Changeset 1c51c8

Timestamp:

Mar 3, 2010, 3:46:03 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:

88d586

Parents:

dbb474

Message:

Added methods for querying molecules using descriptors

Location:

src

Files:

• Descriptors/MoleculeDescriptor.cpp (added)
• Descriptors/MoleculeDescriptor.hpp (added)
• Descriptors/MoleculeDescriptor_impl.hpp (added)
• Makefile.am (modified) (1 diff)
• World.cpp (modified) (4 diffs)
• World.hpp (modified) (5 diffs)
• WorldIterators.cpp (modified) (3 diffs)
• molecule_template.hpp (modified) (1 diff)

src/Makefile.am

@@ -29 +29 @@
 LEGACYHEADER = Legacy/oldmenu.hpp
 
-DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp Descriptors/AtomTypeDescriptor.cpp
-DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp
+DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp Descriptors/AtomIdDescriptor.cpp Descriptors/AtomTypeDescriptor.cpp Descriptors/MoleculeDescriptor.cpp
+DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp Descriptors/AtomIdDescriptor.hpp Descriptors/AtomTypeDescriptor.hpp Descriptors/MoleculeDescriptor.hpp
 
 SOURCE = ${ANALYSISSOURCE} ${ATOMSOURCE} ${PATTERNSOURCE} ${UISOURCE} ${DESCRIPTORSOURCE} ${LEGACYSOURCE} bond.cpp bondgraph.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp errorlogger.cpp graph.cpp helpers.cpp info.cpp leastsquaremin.cpp linkedcell.cpp lists.cpp log.cpp logger.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp World.cpp WorldIterators.cpp

src/World.cpp

@@ -13 +13 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 #include "Actions/ManipulateAtomsProcess.hpp"
 
@@ -22 +24 @@
 }
 
+// Atoms
+
 atom* World::getAtom(AtomDescriptor descriptor){
   return descriptor.find();
@@ -36 +40 @@
 int World::numAtoms(){
   return atoms.size();
+}
+
+// Molecules
+
+molecule *World::getMolecule(MoleculeDescriptor descriptor){
+  return descriptor.find();
+}
+
+std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
+  return descriptor.findAll();
 }
 
@@ -135 +149 @@
 World::AtomSet::iterator World::atomEnd(){
   return atoms.end();
+}
+
+World::MoleculeIterator World::getMoleculeIter(MoleculeDescriptor descr){
+  return MoleculeIterator(descr,this);
+}
+
+World::MoleculeSet::iterator World::moleculeEnd(){
+  return molecules.end();
 }
 

src/World.hpp

@@ -27 +27 @@
 class AtomDescriptor;
 class AtomDescriptor_impl;
+class MoleculeDescriptor;
+class MoleculeDescriptor_impl;
 class ManipulateAtomsProcess;
 template<typename T>
@@ -36 +38 @@
 friend class AtomDescriptor_impl;
 friend class AtomDescriptor;
+friend class MoleculeDescriptor_impl;
+friend class MoleculeDescriptor;
 
 // Actions, calculations etc associated with the World
@@ -77 +81 @@
 
   /**
+   * returns the first molecule that matches a given descriptor.
+   * Do not rely on ordering for descriptors that match more than one molecule.
+   */
+  molecule *getMolecule(MoleculeDescriptor descriptor);
+
+  /**
+   * returns a vector containing all molecules that match a given descriptor
+   */
+  std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
+
+  /**
    * get the number of molecules in the World
    */
@@ -125 +140 @@
 protected:
   /**** Iterators to use internal data structures */
+
+  // Atoms
+
   class AtomIterator {
   public:
@@ -163 +181 @@
   AtomSet::iterator atomEnd();
 
+  // Molecules
+
+  class MoleculeIterator {
+  public:
+    MoleculeIterator();
+    MoleculeIterator(MoleculeDescriptor, World*);
+    MoleculeIterator(const MoleculeIterator&);
+    MoleculeIterator& operator=(const MoleculeIterator&);
+    MoleculeIterator& operator++();     // prefix
+    MoleculeIterator  operator++(int);  // postfix with dummy parameter
+    bool operator==(const MoleculeIterator&);
+    bool operator==(const MoleculeSet::iterator&);
+    bool operator!=(const MoleculeIterator&);
+    bool operator!=(const MoleculeSet::iterator&);
+    molecule* operator*();
+
+    int getCount();
+  protected:
+    void advanceState();
+    MoleculeSet::iterator state;
+    boost::shared_ptr<MoleculeDescriptor_impl>  descr;
+    int index;
+
+    World* world;
+  };
+
+  /**
+   * returns an iterator over all Molecules matching a given descriptor.
+   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
+   */
+  MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
+
+  /**
+   * returns an iterator to the end of the MoleculeSet. Due to overloading this iterator
+   * can be compared to iterators produced by getMoleculeIter (see the mis-matching types).
+   * Thus it can be used to detect when such an iterator is at the end of the list.
+   * used for internal purposes, like MoleculeProcesses and MoleculeCalculations.
+   */
+  MoleculeSet::iterator moleculeEnd();
+
+
   /******* Internal manipulation routines for double callback and Observer mechanism ******/
   void doManipulate(ManipulateAtomsProcess *);

src/WorldIterators.cpp

@@ -8 +8 @@
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
+#include "Descriptors/MoleculeDescriptor.hpp"
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 #include "atom.hpp"
+#include "molecule.hpp"
 #include "World.hpp"
+
+/********************** Atoms *************************/
 
 World::AtomIterator::AtomIterator(){
@@ -76 +81 @@
 
 void World::AtomIterator::advanceState(){
+  // go forward until we have a matching atom or the end is reached
   while((state!=world->atoms.end()) && (!descr->predicate(*state))){
     ++state;
@@ -85 +91 @@
   return index;
 }
+
+/*********************************** Molecules ************************/
+
+World::MoleculeIterator::MoleculeIterator(){
+  state = World::get()->moleculeEnd();
+}
+
+World::MoleculeIterator::MoleculeIterator(MoleculeDescriptor _descr, World* _world) :
+    descr(_descr.get_impl()),
+    index(0),
+    world(_world)
+{
+  state = world->molecules.begin();
+  advanceState();
+}
+
+World::MoleculeIterator::MoleculeIterator(const MoleculeIterator& rhs) :
+    state(rhs.state),
+    descr(rhs.descr),
+    index(rhs.index),
+    world(rhs.world)
+  {}
+
+World::MoleculeIterator& World::MoleculeIterator::operator=(const MoleculeIterator& rhs)
+{
+  if(&rhs!=this){
+    state=rhs.state;
+    descr=rhs.descr;
+    index=rhs.index;
+    world=rhs.world;
+  }
+  return *this;
+}
+
+World::MoleculeIterator& World::MoleculeIterator::operator++(){
+  ++state;
+  ++index;
+  advanceState();
+  return *this;
+}
+
+World::MoleculeIterator World::MoleculeIterator::operator++(int){
+  MoleculeIterator res(*this);
+  ++(*this);
+  return res;
+}
+
+bool World::MoleculeIterator::operator==(const MoleculeIterator& rhs){
+  return state==rhs.state;
+}
+
+bool World::MoleculeIterator::operator==(const World::MoleculeSet::iterator& rhs){
+  return state==rhs;
+}
+
+bool World::MoleculeIterator::operator!=(const MoleculeIterator& rhs){
+  return state!=rhs.state;
+}
+
+bool World::MoleculeIterator::operator!=(const World::MoleculeSet::iterator& rhs){
+  return state!=rhs;
+}
+
+molecule* World::MoleculeIterator::operator*(){
+  return (*state).second;
+}
+
+void World::MoleculeIterator::advanceState(){
+  while((state!=world->molecules.end()) && (!descr->predicate(*state))){
+    ++state;
+    ++index;
+  }
+}
+
+int World::MoleculeIterator::getCount(){
+  return index;
+}
+

src/molecule_template.hpp

@@ -16 +16 @@
 #endif
 
+#include "atom.hpp"
 /********************************************** declarations *******************************/