Changeset 8652a30 for src/Fragmentation/Exporters/ExportGraph.hpp

Timestamp:

Apr 8, 2013, 11:56:08 AM (12 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:

3b0d2a

Parents:

22b786

git-author:

Frederik Heber <heber@…> (03/03/13 08:03:22)

git-committer:

Frederik Heber <heber@…> (04/08/13 11:56:08)

Message:

Moved some functions from ExportGraph_ToFiles into ExportGraph.

• this is preparatory for ExportGraph_ToJobs as the functions for creating molecules are needed there, too.

File:

• src/Fragmentation/Exporters/ExportGraph.hpp (modified) (2 diffs)

src/Fragmentation/Exporters/ExportGraph.hpp

@@ -14 +14 @@
 #endif
 
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Fragmentation/Exporters/ExportGraph.hpp"
+#include "MoleculeListClass.hpp"
+
 #include "Fragmentation/Graph.hpp"
+
+class ListOfLocalAtoms_t;
+class molecule;
 
 /** ExportGraph is an interface definition of a class that takes a fragmented
@@ -27 +34 @@
 {
 public:
-        ExportGraph(const Graph &_graph);
+  ExportGraph(
+      const Graph &_graph,
+      const enum HydrogenTreatment _treatment,
+      const enum HydrogenSaturation _saturation);
         virtual ~ExportGraph();
 
-        virtual void operator()()=0;
+        virtual void operator()();
+
+private:
+
+  void prepareMolecule();
+  molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
+  int StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
+  void CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
 
 protected:
-        const Graph &TotalGraph;
+  const Graph &TotalGraph;
+  //!> internal list of created molecules
+  MoleculeListClass BondFragments;
+  //!> whether to always add already present hydrogens or not
+  const enum HydrogenTreatment treatment;
+  //!> whether to saturate dangling bonds or not
+  const enum HydrogenSaturation saturation;
 };