Changeset 77b350 for src

Timestamp:

Dec 3, 2012, 9:50:02 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:

54a561

Parents:

7b6b21f

git-author:

Frederik Heber <heber@…> (09/25/12 17:31:00)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:02)

Message:

HomologyGraph may now be created from a given KeySet referring to World's atoms.

• HomologyContainer now contains HomologyGraph as keys in a multimap and it stores a (rudimentary) fragment and an energy value.

Location:

src/Fragmentation

Files:

• Homology/HomologyContainer.cpp (modified) (1 diff)
• Homology/HomologyContainer.hpp (modified) (2 diffs)
• Homology/HomologyGraph.cpp (modified) (1 diff)
• Homology/HomologyGraph.hpp (modified) (3 diffs)
• Homology/HomologyGraph_getFromKeyset.cpp (added)
• Homology/unittests/HomologyContainerUnitTest.cpp (modified) (1 diff)
• Homology/unittests/Makefile.am (modified) (1 diff)
• Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added)
• Makefile.am (modified) (1 diff)

src/Fragmentation/Homology/HomologyContainer.cpp

@@ -41 +41 @@
 #include "Fragmentation/Graph.hpp"
 
-HomologyContainer::HomologyContainer(const Graph &keysets, const std::map< KeySet, double> &values)
-{
-  for (Graph::const_iterator iter = keysets.begin();
-      iter != keysets.end();
-      ++iter) {
-
-  }
-}

src/Fragmentation/Homology/HomologyContainer.hpp

@@ -16 +16 @@
 
 #include <map>
+#include <vector>
 
-#include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/Homology/HomologyGraph.hpp"
 
-class Graph;
+class Fragment
+{
+public:
+  typedef std::vector<double> position_t;
+  typedef std::vector< position_t > positions_t;
+  typedef std::vector< double > charges_t;
+  typedef std::pair< position_t, double> nucleus_t;
+  typedef std::vector< nucleus_t > nuclei_t;
+  Fragment() {}
+  Fragment(const positions_t &_positions, const charges_t &_charges) {}
+};
+
 
 /** This class takes all KeySets in a Graph, checks for those that homologues
@@ -35 +47 @@
 {
 public:
-  HomologyContainer(const Graph &keysets, const std::map< KeySet, double> &values);
+  typedef double energy_t;
+  typedef std::pair<Fragment, energy_t> value_t;
+  typedef std::multimap< HomologyGraph, value_t> container_t;
+  typedef std::pair< container_t::const_iterator, container_t::const_iterator> range_t;
+public:
+  /** Default Constructor of class HomologyContainer.
+   *
+   */
+  HomologyContainer() {}
+
+  /** Constructor of class HomologyContainer.
+   *
+   * @param values values with with to initially fill the container
+   */
+  HomologyContainer(const container_t &values) :
+    container(values)
+  {}
+  /** Destructor of class HomologyContainer.
+   *
+   */
   ~HomologyContainer() {}
 
+  /** Inserter for more graphs along with values.
+   *
+   * @param values graph and values to insert
+   */
+  void insert(const container_t &values) {
+    container.insert(values.begin(), values.end());
+  }
+
+  /** Returns iterator range with all contained graphs homologous to the given \a graph.
+   *
+   * @param graph graph to match
+   * @return iterator range with all matches
+   */
+  range_t getHomologousGraphs(const HomologyGraph &graph) {
+    return container.equal_range(graph);
+  }
+
 private:
-  typedef double value_t;
-  typedef std::multimap< KeySet, value_t> container_t;
+  //!> multimap containing all homologous graph under same key but each with its value
+  container_t container;
 };
 

src/Fragmentation/Homology/HomologyGraph.cpp

@@ -38 +38 @@
 
 #include "HomologyGraph.hpp"
+
+
+HomologyGraph::HomologyGraph(const KeySet &keyset) :
+  nodes(detail::getNodesFromKeySet(keyset)),
+  edges(detail::getEdgesFromKeySet(keyset))
+{}
 
 bool HomologyGraph::operator<(const HomologyGraph &graph) const

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -19 +19 @@
 #include "Fragmentation/Homology/FragmentEdge.hpp"
 #include "Fragmentation/Homology/FragmentNode.hpp"
+
+class KeySet;
 
 /** This class contains the representation of a molecular fragment as a graph.
@@ -58 +60 @@
   {}
 
+  /** Constructor for class HomologyGraph from a keyset (i.e. from atoms in the World).
+   *
+   * @param keyset global ids of atoms to pick
+   */
+  HomologyGraph(const KeySet &keyset);
+
   /** Destructor for class HomologyGraph.
    *
@@ -86 +94 @@
 };
 
+// define some helpers outside to allow for light-weight unit testing
+namespace detail {
+  const HomologyGraph::nodes_t getNodesFromKeySet(const KeySet &keyset);
+  const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset);
+};
+
 
 #endif /* HOMOLOGYGRAPH_HPP_ */

src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp

@@ -60 +60 @@
 void HomologyContainerTest::setUp()
 {
-  Graph keysets;
-  std::map< KeySet, double> values;
-  Keys = new HomologyContainer(keysets, values);
+//  Keys = new HomologyContainer(keysets, values);
 }
 

src/Fragmentation/Homology/unittests/Makefile.am

@@ -50 +50 @@
 HomologyGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp \
-        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp
+        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp \
+        ../Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp
 HomologyGraphUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
 

src/Fragmentation/Makefile.am

@@ -9 +9 @@
         Fragmentation/Homology/HomologyContainer.cpp \
         Fragmentation/Homology/HomologyGraph.cpp \
+        Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp \
         Fragmentation/AdaptivityMap.cpp \
         Fragmentation/BondsPerShortestPath.cpp \