Changeset 27e464 for src/molecule.cpp

Timestamp:

Jan 29, 2015, 7:38:10 AM (10 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:

7912e9, eea0bb

Parents:

0ac85c3 (diff), 2050b2 (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 'Refactoring_QtMoleculeList_as_QModel' into Candidate_v1.4.10

File:

• src/molecule.cpp (modified) (5 diffs)

src/molecule.cpp ¶

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <cstring>
+#include <algorithm>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
+#include <cstring>
 
 #include <gsl/gsl_inline.h>
@@ -102 +103 @@
 molecule::~molecule()
 {
+  // inform all UI elements about imminent removal before anything is lost
+  {
+    OBSERVE;
+    NOTIFY(AboutToBeRemoved);
+  }
   CleanupMolecule();
 };
@@ -648 +654 @@
 void removeAtomsinMolecule(molecule *&_mol)
 {
+  // copy list of atoms from molecule as it will be changed
+  std::vector<atom *> atoms;
+  atoms.resize(_mol->getAtomCount(), NULL);
+  std::copy(_mol->begin(), _mol->end(), atoms.begin());
   // remove each atom from world
-  for(molecule::iterator AtomRunner = _mol->begin(); !_mol->empty(); AtomRunner = _mol->begin())
+  for(std::vector<atom *>::iterator AtomRunner = atoms.begin();
+      AtomRunner != atoms.end(); ++AtomRunner)
     World::getInstance().destroyAtom(*AtomRunner);
   // make sure that pointer os not usable
@@ -934 +945 @@
     output << "Map is ";
     for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      if ((*iter)->father == NULL) {
+      if ((*iter)->getFather() == NULL) {
         AtomicMap[(*iter)->getNr()] = -2;
       } else {
@@ -940 +951 @@
       //for (int i=0;i<AtomCount;i++) { // search atom
         //for (int j=0;j<OtherMolecule->getAtomCount();j++) {
-          //LOG(4, "Comparing father " << (*iter)->father << " with the other one " << (*runner)->father << ".");
-          if ((*iter)->father == (*runner))
+          //LOG(4, "Comparing father " << (*iter)->getFather() << " with the other one " << (*runner)->getFather() << ".");
+          if ((*iter)->getFather() == (*runner))
             AtomicMap[(*iter)->getNr()] = (*runner)->getNr();
         }