Changeset e6a9c1 for src/World.hpp

Timestamp:

Mar 4, 2010, 10:40:52 AM (16 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

63b56a7

Parents:

6a661c (diff), 66e95e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'MenuRefactoring' into QT4Refactoring

Conflicts:

molecuilder/src/Makefile.am

File:

• src/World.hpp (modified) (6 diffs)

src/World.hpp

@@ -27 +27 @@
 class AtomDescriptor;
 class AtomDescriptor_impl;
+class MoleculeDescriptor;
+class MoleculeDescriptor_impl;
 class ManipulateAtomsProcess;
 template<typename T>
@@ -36 +38 @@
 friend class AtomDescriptor_impl;
 friend class AtomDescriptor;
+friend class MoleculeDescriptor_impl;
+friend class MoleculeDescriptor;
 
 // Actions, calculations etc associated with the World
@@ -77 +81 @@
 
   /**
+   * returns the first molecule that matches a given descriptor.
+   * Do not rely on ordering for descriptors that match more than one molecule.
+   */
+  molecule *getMolecule(MoleculeDescriptor descriptor);
+
+  /**
+   * returns a vector containing all molecules that match a given descriptor
+   */
+  std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
+
+  /**
    * get the number of molecules in the World
    */
@@ -117 +132 @@
 
   /**
+   * used when changing an atom Id.
+   * Unless you are calling this method from inside an atom don't fiddle with the third parameter.
+   *
+   * Return value indicates wether the change could be done or not.
+   */
+  bool changeAtomId(atomId_t oldId, atomId_t newId, atom* target=0);
+
+  /**
    * Produces a process that calls a function on all Atoms matching a given descriptor. The process is not
    * called at this time, so it can be passed around, stored inside menuItems etc.
@@ -125 +148 @@
 protected:
   /**** Iterators to use internal data structures */
+
+  // Atoms
+
   class AtomIterator {
   public:
@@ -163 +189 @@
   AtomSet::iterator atomEnd();
 
+  // Molecules
+
+  class MoleculeIterator {
+  public:
+    MoleculeIterator();
+    MoleculeIterator(MoleculeDescriptor, World*);
+    MoleculeIterator(const MoleculeIterator&);
+    MoleculeIterator& operator=(const MoleculeIterator&);
+    MoleculeIterator& operator++();     // prefix
+    MoleculeIterator  operator++(int);  // postfix with dummy parameter
+    bool operator==(const MoleculeIterator&);
+    bool operator==(const MoleculeSet::iterator&);
+    bool operator!=(const MoleculeIterator&);
+    bool operator!=(const MoleculeSet::iterator&);
+    molecule* operator*();
+
+    int getCount();
+  protected:
+    void advanceState();
+    MoleculeSet::iterator state;
+    boost::shared_ptr<MoleculeDescriptor_impl>  descr;
+    int index;
+
+    World* world;
+  };
+
+  /**
+   * returns an iterator over all Molecules matching a given descriptor.
+   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
+   */
+  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
+
+  /**
+   * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
+   * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
+   * Thus it can be used to detect when such an iterator is at the end of the list.
+   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
+   */
+  MoleculeSet::iterator moleculeEnd();
+
+
   /******* Internal manipulation routines for double callback and Observer mechanism ******/
   void doManipulate(ManipulateAtomsProcess *);
 
 private:
+
+  atomId_t getNextAtomId();
+  void releaseAtomId(atomId_t);
+  bool reserveAtomId(atomId_t);
+
   periodentafel *periode;
   AtomSet atoms;
+  std::set<atomId_t> atomIdPool; //<!stores the pool for all available AtomIds below currAtomId
   atomId_t currAtomId; //!< stores the next available Id for atoms
   MoleculeSet molecules;