Changeset 9317be

Timestamp:

Oct 20, 2011, 1:20:03 PM (13 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:

539f32

Parents:

025048

git-author:

Frederik Heber <heber@…> (10/20/11 13:18:47)

git-committer:

Frederik Heber <heber@…> (10/20/11 13:20:03)

Message:

Replaced molecule::atomVector by World::AtomComposite everywhere.

Location:

src

Files:

• Actions/GraphAction/SubgraphDissectionAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/BondFileAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (1 diff)
• Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) (1 diff)
• Analysis/unittests/CountBondsUnitTest.cpp (modified) (1 diff)
• Graph/unittests/BondGraphUnitTest.cpp (modified) (2 diffs)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (1 diff)

src/Actions/GraphAction/SubgraphDissectionAction.cpp

@@ -93 +93 @@
   if (mol->getBondCount() == 0) {
     BondGraph *BG = World::getInstance().getBondGraph();
-    molecule::atomVector Set = mol->getAtomSet();
+    World::AtomComposite Set = mol->getAtomSet();
     BG->CreateAdjacency(Set);
 //    if (mol->getBondCount() == 0) {

src/Actions/MoleculeAction/BondFileAction.cpp

@@ -50 +50 @@
         << ", adding " << params.id_offset << " to each id.");
     ifstream input(params.bondfile.string().c_str());
-    molecule::atomVector Set = mol->getAtomSet();
+    World::AtomComposite Set = mol->getAtomSet();
     World::getInstance().getBondGraph()->CreateAdjacencyListFromDbondFile(Set, &input, params.skiplines, params.id_offset);
     input.close();

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -73 +73 @@
   molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   filler->SetNameFromFilename(params.fillername.string().c_str());
-  molecule::atomVector Set = filler->getAtomSet();
+  World::AtomComposite Set = filler->getAtomSet();
   World::getInstance().getBondGraph()->CreateAdjacency(Set);
 

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -83 +83 @@
 //    filler->AddBond(first, third, 1);
 //    filler->AddBond(second, third, 1);
-  molecule::atomVector Set = filler->getAtomSet();
+  World::AtomComposite Set = filler->getAtomSet();
   World::getInstance().getBondGraph()->CreateAdjacency(Set);
 //    filler->SetNameFromFilename("water");

src/Analysis/unittests/AnalysisBondsUnitTest.cpp

@@ -109 +109 @@
   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(5,5) );
 
-  molecule::atomVector Set = TestMolecule->getAtomSet();
+  World::AtomComposite Set = TestMolecule->getAtomSet();
   BG->CreateAdjacency(Set);
 };

src/Analysis/unittests/CountBondsUnitTest.cpp

@@ -112 +112 @@
 
   // construct bond graphs
-  molecule::atomVector Set1 = TestMolecule1->getAtomSet();
+  World::AtomComposite Set1 = TestMolecule1->getAtomSet();
   BG->CreateAdjacency(Set1);
   CPPUNIT_ASSERT( TestMolecule1->getBondCount() != 0);
-  molecule::atomVector Set2 = TestMolecule2->getAtomSet();
+  World::AtomComposite Set2 = TestMolecule2->getAtomSet();
   BG->CreateAdjacency(Set2);
   CPPUNIT_ASSERT( TestMolecule2->getBondCount() != 0);

src/Graph/unittests/BondGraphUnitTest.cpp

@@ -151 +151 @@
   Runner++;
   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
-  molecule::atomVector Set = TestMolecule->getAtomSet();
+  World::AtomComposite Set = TestMolecule->getAtomSet();
   BG->CreateAdjacency(Set);
   CPPUNIT_ASSERT( TestMolecule->getBondCount() != 0);
@@ -163 +163 @@
 
   CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(dummy) );
-  molecule::atomVector Set = TestMolecule->getAtomSet();
+  World::AtomComposite Set = TestMolecule->getAtomSet();
   BG->CreateAdjacency(Set);
   CPPUNIT_ASSERT( TestMolecule->getBondCount() != 0);

src/molecule.cpp

@@ -233 +233 @@
 }
 
-molecule::atomVector molecule::getAtomSet() const
-{
-  atomVector vector_of_atoms;
+World::AtomComposite molecule::getAtomSet() const
+{
+  World::AtomComposite vector_of_atoms;
   BOOST_FOREACH(atom *_atom, atoms)
     vector_of_atoms.push_back(_atom);

src/molecule.hpp

@@ -69 +69 @@
 public:
   typedef ATOMSET(std::list) atomSet;
-  typedef ATOMSET(std::vector) atomVector;
   typedef std::set<atomId_t> atomIdSet;
   typedef ObservedIterator<atomSet> iterator;
@@ -125 +124 @@
   virtual bool changeId(atomId_t newId);
 
-  atomVector getAtomSet() const;
+  World::AtomComposite getAtomSet() const;
 
   iterator begin();

src/molecule_fragmentation.cpp

@@ -681 +681 @@
       ++iter) {
     // correct bond degree
-    molecule::atomVector Set = (*iter)->getAtomSet();
+    World::AtomComposite Set = (*iter)->getAtomSet();
     World::getInstance().getBondGraph()->CorrectBondDegree(Set);
   }