Changeset e73ad9a for src/molecule.hpp

Timestamp:

Mar 2, 2011, 9:53:08 PM (15 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:

1a4d4fe

Parents:

2e4105

git-author:

Frederik Heber <heber@…> (02/25/11 20:52:50)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

Moved CyclicStructureAnalysis from molecule_graph.cpp into own functor in Graph/.

• libMolecuilderGraph needed by libMolecuilderAction and libMolecuilder now.
• replacing call to CyclicStructureAnalysis in molecule::FragmentMolecule() required removing MinimumRingSize from ::FragmentBOSSANOVA() and ::CheckOrderAtSite().
• replaced call in DepthFirstSearchAction.

File:

• src/molecule.hpp (modified) (3 diffs)

src/molecule.hpp

@@ -210 +210 @@
   // Graph analysis
   MoleculeLeafClass * DepthFirstSearchAnalysis(std::deque<bond *> *&BackEdgeStack) const;
-  void CyclicStructureAnalysis(std::deque<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
   bool PickLocalBackEdges(atom **ListOfLocalAtoms, std::deque<bond *> *&ReferenceStack, std::deque<bond *> *&LocalStack) const;
   bond * FindNextUnused(atom *vertex) const;
@@ -224 +223 @@
   /// Fragment molecule by two different approaches:
   int FragmentMolecule(int Order, std::string &prefix);
-  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
+  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path = "");
   bool StoreBondsToFile(std::string filename, std::string path = "");
   bool StoreAdjacencyToFile(std::string filename, std::string path = "");
@@ -235 +234 @@
 
   /// -# BOSSANOVA
-  void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
+  void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack);
   int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
   bool BuildInducedSubgraph(const molecule *Father);