Changeset 90c4280 for src/World.cpp

Timestamp:

Jul 15, 2010, 3:30:55 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

61d655e

Parents:

c084cc

Message:

Added several methods for selecting specific atoms in the World

File:

• src/World.cpp (modified) (4 diffs)

src/World.cpp

@@ -9 +9 @@
 
 #include "World.hpp"
-#include "Patterns/ObservedContainer_impl.hpp"
+
+#include <functional>
 
 #include "atom.hpp"
@@ -28 +29 @@
 
 #include "Patterns/Singleton_impl.hpp"
+#include "Patterns/ObservedContainer_impl.hpp"
 
 using namespace std;
@@ -485 +487 @@
 }
 
+/************************** Selection of Atoms and molecules ******************/
+
+// Atoms
+
+void World::clearAtomSelection(){
+  selectedAtoms.clear();
+}
+
+void World::selectAtom(atom *atom){
+  ASSERT(atom,"Invalid pointer in selection of atom");
+  selectedAtoms[atom->getId()]=atom;
+}
+
+void World::selectAtom(atomId_t id){
+  ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
+  selectedAtoms[id]=atoms[id];
+}
+
+void World::selectAllAtoms(AtomDescriptor descr){
+  internal_AtomIterator begin = getAtomIter_internal(descr);
+  internal_AtomIterator end = atomEnd_internal();
+  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
+  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
+}
+
+void World::selectAtomsOfMolecule(molecule *_mol){
+  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
+  // need to make it const to get the fast iterators
+  const molecule *mol = _mol;
+  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
+  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
+}
+
+void World::selectAtomsOfMolecule(moleculeId_t id){
+  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
+  selectAtomsOfMolecule(molecules[id]);
+}
+
+// Molecules
+
+void World::clearMoleculeSelection(){
+  selectedMolecules.clear();
+}
+
+void World::selectMolecule(molecule *mol){
+  ASSERT(mol,"Invalid pointer to molecule in selection");
+  selectedMolecules[mol->getId()]=mol;
+}
+
+void World::selectMolecule(moleculeId_t id){
+  ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
+  selectedMolecules[id]=molecules[id];
+}
+
+void World::selectAllMoleculess(MoleculeDescriptor descr){
+  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
+  internal_MoleculeIterator end = moleculeEnd_internal();
+  void (World::*func)(molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
+  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
+}
+
+void World::selectMoleculeOfAtom(atom *atom){
+  ASSERT(atom,"Invalid atom pointer in selection of MoleculeOfAtom");
+  molecule *mol=atom->getMolecule();
+  // the atom might not be part of a molecule
+  if(mol){
+    selectMolecule(mol);
+  }
+}
+
+void World::selectMoleculeOfAtom(atomId_t id){
+  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
+  selectMoleculeOfAtom(atoms[id]);
+}
+
 /******************************* Singleton Stuff **************************/
 
@@ -494 +571 @@
     ExitFlag(0),
     atoms(this),
+    selectedAtoms(this),
     currAtomId(0),
     lastAtomPoolSize(0),
     numAtomDefragSkips(0),
     molecules(this),
+    selectedMolecules(this),
     currMoleculeId(0),
     molecules_deprecated(new MoleculeListClass(this))