Changeset 9106c6 for src/molecule.cpp

Timestamp:

Jul 28, 2010, 1:48:50 PM (15 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:

0bb05a

Parents:

b1a39b (diff), a7b777c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'StructureRefactoring' into stable

File:

• src/molecule.cpp (modified) (12 diffs)

src/molecule.cpp

@@ -49 +49 @@
 molecule::molecule(const periodentafel * const teil) :
   Observable("molecule"),
-  elemente(teil),  MDSteps(0),  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0),
+  elemente(teil),  MDSteps(0),  BondCount(0), NoNonHydrogen(0), NoNonBonds(0),
   NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
-  formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
 {
 
-  // other stuff
-  for(int i=MAX_ELEMENTS;i--;)
-    ElementsInMolecule[i] = 0;
   strcpy(name,World::getInstance().getDefaultName().c_str());
 };
@@ -101 +97 @@
 }
 
-const std::string molecule::getFormula(){
-  return *formula;
-}
-
-std::string molecule::calcFormula(){
-  std::map<atomicNumber_t,unsigned int> counts;
-  stringstream sstr;
-  periodentafel *periode = World::getInstance().getPeriode();
-  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-    counts[(*iter)->type->getNumber()]++;
-  }
-  std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
-  for(iter = counts.rbegin(); iter != counts.rend(); ++iter) {
-    atomicNumber_t Z = (*iter).first;
-    sstr << periode->FindElement(Z)->symbol << (*iter).second;
-  }
-  return sstr.str();
+const Formula &molecule::getFormula(){
+  return formula;
+}
+
+unsigned int molecule::getElementCount(){
+  return formula.getElementCount();
+}
+
+bool molecule::hasElement(const element *element) const{
+  return formula.hasElement(element);
+}
+
+bool molecule::hasElement(atomicNumber_t Z) const{
+  return formula.hasElement(Z);
+}
+
+bool molecule::hasElement(const string &shorthand) const{
+  return formula.hasElement(shorthand);
 }
 
@@ -210 +207 @@
     pointer->sort = &pointer->nr;
     if (pointer->type != NULL) {
-      if (ElementsInMolecule[pointer->type->Z] == 0)
-        ElementCount++;
-      ElementsInMolecule[pointer->type->Z]++; // increase number of elements
+      formula += pointer->type;
       if (pointer->type->Z != 1)
         NoNonHydrogen++;
@@ -651 +646 @@
 
   // copy values
-  copy->CountElements();
   if (hasBondStructure()) {  // if adjaceny list is present
     copy->BondDistance = BondDistance;
@@ -774 +768 @@
   ASSERT(pointer, "Null pointer passed to molecule::RemoveAtom().");
   OBSERVE;
-  if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
-    ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
-  } else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
-  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
-    ElementCount--;
+  formula-=pointer->type;
   RemoveBonds(pointer);
   erase(pointer);
@@ -793 +782 @@
   if (pointer == NULL)
     return false;
-  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
-    ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
-  else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
-  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
-    ElementCount--;
+  formula-=pointer->type;
   erase(pointer);
   return true;
@@ -871 +855 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-  CountElements();
 
   for (int i=0;i<MAX_ELEMENTS;++i) {
@@ -898 +881 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-  CountElements();
 
   if (output == NULL) {
@@ -940 +922 @@
 bool molecule::Checkout(ofstream * const output)  const
 {
-  return elemente->Checkout(output, ElementsInMolecule);
+  return formula.checkOut(output);
 };
 
@@ -998 +980 @@
 };
 
-/** Brings molecule::ElementCount and molecule::ElementsInMolecule up-to-date.
- */
-void molecule::CountElements()
-{
-  for(int i=MAX_ELEMENTS;i--;)
-    ElementsInMolecule[i] = 0;
-  ElementCount = 0;
-
-  SetIndexedArrayForEachAtomTo ( ElementsInMolecule, &element::Z, &Increment, 1);
-
-  for(int i=MAX_ELEMENTS;i--;)
-    ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
-};
-
 /** Determines whether two molecules actually contain the same atoms and coordination.
  * \param *out output stream for debugging
@@ -1030 +998 @@
   /// first count both their atoms and elements and update lists thereby ...
   //Log() << Verbose(0) << "Counting atoms, updating list" << endl;
-  CountElements();
-  OtherMolecule->CountElements();
 
   /// ... and compare:
@@ -1041 +1007 @@
     } else Log() << Verbose(4) << "AtomCounts match: " << getAtomCount() << " == " << OtherMolecule->getAtomCount() << endl;
   }
-  /// -# ElementCount
+  /// -# Formula
   if (result) {
-    if (ElementCount != OtherMolecule->ElementCount) {
-      DoLog(4) && (Log() << Verbose(4) << "ElementCount don't match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl);
+    if (formula != OtherMolecule->formula) {
+      DoLog(4) && (Log() << Verbose(4) << "Formulas don't match: " << formula << " == " << OtherMolecule->formula << endl);
       result = false;
-    } else Log() << Verbose(4) << "ElementCount match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl;
-  }
-  /// -# ElementsInMolecule
-  if (result) {
-    for (flag=MAX_ELEMENTS;flag--;) {
-      //Log() << Verbose(5) << "Element " <<  flag << ": " << ElementsInMolecule[flag] << " <-> " << OtherMolecule->ElementsInMolecule[flag] << "." << endl;
-      if (ElementsInMolecule[flag] != OtherMolecule->ElementsInMolecule[flag])
-        break;
-    }
-    if (flag < MAX_ELEMENTS) {
-      DoLog(4) && (Log() << Verbose(4) << "ElementsInMolecule don't match." << endl);
-      result = false;
-    } else Log() << Verbose(4) << "ElementsInMolecule match." << endl;
+    } else Log() << Verbose(4) << "Formulas match: " << formula << " == " << OtherMolecule->formula << endl;
   }
   /// then determine and compare center of gravity for each molecule ...