source: src/MoleculeListClass.hpp@ 402f2c

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 402f2c was 02ce36, checked in by Frederik Heber <heber@…>, 14 years ago

We now require CodePatterns 1.2.0.

  • this is due to the updated Observer structure and multi_array MemDebug bugfix.
  • Property mode set to 100644
File size: 1.6 KB
Line 
1/*
2 * MoleculeListClass.hpp
3 *
4 * Created on: Oct 20, 2011
5 * Author: heber
6 */
7
8#ifndef MOLECULELISTCLASS_HPP_
9#define MOLECULELISTCLASS_HPP_
10
11#ifdef HAVE_CONFIG_H
12#include <config.h>
13#endif
14
15#include <iosfwd>
16#include <list>
17#include <string>
18
19#include "CodePatterns/Observer/Observable.hpp"
20#include "CodePatterns/Observer/ObservedIterator.hpp"
21#include "CodePatterns/Cacheable.hpp"
22
23#include "Parser/ParserTypes.hpp"
24
25class molecule;
26class periodentafel;
27class World;
28
29typedef std::list<molecule *> MoleculeList;
30typedef std::pair<MoleculeList::iterator, bool> MoleculeListTest;
31
32
33/** A list of \a molecule classes.
34 */
35class MoleculeListClass : public Observable
36{
37public:
38 MoleculeList ListOfMolecules; //!< List of the contained molecules
39 int MaxIndex;
40
41 MoleculeListClass(World *world);
42 ~MoleculeListClass();
43
44 bool AddHydrogenCorrection(std::string &path);
45 bool StoreForcesFile(std::string &path, int *SortIndex);
46 void insert(molecule *mol);
47 void erase(molecule *mol);
48 molecule * ReturnIndex(int index);
49 bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex, ParserTypes type);
50 int NumberOfActiveMolecules();
51 void Enumerate(std::ostream *out);
52 void Output(std::ostream *out);
53 int CountAllAtoms() const;
54
55 // Methods moved here from the menus
56 // TODO: more refactoring needed on these methods
57 void createNewMolecule(periodentafel *periode);
58 void loadFromXYZ(periodentafel *periode);
59 void setMoleculeFilename();
60 void parseXYZIntoMolecule();
61 void eraseMolecule();
62
63private:
64 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
65};
66
67#endif /* MOLECULELISTCLASS_HPP_ */
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