Changeset c67ff9 for src/molecule.hpp

Timestamp:

Mar 30, 2012, 9:16:31 AM (14 years ago)

Author:

Frederik Heber <heber@…>

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, 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:

9e1d01

Parents:

8e1f901

git-author:

Frederik Heber <heber@…> (03/21/12 11:56:06)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:16:31)

Message:

Added molecule::getBoundingShape() and unit test MoleculeUnitTest on it.

• We now simply have a function to get a sphere as a suitable bounding shape which allows easy construction of a new cluster.

File:

• src/molecule.hpp (modified) (6 diffs)

src/molecule.hpp

@@ -33 +33 @@
 #include "IdPool_policy.hpp"
 #include "IdPool.hpp"
+#include "Shapes/Shape.hpp"
 #include "types.hpp"
 
@@ -49 +50 @@
 class MoleculeLeafClass;
 class MoleculeListClass;
-class periodentafel;
+class MoleculeUnittest;
 class RealSpaceMatrix;
 class Vector;
-class Shape;
 
 /************************************* Class definitions ****************************************/
@@ -61 +61 @@
 class molecule : public Observable
 {
+  //!> grant unit test access
+  friend class MoleculeUnittest;
+  //!> function may access cstor
   friend molecule *NewMolecule();
+  //!> function may access dstor
   friend void DeleteMolecule(molecule *);
 
@@ -138 +142 @@
     return atomIds.find(key);
   }
+
+  /** Returns the set of atomic ids contained in this molecule.
+   *
+   * @return set of atomic ids
+   */
   const atomIdSet & getAtomIds() const {
     return atomIds.getAtomIds();
@@ -189 +198 @@
 
 public:
+
+  /** Function to create a bounding spherical shape for the currently associated atoms.
+   *
+   */
+  Shape getBoundingShape() const;
 
   /// remove atoms from molecule.
@@ -241 +255 @@
   bond * CopyBond(atom *left, atom *right, bond *CopyBond);
 
-  molecule *CopyMolecule() const;
+  molecule *CopyMolecule(const Vector &offset = zeroVec) const;
   molecule* CopyMoleculeFromSubRegion(const Shape&) const;