Changeset 9511c7

Timestamp:

Dec 3, 2012, 9:49:30 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:

b9401e

Parents:

06f41f3

git-author:

Frederik Heber <heber@…> (09/19/12 14:03:25)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

CheckAgainstAdjacencyFile is now instantiated in FragmentationAction not in Fragmentation.

• CheckAgainstAdjacencyFile was changed to have the adjacency structure from the file for precisely this purpose.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)
• Fragmentation/Fragmentation.cpp (modified) (2 diffs)
• Fragmentation/Fragmentation.hpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp ¶

@@ -39 +39 @@
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Graph/CheckAgainstAdjacencyFile.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
+#include "Helpers/defs.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
@@ -83 +85 @@
   LOG(1, "INFO: There are " << clusters.size()  << " molecules to consider.");
 
+  // parse in Adjacency file
+  std::ifstream File;
+  std::string filename;
+  filename = params.prefix.get() + ADJACENCYFILE;
+  File.open(filename.c_str(), ios::out);
+  CheckAgainstAdjacencyFile FileChecker(File);
+
   DepthFirstSearchAnalysis DFS;
   start = clock();
@@ -102 +111 @@
     LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
         << " atoms, out of " << mol->getAtomCount() << ".");
-    Fragmentation Fragmenter(mol, params.DoSaturation.get() ? DoSaturate : DontSaturate);
+    Fragmentation Fragmenter(mol, FileChecker, params.DoSaturation.get() ? DoSaturate : DontSaturate);
     Fragmenter.setOutputTypes(params.types.get());
 

src/Fragmentation/Fragmentation.cpp ¶

@@ -66 +66 @@
  *
  * \param _mol molecule for internal use (looking up atoms)
+ * \param _FileChecker instance contains adjacency parsed from elsewhere
  * \param _saturation whether to treat hydrogen special and saturate dangling bonds or not
  */
-Fragmentation::Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation) :
+Fragmentation::Fragmentation(molecule *_mol, CheckAgainstAdjacencyFile &_FileChecker, const enum HydrogenSaturation _saturation) :
   mol(_mol),
-  saturation(_saturation)
+  saturation(_saturation),
+  FileChecker(_FileChecker)
 {}
 
@@ -131 +133 @@
   // === compare it with adjacency file ===
   {
-    std::ifstream File;
-    std::string filename;
-    filename = prefix + ADJACENCYFILE;
-    File.open(filename.c_str(), ios::out);
-    LOG(1, "Looking at bond structure stored in adjacency file and comparing to present one ... ");
-
-    CheckAgainstAdjacencyFile FileChecker(File);
     const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
     FragmentationToDo = FragmentationToDo && FileChecker(globalids);

src/Fragmentation/Fragmentation.hpp ¶

@@ -26 +26 @@
 class atom;
 class AtomMask_t;
+class CheckAgainstAdjacencyFile;
 class Graph;
 class KeySet;
@@ -33 +34 @@
 {
 public:
-  Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation);
+  Fragmentation(molecule *_mol, CheckAgainstAdjacencyFile &_FileChecker, const enum HydrogenSaturation _saturation);
   ~Fragmentation();
 
@@ -64 +65 @@
   //!> list of parser types for which a configuration file per fragment is stored
   std::vector<std::string> typelist;
+  //!> reference to an external adjacency for comparison
+  CheckAgainstAdjacencyFile &FileChecker;
 };