Changeset 2b7d1b

Timestamp:

Aug 11, 2010, 4:31:34 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:

701ad6, fa7989

Parents:

31fb1d

git-author:

Frederik Heber <heber@…> (07/29/10 12:07:40)

git-committer:

Frederik Heber <heber@…> (08/11/10 16:31:34)

Message:

Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.

• also rewrote the function a bit:
  • no more copying of atoms
  • we just take the molecule out of the MoleculeLeafs
  • molecule that contains all atoms is destroyed including all original atoms (they are copied by DFS).

Location:

src

Files:

• Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (6 diffs)
• Parser/PcpParser.cpp (modified) (2 diffs)
• config.cpp (modified) (2 diffs)
• molecule.hpp (modified) (1 diff)
• moleculelist.cpp (modified) (1 diff)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -24 +24 @@
 #include "molecule.hpp"
 #include "stackclass.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
 
@@ -44 +45 @@
 {}
 
+/** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
+ */
 void FragmentationSubgraphDissection() {
   ActionRegistry::getInstance().getActionByName(FragmentationSubgraphDissectionAction::NAME)->call(Action::NonInteractive);
@@ -59 +62 @@
 Action::state_ptr FragmentationSubgraphDissectionAction::performCall() {
   DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
-  // @TODO rather do the dissection afterwards
+
   MoleculeListClass *molecules = World::getInstance().getMolecules();
   config * const configuration = World::getInstance().getConfig();
@@ -101 +104 @@
     return Action::failure;
   }
+<<<<<<< HEAD
 
   // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
@@ -143 +147 @@
   // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms.
   // 4d. destroy the original molecule
+=======
+  int FragmentCounter = Subgraphs->Count();
+
+  // TODO: When DepthFirstSearchAnalysis does not use AddCopyAtom() anymore, we don't need to delete all original atoms
+  // 3. destroy the original molecule
+>>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   for (molecule::iterator AtomRunner = mol->begin(); !mol->empty(); AtomRunner = mol->begin())
     World::getInstance().destroyAtom(*AtomRunner);
   World::getInstance().destroyMolecule(mol);
 
+<<<<<<< HEAD
   // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
   // TODO: check whether this is really not needed anymore
   // 4e. free Leafs
   MolecularWalker = Subgraphs;
+=======
+  // 4. free Leafs
+  MoleculeLeafClass *MolecularWalker = Subgraphs;
+>>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -156 +171 @@
   }
   delete(MolecularWalker);
+<<<<<<< HEAD
   delete[](moleculelist);
+=======
+>>>>>>> Merged MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() into FragmenationSubgraphDissectionAction.
   DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
 

src/Parser/PcpParser.cpp

@@ -16 +16 @@
 #include <iomanip>
 
+//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
 #include "config.hpp"
@@ -356 +357 @@
   // 4. dissect the molecule into connected subgraphs
   // don't do this here ...
-  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  //FragmentationSubgraphDissection();
   //delete(mol);
 

src/config.cpp

@@ -15 +15 @@
 #include <cstring>
 
+//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -856 +857 @@
   // 4. dissect the molecule into connected subgraphs
   // don't do this here ...
-  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  //FragmentationSubgraphDissection();
   //delete(mol);
 

src/molecule.hpp

@@ -367 +367 @@
   void Enumerate(ostream *out);
   void Output(ofstream *out);
-  void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
   int CountAllAtoms() const;
 

src/moleculelist.cpp

@@ -585 +585 @@
 };
 
-/** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
- * \param *out output stream for debugging
- * \param *periode periodentafel
- * \param *configuration config with BondGraph
- */
-void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
-{
-  // 0a. remove all present molecules
-  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
-  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
-    erase(*MolRunner);
-    World::getInstance().destroyMolecule(*MolRunner);
-  }
-  // 0b. remove all bonds and construct a molecule with all atoms
-  molecule *mol = World::getInstance().createMolecule();
-  vector <atom *> allatoms = World::getInstance().getAllAtoms();
-  for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
-      delete(*BondRunner);
-    mol->AddAtom(*AtomRunner);
-  }
-
-  // 1. dissect the molecule into connected subgraphs
-  if (configuration->BG != NULL) {
-    if (!configuration->BG->ConstructBondGraph(mol)) {
-      World::getInstance().destroyMolecule(mol);
-      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
-      return;
-    }
-  } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
-    return;
-  }
-
-  // 2. scan for connected subgraphs
-  MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
-  class StackClass<bond *> *BackEdgeStack = NULL;
-  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
-  delete(BackEdgeStack);
-  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
-    World::getInstance().destroyMolecule(mol);
-    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
-    return;
-  }
-
-  // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
-  // the original one as parsed in)
-  // TODO: Optimize this, when molecules just contain pointer list of global atoms!
-
-  // 4a. create array of molecules to fill
-  const int MolCount = Subgraphs->next->Count();
-  char number[MAXSTRINGSIZE];
-  molecule **molecules = new molecule *[MolCount];
-  MoleculeLeafClass *MolecularWalker = Subgraphs;
-  for (int i=0;i<MolCount;i++) {
-    MolecularWalker = MolecularWalker->next;
-    molecules[i] = World::getInstance().createMolecule();
-    molecules[i]->ActiveFlag = true;
-    strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
-    if (MolCount > 1) {
-      sprintf(number, "-%d", i+1);
-      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
-    }
-    DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << ", id is " << molecules[i]->getId() << endl);
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); iter != MolecularWalker->Leaf->end(); ++iter) {
-      DoLog(1) && (Log() << Verbose(1) << **iter << endl);
-    }
-    insert(molecules[i]);
-  }
-
-  // 4b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
-  int FragmentCounter = 0;
-  map<int, atom *> AtomToFragmentMap;
-  MolecularWalker = Subgraphs;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    for (molecule::iterator iter = MolecularWalker->Leaf->begin(); !MolecularWalker->Leaf->empty(); iter = MolecularWalker->Leaf->begin()) {
-      atom * Walker = *iter;
-      DoLog(1) && (Log() << Verbose(1) << "Re-linking " << Walker << "..." << endl);
-      MolecularWalker->Leaf->erase(iter);
-      molecules[FragmentCounter]->AddAtom(Walker);    // counting starts at 1
-    }
-    FragmentCounter++;
-  }
-  World::getInstance().destroyMolecule(mol);
-
-  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
-  // TODO: check whether this is really not needed anymore
-  // 4e. free Leafs
-  MolecularWalker = Subgraphs;
-  while (MolecularWalker->next != NULL) {
-    MolecularWalker = MolecularWalker->next;
-    delete(MolecularWalker->previous);
-  }
-  delete(MolecularWalker);
-  delete[](molecules);
-  DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
-};
-
 /** Count all atoms in each molecule.
  * \return number of atoms in the MoleculeListClass.