Changeset 90c4280


Ignore:
Timestamp:
Jul 15, 2010, 3:30:55 PM (14 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

Location:
src
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • src/World.cpp

    rc084cc r90c4280  
    99
    1010#include "World.hpp"
    11 #include "Patterns/ObservedContainer_impl.hpp"
     11
     12#include <functional>
    1213
    1314#include "atom.hpp"
     
    2829
    2930#include "Patterns/Singleton_impl.hpp"
     31#include "Patterns/ObservedContainer_impl.hpp"
    3032
    3133using namespace std;
     
    485487}
    486488
     489/************************** Selection of Atoms and molecules ******************/
     490
     491// Atoms
     492
     493void World::clearAtomSelection(){
     494  selectedAtoms.clear();
     495}
     496
     497void World::selectAtom(atom *atom){
     498  ASSERT(atom,"Invalid pointer in selection of atom");
     499  selectedAtoms[atom->getId()]=atom;
     500}
     501
     502void World::selectAtom(atomId_t id){
     503  ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
     504  selectedAtoms[id]=atoms[id];
     505}
     506
     507void World::selectAllAtoms(AtomDescriptor descr){
     508  internal_AtomIterator begin = getAtomIter_internal(descr);
     509  internal_AtomIterator end = atomEnd_internal();
     510  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
     511  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
     512}
     513
     514void World::selectAtomsOfMolecule(molecule *_mol){
     515  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
     516  // need to make it const to get the fast iterators
     517  const molecule *mol = _mol;
     518  void (World::*func)(atom*) = &World::selectAtom; // needed for type resolution of overloaded function
     519  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
     520}
     521
     522void World::selectAtomsOfMolecule(moleculeId_t id){
     523  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
     524  selectAtomsOfMolecule(molecules[id]);
     525}
     526
     527// Molecules
     528
     529void World::clearMoleculeSelection(){
     530  selectedMolecules.clear();
     531}
     532
     533void World::selectMolecule(molecule *mol){
     534  ASSERT(mol,"Invalid pointer to molecule in selection");
     535  selectedMolecules[mol->getId()]=mol;
     536}
     537
     538void World::selectMolecule(moleculeId_t id){
     539  ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
     540  selectedMolecules[id]=molecules[id];
     541}
     542
     543void World::selectAllMoleculess(MoleculeDescriptor descr){
     544  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
     545  internal_MoleculeIterator end = moleculeEnd_internal();
     546  void (World::*func)(molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
     547  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
     548}
     549
     550void World::selectMoleculeOfAtom(atom *atom){
     551  ASSERT(atom,"Invalid atom pointer in selection of MoleculeOfAtom");
     552  molecule *mol=atom->getMolecule();
     553  // the atom might not be part of a molecule
     554  if(mol){
     555    selectMolecule(mol);
     556  }
     557}
     558
     559void World::selectMoleculeOfAtom(atomId_t id){
     560  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
     561  selectMoleculeOfAtom(atoms[id]);
     562}
     563
    487564/******************************* Singleton Stuff **************************/
    488565
     
    494571    ExitFlag(0),
    495572    atoms(this),
     573    selectedAtoms(this),
    496574    currAtomId(0),
    497575    lastAtomPoolSize(0),
    498576    numAtomDefragSkips(0),
    499577    molecules(this),
     578    selectedMolecules(this),
    500579    currMoleculeId(0),
    501580    molecules_deprecated(new MoleculeListClass(this))
  • src/World.hpp

    rc084cc r90c4280  
    222222   * All these iterators are observed to track changes.
    223223   * There is a corresponding protected section with unobserved iterators,
    224    * which ca be used internally when the extra speed is needed
     224   * which can be used internally when the extra speed is needed
    225225   */
    226226
     
    239239  typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
    240240
     241  /**
     242   * returns an iterator over all Molecules matching a given descriptor.
     243   * This iterator is observed, so don't keep it around unnecessary to
     244   * avoid unintended blocking.
     245   */
    241246  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
    242247  MoleculeIterator getMoleculeIter();
    243248
    244249  MoleculeIterator moleculeEnd();
     250
     251  /******** Selections of molecules and Atoms *************/
     252  void clearAtomSelection();
     253  void selectAtom(atom*);
     254  void selectAtom(atomId_t);
     255  void selectAllAtoms(AtomDescriptor);
     256  void selectAtomsOfMolecule(molecule*);
     257  void selectAtomsOfMolecule(moleculeId_t);
     258
     259  void clearMoleculeSelection();
     260  void selectMolecule(molecule*);
     261  void selectMolecule(moleculeId_t);
     262  void selectAllMoleculess(MoleculeDescriptor);
     263  void selectMoleculeOfAtom(atom*);
     264  void selectMoleculeOfAtom(atomId_t);
    245265
    246266protected:
     
    311331
    312332  AtomSet atoms;
     333  AtomSet selectedAtoms;
    313334  typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
    314335  /**
     
    323344
    324345  MoleculeSet molecules;
     346  MoleculeSet selectedMolecules;
    325347  typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
    326348  /**
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