Changeset 0fad93

Timestamp:

Dec 3, 2012, 9:50:01 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:

5197e5

Parents:

91207d

git-author:

Frederik Heber <heber@…> (09/20/12 16:31:44)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

Renamed CheckAgainstAdjacencyFile -> AdjacencyList.

• operator() is now CheckAgainstSubset().

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (2 diffs)
• Fragmentation/Fragmentation.cpp (modified) (3 diffs)
• Fragmentation/Fragmentation.hpp (modified) (3 diffs)
• Graph/AdjacencyList.cpp (moved) (moved from src/Graph/CheckAgainstAdjacencyFile.cpp ) (12 diffs)
• Graph/AdjacencyList.hpp (moved) (moved from src/Graph/CheckAgainstAdjacencyFile.hpp ) (4 diffs)
• Graph/Makefile.am (modified) (2 diffs)
• Graph/unittests/AdjacencyListUnitTest.cpp (moved) (moved from src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp ) (11 diffs)
• Graph/unittests/AdjacencyListUnitTest.hpp (moved) (moved from src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp ) (6 diffs)
• Graph/unittests/Makefile.am (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -41 +41 @@
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
+#include "Graph/AdjacencyList.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "Helpers/defs.hpp"
@@ -95 +95 @@
   filename = params.prefix.get() + ADJACENCYFILE;
   File.open(filename.c_str(), ios::out);
-  CheckAgainstAdjacencyFile FileChecker(File);
+  AdjacencyList FileChecker(File);
 
   DepthFirstSearchAnalysis DFS;

src/Fragmentation/Fragmentation.cpp

@@ -54 +54 @@
 #include "Fragmentation/UniqueFragments.hpp"
 #include "Graph/BondGraph.hpp"
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
+#include "Graph/AdjacencyList.hpp"
 #include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
@@ -66 +66 @@
  * \param _saturation whether to treat hydrogen special and saturate dangling bonds or not
  */
-Fragmentation::Fragmentation(molecule *_mol, CheckAgainstAdjacencyFile &_FileChecker, const enum HydrogenSaturation _saturation) :
+Fragmentation::Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenSaturation _saturation) :
   mol(_mol),
   saturation(_saturation),
@@ -124 +124 @@
   {
     const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
-    FragmentationToDo = FragmentationToDo && FileChecker(globalids);
+    FragmentationToDo = FragmentationToDo && FileChecker.CheckAgainstSubset(globalids);
   }
 

src/Fragmentation/Fragmentation.hpp

@@ -27 +27 @@
 class atom;
 class AtomMask_t;
-class CheckAgainstAdjacencyFile;
+class AdjacencyList;
 class KeySet;
 class molecule;
@@ -34 +34 @@
 {
 public:
-  Fragmentation(molecule *_mol, CheckAgainstAdjacencyFile &_FileChecker, const enum HydrogenSaturation _saturation);
+  Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenSaturation _saturation);
   ~Fragmentation();
 
@@ -64 +64 @@
   const enum HydrogenSaturation saturation;
   //!> reference to an external adjacency for comparison
-  CheckAgainstAdjacencyFile &FileChecker;
+  AdjacencyList &FileChecker;
   //!> Resulting Graph with all keysets
   Graph TotalGraph;

src/Graph/AdjacencyList.cpp

@@ -22 +22 @@
 
 /*
- * CheckAgainstAdjacencyFile.cpp
+ * AdjacencyList.cpp
  *
  *  Created on: Mar 3, 2011
@@ -40 +40 @@
 #include <utility>
 
-#include "CheckAgainstAdjacencyFile.hpp"
+#include "AdjacencyList.hpp"
 
 #include "Atom/atom.hpp"
@@ -51 +51 @@
 #include "World.hpp"
 
-/** Constructor of class CheckAgainstAdjacencyFile.
+/** Constructor of class AdjacencyList.
  *
  * \param File file to parser
  */
-CheckAgainstAdjacencyFile::CheckAgainstAdjacencyFile(std::istream &File) :
+AdjacencyList::AdjacencyList(std::istream &File) :
   NonMatchNumber(0)
 {
@@ -63 +63 @@
 }
 
-CheckAgainstAdjacencyFile::~CheckAgainstAdjacencyFile()
+AdjacencyList::~AdjacencyList()
 {}
 
@@ -71 +71 @@
  * @return true - everything ok, false - error while parsing
  */
-bool CheckAgainstAdjacencyFile::ParseInInternalMap(std::istream &File)
+bool AdjacencyList::ParseInInternalMap(std::istream &File)
 {
   if (File.fail()) {
@@ -113 +113 @@
  * @param atomids set of atomic ids to check (must be global ids, i.e. from atom::getId())
  */
-void CheckAgainstAdjacencyFile::CreateExternalMap(const atomids_t &atomids)
+void AdjacencyList::CreateExternalMap(const atomids_t &atomids)
 {
   ExternalAtomBondMap.clear();
@@ -120 +120 @@
     const atomId_t WalkerId = *iter;
     ASSERT(WalkerId != (size_t)-1,
-        "CheckAgainstAdjacencyFile::CreateExternalMap() - Walker has no id.");
+        "AdjacencyList::CreateExternalMap() - Walker has no id.");
     const atom *Walker = World::getInstance().getAtom(AtomById(WalkerId));
     ASSERT( Walker != NULL,
-        "CheckAgainstAdjacencyFile::CreateExternalMap() - Walker id "+toString(*iter)
+        "AdjacencyList::CreateExternalMap() - Walker id "+toString(*iter)
         +" is not associated to any of World's atoms.");
     const BondList& ListOfBonds = Walker->getListOfBonds();
@@ -132 +132 @@
       const atomId_t id = (*Runner)->GetOtherAtom(Walker)->getId();
       ASSERT(id != (size_t)-1,
-          "CheckAgainstAdjacencyFile::CreateExternalMap() - OtherAtom has not id.");
+          "AdjacencyList::CreateExternalMap() - OtherAtom has not id.");
       ExternalAtomBondMap.insert( std::make_pair(WalkerId, id) );
     }
@@ -141 +141 @@
  * \return true - structure is equal, false - not equivalence
  */
-bool CheckAgainstAdjacencyFile::operator()(const atomids_t &atomids)
+bool AdjacencyList::CheckAgainstSubset(const atomids_t &atomids)
 {
   LOG(0, "STATUS: Looking at bond structure of given ids and comparing against stored in adjacency file... ");
@@ -156 +156 @@
 }
 
-CheckAgainstAdjacencyFile::KeysSet CheckAgainstAdjacencyFile::getKeys(const CheckAgainstAdjacencyFile::AtomBondRange &_range) const
+AdjacencyList::KeysSet AdjacencyList::getKeys(const AdjacencyList::AtomBondRange &_range) const
 {
   KeysSet Keys;
@@ -167 +167 @@
 }
 
-CheckAgainstAdjacencyFile::ValuesSet CheckAgainstAdjacencyFile::getValues(const CheckAgainstAdjacencyFile::AtomBondRange&_range) const
+AdjacencyList::ValuesSet AdjacencyList::getValues(const AdjacencyList::AtomBondRange&_range) const
 {
   ValuesSet Values;
@@ -208 +208 @@
  * @return true - both maps are the same, false - both maps diverge by NonMatchNumber counts.
  */
-bool CheckAgainstAdjacencyFile::CompareInternalExternalMap()
+bool AdjacencyList::CompareInternalExternalMap()
 {
   NonMatchNumber = 0;

src/Graph/AdjacencyList.hpp

@@ -1 +1 @@
 /*
- * CheckAgainstAdjacencyFile.hpp
+ * AdjacencyList.hpp
  *
  *  Created on: Mar 3, 2011
@@ -6 +6 @@
  */
 
-#ifndef CHECKAGAINSTADJACENCYFILE_HPP_
-#define CHECKAGAINSTADJACENCYFILE_HPP_
+#ifndef ADJACENCYLIST_HPP_
+#define ADJACENCYLIST_HPP_
 
 // include config.h
@@ -23 +23 @@
 class atom;
 
-/** This class contains the bond structure inside an internal map of atoms which
- * each bond neighbor parsed from an external file.
+/** This class contains the adjacency structure inside an internal map of atoms.
+ *
+ * The adjacency structure is either from a file or from a given set of atoms.
  *
  * We may compare a subset of atoms against this internal bond structure. It is
  * true it is a true subset of the bond structure.
  */
-class CheckAgainstAdjacencyFile
+class AdjacencyList
 {
   //!> Unit test is granted access to internal data
-  friend class CheckAgainstAdjacencyFileTest;
+  friend class AdjacencyListTest;
 public:
-  CheckAgainstAdjacencyFile(std::istream &File);
-  ~CheckAgainstAdjacencyFile();
-
   typedef std::vector<atomId_t> atomids_t;
 
-  bool operator()(const atomids_t &atoms);
+  AdjacencyList(std::istream &File);
+  AdjacencyList(const atomids_t &atoms);
+  ~AdjacencyList();
+
+  bool CheckAgainstSubset(const atomids_t &atoms);
 
 private:
@@ -59 +61 @@
 };
 
-#endif /* CHECKAGAINSTADJACENCYFILE_HPP_ */
+#endif /* ADJACENCYLIST_HPP_ */

src/Graph/Makefile.am

@@ -6 +6 @@
         Graph/BreadthFirstSearchAdd.cpp \
         Graph/BuildInducedSubgraph.cpp \
-        Graph/CheckAgainstAdjacencyFile.cpp \
+        Graph/AdjacencyList.cpp \
         Graph/ConnectedSubgraph.cpp \
         Graph/CyclicStructureAnalysis.cpp \
@@ -15 +15 @@
         Graph/BreadthFirstSearchAdd.hpp \
         Graph/BuildInducedSubgraph.hpp \
-        Graph/CheckAgainstAdjacencyFile.hpp \
+        Graph/AdjacencyList.hpp \
         Graph/ConnectedSubgraph.hpp \
         Graph/CyclicStructureAnalysis.hpp \

src/Graph/unittests/AdjacencyListUnitTest.cpp

@@ -22 +22 @@
 
 /*
- * CheckAgainstAdjacencyFileUnitTest.cpp
+ * AdjacencyListUnitTest.cpp
  *
  *  Created on: Oct 17, 2011
@@ -33 +33 @@
 #endif
 
-#include "CheckAgainstAdjacencyFileUnitTest.hpp"
+#include "AdjacencyListUnitTest.hpp"
 
 #include <cppunit/CompilerOutputter.h>
@@ -52 +52 @@
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
+#include "Graph/AdjacencyList.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
@@ -63 +63 @@
 /********************************************** Test classes **************************************/
 // Registers the fixture into the 'registry'
-CPPUNIT_TEST_SUITE_REGISTRATION( CheckAgainstAdjacencyFileTest );
+CPPUNIT_TEST_SUITE_REGISTRATION( AdjacencyListTest );
 
 static std::string adjacencyfile ="\
@@ -115 +115 @@
 
 // set up and tear down
-void CheckAgainstAdjacencyFileTest::setUp()
+void AdjacencyListTest::setUp()
 {
   // failing asserts should be thrown
@@ -148 +148 @@
 }
 
-void CheckAgainstAdjacencyFileTest::tearDown()
+void AdjacencyListTest::tearDown()
 {
   comparisonMap.clear();
@@ -161 +161 @@
 }
 
-/** Unit tests for CheckAgainstAdjacencyFile::CreateExternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::CreateExternalMapTest()
+/** Unit tests for AdjacencyList::CreateExternalMap().
+ *
+ */
+void AdjacencyListTest::CreateExternalMapTest()
 {
   std::stringstream input;
-  CheckAgainstAdjacencyFile fileChecker(input);
+  AdjacencyList fileChecker(input);
   fileChecker.CreateExternalMap(atomIds);
 
@@ -190 +190 @@
 }
 
-/** Unit tests for CheckAgainstAdjacencyFile::ParseInInternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::ParseInInternalMapTest()
+/** Unit tests for AdjacencyList::ParseInInternalMap().
+ *
+ */
+void AdjacencyListTest::ParseInInternalMapTest()
 {
   std::stringstream input(adjacencyfile);
-  CheckAgainstAdjacencyFile fileChecker(input);
+  AdjacencyList fileChecker(input);
   std::vector<atomId_t> noids;
   fileChecker.CreateExternalMap(noids);
@@ -218 +218 @@
 }
 
-/** Unit tests for CheckAgainstAdjacencyFile::CompareInternalExternalMap().
- *
- */
-void CheckAgainstAdjacencyFileTest::CompareInternalExternalMapTest()
+/** Unit tests for AdjacencyList::CompareInternalExternalMap().
+ *
+ */
+void AdjacencyListTest::CompareInternalExternalMapTest()
 {
   std::stringstream input(adjacencyfile);
-  CheckAgainstAdjacencyFile fileChecker(input);
+  AdjacencyList fileChecker(input);
 
   // assert equality before parsing (empty sets should always return true)
@@ -240 +240 @@
 }
 
-/** Unit tests for CheckAgainstAdjacencyFile::operator()().
- *
- */
-void CheckAgainstAdjacencyFileTest::operatorTest()
+/** Unit tests for AdjacencyList::operator()().
+ *
+ */
+void AdjacencyListTest::CheckAgainstSubsetTest()
 {
   {
     // parse right
     std::stringstream input(adjacencyfile);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker(atomIds) );
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(atomIds) );
   }
   {
     // parse wrong1 (more atoms in the world than in file, hence wrong)
     std::stringstream input(wrongadjacencyfile1);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
   }
   {
@@ -264 +264 @@
     // parse wrong1 (more atoms in the world than in file, hence wrong)
     std::stringstream input(wrongadjacencyfile1);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( fileChecker(validids) );
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( fileChecker.CheckAgainstSubset(validids) );
   }
   {
     // parse wrong2 (there is no atom 10, but present in file. hence true)
     std::stringstream input(wrongadjacencyfile2);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
   }
   {
     // parse wrong3 (6 is not connected)
     std::stringstream input(wrongadjacencyfile3);
-    CheckAgainstAdjacencyFile fileChecker(input);
-    CPPUNIT_ASSERT( !fileChecker(atomIds) );
-  }
-}
+    AdjacencyList fileChecker(input);
+    CPPUNIT_ASSERT( !fileChecker.CheckAgainstSubset(atomIds) );
+  }
+}

src/Graph/unittests/AdjacencyListUnitTest.hpp

@@ -1 +1 @@
 /*
- * CheckAgainstAdjacencyFileUnitTest.hpp
+ * AdjacencyListUnitTest.hpp
  *
  *  Created on: Oct 17, 2011
@@ -6 +6 @@
  */
 
-#ifndef CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_
-#define CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_
+#ifndef UNITTEST_HPP_
+#define UNITTEST_HPP_
 
 // include config.h
@@ -17 +17 @@
 #include <cppunit/extensions/HelperMacros.h>
 
-#include "Graph/CheckAgainstAdjacencyFile.hpp"
+#include "Graph/AdjacencyList.hpp"
 #include "types.hpp"
 
@@ -27 +27 @@
 class World;
 
-class CheckAgainstAdjacencyFileTest : public CppUnit::TestFixture
+class AdjacencyListTest : public CppUnit::TestFixture
 {
-  CPPUNIT_TEST_SUITE( CheckAgainstAdjacencyFileTest );
+  CPPUNIT_TEST_SUITE( AdjacencyListTest );
   CPPUNIT_TEST ( CreateExternalMapTest );
   CPPUNIT_TEST ( ParseInInternalMapTest );
   CPPUNIT_TEST ( CompareInternalExternalMapTest );
-  CPPUNIT_TEST ( operatorTest );
+  CPPUNIT_TEST ( CheckAgainstSubsetTest );
   CPPUNIT_TEST_SUITE_END();
 
@@ -43 +43 @@
   void ParseInInternalMapTest();
   void CompareInternalExternalMapTest();
-  void operatorTest();
+  void CheckAgainstSubsetTest();
 
 private:
-  CheckAgainstAdjacencyFile::AtomBondMap comparisonMap;
+  AdjacencyList::AtomBondMap comparisonMap;
   std::vector<atom *> atoms;
   std::vector<atomId_t> atomIds;
@@ -52 +52 @@
 };
 
-#endif /* CHECKADJACENCYAGAINSTFILEUNITTEST_HPP_ */
+#endif /* UNITTEST_HPP_ */

src/Graph/unittests/Makefile.am

@@ -3 +3 @@
 
 GRAPHTESTSSOURCES = \
-        ../Graph/unittests/BondGraphUnitTest.cpp \
-        ../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp
+        ../Graph/unittests/AdjacencyListUnitTest.cpp \
+        ../Graph/unittests/BondGraphUnitTest.cpp
 
 GRAPHTESTSHEADERS = \
-        ../Graph/unittests/BondGraphUnitTest.hpp \
-        ../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp
+        ../Graph/unittests/AdjacencyListUnitTest.hpp \
+        ../Graph/unittests/BondGraphUnitTest.hpp
 
 GRAPHTESTS = \
-        BondGraphUnitTest \
-        CheckAgainstAdjacencyFileUnitTest
+        AdjacencyListUnitTest \
+        BondGraphUnitTest
 
 
@@ -32 +32 @@
 
 
+AdjacencyListUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        ../Graph/unittests/AdjacencyListUnitTest.cpp \
+        ../Graph/unittests/AdjacencyListUnitTest.hpp
+AdjacencyListUnitTest_LDADD = ${ALLLIBS}
+
 BondGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ../Graph/unittests/BondGraphUnitTest.cpp \
@@ -37 +42 @@
 BondGraphUnitTest_LDADD = ${GRAPHLIBS}
 
-CheckAgainstAdjacencyFileUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
-        ../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp \
-        ../Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp
-CheckAgainstAdjacencyFileUnitTest_LDADD = ${ALLLIBS}
-