Changeset d03bb1 for src

Timestamp:

Jul 21, 2010, 1:55:18 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:

a6d6a9

Parents:

574ddc1

Message:

Added methods to produce formulas from strings

Location:

src

Files:

• Formula.cpp (modified) (4 diffs)
• Formula.hpp (modified) (5 diffs)

src/Formula.cpp

@@ -26 +26 @@
 {}
 
+Formula::Formula(const string &formula) :
+  numElements(0)
+{
+  fromString(formula);
+}
+
 Formula::~Formula()
 {}
@@ -42 +48 @@
   }
   return sstr.str();
+}
+
+// quick function used for parsing
+bool isInRange(pair<char,char> range,char character){
+  return range.first<=character && character<=range.second;
+}
+
+void Formula::fromString(const std::string &formula) throw(ParseError){
+  // some constants needed for parsing... Assumes ASCII, change if other encodings are used
+  static const pair<char,char> CapitalLetters = make_pair('A','Z');
+  static const pair<char,char> SmallLetters = make_pair('a','z');
+  static const pair<char,char> Numbers = make_pair('0','9');
+  // clean the formula
+  clear();
+  string::const_iterator end = formula.end(); // will be used frequently
+  for(string::const_iterator it=formula.begin();it!=end;){
+    string shorthand;
+    // Atom names start with a capital letter
+    if(!isInRange(CapitalLetters,(*it)))
+      throw(ParseError(__FILE__,__LINE__));
+    shorthand+=(*it++);
+    // the rest of the name follows
+    while(it!=end && isInRange(SmallLetters,(*it)))
+      shorthand+=(*it++);
+    // now we can count the occurences
+    int count = 0;
+    while(it!=end && isInRange(Numbers,(*it)))
+      count = (count*10) + ((*it++)-Numbers.first);
+    // one is implicit
+    count = (count!=0)?count:1;
+    // done, we can get the next one
+    addElements(shorthand,count);
+  }
 }
 
@@ -122 +161 @@
 }
 
+void Formula::addElements(const element *element,unsigned int count){
+  ASSERT(element,"Invalid pointer in Formula::addElements(element*)");
+  addElements(element->getNumber(),count);
+}
+
+void Formula::addElements(atomicNumber_t Z,unsigned int count){
+  if(count==0) return;
+  ASSERT(Z>0,"Invalid atomic Number");
+  ASSERT(World::getInstance().getPeriode()->FindElement(Z),"No Element with this number in Periodentafel");
+  elementCounts.resize(Z); // No-op when we already have the right size
+  // might need to update number of elements
+  if(!elementCounts[Z-1]){
+    numElements++;
+  }
+  elementCounts[Z-1]+=count;
+}
+
+void Formula::addElements(const string &shorthand,unsigned int count){
+  element * element = World::getInstance().getPeriode()->FindElement(shorthand);
+  addElements(element,count);
+}
+
 const unsigned int &Formula::operator[](const element *element) const{
   ASSERT(element,"Invalid pointer in access of Formula");
@@ -181 +242 @@
 Formula::const_reverse_iterator Formula::rend() const{
   return const_reverse_iterator(begin());
+}
+
+void Formula::clear(){
+  elementCounts.clear();
+  numElements = 0;
 }
 

src/Formula.hpp

@@ -12 +12 @@
 #include <iosfwd>
 #include <iterator>
+
+#include "Exceptions/ParseError.hpp"
 
 #include "types.hpp"
@@ -53 +55 @@
 
   Formula();
+  Formula(const std::string&);
   Formula(const Formula&);
   virtual ~Formula();
@@ -59 +62 @@
 
   std::string toString() const;
+  void fromString(const std::string&) throw(ParseError);
   bool checkOut(std::ostream*) const;
 
@@ -73 +77 @@
   void operator-=(atomicNumber_t);
   void operator-=(const std::string&);
+
+  void addElements(const element*,unsigned int);
+  void addElements(atomicNumber_t,unsigned int);
+  void addElements(const std::string&,unsigned int);
 
   // only const versions, because someone might try to increment a previously
@@ -93 +101 @@
   const_reverse_iterator rend()   const;
 
+  void clear();
+
 private:
   mutable set_t elementCounts; // we might need to resize even at const places