Changeset 3501d2

Timestamp:

Dec 3, 2012, 9:49:06 AM (12 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:

bf42a0

Parents:

2a0eb0

git-author:

Frederik Heber <heber@…> (09/19/12 10:11:12)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:06)

Message:

REFACTOR: CheckAgainstAdjacencyFile now gets File in cstor.

• we cannot have multiple files, but we may have multiple fragmentations. Hence, CheckAgainstAdjacencyFile should get and parse the File in its cstor and get a set of atoms in its operator() to check against.

Location:

src

Files:

• Fragmentation/Fragmentation.cpp (modified) (1 diff)
• Graph/CheckAgainstAdjacencyFile.cpp (modified) (4 diffs)
• Graph/CheckAgainstAdjacencyFile.hpp (modified) (2 diffs)
• Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) (7 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -136 +136 @@
     LOG(1, "Looking at bond structure stored in adjacency file and comparing to present one ... ");
 
-    CheckAgainstAdjacencyFile FileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
-    FragmentationToDo = FragmentationToDo && FileChecker(File);
+    CheckAgainstAdjacencyFile FileChecker(File);
+    FragmentationToDo = FragmentationToDo && FileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
   }
 

src/Graph/CheckAgainstAdjacencyFile.cpp

@@ -51 +51 @@
 #include "World.hpp"
 
-CheckAgainstAdjacencyFile::CheckAgainstAdjacencyFile(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd) :
+/** Constructor of class CheckAgainstAdjacencyFile.
+ *
+ * \param File file to parser
+ */
+CheckAgainstAdjacencyFile::CheckAgainstAdjacencyFile(std::istream &File) :
   status(true),
   NonMatchNumber(0)
 {
-  CreateInternalMap(AtomMapBegin, AtomMapEnd);
+  ParseInExternalMap(File);
 }
 
@@ -113 +117 @@
  * @param AtomMapEnd iterator pointing past end of map (think of World's SelectionIterator)
  */
-void CheckAgainstAdjacencyFile::CreateInternalMap(World::AtomSet::const_iterator &AtomMapBegin, World::AtomSet::const_iterator &AtomMapEnd)
+void CheckAgainstAdjacencyFile::CreateInternalMap(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd)
 {
   InternalAtomBondMap.clear();
@@ -136 +140 @@
 
 /** Checks contents of adjacency file against bond structure in structure molecule.
- * \param File file to parser
  * \return true - structure is equal, false - not equivalence
  */
-bool CheckAgainstAdjacencyFile::operator()(std::istream &File)
+bool CheckAgainstAdjacencyFile::operator()(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd)
 {
   LOG(0, "STATUS: Looking at bond structure stored in adjacency file and comparing to present one ... ");
@@ -145 +148 @@
   bool status = true;
 
-  status = status && ParseInExternalMap(File);
+  if (InternalAtomBondMap.empty())
+    CreateInternalMap(AtomMapBegin, AtomMapEnd);
+
   status = status && CompareInternalExternalMap();
 

src/Graph/CheckAgainstAdjacencyFile.hpp

@@ -28 +28 @@
   friend class CheckAgainstAdjacencyFileTest;
 public:
-  CheckAgainstAdjacencyFile(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd);
+  CheckAgainstAdjacencyFile(std::istream &File);
   ~CheckAgainstAdjacencyFile();
 
-  bool operator()(std::istream &File);
+  bool operator()(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd);
 
 private:
@@ -47 +47 @@
   ValuesSet getValues(const AtomBondRange&_range) const;
 
-  void CreateInternalMap(World::AtomSet::const_iterator &AtomMapBegin, World::AtomSet::const_iterator &AtomMapEnd);
+  void CreateInternalMap(World::AtomSet::const_iterator AtomMapBegin, World::AtomSet::const_iterator AtomMapEnd);
   bool ParseInExternalMap(std::istream &File);
   bool CompareInternalExternalMap();

src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp

@@ -101 +101 @@
 void CheckAgainstAdjacencyFileTest::setUp()
 {
+  // failing asserts should be thrown
+  ASSERT_DO(Assert::Throw);
+
   const element *hydrogen = World::getInstance().getPeriode()->FindElement(1);
   CPPUNIT_ASSERT(hydrogen != NULL);
-
-  // failing asserts should be thrown
-  ASSERT_DO(Assert::Throw);
 
   TestMolecule = World::getInstance().createMolecule();
@@ -148 +148 @@
 void CheckAgainstAdjacencyFileTest::CreateInternalMapTest()
 {
+  std::stringstream input;
+  CheckAgainstAdjacencyFile fileChecker(input);
   World::getInstance().selectAllAtoms(AllAtoms());
-  CheckAgainstAdjacencyFile fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
+  const World &world = World::getInstance();
+  fileChecker.CreateInternalMap(world.beginAtomSelection(), world.endAtomSelection());
 
   // check size (it's 8*2 + 2*1 = 18 keys)
@@ -178 +181 @@
   std::stringstream input(adjacencyfile);
   World::getInstance().selectAllAtoms(NoAtoms());
-  CheckAgainstAdjacencyFile fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
-  fileChecker.ParseInExternalMap(input);
+  CheckAgainstAdjacencyFile fileChecker(input);
+  fileChecker.CreateInternalMap(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
 
   // check size (it's 8*2 + 2*1 = 18 keys)
@@ -204 +207 @@
 void CheckAgainstAdjacencyFileTest::CompareInternalExternalMapTest()
 {
-  World::getInstance().selectAllAtoms(AllAtoms());
-  CheckAgainstAdjacencyFile fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
+  std::stringstream input(adjacencyfile);
+  CheckAgainstAdjacencyFile fileChecker(input);
 
   // assert non-equality before parsing
@@ -213 +216 @@
 
   // parse
-  std::stringstream input(adjacencyfile);
-  fileChecker.ParseInExternalMap(input);
+  World::getInstance().selectAllAtoms(AllAtoms());
+  fileChecker.CreateInternalMap(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
 
   // assert equality after parsing
@@ -228 +231 @@
 {
   World::getInstance().selectAllAtoms(AllAtoms());
-  CheckAgainstAdjacencyFile fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
   {
     // parse right
     std::stringstream input(adjacencyfile);
-    CPPUNIT_ASSERT( fileChecker(input) );
+    CheckAgainstAdjacencyFile fileChecker(input);
+    CPPUNIT_ASSERT( fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection()) );
   }
   {
     // parse wrong1
     std::stringstream input(wrongadjacencyfile1);
-    CPPUNIT_ASSERT( !fileChecker(input) );
+    CheckAgainstAdjacencyFile fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection()) );
   }
   {
@@ -244 +248 @@
 #ifndef NDEBUG
     std::cout << "The following Assert failures are intended and do not indicate a failure of the test." << std::endl;
-    CPPUNIT_ASSERT_THROW( fileChecker(input), Assert::AssertionFailure );
+    CPPUNIT_ASSERT_THROW( CheckAgainstAdjacencyFile fileChecker(input), Assert::AssertionFailure );
 #else
-    CPPUNIT_ASSERT( !fileChecker(input) );
+    CheckAgainstAdjacencyFile fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection()) );
 #endif
   }