Changeset ca8bea for src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

Timestamp:

Dec 3, 2012, 9:49:59 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:

dcbb5d

Parents:

de0af2

git-author:

Frederik Heber <heber@…> (09/20/12 12:37:12)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:59)

Message:

ExportGraph_ToFiles performs now the storing of the generated Graph to files.

• FragmentMolecule now fills an internal graph.
• ExportGraph_ToFiles gets graph in cstor and writes the contained KeySets to file on call of operator().

File:

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

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

@@ -14 +14 @@
 #endif
 
+#include <string>
+#include <vector>
+
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Exporters/ExportGraph.hpp"
+#include "MoleculeListClass.hpp"
+
+class ListOfLocalAtoms_t;
 
 /** ExportGraph_ToFiles implements an ExportGraph as storing all fragmentary
@@ -22 +29 @@
 {
 public:
-        ExportGraph_ToFiles();
+        ExportGraph_ToFiles(const Graph &_graph, molecule *&_mol, const enum HydrogenSaturation _saturation);
+        virtual ~ExportGraph_ToFiles();
 
         void operator()();
+
+        void setPrefix(const std::string &_prefix) {
+          prefix = _prefix;
+        }
+
+        void setOutputTypes(const std::vector<std::string> &_typelist) {
+          typelist = _typelist;
+        }
+
+private:
+
+        void prepareMolecule();
+  molecule * StoreFragmentFromKeySet(molecule *mol, KeySet &Leaflet, bool IsAngstroem);
+  int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
+  void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
+  bool CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex);
+
+
+private:
+  //!> molecule as reference
+  molecule *mol;
+  //!> internal list of created molecules
+        MoleculeListClass BondFragments;
+        //!> prefix for fragment files
+        std::string prefix;
+  //!> list of parser types for which a configuration file per fragment is stored
+  std::vector<std::string> typelist;
+  //!> whether to saturate dangling bonds or not
+  const enum HydrogenSaturation saturation;
 };