Changeset e23fec for src

Timestamp:

Feb 10, 2015, 2:04:40 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:

c26617

Parents:

917300

git-author:

Frederik Heber <heber@…> (01/25/15 12:34:57)

git-committer:

Frederik Heber <heber@…> (02/10/15 14:04:40)

Message:

Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId().

• I just stumbled over this, trying to recreate bonds from removed atoms and Contains looks for the Nr not the Id ...

Location:

src

Files:

• Bond/BondInfo.cpp (modified) (1 diff)
• Bond/bond.cpp (modified) (1 diff)
• Bond/bond.hpp (modified) (2 diffs)
• Fragmentation/PowerSetGenerator.cpp (modified) (1 diff)

src/Bond/BondInfo.cpp

@@ -68 +68 @@
   const BondList &rightbonds = rightatom->getListOfBonds();
   boost::function< bool (const bond::ptr )> leftpredicate =
-      boost::bind(static_cast<bool (bond::*)(const int) const>(&bond::Contains), _1, rightid);
+      boost::bind(static_cast<bool (bond::*)(const atomId_t) const>(&bond::ContainsId), _1, rightid);
   boost::function< bool (const bond::ptr )> rightpredicate =
-      boost::bind(static_cast<bool (bond::*)(const int) const>(&bond::Contains), _1, leftid);
+      boost::bind(static_cast<bool (bond::*)(const atomId_t) const>(&bond::ContainsId), _1, leftid);
   if ((std::find_if(leftbonds.begin(), leftbonds.end(), leftpredicate) != leftbonds.end())
       || (std::find_if(rightbonds.begin(), rightbonds.end(), rightpredicate) != rightbonds.end())) {

src/Bond/bond.cpp

@@ -125 +125 @@
  * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
  */
-bool bond::Contains(const int number) const
+bool bond::ContainsNr(const int number) const
 {
   return ((leftatom->getNr() == number) || (rightatom->getNr() == number));
+};
+
+/** Checks if an atom exists in a bond.
+ * \param Nr index of atom
+ * \return true if it is either bond::leftatom or bond::rightatom, false otherwise
+ */
+bool bond::ContainsId(const atomId_t number) const
+{
+  return ((leftatom->getId() == number) || (rightatom->getId() == number));
 };
 

src/Bond/bond.hpp

@@ -19 +19 @@
 
 #include <boost/shared_ptr.hpp>
+
+#include "types.hpp"
 
 #include "Bond/bond_observable.hpp"
@@ -51 +53 @@
 
   bool Contains(const ParticleInfo * const ptr) const;
-  bool Contains(const int nr) const;
+  bool ContainsNr(const int nr) const;
+  bool ContainsId(const atomId_t nr) const;
   double GetDistance() const;
   double GetDistanceSquared() const;

src/Fragmentation/PowerSetGenerator.cpp

@@ -131 +131 @@
     for (TouchedList_t::const_iterator iter = TouchedList.begin();
         iter != TouchedList.end(); ++iter) {
-      if ((*Binder)->Contains(*iter))   // if we added this very endpiece
+      if ((*Binder)->ContainsNr(*iter))   // if we added this very endpiece
         SetDimension++;
     }