Changeset e472eab

Timestamp:

Jul 25, 2010, 9:41:34 PM (14 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:

521bbf

Parents:

8d4aa1

Message:

Added new all/none selection actions for atoms and molecules.

• new function World::getSelected...() needed for Undo/Redo of new (Not)AllAtoms/AllMoleculesActions.

Location:

src

Files:

• Actions/Makefile.am (modified) (1 diff)
• Actions/MapOfActions.cpp (modified) (7 diffs)
• Actions/SelectionAction/AllAtomsAction.cpp (added)
• Actions/SelectionAction/AllAtomsAction.hpp (added)
• Actions/SelectionAction/AllMoleculesAction.cpp (added)
• Actions/SelectionAction/AllMoleculesAction.hpp (added)
• Actions/SelectionAction/NotAllAtomsAction.cpp (added)
• Actions/SelectionAction/NotAllAtomsAction.hpp (added)
• Actions/SelectionAction/NotAllMoleculesAction.cpp (added)
• Actions/SelectionAction/NotAllMoleculesAction.hpp (added)
• World.cpp (modified) (4 diffs)
• World.hpp (modified) (1 diff)

src/Actions/Makefile.am

@@ -114 +114 @@
 
 SELECTIONACTIONSOURCE = \
+        SelectionAction/AllAtomsAction.cpp \
+        SelectionAction/AllMoleculesAction.cpp \
         SelectionAction/AtomByIdAction.cpp \
         SelectionAction/MoleculeByIdAction.cpp \
+        SelectionAction/NotAllAtomsAction.cpp \
+        SelectionAction/NotAllMoleculesAction.cpp \
         SelectionAction/NotAtomByIdAction.cpp \
         SelectionAction/NotMoleculeByIdAction.cpp
 SELECTIONACTIONHEADER = \
+        SelectionAction/AllAtomsAction.hpp \
+        SelectionAction/AllMoleculesAction.hpp \
         SelectionAction/AtomByIdAction.hpp \
         SelectionAction/MoleculeByIdAction.hpp \
+        SelectionAction/NotAllAtomsAction.hpp \
+        SelectionAction/NotAllMoleculesAction.hpp \
         SelectionAction/NotAtomByIdAction.hpp \
         SelectionAction/NotMoleculeByIdAction.hpp

src/Actions/MapOfActions.cpp

@@ -64 +64 @@
 #include "Actions/ParserAction/LoadXyzAction.hpp"
 #include "Actions/ParserAction/SaveXyzAction.hpp"
+#include "Actions/SelectionAction/AllAtomsAction.hpp"
+#include "Actions/SelectionAction/AllMoleculesAction.hpp"
 #include "Actions/SelectionAction/AtomByIdAction.hpp"
 #include "Actions/SelectionAction/MoleculeByIdAction.hpp"
+#include "Actions/SelectionAction/NotAllAtomsAction.hpp"
+#include "Actions/SelectionAction/NotAllMoleculesAction.hpp"
 #include "Actions/SelectionAction/NotAtomByIdAction.hpp"
 #include "Actions/SelectionAction/NotMoleculeByIdAction.hpp"
@@ -236 +240 @@
   DescriptionMap["periodic"] = "system is constraint to periodic boundary conditions (y/n)";
   DescriptionMap["position"] = "position in R^3 space";
+  DescriptionMap["select-all-atoms"] = "select all atoms";
+  DescriptionMap["select-all-molecules"] = "select all molecules";
   DescriptionMap["select-atom-by-id"] = "select an atom by index";
   DescriptionMap["select-molecule-by-id"] = "select a molecule by index";
   DescriptionMap["start-step"] = "first or start step";
+  DescriptionMap["unselect-all-atoms"] = "unselect all atoms";
+  DescriptionMap["unselect-all-molecules"] = "unselect all molecules";
   DescriptionMap["unselect-atom-by-id"] = "unselect an atom by index";
   DescriptionMap["unselect-molecule-by-id"] = "unselect a molecule by index";
@@ -343 +351 @@
   TypeMap["periodic"] = &typeid(bool);
   TypeMap["position"] = &typeid(VectorValue);
+  TypeMap["select-all-atoms"] = &typeid(void);
+  TypeMap["select-all-molecules"] = &typeid(void);
   TypeMap["select-atom-by-id"] = &typeid(atom);
   TypeMap["select-molecule-by-id"] = &typeid(molecule);
   TypeMap["start-step"] = &typeid(int);
+  TypeMap["unselect-all-atoms"] = &typeid(void);
+  TypeMap["unselect-all-molecules"] = &typeid(void);
   TypeMap["unselect-atom-by-id"] = &typeid(atom);
   TypeMap["unselect-molecule-by-id"] = &typeid(molecule);
@@ -475 +487 @@
   generic.insert("save-temperature");
   generic.insert("scale-box");
+  generic.insert("select-all-atoms");
+  generic.insert("select-all-molecules");
+  generic.insert("select-atom-by-id");
+  generic.insert("select-molecule-by-id");
   generic.insert("set-basis");
   generic.insert("set-output");
@@ -480 +496 @@
   generic.insert("suspend-in-water");
   generic.insert("translate-mol");
+  generic.insert("unselect-all-atoms");
+  generic.insert("unselect-all-molecules");
+  generic.insert("unselect-atom-by-id");
+  generic.insert("unselect-molecule-by-id");
         generic.insert("verbose");
   generic.insert("verlet-integrate");
@@ -507 +527 @@
   hidden.insert("periodic");
   hidden.insert("position");
-  hidden.insert("select-atom-by-id");
-  hidden.insert("select-molecule-by-id");
   hidden.insert("start-step");
-  hidden.insert("unselect-atom-by-id");
-  hidden.insert("unselect-molecule-by-id");
 }
 
@@ -790 +806 @@
   new ParserSaveXyzAction();
 
+  new SelectionAllAtomsAction();
+  new SelectionAllMoleculesAction();
   new SelectionAtomByIdAction();
   new SelectionMoleculeByIdAction();
+  new SelectionNotAllAtomsAction();
+  new SelectionNotAllMoleculesAction();
   new SelectionNotAtomByIdAction();
   new SelectionNotMoleculeByIdAction();

src/World.cpp

@@ -558 +558 @@
 }
 
-size_t World::countSelectedAtoms() {
+size_t World::countSelectedAtoms() const {
   size_t count = 0;
-  for (internal_AtomIterator iter = getAtomIter_internal(AllAtoms()); iter != atomEnd_internal(); ++iter)
+  for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
     count++;
   return count;
 }
 
-bool World::isSelected(atom *atom) {
+bool World::isSelected(atom *atom) const {
   return selectedAtoms.find(atom->getId()) != selectedAtoms.end();
 }
+
+const std::vector<atom *> World::getSelectedAtoms() const {
+  std::vector<atom *> returnAtoms;
+  returnAtoms.resize(countSelectedAtoms());
+  int count = 0;
+  for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
+    returnAtoms[count++] = iter->second;
+  return returnAtoms;
+}
+
 
 // Molecules
@@ -585 +595 @@
 }
 
-void World::selectAllMoleculess(MoleculeDescriptor descr){
+void World::selectAllMolecules(MoleculeDescriptor descr){
   internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
   internal_MoleculeIterator end = moleculeEnd_internal();
@@ -616 +626 @@
 }
 
-void World::unselectAllMoleculess(MoleculeDescriptor descr){
+void World::unselectAllMolecules(MoleculeDescriptor descr){
   internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
   internal_MoleculeIterator end = moleculeEnd_internal();
@@ -637 +647 @@
 }
 
-size_t World::countSelectedMolecules() {
+size_t World::countSelectedMolecules() const {
   size_t count = 0;
-  for (internal_MoleculeIterator iter = getMoleculeIter_internal(AllMolecules()); iter != moleculeEnd_internal(); ++iter)
+  for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
     count++;
   return count;
 }
 
-bool World::isSelected(molecule *mol) {
+bool World::isSelected(molecule *mol) const {
   return selectedMolecules.find(mol->getId()) != selectedMolecules.end();
+}
+
+const std::vector<molecule *> World::getSelectedMolecules() const {
+  std::vector<molecule *> returnMolecules;
+  returnMolecules.resize(countSelectedMolecules());
+  int count = 0;
+  for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
+    returnMolecules[count++] = iter->second;
+  return returnMolecules;
 }
 

src/World.hpp

@@ -264 +264 @@
   void unselectAtomsOfMolecule(molecule*);
   void unselectAtomsOfMolecule(moleculeId_t);
-  size_t countSelectedAtoms();
-  bool isSelected(atom *_atom);
+  size_t countSelectedAtoms() const;
+  bool isSelected(atom *_atom) const;
+  const std::vector<atom *> getSelectedAtoms() const;
 
   void clearMoleculeSelection();
   void selectMolecule(molecule*);
   void selectMolecule(moleculeId_t);
-  void selectAllMoleculess(MoleculeDescriptor);
+  void selectAllMolecules(MoleculeDescriptor);
   void selectMoleculeOfAtom(atom*);
   void selectMoleculeOfAtom(atomId_t);
   void unselectMolecule(molecule*);
   void unselectMolecule(moleculeId_t);
-  void unselectAllMoleculess(MoleculeDescriptor);
+  void unselectAllMolecules(MoleculeDescriptor);
   void unselectMoleculeOfAtom(atom*);
   void unselectMoleculeOfAtom(atomId_t);
-  size_t countSelectedMolecules();
-  bool isSelected(molecule *_mol);
+  size_t countSelectedMolecules() const;
+  bool isSelected(molecule *_mol) const;
+  const std::vector<molecule *> getSelectedMolecules() const;
 
   /******************** Iterators to selections *****************/