Changeset 43587e

Timestamp:

Oct 18, 2009, 6:12:53 PM (15 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:

9eefda

Parents:

ce7cc5

Message:

Refactored molecule::BuildInducedSubgraph()

• new functions BuildInducedSubgraph_Init(), BuildInducedSubgraph_FillParentList(), BuildInducedSubgraph_CreateBondsFromParentList(), BuildInducedSubgraph_Finalize()

File:

• src/molecule_graph.cpp (modified) (4 diffs)

src/molecule_graph.cpp

@@ -1154 +1154 @@
 };
 
-
-/** Adds bond structure to this molecule from \a Father molecule.
- * This basically causes this molecule to become an induced subgraph of the \a Father, i.e. for every bond in Father
- * with end points present in this molecule, bond is created in this molecule.
- * Special care was taken to ensure that this is of complexity O(N), where N is the \a Father's molecule::AtomCount.
- * \param *out output stream for debugging
- * \param *Father father molecule
- * \return true - is induced subgraph, false - there are atoms with fathers not in \a Father
- * \todo not checked, not fully working probably
- */
-bool molecule::BuildInducedSubgraph(ofstream *out, const molecule *Father)
-{
-  atom *Walker = NULL, *OtherAtom = NULL;
-  bool status = true;
-  atom **ParentList = Malloc<atom*>(Father->AtomCount, "molecule::BuildInducedSubgraph: **ParentList");
-
-  *out << Verbose(2) << "Begin of BuildInducedSubgraph." << endl;
-
+void BuildInducedSubgraph_Init(ofstream *out, atom **&ParentList, int AtomCount)
+{
   // reset parent list
+  ParentList = Malloc<atom*>(AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
   *out << Verbose(3) << "Resetting ParentList." << endl;
-  for (int i=Father->AtomCount;i--;)
+  for (int i=AtomCount;i--;)
     ParentList[i] = NULL;
-
+};
+
+void BuildInducedSubgraph_FillParentList(ofstream *out, const molecule *mol, const molecule *Father, atom **&ParentList)
+{
   // fill parent list with sons
   *out << Verbose(3) << "Filling Parent List." << endl;
-  Walker = start;
-  while (Walker->next != end) {
+  atom *Walker = mol->start;
+  while (Walker->next != mol->end) {
     Walker = Walker->next;
     ParentList[Walker->father->nr] = Walker;
@@ -1187 +1175 @@
   }
 
+};
+
+void BuildInducedSubgraph_Finalize(ofstream *out, atom **&ParentList)
+{
+  Free(&ParentList);
+};
+
+bool BuildInducedSubgraph_CreateBondsFromParent(ofstream *out, molecule *mol, const molecule *Father, atom **&ParentList)
+{
+  bool status = true;
+  atom *Walker = NULL;
+  atom *OtherAtom = NULL;
   // check each entry of parent list and if ok (one-to-and-onto matching) create bonds
   *out << Verbose(3) << "Creating bonds." << endl;
@@ -1200 +1200 @@
           if (ParentList[OtherAtom->nr] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
             *out << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->Name << " and " << ParentList[OtherAtom->nr]->Name << "." << endl;
-            AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
+            mol->AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
           }
         }
@@ -1206 +1206 @@
     }
   }
-
-  Free(&ParentList);
+  return status;
+};
+
+/** Adds bond structure to this molecule from \a Father molecule.
+ * This basically causes this molecule to become an induced subgraph of the \a Father, i.e. for every bond in Father
+ * with end points present in this molecule, bond is created in this molecule.
+ * Special care was taken to ensure that this is of complexity O(N), where N is the \a Father's molecule::AtomCount.
+ * \param *out output stream for debugging
+ * \param *Father father molecule
+ * \return true - is induced subgraph, false - there are atoms with fathers not in \a Father
+ * \todo not checked, not fully working probably
+ */
+bool molecule::BuildInducedSubgraph(ofstream *out, const molecule *Father)
+{
+  bool status = true;
+  atom **ParentList = NULL;
+
+  *out << Verbose(2) << "Begin of BuildInducedSubgraph." << endl;
+  BuildInducedSubgraph_Init(out, ParentList, Father->AtomCount);
+  BuildInducedSubgraph_FillParentList(out, this, Father, ParentList);
+  status = BuildInducedSubgraph_CreateBondsFromParent(out, this, Father, ParentList);
+  BuildInducedSubgraph_Finalize(out, ParentList);
   *out << Verbose(2) << "End of BuildInducedSubgraph." << endl;
   return status;