Changeset 99752a

Timestamp:

Mar 2, 2011, 9:53:07 PM (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:

53d6b2

Parents:

c6123b

git-author:

Frederik Heber <heber@…> (02/25/11 15:40:39)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:07)

Message:

Moved FillBondStructureFromReference from MoleculeLeafClass to molecule.

Location:

src

Files:

• Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (2 diffs)
• molecule.hpp (modified) (3 diffs)
• molecule_fragmentation.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -58 +58 @@
       Subgraphs = Subgraphs->next;
       ListOfAtoms = NULL;
-      Subgraphs->FillBondStructureFromReference(mol, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
+      Subgraphs->Leaf->FillBondStructureFromReference(mol, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
       LocalBackEdgeStack = new std::deque<bond *>; // no need to have it Subgraphs->Leaf->BondCount size
       Subgraphs->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -124 +124 @@
       while (MoleculeWalker->next != NULL) {
         ListOfAtoms = NULL;
-        MoleculeWalker->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
+        MoleculeWalker->Leaf->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
         molecules->insert(MoleculeWalker->Leaf);
         MoleculeWalker = MoleculeWalker->next;
@@ -130 +130 @@
       molecules->insert(MoleculeWalker->Leaf);
       ListOfAtoms = NULL;
-      MoleculeWalker->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
+      MoleculeWalker->Leaf->FillBondStructureFromReference(mol, ListOfAtoms, true);  // we want to keep the created ListOfLocalAtoms
     }
 

src/molecule.hpp

@@ -184 +184 @@
 
   /// Initialising routines in fragmentation
-  void CreateAdjacencyListFromDbondFile(ifstream *output,unsigned int skiplines,int id_offset);
   void OutputBondsList() const;
   void CyclicBondAnalysis() const;
@@ -228 +227 @@
   // Recognize doubly appearing molecules in a list of them
   int * GetFatherSonAtomicMap(molecule *OtherMolecule);
+  bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
   bool FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount);
 
@@ -300 +300 @@
 
   bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
-  bool FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList = false);
   bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
   bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);

src/molecule_fragmentation.cpp

@@ -685 +685 @@
     // fill the bond structure of the individually stored subgraphs
     ListOfAtoms = NULL;
-    MolecularWalker->FillBondStructureFromReference(this, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
+    MolecularWalker->Leaf->FillBondStructureFromReference(this, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     LocalBackEdgeStack = new std::deque<bond *>; // (MolecularWalker->Leaf->BondCount);

src/molecule_graph.cpp

@@ -72 +72 @@
 
 /************************************* Functions for class molecule *********************************/
+
+/** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
+ * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
+ * \param *reference reference molecule with the bond structure to be copied
+ * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
+ * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
+ * \return true - success, false - failure
+ */
+bool molecule::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
+{
+  atom *OtherWalker = NULL;
+  atom *Father = NULL;
+  bool status = true;
+  int AtomNo;
+
+  DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
+  // fill ListOfLocalAtoms if NULL was given
+  if (!FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount())) {
+    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
+    return false;
+  }
+
+  if (status) {
+    DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for molecule " << getName() << "." << endl);
+    // remove every bond from the list
+    for_each(begin(), end(),
+        boost::bind(&BondedParticle::ClearBondsAtStep,_1,WorldTime::getTime()));
+
+
+    for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+      Father = (*iter)->GetTrueFather();
+      AtomNo = Father->getNr(); // global id of the current walker
+      const BondList& ListOfBonds = Father->getListOfBonds();
+      for (BondList::const_iterator Runner = ListOfBonds.begin();
+          Runner != ListOfBonds.end();
+          ++Runner) {
+        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr()]; // local copy of current bond partner of walker
+        if (OtherWalker != NULL) {
+          if (OtherWalker->getNr() > (*iter)->getNr())
+            AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
+        } else {
+          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr() << "] is NULL!" << endl);
+          status = false;
+        }
+      }
+    }
+  }
+
+  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
+    // free the index lookup list
+    delete[](ListOfLocalAtoms);
+  }
+  DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
+  return status;
+};
 
 /** Checks for presence of bonds within atom list.

src/moleculelist.cpp

@@ -777 +777 @@
 };
 
-/** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
- * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
- * \param *out output stream for debugging
- * \param *reference reference molecule with the bond structure to be copied
- * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
- * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \return true - success, false - failure
- */
-bool MoleculeLeafClass::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
-{
-  atom *OtherWalker = NULL;
-  atom *Father = NULL;
-  bool status = true;
-  int AtomNo;
-
-  DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
-  // fill ListOfLocalAtoms if NULL was given
-  if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms, reference->getAtomCount())) {
-    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
-    return false;
-  }
-
-  if (status) {
-    DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
-    // remove every bond from the list
-    for_each(Leaf->begin(), Leaf->end(),
-        boost::bind(&BondedParticle::ClearBondsAtStep,_1,WorldTime::getTime()));
-
-
-    for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
-      Father = (*iter)->GetTrueFather();
-      AtomNo = Father->getNr(); // global id of the current walker
-      const BondList& ListOfBonds = Father->getListOfBonds();
-      for (BondList::const_iterator Runner = ListOfBonds.begin();
-          Runner != ListOfBonds.end();
-          ++Runner) {
-        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr()]; // local copy of current bond partner of walker
-        if (OtherWalker != NULL) {
-          if (OtherWalker->getNr() > (*iter)->getNr())
-            Leaf->AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
-        } else {
-          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->getNr() << "] is NULL!" << endl);
-          status = false;
-        }
-      }
-    }
-  }
-
-  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
-    // free the index lookup list
-    delete[](ListOfLocalAtoms);
-  }
-  DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
-  return status;
-};
-
 /** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
  * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.