Changeset 951aa6 for src

Timestamp:

Feb 11, 2016, 8:07:50 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:

db842b

Parents:

29f7c1

git-author:

Frederik Heber <heber@…> (12/29/15 19:50:22)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:07:50)

Message:

Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen().

• we don't do these as Cacheables anymore.

Location:

src

Files:

• molecule.cpp (modified) (2 diffs)
• molecule.hpp (modified) (2 diffs)

src/molecule.cpp

@@ -957 +957 @@
 }
 
-/** Brings molecule::AtomCount and atom::*Name up-to-date.
- * \param *out output stream for debugging
- */
-size_t molecule::doCountNoNonHydrogen() const
-{
-  int temp = 0;
-  // go through atoms and look for new ones
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter)
-    if ((*iter)->getType()->getAtomicNumber() != 1) // count non-hydrogen atoms whilst at it
-      ++temp;
-  return temp;
-};
-
-/** Counts the number of present bonds.
- * \return number of bonds
- */
-int molecule::doCountBonds() const
-{
-  unsigned int counter = 0;
-  for(molecule::const_iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner) {
-    const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
-    for(BondList::const_iterator BondRunner = ListOfBonds.begin();
-        BondRunner != ListOfBonds.end();
-        ++BondRunner)
-      if ((*BondRunner)->leftatom == *AtomRunner)
-        counter++;
-  }
-  return counter;
-}
-
-
 /** Returns an index map for two father-son-molecules.
  * The map tells which atom in this molecule corresponds to which one in the other molecul with their fathers.
@@ -1202 +1171 @@
 }
 
-void molecule::resetFormula()
-{
-  // clear
-  formula.clear();
-
-  for (molecule::const_iterator iter = const_cast<const molecule *>(this)->begin();
-      iter != const_cast<const molecule *>(this)->end(); ++iter)
-    formula+=(*iter)->getType();
-}
-
 void molecule::select()
 {

src/molecule.hpp

@@ -135 +135 @@
   const std::string getName() const;
   int getAtomCount() const;
-  size_t doCountNoNonHydrogen() const;
-  int doCountBonds() const;
   size_t getNoNonHydrogen() const{
     return NoNonHydrogen;
@@ -275 +273 @@
    */
   void setAtomName(atom *_atom) const;
-
-  /** Resets the formula for this molecule.
-   *
-   * This is required in case an atom changes its element as we then don't
-   * have any knowledge about its previous element anymore.
-   */
-  void resetFormula();
 
   //!> grant World (only) access to selection state changers