Changeset 49c059 for src/molecule.hpp

Timestamp:

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

2fa1dc

Parents:

1a4d4fe

git-author:

Frederik Heber <heber@…> (02/25/11 22:15:31)

git-committer:

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

Message:

Moved DepthFirstSearchAnalysis into functor in Graph/.

Smaller fixes:

• molecule::CorrectBondDegree() - does not rely on BondCount which was not necessary anyway.

• DFS does not copy atoms or molecules anymore but reinitiates the current molecule structure with present atoms, used new class ConnectedSubgraph for that. New functions:
  • UpdateMoleculeStructure() - reinstantiates molecules.
  • getMoleculeStructure() - puts molecules into chained list.
• adapted because of that:
  • DepthFirstSearchAction: uses DFS and CSA functors, also UpdateMoleculeStructure() such that CSA has current structure.
  • FragmentationAction: assumes connectivity fully present, DFS created.
  • SubgraphDissectionAction: uses DFS and UpdateMoleculeStructure().
  • molecule::FragmentMolecule(): no more DFS, instead DFS has to happen beforehand and is given as parameter, used to obtain chained list for compatibility for the moment.
• DepthFirstSearchAnalysis::SetNextComponentNumber() bugfix due to wrong assert.

TESTFIXES:

• Fragmentation and regression test Fragmentation/FragmentMolecule: FragmentationAction now needs SubgraphDissectionAction beforehand.
• shifted id (down by one) due to non-copying (before: one big molecule, copied and split up system started at 1, now it starts at 0):
  • (Un)Selection/Atoms/AllAtomsOfMolecule
  • Analysis/SurfaceCorrelation
  • (Un)Selection/Molecules/MoleculeById (also renamed post-files accordingly)
  • (Un)Selection/Molecules/MoleculeByName

File:

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

src/molecule.hpp

@@ -39 +39 @@
 class BondedParticle;
 class BondGraph;
+class DepthFirstSearchAnalysis;
 class element;
 class ForceMatrix;
@@ -204 +205 @@
   /// Initialising routines in fragmentation
   void OutputBondsList() const;
-  void CyclicBondAnalysis() const;
-  void OutputGraphInfoPerAtom() const;
-  void OutputGraphInfoPerBond() const;
-
-  // Graph analysis
-  MoleculeLeafClass * DepthFirstSearchAnalysis(std::deque<bond *> *&BackEdgeStack) const;
-  bool PickLocalBackEdges(atom **ListOfLocalAtoms, std::deque<bond *> *&ReferenceStack, std::deque<bond *> *&LocalStack) const;
-  bond * FindNextUnused(atom *vertex) const;
-  void SetNextComponentNumber(atom *vertex, int nr) const;
-  void ResetAllBondsToUnused() const;
-  int CountCyclicBonds();
-  bool CheckForConnectedSubgraph(KeySet *Fragment);
+
   bond * CopyBond(atom *left, atom *right, bond *CopyBond);
 
@@ -222 +212 @@
 
   /// Fragment molecule by two different approaches:
-  int FragmentMolecule(int Order, std::string &prefix);
+  int FragmentMolecule(int Order, std::string &prefix, DepthFirstSearchAnalysis &DFS);
   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path = "");
   bool StoreBondsToFile(std::string filename, std::string path = "");
@@ -259 +249 @@
 
 private:
-  void init_DFS(struct DFSAccounting&) const;
   int last_atom; //!< number given to last atom
 };