source: src/Atom/atom_bondedparticle.hpp@ 561b94

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 561b94 was f01769, checked in by Frederik Heber <heber@…>, 10 years ago

Replaced World::getAtom() wherever possible by const version.

  • some AtomSet member functions now have const atom ptr instead of atom ptr.
  • molecule can return const and non-const AtomSet.
  • added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion.
  • in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const).
  • Property mode set to 100644
File size: 2.1 KB
Line 
1/*
2 * atom_bondedparticle.hpp
3 *
4 * Created on: Oct 19, 2009
5 * Author: heber
6 */
7
8#ifndef ATOM_BONDEDPARTICLE_HPP_
9#define ATOM_BONDEDPARTICLE_HPP_
10
11
12using namespace std;
13
14/*********************************************** includes ***********************************/
15
16// include config.h
17#ifdef HAVE_CONFIG_H
18#include <config.h>
19#endif
20
21#include <fstream>
22#include <list>
23
24#include "atom_atominfo.hpp"
25#include "atom_bondedparticleinfo.hpp"
26#include "atom_observable.hpp"
27#include "atom_particleinfo.hpp"
28#include "atom_observable.hpp"
29
30/****************************************** forward declarations *****************************/
31
32class bond;
33
34/********************************************** declarations *******************************/
35
36class BondedParticle :
37 public BondedParticleInfo,
38 public virtual ParticleInfo,
39 public virtual AtomInfo,
40 public virtual AtomObservable
41{
42public:
43 BondedParticle();
44 virtual ~BondedParticle();
45
46 bond::ptr addBond(const unsigned int _step, BondedParticle* Partner);
47 bond::ptr addBond(BondedParticle* Partner);
48 void removeBond(const unsigned int _step, BondedParticle* Partner);
49 void removeBond(BondedParticle* Partner);
50 void removeBond(bond::ptr &binder);
51 void removeAllBonds();
52 void removeAllBonds(const unsigned int _step);
53 bool IsBondedTo(const unsigned int _step, const BondedParticle * const BondPartner) const;
54 void ClearBondsAtStep(const unsigned int _step);
55 int CountBonds() const;
56 void OutputBondOfAtom(std::ostream &ost) const;
57 void OutputBonds(ofstream * const BondFile) const;
58 void OutputOrder(ofstream *file) const;
59
60 std::ostream & operator << (std::ostream &ost) const;
61
62protected:
63 bool RegisterBond(const unsigned int _step, bond::ptr const Binder);
64 bool UnregisterBond(const unsigned int _step, bond::ptr const Binder);
65
66 int ContainsBondAtStep(bond::ptr Binder) const;
67
68private:
69 unsigned int findBondsStep(bond::ptr const Binder) const;
70 BondList::const_iterator findBondPartnerAtStep(
71 const unsigned int _step,
72 BondedParticle * const Partner) const;
73};
74
75std::ostream & operator << (std::ostream &ost, const BondedParticle &a);
76
77#endif /* ATOM_BONDEDPARTICLE_HPP_ */
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