Changeset b8d1aeb for src/moleculelist.cpp

Timestamp:

Feb 2, 2010, 11:38:06 AM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

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, Candidate_v1.7.0, 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:

7ba324

Parents:

9fe36b (diff), 2ededc2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'MenuRefactoring' into QT4Refactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am

File:

• src/moleculelist.cpp (modified) (6 diffs)

src/moleculelist.cpp

@@ -4 +4 @@
  *
  */
+
+#include <cstring>
 
 #include "atom.hpp"
@@ -405 +407 @@
   input.open(line.c_str());
   if (input == NULL) {
-    eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
-    performCriticalExit();
+    Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
     return false;
   }
@@ -743 +744 @@
 /** 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 *mol molecule with atoms to dissect
+ * \param *periode periodentafel
  * \param *configuration config with BondGraph
  */
-void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
-{
+void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
+{
+  molecule *mol = new molecule(periode);
+  atom *Walker = NULL;
+  atom *Advancer = NULL;
+  bond *Binder = NULL;
+  bond *Stepper = NULL;
+  // 0. gather all atoms into single molecule
+  for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
+    // shift all atoms to new molecule
+    Advancer = (*MolRunner)->start->next;
+    while (Advancer != (*MolRunner)->end) {
+      Walker = Advancer;
+      Advancer = Advancer->next;
+      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      unlink(Walker);
+      Walker->father = Walker;
+      mol->AddAtom(Walker);    // counting starts at 1
+    }
+    // remove all bonds
+    Stepper = (*MolRunner)->first->next;
+    while (Stepper != (*MolRunner)->last) {
+      Binder = Stepper;
+      Stepper = Stepper->next;
+      delete(Binder);
+    }
+    // remove the molecule
+    delete(*MolRunner);
+    ListOfMolecules.erase(MolRunner);
+  }
+
   // 1. dissect the molecule into connected subgraphs
   configuration->BG->ConstructBondGraph(mol);
@@ -763 +793 @@
   // 4a. create array of molecules to fill
   const int MolCount = Subgraphs->next->Count();
+  char number[MAXSTRINGSIZE];
   molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
   for (int i=0;i<MolCount;i++) {
     molecules[i] = (molecule*) new molecule(mol->elemente);
     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);
+    }
+    cout << "MolName is " << molecules[i]->name << endl;
     insert(molecules[i]);
   }
@@ -774 +811 @@
   int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
   MoleculeLeafClass *MolecularWalker = Subgraphs;
-  atom *Walker = NULL;
+  Walker = NULL;
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
@@ -803 +840 @@
     }
   }
-  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintained their ListOfBonds, but we have to remove them from first..last list
-  bond *Binder = mol->first;
+  // 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
+  Binder = mol->first;
   while (mol->first->next != mol->last) {
     Binder = mol->first->next;