Changeset 8ea3e7 for src/Actions/MoleculeAction

Timestamp:

Jun 13, 2012, 5:39:03 PM (13 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:

97f9b9

Parents:

2382d7

git-author:

Frederik Heber <heber@…> (05/10/12 09:22:07)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:39:03)

Message:

CopyMolecule can now copy all currently selected molecules.

• this is both removal of molecule as parameter and enhancing the Action.
• also we added new UndoRedoHelper RemoveMoleculesWithAtomsByIds.
• CopyMoleculeAction::performRedo() simply calls performCall() which is now possible due to new parameter structure.
• TESTFIX: as we no longer specify the molecule to copy as argument of copy-molecule, regression test Molecules/Copy has been changed to prior select-molecule-by-id.

Location:

src/Actions/MoleculeAction

Files:

• CopyAction.cpp (modified) (5 diffs)
• CopyAction.def (modified) (1 diff)

src/Actions/MoleculeAction/CopyAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "Actions/UndoRedoHelpers.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
@@ -31 +32 @@
 #include <fstream>
 #include <string>
+#include <vector>
 
 #include "Actions/MoleculeAction/CopyAction.hpp"
@@ -40 +42 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-Action::state_ptr MoleculeCopyAction::performCall() {
-  molecule *copy = NULL;
+Action::state_ptr MoleculeCopyAction::performCall()
+{
+  std::vector<moleculeId_t> molecules;
+  for (World::MoleculeSelectionConstIterator iter = World::getInstance().beginMoleculeSelection();
+      iter != World::getInstance().endMoleculeSelection(); ++iter) {
+    molecule * const copy = (iter->second)->CopyMolecule();
+    Vector *Center = (iter->second)->DetermineCenterOfAll();
+    *Center *= -1.;
+    *Center += params.position.get();
+    copy->Translate(Center);
+    delete(Center);
+    molecules.push_back(copy->getId());
+  }
 
-  copy = params.mol.get()->CopyMolecule();
-  Vector *Center = params.mol.get()->DetermineCenterOfAll();
-  *Center *= -1.;
-  *Center += params.position.get();
-  copy->Translate(Center);
-  delete(Center);
-
-  return Action::state_ptr(new MoleculeCopyState(copy,params));
+  return Action::state_ptr(new MoleculeCopyState(molecules,params));
 }
 
@@ -56 +62 @@
   MoleculeCopyState *state = assert_cast<MoleculeCopyState*>(_state.get());
 
-  state->copy->removeAtomsinMolecule();
-  World::getInstance().destroyMolecule(state->copy);
+  RemoveMoleculesWithAtomsByIds(state->copies);
 
   return Action::state_ptr(_state);
@@ -63 +68 @@
 
 Action::state_ptr MoleculeCopyAction::performRedo(Action::state_ptr _state){
-  MoleculeCopyState *state = assert_cast<MoleculeCopyState*>(_state.get());
-
-  molecule *copy = state->params.mol.get()->CopyMolecule();
-  Vector *Center = state->params.mol.get()->DetermineCenterOfAll();
-  *Center *= -1.;
-  *Center += state->params.position.get();
-  copy->Translate(Center);
-  delete(Center);
-
-  return Action::state_ptr(new MoleculeCopyState(copy,state->params));
+  return performCall();
 }
 

src/Actions/MoleculeAction/CopyAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class MoleculeListClass;
+#include <vector>
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (const molecule *)(Vector)
-#define paramtokens ("copy-molecule")("position")
-#define paramdescriptions ("molecule to copy")("position in R^3 space")
+#define paramtypes (Vector)
+#define paramtokens ("position")
+#define paramdescriptions ("position in R^3 space")
 #undef paramdefaults
-#define paramreferences (mol)(position)
+#define paramreferences (position)
 
-#define statetypes (molecule *)
-#define statereferences (copy)
+#define statetypes (const std::vector<moleculeId_t>)
+#define statereferences (copies)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS