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 c37c20 was             6aad6f, checked in by Frederik Heber <heber@…>, 14 years ago | 
        
          | 
FIX: molecule::containsAtom() is now const and has const param, added AtomIdSet::contains().
 AtomIdSet::contains() is predicate to whether id is contained, added unit
test function.
also added molecule::containsAtom() on atomic id only.
 | 
        
          | 
              
Property                 mode
 set to                 100644 | 
        
          | File size:
            1.8 KB | 
      
      
| Rev | Line |  | 
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| [5e6534] | 1 | /* | 
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|  | 2 | * AtomIdSet.hpp | 
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|  | 3 | * | 
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|  | 4 | *  Created on: Feb 21, 2012 | 
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|  | 5 | *      Author: heber | 
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|  | 6 | */ | 
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|  | 7 |  | 
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|  | 8 | #ifndef ATOMIDSET_HPP_ | 
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|  | 9 | #define ATOMIDSET_HPP_ | 
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|  | 10 |  | 
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|  | 11 |  | 
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|  | 12 | // include config.h | 
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|  | 13 | #ifdef HAVE_CONFIG_H | 
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|  | 14 | #include <config.h> | 
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|  | 15 | #endif | 
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|  | 16 |  | 
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|  | 17 | #include <boost/iterator/transform_iterator.hpp> | 
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|  | 18 |  | 
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|  | 19 | #include <set> | 
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|  | 20 | #include <vector> | 
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|  | 21 |  | 
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|  | 22 | #include "types.hpp" | 
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|  | 23 |  | 
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|  | 24 | class atom; | 
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|  | 25 | struct FromIdToAtom : | 
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|  | 26 | public std::unary_function<atom *, atomId_t> | 
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|  | 27 | { | 
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|  | 28 | atom * operator()(atomId_t id) const; | 
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|  | 29 | }; | 
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|  | 30 |  | 
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|  | 31 | /** AtomIdSet is a set of atomic ids that however behave as a set of atoms. | 
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|  | 32 | * | 
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|  | 33 | * This class represents an iterable set of atoms that is however only stored as | 
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|  | 34 | * ids internally. | 
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|  | 35 | */ | 
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|  | 36 | class AtomIdSet | 
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|  | 37 | { | 
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|  | 38 | public: | 
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|  | 39 | typedef std::set<atomId_t> atomIdSet; | 
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|  | 40 | typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator; | 
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|  | 41 | typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator; | 
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|  | 42 |  | 
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|  | 43 | AtomIdSet(const atomIdSet &_atoms); | 
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|  | 44 | AtomIdSet(const std::vector<atom *> &_atoms); | 
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|  | 45 | AtomIdSet(); | 
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|  | 46 | ~AtomIdSet(); | 
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|  | 47 |  | 
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|  | 48 | iterator begin(); | 
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|  | 49 | const_iterator begin() const; | 
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|  | 50 | iterator end(); | 
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|  | 51 | const_iterator end() const; | 
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|  | 52 | bool empty() const; | 
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|  | 53 | size_t size() const; | 
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| [6aad6f] | 54 | bool contains(const atom * const key) const; | 
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|  | 55 | bool contains(const atomId_t &id) const; | 
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| [5e6534] | 56 | const_iterator find(const atom * const key) const; | 
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|  | 57 | const_iterator find(const atomId_t &id) const; | 
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|  | 58 | std::pair<iterator, bool> insert(const atom * const key); | 
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|  | 59 | std::pair<iterator, bool> insert(const atomId_t &id); | 
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|  | 60 | const_iterator erase(const_iterator &loc); | 
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|  | 61 | const_iterator erase(const atom * const key); | 
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|  | 62 | const_iterator erase(const atomId_t &id); | 
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|  | 63 |  | 
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|  | 64 | /** Getter for internal set of atoms. | 
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|  | 65 | * | 
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|  | 66 | * @return set of atomic ids | 
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|  | 67 | */ | 
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|  | 68 | const atomIdSet & getAtomIds() const { | 
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|  | 69 | return atoms; | 
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|  | 70 | } | 
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|  | 71 |  | 
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|  | 72 | private: | 
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|  | 73 | //!> internal atoms stored by their ids | 
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|  | 74 | atomIdSet atoms; | 
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|  | 75 | }; | 
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|  | 76 |  | 
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|  | 77 |  | 
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|  | 78 | #endif /* ATOMIDSET_HPP_ */ | 
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