Ignore:
Timestamp:
Oct 14, 2013, 11:42:03 PM (11 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:
adb51ab
Parents:
8dbcaf
git-author:
Frederik Heber <heber@…> (09/25/13 08:49:20)
git-committer:
Frederik Heber <heber@…> (10/14/13 23:42:03)
Message:

Added option DoCyclesFull to FragmentationAction.

  • FIX: Fragmentation::Fragmentation() has no need for a ref to DFS anymore.
  • DFS in FragmentationAction is now used for Cycle detection only.
  • CyclicStructureAnalysis::RetrieveCycleMembers() also fills internal vector with all found cycles (as KeySet's), with a getter.
File:
1 edited

Legend:

Unmodified
Added
Removed
  • src/Graph/CyclicStructureAnalysis.hpp

    r8dbcaf rfe0cb8  
    1616#include <deque>
    1717#include <map>
     18#include <vector>
    1819
    1920#include "Bond/bond.hpp"
    2021#include "Bond/GraphEdge.hpp"
     22#include "Fragmentation/KeySet.hpp"
    2123#include "Fragmentation/HydrogenSaturation_enum.hpp"
    2224#include "Helpers/defs.hpp"
     
    2931{
    3032public:
     33  //!> typedef for specifying a cycle
     34  typedef KeySet cycle_t;
     35  //!> typedef for specifying many cycles
     36  typedef std::vector< cycle_t > cycles_t;
     37
    3138  explicit CyclicStructureAnalysis(const enum HydrogenTreatment _treatment);
    3239  ~CyclicStructureAnalysis();
     
    3744  const std::map<atomId_t, int >& getMinimumRingSize() const;
    3845
     46  /** Getter for all found cycles.
     47   *
     48   */
     49  cycles_t getAllCycles() const {
     50    return allcycles;
     51  }
     52
    3953private:
     54
    4055  // init or reset
    4156  void InitNode(atomId_t atom_id);
     
    5974  atom *Root;
    6075
     76  //!> container for all found cycles, note that these are global ids
     77  cycles_t allcycles;
     78
    6179  //!> whether to treat hydrogen special or not
    6280  const enum HydrogenTreatment treatment;
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