Changeset be97a8 for src/Descriptors

Timestamp:

Jul 20, 2010, 1:01:11 PM (15 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, Candidate_v1.7.0, 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:

3d078d, 4b6777, c644a5

Parents:

ba9f5b (diff), 818eda (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'StructureRefactoring' into stable

Conflicts:

test_all.sh

• test_all.sh was modified by Till in StructureRefactoring (these changes taken over).
• World::setDomain() was missing OBSERVE macro.
• MapOfActions: "molecule-by-name" needs String not Molecule.
• TESTFIX: Tesselations/defs.in - paths changed such that @srcdir@ may be absolute.
• TESTFIX: Tesselations/heptan/1.5/NonConvexEnvelope.dat - exchanged due to same surface but different polygon triangulation.
• TESTFIX: Domain/4 molecule-by-id changed from 208 to 207 due to different handling of molecule ids.

Location:

src/Descriptors

Files:

• AtomDescriptor.cpp (modified) (4 diffs)
• AtomDescriptor_impl.hpp (modified) (1 diff)
• AtomIdDescriptor.cpp (modified) (2 diffs)
• AtomSelectionDescriptor.cpp (added)
• AtomSelectionDescriptor.hpp (added)
• AtomSelectionDescriptor_impl.hpp (added)
• MoleculeDescriptor.cpp (modified) (3 diffs)
• MoleculeDescriptor_impl.hpp (modified) (1 diff)
• MoleculeIdDescriptor.cpp (modified) (2 diffs)
• MoleculeSelectionDescriptor.cpp (added)
• MoleculeSelectionDescriptor.hpp (added)
• MoleculeSelectionDescriptor_impl.hpp (added)

src/Descriptors/AtomDescriptor.cpp

@@ -13 +13 @@
 #include "World.hpp"
 #include "atom.hpp"
+#include "Patterns/ObservedContainer_impl.hpp"
 
 #include <boost/bind.hpp>
@@ -20 +21 @@
 using namespace std;
 
-typedef World::AtomSet::iterator atoms_iter_t;
+typedef World::AtomSet::internal_iterator atoms_iter_t;
 
 /************************ Forwarding object **************************************/
@@ -73 +74 @@
 
 atom* AtomDescriptor_impl::find() {
-  World::AtomSet atoms = getAtoms();
-  atoms_iter_t res = find_if(atoms.begin(),atoms.end(),boost::bind(&AtomDescriptor_impl::predicate,this,_1));
-  return (res!=atoms.end())?((*res).second):0;
+  World::AtomSet &atoms = getAtoms();
+  atoms_iter_t res = find_if(atoms.begin_internal(),atoms.end_internal(),boost::bind(&AtomDescriptor_impl::predicate,this,_1));
+  return (res!=atoms.end_internal())?((*res).second):0;
 }
 
@@ -81 +82 @@
   vector<atom*> res;
   World::AtomSet atoms = getAtoms();
-  atoms_iter_t iter;
-  for(iter=atoms.begin();iter!=atoms.end();++iter) {
-    if(predicate(*iter)){
-      res.push_back((*iter).second);
-    }
+  for_each(atoms.begin_internal(),
+           atoms.end_internal(),
+           boost::bind(&AtomDescriptor_impl::checkAndAdd,
+                       this,&res,_1));
+  return res;
+}
+
+void AtomDescriptor_impl::checkAndAdd(std::vector<atom*> *v,std::pair<atomId_t,atom*> p){
+  if(predicate(p)){
+    v->push_back(p.second);
   }
-  return res;
 }
 

src/Descriptors/AtomDescriptor_impl.hpp

@@ -50 +50 @@
    */
   World::AtomSet& getAtoms();
+
+  void checkAndAdd(std::vector<atom*>*,std::pair<atomId_t,atom*>);
 };
 

src/Descriptors/AtomIdDescriptor.cpp

@@ -12 +12 @@
 
 #include "atom.hpp"
+#include "Patterns/ObservedContainer_impl.hpp"
 
 using namespace std;
@@ -32 +33 @@
 
 atom *AtomIdDescriptor_impl::find(){
-  World::AtomSet atoms = getAtoms();
+  World::AtomSet &atoms = getAtoms();
   World::AtomSet::iterator res = atoms.find(id);
   return (res!=atoms.end())?((*res).second):0;

src/Descriptors/MoleculeDescriptor.cpp

@@ -12 +12 @@
 
 #include "World.hpp"
+#include "Patterns/ObservedContainer_impl.hpp"
 
 #include "molecule.hpp"
@@ -20 +21 @@
 using namespace std;
 
-typedef World::MoleculeSet::iterator molecules_iter_t;
+typedef World::MoleculeSet::internal_iterator molecules_iter_t;
 
 /************************ Forwarding object **************************************/
@@ -73 +74 @@
 
 molecule* MoleculeDescriptor_impl::find() {
-  World::MoleculeSet molecules = getMolecules();
-  molecules_iter_t res = find_if(molecules.begin(),molecules.end(),boost::bind(&MoleculeDescriptor_impl::predicate,this,_1));
-  return (res!=molecules.end())?((*res).second):0;
+  World::MoleculeSet &molecules = getMolecules();
+  molecules_iter_t res = find_if(molecules.begin_internal(),molecules.end_internal(),boost::bind(&MoleculeDescriptor_impl::predicate,this,_1));
+  return (res!=molecules.end_internal())?((*res).second):0;
 }
 
 vector<molecule*> MoleculeDescriptor_impl::findAll() {
   vector<molecule*> res;
-  World::MoleculeSet molecules = getMolecules();
-  molecules_iter_t iter;
-  for(iter=molecules.begin();iter!=molecules.end();++iter) {
-    if(predicate(*iter)){
-      res.push_back((*iter).second);
-    }
+  World::MoleculeSet &molecules = getMolecules();
+  for_each(molecules.begin_internal(),
+           molecules.end_internal(),
+           boost::bind(&MoleculeDescriptor_impl::checkAndAdd,
+                       this,&res,_1));
+  return res;
+}
+
+void MoleculeDescriptor_impl::checkAndAdd(std::vector<molecule*> *v,std::pair<moleculeId_t,molecule*> p){
+  if(predicate(p)){
+    v->push_back(p.second);
   }
-  return res;
 }
 

src/Descriptors/MoleculeDescriptor_impl.hpp

@@ -50 +50 @@
    */
   World::MoleculeSet& getMolecules();
+
+  void checkAndAdd(std::vector<molecule*>*,std::pair<moleculeId_t,molecule*>);
 };
 

src/Descriptors/MoleculeIdDescriptor.cpp

@@ -10 +10 @@
 #include "MoleculeIdDescriptor.hpp"
 #include "MoleculeIdDescriptor_impl.hpp"
+
+#include "Patterns/ObservedContainer_impl.hpp"
 
 #include "molecule.hpp"
@@ -32 +34 @@
 
 molecule *MoleculeIdDescriptor_impl::find(){
-  World::MoleculeSet molecules = getMolecules();
+  World::MoleculeSet &molecules = getMolecules();
   World::MoleculeSet::iterator res = molecules.find(id);
   return (res!=molecules.end())?((*res).second):0;