Changeset ac9b56

Timestamp:

Feb 2, 2010, 3:53:04 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

f721c6

Parents:

e3c8b4

Message:

Added simple way to retrieve formula of a molecule using caching

Location:

src

Files:

• molecule.cpp (modified) (3 diffs)
• molecule.hpp (modified) (3 diffs)

src/molecule.cpp

@@ -6 +6 @@
 
 #include <cstring>
+#include <boost/bind.hpp>
 
 #include "atom.hpp"
@@ -32 +33 @@
   first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0), 
   BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
-  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start)
+  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start),
+  formula(this,boost::bind(&molecule::calcFormula,this))
 {
   // init atom chain list
@@ -72 +74 @@
   strncpy(name,_name.c_str(),MAXSTRINGSIZE);
   FINISH_OBSERVER;
+}
+
+const std::string molecule::getFormula(){
+  return *formula;
+}
+
+std::string molecule::calcFormula(){
+  int Counts[MAX_ELEMENTS];
+  stringstream sstr;
+  for (int j = 0; j<MAX_ELEMENTS;j++)
+    Counts[j] = 0;
+  for(atom *Walker = start; Walker != end; Walker = Walker->next) {
+    Counts[Walker->type->Z]++;
+  }
+  for(element* Elemental = elemente->end; Elemental != elemente->start; Elemental = Elemental->previous) {
+    if (Counts[Elemental->Z] != 0)
+      sstr << Elemental->symbol << Counts[Elemental->Z];
+  }
+  return sstr.str();
 }
 

src/molecule.hpp

@@ -33 +33 @@
 #include "tesselation.hpp"
 #include "Patterns/Observer.hpp"
+#include "Patterns/Cacheable.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -105 +106 @@
     char name[MAXSTRINGSIZE];         //!< arbitrary name
 
+  private:
+    Cacheable<string> formula;
+
 public:
   molecule(const periodentafel * const teil);
@@ -112 +116 @@
   const std::string getName();
   void setName(const std::string);
+  const std::string getFormula();
+  std::string calcFormula();
 
   // re-definition of virtual functions from PointCloud