Changeset 715b67

Timestamp:

Mar 1, 2011, 10:16:39 AM (14 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:

d4a44c

Parents:

7adf0f

git-author:

Frederik Heber <heber@…> (02/18/11 14:43:09)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

Renamed BondGraph::ConstructBondGraph -> CreateAdjacencyForMolecule.

• first step in moving CreateAdjacencyList over to class BondGraph.

Location:

src

Files:

• Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/SaveBondsAction.cpp (modified) (1 diff)
• bondgraph.cpp (modified) (1 diff)
• bondgraph.hpp (modified) (1 diff)
• unittests/AnalysisBondsUnitTest.cpp (modified) (1 diff)
• unittests/BondGraphUnitTest.cpp (modified) (3 diffs)
• unittests/CountBondsUnitTest.cpp (modified) (1 diff)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -92 +92 @@
   if (BondCount == 0) {
     BondGraph *BG = World::getInstance().getBondGraph();
-    if (!BG->ConstructBondGraph(mol)) {
+    if (!BG->CreateAdjacencyForMolecule(mol)) {
       World::getInstance().destroyMolecule(mol);
       DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -73 +73 @@
   molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   filler->SetNameFromFilename(params.fillername.string().c_str());
-  World::getInstance().getBondGraph()->ConstructBondGraph(filler);
+  World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(filler);
 
   // call routine

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -84 +84 @@
 //    filler->AddBond(first, third, 1);
 //    filler->AddBond(second, third, 1);
-  World::getInstance().getBondGraph()->ConstructBondGraph(filler);
+  World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(filler);
 //    filler->SetNameFromFilename("water");
   // TODO: Remove the erasure of molecule when saving does not depend on them anymore.

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -49 +49 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Storing adjacency to path " << params.adjacencyfile << "." << endl);
-    World::getInstance().getBondGraph()->ConstructBondGraph(mol);
+    World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(mol);
     // TODO: sollte stream nicht filename benutzen, besser fuer unit test
     mol->StoreAdjacencyToFile(params.adjacencyfile.leaf(), params.adjacencyfile.branch_path().string());

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -49 +49 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << params.bondsfile << "." << endl);
-    World::getInstance().getBondGraph()->ConstructBondGraph(mol);
+    World::getInstance().getBondGraph()->CreateAdjacencyForMolecule(mol);
     // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
     mol->StoreBondsToFile(params.bondsfile.leaf(), params.bondsfile.branch_path().string());

src/bondgraph.cpp

@@ -89 +89 @@
 };
 
-bool BondGraph::ConstructBondGraph(molecule * const mol)
+bool BondGraph::CreateAdjacencyForMolecule(molecule * const mol)
 {
   Info FunctionInfo(__func__);

src/bondgraph.hpp

@@ -51 +51 @@
   bool LoadBondLengthTable(std::istream &input);
 
-  /** Parses the bond lengths in a given file and puts them int a matrix form.
-   * \param *out output stream for debugging
+  /** Creates the bond list for all atoms in a given molecule.
    * \param *mol molecule with atoms
    * \return true - success, false - failed to construct bond structure
    */
-  bool ConstructBondGraph(molecule * const mol);
+  bool CreateAdjacencyForMolecule(molecule * const mol);
 
   /** Returns the entry for a given index pair.

src/unittests/AnalysisBondsUnitTest.cpp

@@ -109 +109 @@
   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(5,5) );
 
-  BG->ConstructBondGraph(TestMolecule);
+  BG->CreateAdjacencyForMolecule(TestMolecule);
 };
 

src/unittests/BondGraphUnitTest.cpp

@@ -139 +139 @@
 };
 
-/** UnitTest for BondGraphTest::ConstructBondGraph().
+/** UnitTest for BondGraphTest::CreateAdjacencyForMolecule().
  */
 void BondGraphTest::ConstructGraphFromTableTest()
@@ -147 +147 @@
   Runner++;
   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );
+  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule) );
   CPPUNIT_ASSERT_EQUAL( true , (*Walker)->IsBondedTo(WorldTime::getTime(), (*Runner)) );
 };
 
-/** UnitTest for BondGraphTest::ConstructBondGraph().
+/** UnitTest for BondGraphTest::CreateAdjacencyForMolecule().
  */
 void BondGraphTest::ConstructGraphFromCovalentRadiiTest()
@@ -157 +157 @@
 
   CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(dummy) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );
+  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule) );
 
   // this cannot be assured using dynamic IDs

src/unittests/CountBondsUnitTest.cpp

@@ -112 +112 @@
 
   // construct bond graphs
-  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule1) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule2) );
+  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule1) );
+  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule2) );
 //  TestMolecule1->Output((ofstream *)&cout);
 //  TestMolecule1->OutputBondsList();