Changeset 1fd675 for src/Actions/FragmentationAction

Timestamp:

Aug 28, 2010, 12:57:56 AM (15 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:

966e12

Parents:

53d01c

git-author:

Frederik Heber <heber@…> (08/26/10 21:05:34)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:57:56)

Message:

All Actions are converted to the new macro framework.

• included all three values that have been used to create or convert the files
  • createdef.sh
  • createCpp.sh
  • createHeader.sh

Location:

src/Actions/FragmentationAction

Files:

• DepthFirstSearchAction.cpp (modified) (4 diffs)
• DepthFirstSearchAction.def (added)
• DepthFirstSearchAction.hpp (modified) (1 diff)
• FragmentationAction.cpp (modified) (3 diffs)
• FragmentationAction.def (added)
• FragmentationAction.hpp (modified) (1 diff)
• SubgraphDissectionAction.cpp (modified) (4 diffs)
• SubgraphDissectionAction.def (added)
• SubgraphDissectionAction.hpp (modified) (1 diff)

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -20 +20 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
-#include "Actions/ActionRegistry.hpp"
 #include "atom.hpp"
 #include "bondgraph.hpp"
@@ -38 +36 @@
 using namespace std;
 
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Dialog.hpp"
-#include "Actions/ValueStorage.hpp"
+#include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
 
-const char FragmentationDepthFirstSearchAction::NAME[] = "depth-first-search";
-
-FragmentationDepthFirstSearchAction::FragmentationDepthFirstSearchAction() :
-  Action(NAME)
-{}
-
-FragmentationDepthFirstSearchAction::~FragmentationDepthFirstSearchAction()
-{}
-
-void FragmentationDepthFirstSearch(double distance) {
-  ValueStorage::getInstance().setCurrentValue(FragmentationDepthFirstSearchAction::NAME, distance);
-  ActionRegistry::getInstance().getActionByName(FragmentationDepthFirstSearchAction::NAME)->call(Action::NonInteractive);
-};
-
-void FragmentationDepthFirstSearchAction::getParametersfromValueStorage()
-{};
-
-Dialog* FragmentationDepthFirstSearchAction::fillDialog(Dialog *dialog) {
-  ASSERT(dialog,"No Dialog given when filling action dialog");
-
-  dialog->queryDouble(NAME, ValueStorage::getInstance().getDescription(NAME));
-
-  return dialog;
-}
-
+// and construct the stuff
+#include "DepthFirstSearchAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
 Action::state_ptr FragmentationDepthFirstSearchAction::performCall() {
-  double distance;
-
-  ValueStorage::getInstance().queryCurrentValue(NAME, distance);
+  // obtain information
+  getParametersfromValueStorage();
 
   DoLog(1) && (Log() << Verbose(1) << "Depth-First-Search Analysis." << endl);
@@ -79 +53 @@
   class StackClass<bond *> *BackEdgeStack = NULL;
   class StackClass<bond *> *LocalBackEdgeStack = NULL;
-  mol->CreateAdjacencyList(distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+  mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   if (Subgraphs != NULL) {
@@ -121 +95 @@
   return NAME;
 }
+/** =========== end of function ====================== */

src/Actions/FragmentationAction/DepthFirstSearchAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-void FragmentationDepthFirstSearch(double distance);
-
-class FragmentationDepthFirstSearchAction : public Action {
-  friend void FragmentationDepthFirstSearch(double distance);
-
-public:
-  FragmentationDepthFirstSearchAction();
-  virtual ~FragmentationDepthFirstSearchAction();
-
-  bool canUndo();
-  bool shouldUndo();
-
-  virtual const std::string getName();
-protected:
-  virtual Dialog * fillDialog(Dialog *dialog);
-private:
-  virtual void getParametersfromValueStorage();
-  virtual Action::state_ptr performCall();
-  virtual Action::state_ptr performUndo(Action::state_ptr);
-  virtual Action::state_ptr performRedo(Action::state_ptr);
-
-  static const char NAME[];
-};
+#include "DepthFirstSearchAction.def"
+#include "Action_impl_header.hpp"
 
 #endif /* DEPTHFIRSTSEARCHACTION_HPP_ */

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -20 +20 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/FragmentationAction/FragmentationAction.hpp"
-#include "Actions/ActionRegistry.hpp"
 #include "atom.hpp"
 #include "bondgraph.hpp"
@@ -36 +34 @@
 using namespace std;
 
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Dialog.hpp"
-#include "Actions/ValueStorage.hpp"
+#include "Actions/FragmentationAction/FragmentationAction.hpp"
 
-const char FragmentationFragmentationAction::NAME[] = "fragment-mol";
-
-FragmentationFragmentationAction::FragmentationFragmentationAction() :
-  Action(NAME)
-{}
-
-FragmentationFragmentationAction::~FragmentationFragmentationAction()
-{}
-
-void FragmentationFragmentation(std::string &path, double distance, int order) {
-  ValueStorage::getInstance().setCurrentValue(FragmentationFragmentationAction::NAME, path);
-  ValueStorage::getInstance().setCurrentValue("distance", distance);
-  ValueStorage::getInstance().setCurrentValue("order", order);
-  ActionRegistry::getInstance().getActionByName(FragmentationFragmentationAction::NAME)->call(Action::NonInteractive);
-};
-
-void FragmentationFragmentationAction::getParametersfromValueStorage()
-{};
-
-Dialog* FragmentationFragmentationAction::fillDialog(Dialog *dialog) {
-  ASSERT(dialog,"No Dialog given when filling action dialog");
-
-  dialog->queryString(NAME, ValueStorage::getInstance().getDescription(NAME));
-  dialog->queryDouble("distance", ValueStorage::getInstance().getDescription("distance"));
-  dialog->queryInt("order", ValueStorage::getInstance().getDescription("order"));
-
-  return dialog;
-}
-
+// and construct the stuff
+#include "FragmentationAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
 Action::state_ptr FragmentationFragmentationAction::performCall() {
   clock_t start,end;
   molecule *mol = NULL;
-  double distance = -1.;
-  int order = 0;
-  std::string path;
   config *configuration = World::getInstance().getConfig();
   int ExitFlag = 0;
 
-  ValueStorage::getInstance().queryCurrentValue(NAME, path);
-  ValueStorage::getInstance().queryCurrentValue("distance", distance);
-  ValueStorage::getInstance().queryCurrentValue("order", order);
+  // obtain information
+  getParametersfromValueStorage();
 
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
     ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
-    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << distance << " angstroem, order of " << order << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << params.distance << " angstroem, order of " << params.order << "." << endl);
     DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
     start = clock();
-    mol->CreateAdjacencyList(distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+    mol->CreateAdjacencyList(params.distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
     DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
     if (mol->hasBondStructure()) {
-      ExitFlag = mol->FragmentMolecule(order, path);
+      ExitFlag = mol->FragmentMolecule(params.order, params.path);
     }
     World::getInstance().setExitFlag(ExitFlag);
@@ -119 +86 @@
   return NAME;
 }
+/** =========== end of function ====================== */

src/Actions/FragmentationAction/FragmentationAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-void FragmentationFragmentation(std::string &path, double distance, int order);
-
-class FragmentationFragmentationAction : public Action {
-  friend void FragmentationFragmentation(std::string &path, double distance, int order);
-
-public:
-  FragmentationFragmentationAction();
-  virtual ~FragmentationFragmentationAction();
-
-  bool canUndo();
-  bool shouldUndo();
-
-  virtual const std::string getName();
-protected:
-  virtual Dialog * fillDialog(Dialog *dialog);
-private:
-  virtual void getParametersfromValueStorage();
-  virtual Action::state_ptr performCall();
-  virtual Action::state_ptr performUndo(Action::state_ptr);
-  virtual Action::state_ptr performRedo(Action::state_ptr);
-
-  static const char NAME[];
-};
+#include "FragmentationAction.def"
+#include "Action_impl_header.hpp"
 
 #endif /* FRAGMENTATIONACTION_HPP_ */

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -20 +20 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
-#include "Actions/ActionRegistry.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
@@ -38 +36 @@
 #include <string>
 
+typedef std::map< moleculeId_t, std::vector<atomId_t> > MolAtomList;
+
 using namespace std;
 
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Dialog.hpp"
-#include "Actions/ValueStorage.hpp"
+#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 
-// memento to remember the state when undoing
+// and construct the stuff
+#include "SubgraphDissectionAction.def"
+#include "Action_impl_pre.hpp"
+/** =========== define the function ====================== */
+Action::state_ptr FragmentationSubgraphDissectionAction::performCall() {
+  // obtain information
+  getParametersfromValueStorage();
 
-typedef std::map< moleculeId_t, std::vector<atomId_t> > MolAtomList;
-
-class FragmentationSubgraphDissectionState : public ActionState {
-public:
-  FragmentationSubgraphDissectionState(const MolAtomList &_moleculelist) :
-   moleculelist(_moleculelist)
-  {}
-  MolAtomList moleculelist;
-};
-
-const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
-
-FragmentationSubgraphDissectionAction::FragmentationSubgraphDissectionAction() :
-  Action(NAME)
-{}
-
-FragmentationSubgraphDissectionAction::~FragmentationSubgraphDissectionAction()
-{}
-
-/** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
- */
-void FragmentationSubgraphDissection() {
-  ActionRegistry::getInstance().getActionByName(FragmentationSubgraphDissectionAction::NAME)->call(Action::NonInteractive);
-};
-
-void FragmentationSubgraphDissectionAction::getParametersfromValueStorage()
-{};
-
-Dialog* FragmentationSubgraphDissectionAction::fillDialog(Dialog *dialog) {
-  ASSERT(dialog,"No Dialog given when filling action dialog");
-
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
-
-  return dialog;
-}
-
-
-Action::state_ptr FragmentationSubgraphDissectionAction::performCall() {
   DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
 
@@ -97 +63 @@
     moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
   }
-  FragmentationSubgraphDissectionState *UndoState = new FragmentationSubgraphDissectionState(moleculelist);
+  FragmentationSubgraphDissectionState *UndoState = new FragmentationSubgraphDissectionState(moleculelist, params);
 
   MoleculeListClass *molecules = World::getInstance().getMolecules();
@@ -213 +179 @@
   return NAME;
 }
+/** =========== end of function ====================== */

src/Actions/FragmentationAction/SubgraphDissectionAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 
-void FragmentationSubgraphDissection();
-
-class FragmentationSubgraphDissectionAction : public Action {
-  friend void FragmentationSubgraphDissection();
-
-public:
-  FragmentationSubgraphDissectionAction();
-  virtual ~FragmentationSubgraphDissectionAction();
-
-  bool canUndo();
-  bool shouldUndo();
-
-  virtual const std::string getName();
-protected:
-  virtual Dialog * fillDialog(Dialog *dialog);
-private:
-  virtual void getParametersfromValueStorage();
-  virtual Action::state_ptr performCall();
-  virtual Action::state_ptr performUndo(Action::state_ptr);
-  virtual Action::state_ptr performRedo(Action::state_ptr);
-
-  static const char NAME[];
-};
+#include "SubgraphDissectionAction.def"
+#include "Action_impl_header.hpp"
 
 #endif /* SUBGRAPHDISSECTIONACTION_HPP_ */