Changeset 90c4280 for src/World.hpp

Timestamp:

Jul 15, 2010, 3:30:55 PM (14 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:

61d655e

Parents:

c084cc

Message:

Added several methods for selecting specific atoms in the World

File:

• src/World.hpp (modified) (4 diffs)

src/World.hpp

@@ -222 +222 @@
    * All these iterators are observed to track changes.
    * There is a corresponding protected section with unobserved iterators,
-   * which ca be used internally when the extra speed is needed
+   * which can be used internally when the extra speed is needed
    */
 
@@ -239 +239 @@
   typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
 
+  /**
+   * returns an iterator over all Molecules matching a given descriptor.
+   * This iterator is observed, so don't keep it around unnecessary to
+   * avoid unintended blocking.
+   */
   MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
   MoleculeIterator getMoleculeIter();
 
   MoleculeIterator moleculeEnd();
+
+  /******** Selections of molecules and Atoms *************/
+  void clearAtomSelection();
+  void selectAtom(atom*);
+  void selectAtom(atomId_t);
+  void selectAllAtoms(AtomDescriptor);
+  void selectAtomsOfMolecule(molecule*);
+  void selectAtomsOfMolecule(moleculeId_t);
+
+  void clearMoleculeSelection();
+  void selectMolecule(molecule*);
+  void selectMolecule(moleculeId_t);
+  void selectAllMoleculess(MoleculeDescriptor);
+  void selectMoleculeOfAtom(atom*);
+  void selectMoleculeOfAtom(atomId_t);
 
 protected:
@@ -311 +331 @@
 
   AtomSet atoms;
+  AtomSet selectedAtoms;
   typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
   /**
@@ -323 +344 @@
 
   MoleculeSet molecules;
+  MoleculeSet selectedMolecules;
   typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
   /**