Changeset d2a294 for src/moleculelist.cpp

Timestamp:

May 8, 2008, 3:22:41 PM (17 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:

df2fca

Parents:

fc1309

Message:

new function FillListOfLocalAtoms() checks whether List needs filling or is already present, Count() const

Count() is now Count() const
new function FillListOfLocalAtoms() checks for NULL pointers and if found fills the list by calling CreateFatherLookupTable()

File:

• src/moleculelist.cpp (modified) (3 diffs)

src/moleculelist.cpp

@@ -364 +364 @@
   int AtomNo;
 
-  if (ListOfLocalAtoms == NULL) { // allocated initial pointer
-    // count the number of fragments
-    MoleculeLeafClass *MolecularWalker = this;
-    while (MolecularWalker->next != NULL) {
-      MolecularWalker = MolecularWalker->next;
-      FragmentCounter++;
-    }
-    // allocate and set each field to NULL 
-    ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **)*(FragmentCounter+1), "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
-    if (ListOfLocalAtoms == NULL)
-      return false;
-    for (int i=0;i<=FragmentCounter;i++)
-      ListOfLocalAtoms[i] = NULL;
-    FragmentCounter = 0;
-    FreeList = FreeList && true;
-  }
-  if (ListOfLocalAtoms[FragmentCounter] == NULL) { // allocate and fill list of this fragment/subgraph
-    status = status && CreateFatherLookupTable(out, Leaf->start, Leaf->end, ListOfLocalAtoms[FragmentCounter], reference->AtomCount);
-    FreeList = FreeList && true;
+  // fill ListOfLocalAtoms if NULL was given
+  if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
+    *out << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
+    return false;
   }
   
@@ -449 +434 @@
         if (next != NULL)
           next->FillRootStackForSubgraphs(out, RootStack, Order, ++FragmentCounter);
-      } else
+      }  else {
+        *out << Verbose(1) << "Rootstack[" << FragmentCounter  << "] is NULL." << endl;
         return false;
-    }
+      }
+    }
+    FragmentCounter--;
     return true;
+  } else {
+    *out << Verbose(1) << "Rootstack is NULL." << endl;
+    return false;
+  }
+};
+
+/** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
+ * \param *out output stream fro debugging
+ * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
+ * \param &FragmentCounter counts the fragments as we move along the list
+ * \param GlobalAtomCount number of atoms in the complete molecule
+ * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
+ * \return true - succes, false - failure
+ */
+bool MoleculeLeafClass::FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, int &FragmentCounter, int GlobalAtomCount, bool &FreeList)
+{
+  bool status = true;
+  
+  int Counter = Count();
+  if (ListOfLocalAtoms == NULL) { // allocated initial pointer
+    // allocate and set each field to NULL
+    ListOfLocalAtoms = (atom ***) Malloc(sizeof(atom **)*Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
+    if (ListOfLocalAtoms != NULL) {
+      for (int i=0;i<Counter;i++)
+        ListOfLocalAtoms[i] = NULL;
+      FreeList = FreeList && true;
+    } else
+      status = false;
+  }
+  
+  if ((ListOfLocalAtoms != NULL) && (ListOfLocalAtoms[FragmentCounter] == NULL)) { // allocate and fill list of this fragment/subgraph
+    status = status && CreateFatherLookupTable(out, Leaf->start, Leaf->end, ListOfLocalAtoms[FragmentCounter], GlobalAtomCount);
+    FreeList = FreeList && true;
+  }
+  
+  return status;
+};
+
+/** The indices per keyset are compared to the respective father's Atom::nr in each subgraph and thus put into \a **&FragmentList.
+ * \param *out output stream fro debugging
+ * \param *reference reference molecule with the bond structure to be copied
+ * \param *KeySetList list with all keysets
+ * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
+ * \param **&FragmentList list to be allocated and returned
+ * \param &FragmentCounter counts the fragments as we move along the list
+ * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
+ * \retuen true - success, false - failure
+ */
+bool MoleculeLeafClass::AssignKeySetsToFragment(ofstream *out, molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
+{
+  bool status = true;
+  int KeySetCounter = 0;
+  
+  // fill ListOfLocalAtoms if NULL was given
+  if (!FillListOfLocalAtoms(out, ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
+    *out << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
+    return false;
+  }
+
+  // allocate fragment list
+  if (FragmentList == NULL) {
+    KeySetCounter = Count();
+    FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "molecule::FragmentMolecule - **BondFragments");
+    for(int i=0;i<KeySetCounter;i++)
+      FragmentList[i] = NULL;
+    KeySetCounter = 0;
+  }
+  
+  if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
+    // assign scanned keysets
+    if (FragmentList[FragmentCounter] == NULL)
+      FragmentList[FragmentCounter] = new Graph;
+    KeySet *TempSet = new KeySet;
+    for(Graph::iterator runner = KeySetList->begin();runner != KeySetList->end(); runner++) { // key sets contain global numbers!
+      if ( ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr]->nr != -1) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
+        // translate keyset to local numbers
+        for(KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
+          TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->nr]->nr);
+        // insert into FragmentList
+        FragmentList[FragmentCounter]->insert(GraphPair (*TempSet, pair<int,double>(KeySetCounter++, (*runner).second.second)));
+      }
+      TempSet->clear();
+    }
+    delete(TempSet);
+    if (KeySetCounter == 0) {// if there are no keysets, delete the list
+      *out << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl;
+      delete(FragmentList[FragmentCounter]);
+    } else
+      *out << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl;
+    FragmentCounter++;
+    if (next != NULL)
+      next->AssignKeySetsToFragment(out, reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
+    FragmentCounter--;
   } else
-    return false;
+    *out << Verbose(1) << "KeySetList is NULL or empty." << endl;
+  
+  return status;
 };
 
@@ -460 +543 @@
  * \return number of items
  */
-int MoleculeLeafClass::Count()
+int MoleculeLeafClass::Count() const
 {
   if (next != NULL)