Changeset c42e60 for src

Timestamp:

Dec 16, 2010, 5:32:23 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:

1a0987

Parents:

fc5c3a

git-author:

Frederik Heber <heber@…> (12/11/10 21:05:11)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:23)

Message:

Two new descriptors: AtomOfMoleculeSelection, MoleculeOfAtomSelection. Rewrote associated SelectionActions.

• AtomOfMoleculeSelectionDescriptor: represents all atoms of currently selected molecules
• MoleculeOfAtomSelectionDescriptor: represents all molecules of currently selected atoms
• rewrote Selection(Not)AllAtomsOfMoleculeAction: simply uses selectAllAtoms() and descriptor, no parameter anymore
• rewrote Selection(Not)MoleculeOfAtomAction: simply uses selectedAllMolecules() and descriptor, no parameter anymore
• renamed (un)select-molecule-of-atom to (un)select-atoms-molecules.

That is, the SelectionActions are meant to use one selection and turn the
other accordingly. It is a sort of exchange between the two. I can convert
a selection of atoms to molecules and vica versa, but this "mapping" is NOT
injective but always surjective.

Testchange:

• Selection/Atoms/testsuite-selection-atoms-of-molecule.at: Due to the absent parameter now, we first select the molecule by id and then ...

Location:

src

Files:

• Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) (4 diffs)
• Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (modified) (2 diffs)
• Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) (4 diffs)
• Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (modified) (2 diffs)
• Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) (3 diffs)
• Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (modified) (2 diffs)
• Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) (3 diffs)
• Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (modified) (2 diffs)
• Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (added)
• Descriptors/AtomOfMoleculeSelectionDescriptor.hpp (added)
• Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (added)
• Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (added)
• Descriptors/MoleculeOfAtomSelectionDescriptor.hpp (added)
• Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (added)
• Makefile.am (modified) (5 diffs)

src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp

@@ -21 +21 @@
 
 #include "Descriptors/AtomSelectionDescriptor.hpp"
+#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
 #include "atom.hpp"
 #include "molecule.hpp"
@@ -43 +44 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Selecting all atoms of molecule " << params.mol->getName() << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Selecting all atoms of currently selected molecule." << endl);
   std::vector<atom *> selectedAtoms = World::getInstance().getAllAtoms(AtomsBySelection());
-  World::getInstance().selectAtomsOfMolecule(params.mol);
+  World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
   return Action::state_ptr(new SelectionAllAtomsOfMoleculeState(selectedAtoms, params));
 }
@@ -52 +53 @@
   SelectionAllAtomsOfMoleculeState *state = assert_cast<SelectionAllAtomsOfMoleculeState*>(_state.get());
 
-  World::getInstance().unselectAtomsOfMolecule(state->params.mol);
+  World::getInstance().clearAtomSelection();
   BOOST_FOREACH(atom *_atom, state->selectedAtoms)
     World::getInstance().selectAtom(_atom);
@@ -62 +63 @@
   SelectionAllAtomsOfMoleculeState *state = assert_cast<SelectionAllAtomsOfMoleculeState*>(_state.get());
 
-  World::getInstance().selectAtomsOfMolecule(state->params.mol);
+  World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def

@@ -12 +12 @@
 // 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 *)
-#define paramtokens ("select-molecules-atoms")
-#define paramdescriptions ("molecule to select")
+#undef paramtypes
+#undef paramtokens
+#undef paramdescriptions
 #undef paramdefaults
-#define paramreferences (mol)
+#undef paramreferences
 
 #define statetypes (std::vector<atom*>)
@@ -30 +30 @@
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "select all atoms of a molecule"
+#define DESCRIPTION "select all atoms of currently selected molecules"
 #undef SHORTFORM

src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp

@@ -21 +21 @@
 
 #include "Descriptors/AtomSelectionDescriptor.hpp"
+#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
 #include "atom.hpp"
 #include "molecule.hpp"
@@ -43 +44 @@
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Unselecting all atoms of molecule " << params.mol->getName() << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Unselecting all atoms of currently selected molecules." << endl);
   std::vector<atom *> unselectedAtoms = World::getInstance().getAllAtoms(!AtomsBySelection());
-  World::getInstance().unselectAtomsOfMolecule(params.mol);
+  World::getInstance().unselectAllAtoms(AtomsByMoleculeSelection());
   return Action::state_ptr(new SelectionNotAllAtomsOfMoleculeState(unselectedAtoms, params));
 }
@@ -52 +53 @@
   SelectionNotAllAtomsOfMoleculeState *state = assert_cast<SelectionNotAllAtomsOfMoleculeState*>(_state.get());
 
-  World::getInstance().selectAtomsOfMolecule(state->params.mol);
+  World::getInstance().selectAllAtoms(AllAtoms());
   BOOST_FOREACH(atom *_atom, state->unselectedAtoms)
     World::getInstance().unselectAtom(_atom);
@@ -60 +61 @@
 
 Action::state_ptr SelectionNotAllAtomsOfMoleculeAction::performRedo(Action::state_ptr _state){
-  SelectionNotAllAtomsOfMoleculeState *state = assert_cast<SelectionNotAllAtomsOfMoleculeState*>(_state.get());
+  //SelectionNotAllAtomsOfMoleculeState *state = assert_cast<SelectionNotAllAtomsOfMoleculeState*>(_state.get());
 
-  World::getInstance().unselectAtomsOfMolecule(state->params.mol);
+  World::getInstance().unselectAllAtoms(AtomsByMoleculeSelection());
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def

@@ -12 +12 @@
 // 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*)
-#define paramtokens ("unselect-molecules-atoms")
-#define paramdescriptions ("molecule")
+#undef paramtypes
+#undef paramtokens
+#undef paramdescriptions
 #undef paramdefaults
-#define paramreferences (mol)
+#undef paramreferences
 
 #define statetypes (std::vector<atom*>)
@@ -30 +30 @@
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "unselect all atoms of a molecule"
+#define DESCRIPTION "unselect all atoms of currently selected molecules"
 #undef SHORTFORM

src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp

@@ -21 +21 @@
 
 #include "Descriptors/MoleculeDescriptor.hpp"
-#include "atom.hpp"
+#include "Descriptors/MoleculeOfAtomSelectionDescriptor.hpp"
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
@@ -43 +43 @@
 
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
-  DoLog(1) && (Log() << Verbose(1) << "Selecting molecule to which " << params.Walker->getName() << " belongs." << endl);
-  World::getInstance().selectMoleculeOfAtom(params.Walker);
+  DoLog(1) && (Log() << Verbose(1) << "Selecting molecule to currently selected atoms." << endl);
+  World::getInstance().selectAllMolecules(MoleculesByAtomSelection());
   return Action::state_ptr(new SelectionMoleculeOfAtomState(selectedMolecules, params));
 }
@@ -59 +59 @@
 
 Action::state_ptr SelectionMoleculeOfAtomAction::performRedo(Action::state_ptr _state){
-  SelectionMoleculeOfAtomState *state = assert_cast<SelectionMoleculeOfAtomState*>(_state.get());
+  //SelectionMoleculeOfAtomState *state = assert_cast<SelectionMoleculeOfAtomState*>(_state.get());
 
-  World::getInstance().selectMoleculeOfAtom(state->params.Walker);
+  World::getInstance().selectAllMolecules(MoleculesByAtomSelection());
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def

@@ -11 +11 @@
 // 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 atom*)
-#define paramtokens ("select-molecule-of-atom")
-#define paramdescriptions ("one atom of desired molecule")
+#undef paramtypes
+#undef paramtokens
+#undef paramdescriptions
 #undef paramdefaults
-#define paramreferences (Walker)
+#undef paramreferences
 
 #define statetypes (std::vector<molecule*>)
@@ -25 +25 @@
 #define MENUPOSITION 11
 #define ACTIONNAME MoleculeOfAtom
-#define TOKEN "select-molecule-of-atom"
+#define TOKEN "select-atoms-molecules"
 
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "select a molecule to which a given atom belongs"
+#define DESCRIPTION "select all molecules of currently selected atoms"
 #undef SHORTFORM

src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp

@@ -21 +21 @@
 
 #include "Descriptors/MoleculeDescriptor.hpp"
-#include "atom.hpp"
+#include "Descriptors/MoleculeOfAtomSelectionDescriptor.hpp"
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
@@ -43 +43 @@
 
   std::vector<molecule *> unselectedMolecules = World::getInstance().getSelectedMolecules();
-  DoLog(1) && (Log() << Verbose(1) << "Unselecting molecule to which " << params.Walker->getName() << " belongs." << endl);
-  World::getInstance().unselectMoleculeOfAtom(params.Walker);
+  DoLog(1) && (Log() << Verbose(1) << "Unselecting molecule to currently selected atoms." << endl);
+  World::getInstance().unselectAllMolecules(MoleculesByAtomSelection());
   return Action::state_ptr(new SelectionNotMoleculeOfAtomState(unselectedMolecules, params));
 }
@@ -59 +59 @@
 
 Action::state_ptr SelectionNotMoleculeOfAtomAction::performRedo(Action::state_ptr _state){
-  SelectionNotMoleculeOfAtomState *state = assert_cast<SelectionNotMoleculeOfAtomState*>(_state.get());
+  //SelectionNotMoleculeOfAtomState *state = assert_cast<SelectionNotMoleculeOfAtomState*>(_state.get());
 
-  World::getInstance().unselectMoleculeOfAtom(state->params.Walker);
+  World::getInstance().unselectAllMolecules(MoleculesByAtomSelection());
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def

@@ -11 +11 @@
 // 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 atom*)
-#define paramtokens ("unselect-molecule-of-atom")
-#define paramdescriptions ("one atom of desired molecule")
+#undef paramtypes
+#undef paramtokens
+#undef paramdescriptions
 #undef paramdefaults
-#define paramreferences (Walker)
+#undef paramreferences
 
 #define statetypes (std::vector<molecule*>)
@@ -25 +25 @@
 #define MENUPOSITION 21
 #define ACTIONNAME NotMoleculeOfAtom
-#define TOKEN "unselect-molecule-of-atom"
+#define TOKEN "unselect-atoms-molecules"
 
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "unselect a molecule to which a given atom belongs"
+#define DESCRIPTION "unselect all molecules of currently selected atoms"
 #undef SHORTFORM

src/Makefile.am

@@ -84 +84 @@
 
   
-DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
+DESCRIPTORSOURCE = \
+        Descriptors/AtomDescriptor.cpp \
   Descriptors/AtomIdDescriptor.cpp \
+  Descriptors/AtomOfMoleculeSelectionDescriptor.cpp \
   Descriptors/AtomSelectionDescriptor.cpp \
   Descriptors/AtomShapeDescriptor.cpp \
@@ -93 +95 @@
   Descriptors/MoleculeIdDescriptor.cpp \
   Descriptors/MoleculeNameDescriptor.cpp \
+  Descriptors/MoleculeOfAtomSelectionDescriptor.cpp \
   Descriptors/MoleculeOrderDescriptor.cpp \
   Descriptors/MoleculePtrDescriptor.cpp \
@@ -98 +101 @@
                                    
 
-DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp \
+DESCRIPTORHEADER = \
+        Descriptors/AtomDescriptor.hpp \
   Descriptors/AtomIdDescriptor.hpp \
+  Descriptors/AtomOfMoleculeSelectionDescriptor.hpp \
   Descriptors/AtomSelectionDescriptor.hpp \
   Descriptors/AtomShapeDescriptor.hpp \
@@ -107 +112 @@
   Descriptors/MoleculeIdDescriptor.hpp \
   Descriptors/MoleculeNameDescriptor.hpp \
+  Descriptors/MoleculeOfAtomSelectionDescriptor.hpp \
   Descriptors/MoleculeOrderDescriptor.hpp \
   Descriptors/MoleculePtrDescriptor.hpp \
-  Descriptors/MoleculeSelectionDescriptor.cpp
+  Descriptors/MoleculeSelectionDescriptor.hpp
+  
+DESCRIPTORIMPLHEADER = \
+        Descriptors/AtomDescriptor_impl.hpp \
+  Descriptors/AtomIdDescriptor_impl.hpp \
+  Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp \
+  Descriptors/AtomSelectionDescriptor_impl.hpp \
+  Descriptors/AtomShapeDescriptor_impl.hpp \
+  Descriptors/AtomTypeDescriptor_impl.hpp \
+  Descriptors/MoleculeDescriptor_impl.hpp \
+  Descriptors/MoleculeFormulaDescriptor_impl.hpp \
+  Descriptors/MoleculeIdDescriptor_impl.hpp \
+  Descriptors/MoleculeNameDescriptor_impl.hpp \
+  Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp \
+  Descriptors/MoleculeOrderDescriptor_impl.hpp \
+  Descriptors/MoleculePtrDescriptor_impl.hpp \
+  Descriptors/MoleculeSelectionDescriptor_impl.hpp
   
 THERMOSTATSOURCE = \
@@ -193 +215 @@
   ${SHAPEHEADER} \
   ${DESCRIPTORHEADER} \
+  ${DESCRIPTORIMPLHEADER} \
   ${THERMOSTATHEADER} \
   ${TESSELATIONHEADER} \