Changeset 910a5d for src

Timestamp:

Jan 27, 2015, 4:46:25 PM (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:

d05088

Parents:

cf5b40

git-author:

Frederik Heber <heber@…> (01/27/15 11:38:34)

git-committer:

Frederik Heber <heber@…> (01/27/15 16:46:25)

Message:

atom::father is now accessible through getter and setter only.

• this allows to manage signing on and off to and from father to be notified when it's destroyed.

Location:

src

Files:

• Atom/atom.cpp (modified) (1 diff)
• Atom/atom.hpp (modified) (2 diffs)
• Fragmentation/Exporters/HydrogenPool.cpp (modified) (1 diff)
• Fragmentation/Exporters/SaturatedFragment.cpp (modified) (2 diffs)
• Graph/BuildInducedSubgraph.cpp (modified) (2 diffs)
• Parser/PdbParser.cpp (modified) (1 diff)
• molecule.cpp (modified) (2 diffs)
• moleculelist.cpp (modified) (1 diff)

src/Atom/atom.cpp

@@ -125 +125 @@
     return father->GetTrueFather();
   }
-};
+}
+
+void atom::setFather(atom * const _father)
+{
+  father = _father;
+}
 
 /** Sets father to itself or its father in case of copying a molecule.

src/Atom/atom.hpp

@@ -47 +47 @@
   friend atom* NewAtom(atomId_t);
   friend void  DeleteAtom(atom*);
+
+  atom *father;   //!< In many-body bond order fragmentations points to originating atom
+  int *sort;      //!< sort criteria
+
 public:
-    atom *father;   //!< In many-body bond order fragmentations points to originating atom
-    int *sort;      //!< sort criteria
 
   /** Clones this atom.
@@ -130 +132 @@
    */
   const atom *GetTrueFather() const;
+
+  /** Const getter for the atoms father.
+   *
+   * \return father of this atom
+   */
+  atom * const getFather() const
+  { return father; }
+
+  /** Sets the father for this atom.
+   *
+   * \param _father ptr to father atom
+   */
+  void setFather(atom * const _father);
 
   /** Compares the indices of \a this atom with a given \a ptr.

src/Fragmentation/Exporters/HydrogenPool.cpp

@@ -68 +68 @@
   ++HydrogenCount;
 
-  // give warning if pool has more than thereshold
+  // give warning if pool has more than threshold
   if (HydrogenCount >= WARNINGTHRESHOLD) {
     ELOG(2, "HydrogenPool contains more hydrogen atoms than limit.");

src/Fragmentation/Exporters/SaturatedFragment.cpp

@@ -311 +311 @@
   _atom->setFixedIon(true);
   // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
-  _atom->father = _father;
+  _atom->setFather(_father);
   SaturationHydrogens.insert(_atom->getId());
 
@@ -387 +387 @@
   _atom->setFixedIon(replacement->getFixedIon());
   // if we replace hydrogen, we mark it as our father, otherwise we are just an added hydrogen with no father
-  _atom->father = replacement;
+  _atom->setFather(replacement);
   SaturationHydrogens.insert(_atom->getId());
   return _atom;

src/Graph/BuildInducedSubgraph.cpp

@@ -63 +63 @@
   LOG(3, "Filling Parent List.");
   for (molecule::iterator iter = Son->begin(); iter != Son->end(); ++iter) {
-    ParentList[(*iter)->father] = (*iter);
+    ParentList[(*iter)->getFather()] = (*iter);
     // Outputting List for debugging
-    LOG(4, "INFO: ParentList[] of " << (*iter)->father << " is " << *ParentList[(*iter)->father] << ".");
+    LOG(4, "INFO: ParentList[] of " << (*iter)->getFather() << " is " << *ParentList[(*iter)->getFather()] << ".");
   }
 }
@@ -77 +77 @@
   for (molecule::iterator iter = Father->begin(); iter != Father->end(); ++iter) {
     if (ParentList.count(*iter)) {
-      if (ParentList[(*iter)]->father != (*iter)) {
+      if (ParentList[(*iter)]->getFather() != (*iter)) {
         status = false;
       } else {

src/Parser/PdbParser.cpp

@@ -360 +360 @@
 {
   if (additionalAtomData.find(_atom->getId()) != additionalAtomData.end()) {
-  } else if (additionalAtomData.find(_atom->father->getId()) != additionalAtomData.end()) {
+  } else if (additionalAtomData.find(_atom->getFather()->getId()) != additionalAtomData.end()) {
     // use info from direct father
-    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->father->getId()];
+    additionalAtomData[_atom->getId()] = additionalAtomData[_atom->getFather()->getId()];
   } else if (additionalAtomData.find(_atom->GetTrueFather()->getId()) != additionalAtomData.end()) {
     // use info from topmost father

src/molecule.cpp

@@ -934 +934 @@
     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 +940 @@
       //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();
         }

src/moleculelist.cpp

@@ -409 +409 @@
     for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
       //LOG(1, "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
-      if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
-          || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
+      if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->getFather() == NULL)
+          || ((*iter)->getFather()->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
         for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
           //LOG(2, "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");