source: src/molecule.hpp@ 108968

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 108968 was c67ff9, checked in by Frederik Heber <heber@…>, 13 years ago

Added molecule::getBoundingShape() and unit test MoleculeUnitTest on it.

  • We now simply have a function to get a sphere as a suitable bounding shape which allows easy construction of a new cluster.
  • Property mode set to 100755
File size: 8.4 KB
RevLine 
[cee0b57]1/** \file molecule.hpp
[14de469]2 *
[69eb71]3 * Class definitions of atom and molecule, element and periodentafel
[14de469]4 */
5
6#ifndef MOLECULES_HPP_
7#define MOLECULES_HPP_
8
[f66195]9/*********************************************** includes ***********************************/
10
[962d8d]11#ifdef HAVE_CONFIG_H
12#include <config.h>
13#endif
14
[edb93c]15//// STL headers
[14de469]16#include <map>
17#include <set>
[a564be]18#include <stack>
[14de469]19#include <deque>
[d7e30c]20#include <list>
[5e0d1f]21#include <vector>
[14de469]22
[520c8b]23#include <string>
24
[8e1f901]25#include "AtomIdSet.hpp"
[6f0841]26#include "Atom/AtomSet.hpp"
[ad011c]27#include "CodePatterns/Cacheable.hpp"
[02ce36]28#include "CodePatterns/Observer/Observable.hpp"
[30c753]29#include "Descriptors/AtomIdDescriptor.hpp"
[07a47e]30#include "Fragmentation/HydrogenSaturation_enum.hpp"
[389cc8]31#include "Formula.hpp"
[30c753]32#include "Helpers/defs.hpp"
[560bbe]33#include "IdPool_policy.hpp"
34#include "IdPool.hpp"
[c67ff9]35#include "Shapes/Shape.hpp"
[30c753]36#include "types.hpp"
[14de469]37
[f66195]38/****************************************** forward declarations *****************************/
39
40class atom;
41class bond;
[b70721]42class BondedParticle;
43class BondGraph;
[49c059]44class DepthFirstSearchAnalysis;
[f66195]45class element;
46class ForceMatrix;
[dadc74]47class Graph;
[6bd7e0]48class LinkedCell_deprecated;
[14de469]49class molecule;
[2319ed]50class MoleculeLeafClass;
[14de469]51class MoleculeListClass;
[c67ff9]52class MoleculeUnittest;
[1f91f4]53class RealSpaceMatrix;
[f66195]54class Vector;
[14de469]55
56/************************************* Class definitions ****************************************/
57
58/** The complete molecule.
59 * Class incorporates number of types
60 */
[34c43a]61class molecule : public Observable
[e4afb4]62{
[c67ff9]63 //!> grant unit test access
64 friend class MoleculeUnittest;
65 //!> function may access cstor
[cbc5fb]66 friend molecule *NewMolecule();
[c67ff9]67 //!> function may access dstor
[cbc5fb]68 friend void DeleteMolecule(molecule *);
[bd58fb]69
[e4afb4]70public:
[8e1f901]71 typedef AtomIdSet::atomIdSet atomIdSet;
72 typedef AtomIdSet::iterator iterator;
73 typedef AtomIdSet::const_iterator const_iterator;
[e4afb4]74
75 int MDSteps; //!< The number of MD steps in Trajectories
76 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
77 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
78 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
79 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
80 int IndexNr; //!< index of molecule in a MoleculeListClass
81 char name[MAXSTRINGSIZE]; //!< arbitrary name
82
83private:
84 Formula formula;
[458c31]85 Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
86 Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
[e4afb4]87 moleculeId_t id;
[8e1f901]88 AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
[560bbe]89 IdPool<atomId_t, uniqueId> atomIdPool; //!< pool of internal ids such that way may guarantee uniqueness
90
[e4afb4]91protected:
[ac9b56]92
[4d2b33]93 molecule();
[e4afb4]94 virtual ~molecule();
[042f82]95
[cbc5fb]96public:
[520c8b]97 //getter and setter
[73a857]98 const std::string getName() const;
[ea7176]99 int getAtomCount() const;
100 int doCountAtoms();
[458c31]101 int getBondCount() const;
102 int doCountBonds() const;
[73a857]103 moleculeId_t getId() const;
[cbc5fb]104 void setId(moleculeId_t);
[520c8b]105 void setName(const std::string);
[73a857]106 const Formula &getFormula() const;
107 unsigned int getElementCount() const;
[389cc8]108 bool hasElement(const element*) const;
109 bool hasElement(atomicNumber_t) const;
110 bool hasElement(const std::string&) const;
111
[a7a087]112 virtual bool changeId(atomId_t newId);
[520c8b]113
[9317be]114 World::AtomComposite getAtomSet() const;
[3738f0]115
[8e1f901]116 // simply pass on all functions to AtomIdSet
117 iterator begin() {
118 return atomIds.begin();
119 }
120 const_iterator begin() const
121 {
122 return atomIds.begin();
123 }
124 iterator end()
125 {
126 return atomIds.end();
127 }
128 const_iterator end() const
129 {
130 return atomIds.end();
131 }
132 bool empty() const
133 {
134 return atomIds.empty();
135 }
136 size_t size() const
137 {
138 return atomIds.size();
139 }
140 const_iterator find(atom * key) const
141 {
142 return atomIds.find(key);
143 }
[c67ff9]144
145 /** Returns the set of atomic ids contained in this molecule.
146 *
147 * @return set of atomic ids
148 */
[8e1f901]149 const atomIdSet & getAtomIds() const {
150 return atomIds.getAtomIds();
151 }
152
153 std::pair<iterator, bool> insert(atom * const key);
154
[6cfa36]155 bool containsAtom(atom* key);
[bd58fb]156
[2e4105]157private:
158 friend void atom::removeFromMolecule();
159 /** Erase an atom from the list.
160 * \note This should only be called by atom::removeFromMolecule(),
161 * otherwise it is not assured that the atom knows about it.
162 *
163 * @param loc locator to atom in list
164 * @return iterator to just after removed item (compliant with standard)
165 */
166 const_iterator erase(const_iterator loc);
[8e1f901]167
[2e4105]168 /** Erase an atom from the list.
169 * \note This should only be called by atom::removeFromMolecule(),
170 * otherwise it is not assured that the atom knows about it.
171 *
172 * @param *key key to atom in list
173 * @return iterator to just after removed item (compliant with standard)
174 */
175 const_iterator erase(atom * key);
176
[560bbe]177private:
178 friend bool atom::changeNr(int newId);
179 /**
180 * used when changing an ParticleInfo::Nr.
181 * Note that this number is local with this molecule.
182 * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
183 *
184 * @param oldNr old Nr
185 * @param newNr new Nr to set
186 * @param *target ref to atom
187 * @return indicates wether the change could be done or not.
188 */
189 bool changeAtomNr(int oldNr, int newNr, atom* target=0);
190
191 /** Sets the name of the atom.
192 *
193 * The name is set via its element symbol and its internal ParticleInfo::Nr.
194 *
195 * @param _atom atom whose name to set
196 */
197 void setAtomName(atom *_atom) const;
198
[2e4105]199public:
200
[c67ff9]201 /** Function to create a bounding spherical shape for the currently associated atoms.
202 *
203 */
204 Shape getBoundingShape() const;
205
[042f82]206 /// remove atoms from molecule.
207 bool AddAtom(atom *pointer);
208 bool RemoveAtom(atom *pointer);
209 bool UnlinkAtom(atom *pointer);
210 bool CleanupMolecule();
[9df680]211 void removeAtomsinMolecule();
[042f82]212
213 /// Add/remove atoms to/from molecule.
214 atom * AddCopyAtom(atom *pointer);
[e138de]215 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
[cee0b57]216 bond * AddBond(atom *first, atom *second, int degree = 1);
[042f82]217 bool RemoveBond(bond *pointer);
218 bool RemoveBonds(atom *BondPartner);
[e4afb4]219 bool hasBondStructure() const;
[042f82]220
221 /// Find atoms.
222 atom * FindAtom(int Nr) const;
[955b91]223 atom * AskAtom(std::string text);
[59fff1]224 bool isInMolecule(const atom * const _atom);
[042f82]225
226 /// Count and change present atoms' coordination.
[e138de]227 bool CenterInBox();
228 bool BoundInBox();
229 void CenterEdge(Vector *max);
230 void CenterOrigin();
231 void CenterPeriodic();
232 void CenterAtVector(Vector *newcenter);
[042f82]233 void Translate(const Vector *x);
234 void TranslatePeriodically(const Vector *trans);
235 void Mirror(const Vector *x);
236 void Align(Vector *n);
[776b64]237 void Scale(const double ** const factor);
[07a47e]238 void DeterminePeriodicCenter(Vector &center, const enum HydrogenSaturation _saturation = DoSaturate);
[4bb63c]239 Vector * DetermineCenterOfGravity() const;
[e138de]240 Vector * DetermineCenterOfAll() const;
[eddea2]241 Vector * DetermineCenterOfBox() const;
[437922]242 void SetNameFromFilename(const char *filename);
[042f82]243 void SetBoxDimension(Vector *dim);
[3c58f8]244 bool ScanForPeriodicCorrection();
[e138de]245 double VolumeOfConvexEnvelope(bool IsAngstroem);
[1f91f4]246 RealSpaceMatrix getInertiaTensor() const;
247 void RotateToPrincipalAxisSystem(Vector &Axis);
[042f82]248
249 bool CheckBounds(const Vector *x) const;
250 void GetAlignvector(struct lsq_params * par) const;
251
252 /// Initialising routines in fragmentation
[e138de]253 void OutputBondsList() const;
[49c059]254
[266237]255 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
256
[c67ff9]257 molecule *CopyMolecule(const Vector &offset = zeroVec) const;
[c550dd]258 molecule* CopyMoleculeFromSubRegion(const Shape&) const;
[042f82]259
260 /// Fragment molecule by two different approaches:
[e4afb4]261 bool StoreBondsToFile(std::string filename, std::string path = "");
262 bool StoreAdjacencyToFile(std::string filename, std::string path = "");
[9879f6]263 bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
[b9772a]264
[042f82]265 // Recognize doubly appearing molecules in a list of them
[e138de]266 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
[99752a]267 bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
[c6123b]268 bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount);
[042f82]269
270 // Output routines.
[e4afb4]271 bool Output(std::ostream * const output) const;
272 bool OutputTrajectories(ofstream * const output) const;
[e138de]273 void OutputListOfBonds() const;
274 bool OutputXYZ(ofstream * const output) const;
275 bool OutputTrajectoriesXYZ(ofstream * const output);
276 bool Checkout(ofstream * const output) const;
[042f82]277
[c68025]278 // Manipulation routines
279 void flipActiveFlag();
280
[e4afb4]281private:
282 int last_atom; //!< number given to last atom
[14de469]283};
284
[cbc5fb]285molecule *NewMolecule();
286void DeleteMolecule(molecule* mol);
287
[14de469]288
289
290#endif /*MOLECULES_HPP_*/
291
Note: See TracBrowser for help on using the repository browser.