Changeset f761c4 for src/Formula.cpp

Timestamp:

Aug 5, 2010, 7:56:22 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:

a881f5

Parents:

ec149d (diff), 7baf4a (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' of jupiter:molecuilder into StructureRefactoring

File:

• src/Formula.cpp (modified) (5 diffs)

src/Formula.cpp

@@ -55 +55 @@
 
 void Formula::fromString(const std::string &formula) throw(ParseError){
+  // make this transactional, in case an error is thrown
+  Formula res;
+  string::const_iterator begin = formula.begin();
+  string::const_iterator end = formula.end();
+  res.parseFromString(begin,end,static_cast<char>(0));
+  (*this)=res;
+}
+
+int Formula::parseMaybeNumber(string::const_iterator &it,string::const_iterator &end) throw(ParseError){
+  static const range<char> Numbers = makeRange('0',static_cast<char>('9'+1));
+  int count = 0;
+  while(it!=end && Numbers.isInRange(*it))
+    count = (count*10) + ((*it++)-Numbers.first);
+  // one is implicit
+  count = (count!=0)?count:1;
+  return count;
+}
+
+void Formula::parseFromString(string::const_iterator &it,string::const_iterator &end,char delimiter) throw(ParseError){
   // some constants needed for parsing... Assumes ASCII, change if other encodings are used
   static const range<char> CapitalLetters = makeRange('A',static_cast<char>('Z'+1));
   static const range<char> SmallLetters = makeRange('a',static_cast<char>('z'+1));
-  static const range<char> Numbers = makeRange('0',static_cast<char>('9'+1));
+  map<char,char> delimiters;
+  delimiters['('] = ')';
+  delimiters['['] = ']';
   // clean the formula
   clear();
-  string::const_iterator end = formula.end(); // will be used frequently
-  for(string::const_iterator it=formula.begin();it!=end;){
+  for(/*send from above*/;it!=end && *it!=delimiter;/*updated in loop*/){
+    // we might have a sub formula
+    if(delimiters.count(*it)){
+      Formula sub;
+      char nextdelim=delimiters[*it];
+      sub.parseFromString(++it,end,nextdelim);
+      if(!sub.getElementCount()){
+        throw(ParseError(__FILE__,__LINE__));
+      }
+      int count = parseMaybeNumber(++it,end);
+      addFormula(sub,count);
+      continue;
+    }
     string shorthand;
     // Atom names start with a capital letter
@@ -71 +103 @@
     while(it!=end && SmallLetters.isInRange(*it))
       shorthand+=(*it++);
-    // now we can count the occurences
-    int count = 0;
-    while(it!=end && Numbers.isInRange(*it))
-      count = (count*10) + ((*it++)-Numbers.first);
-    // one is implicit
-    count = (count!=0)?count:1;
+    int count = parseMaybeNumber(it,end);
     // test if the shorthand exists
     if(!World::getInstance().getPeriode()->FindElement(shorthand))
@@ -83 +110 @@
     addElements(shorthand,count);
   }
+  if(it==end && delimiter!=0){
+    throw(ParseError(__FILE__,__LINE__));
+  }
 }
 
@@ -93 +123 @@
     *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl;
     for(const_iterator iter=begin(); iter!=end();++iter){
-      (*iter).first->No = No;
       result = result && (*iter).first->Checkout(output, No++, (*iter).second);
     }
@@ -195 +224 @@
 }
 
+void Formula::addFormula(const Formula &formula,unsigned int n){
+  for(Formula::const_iterator iter=formula.begin();iter!=formula.end();++iter){
+    this->addElements(iter->first,iter->second*n);
+  }
+}
+
+enumeration<Formula::key_type> Formula::enumerateElements() const{
+  enumeration<key_type> res(1);
+  for(Formula::const_iterator iter=begin();iter!=end();++iter){
+    res.add(iter->first);
+  }
+  return res;
+}
+
 const unsigned int Formula::operator[](const element *element) const{
   ASSERT(element,"Invalid pointer in access of Formula");