Changeset 2bfc5b for src/Analysis/analysis_bonds.cpp

Timestamp:

Feb 11, 2016, 8:07:11 AM (9 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:

df5b8c

Parents:

ada8df

git-author:

Frederik Heber <heber@…> (12/30/15 10:06:45)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:11)

Message:

Replaced MoleculeListClass in analysis_bonds by vector of molecules.

• TESTFIX: also adapted CountBondsUnitTest.

File:

• src/Analysis/analysis_bonds.cpp (modified) (6 diffs)

src/Analysis/analysis_bonds.cpp

@@ -43 +43 @@
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
-#include "MoleculeListClass.hpp"
 
 /** Calculates the min, mean and maximum bond counts for the given molecule.
@@ -162 +161 @@
  * \param *Interface2Element or NULL
  */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
+int CountHydrogenBridgeBonds(const std::vector<molecule *> &molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
 {
   Info FunctionInfo(__func__);
@@ -175 +174 @@
 
   // go through every molecule
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();
-      MolWalker != molecules->ListOfMolecules.end();
+  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin();
+      MolWalker != molecules.end();
       ++MolWalker) {
     LOG(2, "INFO: Current molecule is " << (*MolWalker)->getName() << ".");
@@ -290 +289 @@
  * \return number of found bonds (\a *first-\a *second)
  */
-int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second)
+int CountBondsOfTwo(const std::vector<molecule *> &molecules, const element * const first, const element * const second)
 {
   int count = 0;
 
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
+  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin();MolWalker != molecules.end(); MolWalker++) {
     molecule::iterator Walker = (*MolWalker)->begin();
     for(;Walker!=(*MolWalker)->end();++Walker){
@@ -324 +323 @@
  * \return number of found bonds (\a *first-\a *second-\a *third, \a *third-\a *second-\a *first, respectively)
  */
-int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third)
+int CountBondsOfThree(const std::vector<molecule *> &molecules, const element * const first, const element * const second, const element * const third)
 {
   int count = 0;
@@ -333 +332 @@
   ElementArray[1] = third;
 
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
+  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin();MolWalker != molecules.end(); MolWalker++) {
     molecule::iterator Walker = (*MolWalker)->begin();
     for(;Walker!=(*MolWalker)->end();++Walker){