //!< index of molecule in a MoleculeListClass
108 char name[MAXSTRINGSIZE]; //!< arbitrary name
109
110 private:
111 Formula formula;
112 Cacheable<int> AtomCount;
113 moleculeId_t id;
114 atomSet atoms; //<!list of atoms
115 atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
116 protected:
117 //void CountAtoms();
118 /**
119 * this iterator type should be used for internal variables, \
120 * since it will not lock
121 */
122 typedef atomSet::iterator internal_iterator;
123
124
125 molecule(const periodentafel * const teil);
126 virtual ~molecule();
127
128
129public:
130 //getter and setter
131 const std::string getName();
132 int getAtomCount() const;
133 int doCountAtoms();
134 moleculeId_t getId();
135 void setId(moleculeId_t);
136 void setName(const std::string);
137 const Formula &getFormula();
138 unsigned int getElementCount();
139 bool hasElement(const element*) const;
140 bool hasElement(atomicNumber_t) const;
141 bool hasElement(const std::string&) const;
142
143 virtual bool changeId(atomId_t newId);
144
145 iterator begin();
146 const_iterator begin() const;
147 iterator end();
148 const_iterator end() const;
149 bool empty() const;
150 size_t size() const;
151 const_iterator erase( const_iterator loc );
152 const_iterator erase( atom * key );
153 const_iterator find ( atom * key ) const;
154 pair<iterator,bool> insert ( atom * const key );
155 bool containsAtom(atom* key);
156
157
158 // re-definition of virtual functions from PointCloud
159 const char * const GetName() const;
160 Vector *GetCenter() const ;
161 TesselPoint *GetPoint() const ;
162 int GetMaxId() const;
163 void GoToNext() const ;
164 void GoToFirst() const ;
165 bool IsEmpty() const ;
166 bool IsEnd() const ;
167
168 // templates for allowing global manipulation of molecule with each atom as single argument
169 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
170 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
171
172 // templates for allowing global copying of molecule with each atom as single argument
173 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
174 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
175
176 // templates for allowing global manipulation of all atoms
177 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
178 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
179 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
180 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
181 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
182 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
183 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;
184 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;
185 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;
186 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;
187
188 // templates for allowing conditional global copying of molecule with each atom as single argument
189 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
190 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
191 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
192 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
193 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
194 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
195 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
196 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
197 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;
198 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;
199 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;
200 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;
201 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;
202 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;
203 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;
204 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;
205
206 // templates for allowing global manipulation of an array with one entry per atom
207 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
208 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
209 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
210 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
211 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
212 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
213 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
214 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
215 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
216 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
217 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
218
219 // templates for allowing global manipulation of each atom by entries in an array
220 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
221 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
222
223 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
224 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
225 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
226 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
227
228 /// remove atoms from molecule.
229 bool AddAtom(atom *pointer);
230 bool RemoveAtom(atom *pointer);
231 bool UnlinkAtom(atom *pointer);
232 bool CleanupMolecule();
233
234 /// Add/remove atoms to/from molecule.
235 atom * AddCopyAtom(atom *pointer);
236 bool AddXYZFile(string filename);
237 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
238 bond * AddBond(atom *first, atom *second, int degree = 1);
239 bool RemoveBond(bond *pointer);
240 bool RemoveBonds(atom *BondPartner);
241 bool hasBondStructure();
242 unsigned int CountBonds() const;
243
244 /// Find atoms.
245 atom * FindAtom(int Nr) const;
246 atom * AskAtom(string text);
247
248 /// Count and change present atoms' coordination.
249 bool CenterInBox();
250 bool BoundInBox();
251 void CenterEdge(Vector *max);
252 void CenterOrigin();
253 void CenterPeriodic();
254 void CenterAtVector(Vector *newcenter);
255 void Translate(const Vector *x);
256 void TranslatePeriodically(const Vector *trans);
257 void Mirror(const Vector *x);
258 void Align(Vector *n);
259 void Scale(const double ** const factor);
260 void DeterminePeriodicCenter(Vector &center);
261 Vector * DetermineCenterOfGravity() const;
262 Vector * DetermineCenterOfAll() const;
263 Vector * DetermineCenterOfBox() const;
264 void SetNameFromFilename(const char *filename);
265 void SetBoxDimension(Vector *dim);
266 void ScanForPeriodicCorrection();
267 bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
268 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
269 double VolumeOfConvexEnvelope(bool IsAngstroem);
270
271 double ConstrainedPotential(struct EvaluatePotential &Params);
272 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
273 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
274 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
275
276 bool CheckBounds(const Vector *x) const;
277 void GetAlignvector(struct lsq_params * par) const;
278
279 /// Initialising routines in fragmentation
280 void CreateAdjacencyListFromDbondFile(ifstream *output);
281 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
282 int CorrectBondDegree() const;
283 void OutputBondsList() const;
284 void CyclicBondAnalysis() const;
285 void OutputGraphInfoPerAtom() const;
286 void OutputGraphInfoPerBond() const;
287
288
289 // Graph analysis
290 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
291 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
292 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
293 bond * FindNextUnused(atom *vertex) const;
294 void SetNextComponentNumber(atom *vertex, int nr) const;
295 void ResetAllBondsToUnused() const;
296 int CountCyclicBonds();
297 bool CheckForConnectedSubgraph(KeySet *Fragment);
298 string GetColor(enum Shading color) const;
299 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
300
301
302 molecule *CopyMolecule();
303 molecule* CopyMoleculeFromSubRegion(const Shape&) const;
304
305 /// Fragment molecule by two different approaches:
306 int FragmentMolecule(int Order, std::string &prefix);
307 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
308 bool StoreBondsToFile(std::string &filename, std::string path = "");
309 bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
310 bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
311 bool ParseOrderAtSiteFromFile(std::string &path);
312 bool StoreOrderAtSiteFile(std::string &path);
313 bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
314 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
315 bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
316 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
317 /// -# BOSSANOVA
318 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
319 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
320 bool BuildInducedSubgraph(const molecule *Father);
321 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
322 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
323 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
324 int GuesstimateFragmentCount(int order);
325
326 // Recognize doubly appearing molecules in a list of them
327 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
328
329 // Output routines.
330 bool Output(std::ostream * const output);
331 bool OutputTrajectories(ofstream * const output);
332 void OutputListOfBonds() const;
333 bool OutputXYZ(ofstream * const output) const;
334 bool OutputTrajectoriesXYZ(ofstream * const output);
335 bool Checkout(ofstream * const output) const;
336 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
337
338 // Manipulation routines
339 void flipActiveFlag();
340
341 private:
342 int last_atom; //!< number given to last atom
343 mutable internal_iterator InternalPointer; //!< internal pointer for PointCloud
344};
345
346molecule *NewMolecule();
347void DeleteMolecule(molecule* mol);
348
349#include "molecule_template.hpp"
350
351/** A list of \a molecule classes.
352 */
353class MoleculeListClass : public Observable {
354 public:
355 MoleculeList ListOfMolecules; //!< List of the contained molecules
356 int MaxIndex;
357
358 MoleculeListClass(World *world);
359 ~MoleculeListClass();
360
361 bool AddHydrogenCorrection(std::string &path);
362 bool StoreForcesFile(std::string &path, int *SortIndex);
363 void insert(molecule *mol);
364 void erase(molecule *mol);
365 molecule * ReturnIndex(int index);
366 bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
367 int NumberOfActiveMolecules();
368 void Enumerate(ostream *out);
369 void Output(ofstream *out);
370 int CountAllAtoms() const;
371
372 // Methods moved here from the menus
373 // TODO: more refactoring needed on these methods
374 void flipChosen();
375 void createNewMolecule(periodentafel *periode);
376 void loadFromXYZ(periodentafel *periode);
377 void setMoleculeFilename();
378 void parseXYZIntoMolecule();
379 void eraseMolecule();
380
381 private:
382 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
383};
384
385
386/** A leaf for a tree of \a molecule class
387 * Wraps molecules in a tree structure
388 */
389class MoleculeLeafClass {
390 public:
391 molecule *Leaf; //!< molecule of this leaf
392 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
393 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
394 MoleculeLeafClass *previous; //!< Previous leaf on this level
395 MoleculeLeafClass *next; //!< Next leaf on this level
396
397 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
398 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
399 ~MoleculeLeafClass();
400
401 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
402 bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
403 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
404 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
405 bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount, bool &FreeList);
406 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
407 int Count() const;
408};
409
410
411#endif /*MOLECULES_HPP_*/
412
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