Changeset 458c31 for src/molecule.hpp

Timestamp:

Mar 1, 2011, 10:16:39 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, 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:

4b5cf8

Parents:

d4a44c

git-author:

Frederik Heber <heber@…> (02/21/11 13:02:57)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

molecule::BondCount is now Cachable and private.

• renamed CountBonds() -> doCountBonds in analogy to AtomCount.

File:

• src/molecule.hpp (modified) (4 diffs)

src/molecule.hpp

@@ -98 +98 @@
   //bond *last;         //!< end of bond list
   int MDSteps; //!< The number of MD steps in Trajectories
-  //int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
-  int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
   mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
   mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
   mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
-  //double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
   bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
   //Vector Center;      //!< Center of molecule in a global box
@@ -111 +108 @@
 private:
   Formula formula;
-  Cacheable<int> AtomCount;
+  Cacheable<int> AtomCount; //!< number of atoms, brought up-to-date by doCountAtoms()
+  Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
   atomSet atoms; //<!list of atoms
@@ -131 +129 @@
   int getAtomCount() const;
   int doCountAtoms();
+  int getBondCount() const;
+  int doCountBonds() const;
   moleculeId_t getId() const;
   void setId(moleculeId_t);
@@ -169 +169 @@
   bool RemoveBonds(atom *BondPartner);
   bool hasBondStructure() const;
-  unsigned int CountBonds() const;
 
   /// Find atoms.