Changeset ca8bea for src/Actions/FragmentationAction

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/Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -37 +37 @@
 #include "Atom/atom.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -111 +112 @@
     LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
         << " atoms, out of " << mol->getAtomCount() << ".");
-    Fragmentation Fragmenter(mol, FileChecker, params.DoSaturation.get() ? DoSaturate : DontSaturate);
-    Fragmenter.setOutputTypes(params.types.get());
+    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
+    Fragmentation Fragmenter(mol, FileChecker, saturation);
 
     // perform fragmentation
@@ -123 +124 @@
         ExitFlag = tempFlag; // if we are the first, we set the standard
     }
+
+    // store molecule's fragment to file
+    ExportGraph_ToFiles exporter(Fragmenter.getGraph(), mol, saturation);
+    exporter.setPrefix(params.prefix.get());
+    exporter.setOutputTypes(params.types.get());
+    exporter();
   }
   World::getInstance().setExitFlag(ExitFlag);
   end = clock();
   LOG(0, "STATUS: Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s.");
+
 
   return Action::success;