Changeset 1c51c8 for src/World.hpp


Ignore:
Timestamp:
Mar 3, 2010, 3:46:03 PM (15 years ago)
Author:
Tillmann Crueger <crueger@…>
Branches:
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
Children:
88d586
Parents:
dbb474
Message:

Added methods for querying molecules using descriptors

File:
1 edited

Legend:

Unmodified
Added
Removed
  • src/World.hpp

    rdbb474 r1c51c8  
    2727class AtomDescriptor;
    2828class AtomDescriptor_impl;
     29class MoleculeDescriptor;
     30class MoleculeDescriptor_impl;
    2931class ManipulateAtomsProcess;
    3032template<typename T>
     
    3638friend class AtomDescriptor_impl;
    3739friend class AtomDescriptor;
     40friend class MoleculeDescriptor_impl;
     41friend class MoleculeDescriptor;
    3842
    3943// Actions, calculations etc associated with the World
     
    7781
    7882  /**
     83   * returns the first molecule that matches a given descriptor.
     84   * Do not rely on ordering for descriptors that match more than one molecule.
     85   */
     86  molecule *getMolecule(MoleculeDescriptor descriptor);
     87
     88  /**
     89   * returns a vector containing all molecules that match a given descriptor
     90   */
     91  std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
     92
     93  /**
    7994   * get the number of molecules in the World
    8095   */
     
    125140protected:
    126141  /**** Iterators to use internal data structures */
     142
     143  // Atoms
     144
    127145  class AtomIterator {
    128146  public:
     
    163181  AtomSet::iterator atomEnd();
    164182
     183  // Molecules
     184
     185  class MoleculeIterator {
     186  public:
     187    MoleculeIterator();
     188    MoleculeIterator(MoleculeDescriptor, World*);
     189    MoleculeIterator(const MoleculeIterator&);
     190    MoleculeIterator& operator=(const MoleculeIterator&);
     191    MoleculeIterator& operator++();     // prefix
     192    MoleculeIterator  operator++(int);  // postfix with dummy parameter
     193    bool operator==(const MoleculeIterator&);
     194    bool operator==(const MoleculeSet::iterator&);
     195    bool operator!=(const MoleculeIterator&);
     196    bool operator!=(const MoleculeSet::iterator&);
     197    molecule* operator*();
     198
     199    int getCount();
     200  protected:
     201    void advanceState();
     202    MoleculeSet::iterator state;
     203    boost::shared_ptr<MoleculeDescriptor_impl>  descr;
     204    int index;
     205
     206    World* world;
     207  };
     208
     209  /**
     210   * returns an iterator over all Molecules matching a given descriptor.
     211   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
     212   */
     213  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
     214
     215  /**
     216   * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
     217   * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
     218   * Thus it can be used to detect when such an iterator is at the end of the list.
     219   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
     220   */
     221  MoleculeSet::iterator moleculeEnd();
     222
     223
    165224  /******* Internal manipulation routines for double callback and Observer mechanism ******/
    166225  void doManipulate(ManipulateAtomsProcess *);
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