Changes in / [255971:d223d5]

Files:

• Makefile.am (modified) (1 diff)
• doc/molecuilder_logo.png (added)
• doc/molecuilder_logo.xcf (added)
• src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) (1 diff)
• src/Actions/CmdAction/FastParsingAction.cpp (modified) (1 diff)
• src/Actions/CmdAction/VerboseAction.cpp (modified) (1 diff)
• src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (1 diff)
• src/Actions/MapOfActions.hpp (modified) (1 diff)
• src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) (3 diffs)
• src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) (1 diff)
• src/Exceptions/Makefile.am (modified) (1 diff)
• src/Formula.cpp (modified) (5 diffs)
• src/Formula.hpp (modified) (4 diffs)
• src/Helpers/Assert.cpp (modified) (5 diffs)
• src/Helpers/Assert.hpp (modified) (5 diffs)
• src/Helpers/Log.hpp (modified) (1 diff)
• src/Helpers/Makefile.am (modified) (1 diff)
• src/Helpers/MemDebug.cpp (modified) (4 diffs)
• src/Helpers/MemDebug.hpp (modified) (2 diffs)
• src/Helpers/helpers.hpp (modified) (1 diff)
• src/LinearAlgebra/Makefile.am (modified) (1 diff)
• src/LinearAlgebra/linearsystemofequations.hpp (modified) (2 diffs)
• src/Makefile.am (modified) (10 diffs)
• src/Parser/Makefile.am (modified) (1 diff)
• src/Parser/TremoloParser.cpp (modified) (1 diff)
• src/UIElements/Makefile.am (modified) (1 diff)
• src/UIElements/QT4/QTDialog.cpp (modified) (1 diff)
• src/UIElements/TextUI/TextDialog.cpp (modified) (2 diffs)
• src/UIElements/TextUI/TextWindow.cpp (modified) (1 diff)
• src/World.cpp (modified) (3 diffs)
• src/atom.cpp (modified) (3 diffs)
• src/atom.hpp (modified) (2 diffs)
• src/builder.cpp (modified) (3 diffs)
• src/defs.hpp (modified) (1 diff)
• src/element.cpp (modified) (2 diffs)
• src/element.hpp (modified) (3 diffs)
• src/molecule.cpp (modified) (11 diffs)
• src/molecule.hpp (modified) (1 diff)
• src/unittests/ActionSequenceTest.cpp (modified) (1 diff)
• src/unittests/FormulaUnittest.cpp (modified) (2 diffs)
• src/unittests/Makefile.am (modified) (1 diff)
• src/unittests/ShapeUnittest.cpp (modified) (1 diff)
• test_all.sh (modified) (1 diff)
• tests/Tesselations/Makefile.am (modified) (1 diff)

Makefile.am

@@ -9 +9 @@
 doc:
         cd doc && make doxygen-docs
+        
+unity:
+        cd src && make unity

src/Actions/AnalysisAction/PointCorrelationAction.hpp

@@ -11 +11 @@
 #include "Actions/Action.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include <vector>
+#include <string>
 
 class element;

src/Actions/CmdAction/FastParsingAction.cpp

@@ -78 +78 @@
 
 Action::state_ptr CommandLineFastParsingAction::performRedo(Action::state_ptr _state){
-  performUndo(_state);
+  return performUndo(_state);
 }
 

src/Actions/CmdAction/VerboseAction.cpp

@@ -76 +76 @@
 
 Action::state_ptr CommandLineVerboseAction::performRedo(Action::state_ptr _state){
-  performUndo(_state);
+  return performUndo(_state);
 }
 

src/Actions/FragmentationAction/SubgraphDissectionAction.hpp

@@ -7 +7 @@
 
 #ifndef SUBGRAPHDISSECTIONACTION_HPP_
-#define SUBGRAPHDISSECTIONACTION_HPP_f
+#define SUBGRAPHDISSECTIONACTION_HPP_
 
 #include "Actions/Action.hpp"

src/Actions/Makefile.am

@@ -209 +209 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(ACTIONSSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

src/Actions/MapOfActions.hpp

@@ -10 +10 @@
 
 #include <boost/program_options.hpp>
+#include <boost/lexical_cast.hpp>
 
 #include <map>

src/Actions/SelectionAction/NotAllAtomsAction.cpp

@@ -28 +28 @@
 // memento to remember the state when undoing
 
-class SelectionAllAtomsState : public ActionState {
+class SelectionNotAllAtomsState : public ActionState {
 public:
-  SelectionAllAtomsState(std::vector<atom*> _selectedAtoms) :
+  SelectionNotAllAtomsState(std::vector<atom*> _selectedAtoms) :
     selectedAtoms(_selectedAtoms)
   {}
@@ -61 +61 @@
   DoLog(1) && (Log() << Verbose(1) << "Unselecting all atoms." << endl);
   World::getInstance().clearAtomSelection();
-  return Action::state_ptr(new SelectionAllAtomsState(selectedAtoms));
+  return Action::state_ptr(new SelectionNotAllAtomsState(selectedAtoms));
 }
 
 Action::state_ptr SelectionNotAllAtomsAction::performUndo(Action::state_ptr _state) {
-  SelectionAllAtomsState *state = assert_cast<SelectionAllAtomsState*>(_state.get());
+  SelectionNotAllAtomsState *state = assert_cast<SelectionNotAllAtomsState*>(_state.get());
 
   World::getInstance().clearAtomSelection();
@@ -71 +71 @@
     World::getInstance().selectAtom(*iter);
 
-  return Action::state_ptr(new SelectionAllAtomsState(state->selectedAtoms));
+  return Action::state_ptr(new SelectionNotAllAtomsState(state->selectedAtoms));
 }
 
 Action::state_ptr SelectionNotAllAtomsAction::performRedo(Action::state_ptr _state){
-  SelectionAllAtomsState *state = assert_cast<SelectionAllAtomsState*>(_state.get());
+  SelectionNotAllAtomsState *state = assert_cast<SelectionNotAllAtomsState*>(_state.get());
 
   World::getInstance().clearAtomSelection();
 
-  return Action::state_ptr(new SelectionAllAtomsState(state->selectedAtoms));
+  return Action::state_ptr(new SelectionNotAllAtomsState(state->selectedAtoms));
 }
 

src/Actions/WorldAction/SetDefaultNameAction.cpp

@@ -79 +79 @@
 
 Action::state_ptr WorldSetDefaultNameAction::performRedo(Action::state_ptr _state){
-  performUndo(_state);
+  return performUndo(_state);
 }
 

src/Actions/WorldAction/SetGaussianBasisAction.cpp

@@ -79 +79 @@
 
 Action::state_ptr WorldSetGaussianBasisAction::performRedo(Action::state_ptr _state){
-  performUndo(_state);
+  return performUndo(_state);
 }
 

src/Exceptions/Makefile.am

@@ -72 +72 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(EXCEPTIONSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

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");

src/Formula.hpp

@@ -16 +16 @@
 
 #include "types.hpp"
+#include "Helpers/helpers.hpp"
 
 class element;
@@ -22 +23 @@
 {
 public:
-  typedef element*                                      key_type;
+  typedef const element*                                key_type;
   typedef unsigned int                                  mapped_type;
   typedef std::pair<key_type, mapped_type>              value_type;
@@ -65 +66 @@
 
   unsigned int getElementCount() const;
-  bool hasElement(const element*)       const;
+  bool hasElement(key_type)             const;
   bool hasElement(atomicNumber_t)       const;
   bool hasElement(const std::string&)   const;
 
-  void operator+=(const element*);
+  void operator+=(key_type);
   void operator+=(atomicNumber_t);
   void operator+=(const std::string&);
 
-  void operator-=(const element*);
+  void operator-=(key_type);
   void operator-=(atomicNumber_t);
   void operator-=(const std::string&);
 
-  void addElements(const element*,unsigned int);
+  void addElements(key_type,unsigned int);
   void addElements(atomicNumber_t,unsigned int);
   void addElements(const std::string&,unsigned int);
 
+  void addFormula(const Formula&,unsigned int);
+
+  enumeration<key_type> enumerateElements() const;
+
   // only const versions, because someone might try to increment a previously
   // not set element
-  const unsigned int operator[](const element*) const;
+  const unsigned int operator[](key_type) const;
   const unsigned int operator[](atomicNumber_t) const;
   const unsigned int operator[](std::string)    const;
@@ -98 +103 @@
 
 private:
+  void parseFromString(std::string::const_iterator&,std::string::const_iterator&,char) throw(ParseError);
+  int parseMaybeNumber(std::string::const_iterator &it,std::string::const_iterator &end) throw(ParseError);
   // this contains all counts of elements in the formula
   // the size of the actual structure might be used in comparisons

src/Helpers/Assert.cpp

@@ -5 +5 @@
  *      Author: crueger
  */
-
-#include "Helpers/MemDebug.hpp"
 
 #include "Helpers/Assert.hpp"
@@ -46 +44 @@
 }
 
-using namespace Assert;
-
 #ifndef NDEBUG
 
-Action _my_assert::defaultAction = Ask;
-std::vector<Assert::hook_t> _my_assert::hooks;
+#ifdef __GNUC__
+#include <cstdlib>
+#include <execinfo.h>
+#include <cxxabi.h>
+#endif
 
-std::map<std::string,bool> _wrapper::ignores;
-const char* _wrapper::message_ptr = "source pointer did not point to object of desired type";
-const char* _wrapper::message_ref = "source reference did not contain object of desired type";
+Assert::Action Assert::_my_assert::defaultAction = Ask;
+std::vector<Assert::hook_t> Assert::_my_assert::hooks;
 
+std::map<std::string,bool> Assert::_wrapper::ignores;
+const char* Assert::_wrapper::message_ptr = "source pointer did not point to object of desired type";
+const char* Assert::_wrapper::message_ref = "source reference did not contain object of desired type";
 
-bool _my_assert::check(const bool res,
-                       const char* condition,
-                       const char* message,
-                       const char* filename,
-                       const int line,
-                       bool& ignore)
+bool Assert::_my_assert::check(const char* condition,
+                               const char* message,
+                               const char* filename,
+                               const int line,
+                               bool& ignore)
 {
-  if(!res){
-    cout << "Assertion \"" << condition << "\" failed in file " << filename << " at line " << line << endl;
-    cout << "Assertion Message: " << message << std::endl;
-    while(true){
-      char choice;
-      if(defaultAction==Ask) {
-        cout << "Please choose: (a)bort, (t)hrow execption, (i)gnore, al(w)ays ignore" << endl;
-        cin >> choice;
-      }
-      else{
-        choice = ActionKeys[defaultAction];
-      }
-      switch(choice){
-        case 'a':
-          return true;
-          break;
-        case 't':
-          throw AssertionFailure(condition,filename,line,message);
-          break;
-        case 'w':
-          ignore = true;
-          // fallthrough
-        case 'i':
-          return false;
-          break;
-      }
+  cout << "Assertion \"" << condition << "\" failed in file " << filename << " at line " << line << endl;
+  cout << "Assertion Message: " << message << std::endl;
+  while(true){
+    char choice;
+    if(defaultAction==Assert::Ask) {
+#ifdef __GNUC__
+      cout << "Please choose: (a)bort, (t)hrow execption, show (b)actrace, (i)gnore, al(w)ays ignore" << endl;
+#else
+      cout << "Please choose: (a)bort, (t)hrow execption, (i)gnore, al(w)ays ignore" << endl;
+#endif /* __GNUC__ */
+      cin >> choice;
+    }
+    else{
+      choice = ActionKeys[defaultAction];
+    }
+    switch(choice){
+      case 'a':
+        return true;
+        break;
+      case 't':
+        throw AssertionFailure(condition,filename,line,message);
+        break;
+#ifdef __GNUC__
+      case 'b':
+        Assert::_my_assert::backtrace(filename,line);
+       break;
+#endif /* __GNUC__ */
+      case 'w':
+        ignore = true;
+        // fallthrough
+      case 'i':
+        return false;
+        break;
     }
   }
@@ -96 +103 @@
 }
 
-void _my_assert::doHooks(){
+#ifdef __GNUC__
+void Assert::_my_assert::backtrace(const char *file, int line){
+  const size_t max_depth = 100;
+  void* stack_addrs[max_depth];
+  size_t stack_depth;
+  char **stack_strings=0;
+  const char *func_name=0;
+  size_t sz = 64;
+
+  // get the backtrace
+  stack_depth   = ::backtrace(stack_addrs,max_depth);
+  stack_strings = backtrace_symbols(stack_addrs, stack_depth);
+  // used later for demangling
+  // reserved here, so we can free it unconditionally
+  char *dm_function = static_cast<char*>(malloc(sz));
+  if(!dm_function){
+    // malloc failed... we are out of luck
+    cout << "cannot provide stack trace due to exhausted memory" << endl;
+    return;
+  }
+
+  cout << "Backtrace from  " << file << "@" << line << ":" << endl;
+
+  // i=2 because we don't want this function, nor the assertion handler
+  for(unsigned int i=2;i<stack_depth-2;++i){
+    // find the mangled function name
+    char *begin = stack_strings[i];
+    // function name starts with a (
+    while(*begin && *begin!='(') ++begin;
+    char *end=begin;
+    while(*end && *end!='+') ++end;
+
+    // see if we found our function name
+    if(*begin && *end){
+      *begin++ = 0;
+      *end = 0;
+      // use the C++ demangler
+
+      int status;
+      char *func_ret = abi::__cxa_demangle(begin, dm_function, &sz, &status);
+      if(func_ret){
+        // abi might have realloced...
+        dm_function = func_ret;
+        func_name = dm_function;
+      }
+      else{
+        // demangling failed... get the function name without demangling
+        func_name = begin;
+      }
+    }
+    else{
+      // function name not found... get the whole line
+      func_name = stack_strings[i];
+    }
+    cout << func_name << endl;
+  }
+  free(dm_function);
+  free(stack_strings); // malloc()ed by backtrace_symbols
+}
+#endif /* __GNUC__ */
+
+void Assert::_my_assert::doHooks(){
   for(vector<hook_t>::reverse_iterator iter = hooks.rbegin(); iter!=hooks.rend(); ++iter ){
     (*iter)();
@@ -102 +170 @@
 }
 
-void _my_assert::addHook(hook_t hook){
+void Assert::_my_assert::addHook(hook_t hook){
   hooks.push_back(hook);
 }
 
-void _my_assert::removeHook(Assert::hook_t hook){
+void Assert::_my_assert::removeHook(Assert::hook_t hook){
   for(vector<hook_t>::iterator iter = hooks.begin(); iter!=hooks.end();){
     if((*iter)==hook){
@@ -117 +185 @@
 }
 
-void _my_assert::setDefault(Assert::Action action){
+void Assert::_my_assert::setDefault(Assert::Action action){
   defaultAction = action;
 }
-Assert::Action _my_assert::getDefault(){
+Assert::Action Assert::_my_assert::getDefault(){
   return defaultAction;
 }
-std::string _my_assert::printDefault(){
+std::string Assert::_my_assert::printDefault(){
   return ActionNames[defaultAction];
 }

src/Helpers/Assert.hpp

@@ -234 +234 @@
       static bool ignore = false;\
       if(!ignore){\
-        if(Assert::_my_assert::check((condition),STRINGIFY(condition),(message),\
-                                     __FILE__,__LINE__,ignore)){\
+        if(!(condition) && Assert::_my_assert::check(STRINGIFY(condition),(message),\
+                                                     __FILE__,__LINE__,ignore)){\
           Assert::_my_assert::doHooks();\
           DEBUG_BREAK;\
@@ -247 +247 @@
                   static bool ignore = false; \
                   if(!ignore){\
-                          if(Assert::_my_assert::check(false,"Exception caught",(message),__FILE__,__LINE__,ignore)){\
+                          if(Assert::_my_assert::check("Exception caught",(message),__FILE__,__LINE__,ignore)){\
                             Assert::_my_assert::doHooks();\
-          DEBUG_BREAK;\
+                            DEBUG_BREAK;\
                           }\
                   }\
@@ -299 +299 @@
     class _my_assert{
     public:
-      static bool check(const bool res,
-                        const char* condition,
+      static bool check(const char* condition,
                         const char* message,
                         const char* filename,
                         const int line,
                         bool& ignore);
+#ifdef __GNUC__
+      static void backtrace(const char *file, int line);
+#endif /* __GNUC__ */
       static void addHook(Assert::hook_t hook);
       static void removeHook(Assert::hook_t hook);
@@ -332 +334 @@
 
       if(!ignore){
-        if(_my_assert::check(dynamic_cast<target>(src)==static_cast<target>(src),"type-safe typecast",
-                                       message_ptr,file,line,ignore)){
+        bool res = dynamic_cast<target>(src)==static_cast<target>(src);
+        if(!res && _my_assert::check("type-safe typecast",message_ptr,file,line,ignore)){
           _my_assert::doHooks();
           DEBUG_BREAK;
@@ -354 +356 @@
       catch(...){
         if(!ignore){
-          if(_my_assert::check(0,"type-safe typecast",message_ref,file,line,ignore)){
+          if(_my_assert::check("type-safe typecast",message_ref,file,line,ignore)){
             _my_assert::doHooks();
             DEBUG_BREAK;

src/Helpers/Log.hpp

@@ -12 +12 @@
 #include "Helpers/logger.hpp"
 
-class logger * Log();
-class errorLogger * eLog();
+class logger & Log();
+class errorLogger & eLog();
 void setVerbosity(int verbosityLevel);
 bool DoLog(int verbose);

src/Helpers/Makefile.am

@@ -69 +69 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(HELPERSSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

src/Helpers/MemDebug.cpp

@@ -72 +72 @@
   // all allocated memory blocks
   struct entry_t {
+    typedef unsigned int checksum_t;
     // we seperate the tracking info from the rest
     // A checksum will be calculated for this part of
@@ -90 +91 @@
     } info;
     bool isIgnored;
-    char checksum;
+    checksum_t checksum;
     entry_t *prev;
     entry_t *next;
@@ -117 +118 @@
   // calculates a simple checksum for the info block
   // the checksum is used to find memory corruptions
-  inline char calcChecksum(entry_t::info_t *info){
+  inline entry_t::checksum_t calcChecksum(entry_t::info_t *info){
     char *buffer = (char*)info;
-    char checksum =0;
+    entry_t::checksum_t checksum =0;
     for(size_t i=0;i<sizeof(entry_t::info_t);i++){
       checksum+=buffer[i];
@@ -154 +155 @@
       cout << "Chunk reserved at: " << pos->info.file << ":" << pos->info.line << endl;
 #endif
+    }
+  }
+
+  void dumpMemory(std::ostream &ost){
+    ost << "Maximum allocated Memory: " << max << " bytes" << endl;
+    ost << "Maximum allocated Memory: " << max << " bytes" << endl;
+    ost << "Currently allocated Memory: " << state <<" bytes" << endl;
+    ost << allocs << " allocated chunks total" << endl;
+    bool corrupted=false;
+    for(entry_t *pos=begin;pos;pos=pos->next){
+      ost << "\nChunk of " << pos->info.nbytes << " bytes" << " still available" << endl;
+#     ifdef __GNUC__
+        ost << "Chunk reserved at: " << pos->info.function
+             << " (" << pos->info.file << ":" << pos->info.line  << ")" << endl;
+#     else
+        ost << "Chunk reserved at: " << pos->info.file << ":" << pos->info.line << endl;
+#     endif
+        ost << "Chunk address: " << pos->info.location << endl;
+        entry_t::checksum_t checksum = calcChecksum(&pos->info);
+        ost << "Checksum of chunk: " << checksum << endl;
+        ost << "Checksum at allocation time: " << pos->checksum << endl;
+        if(checksum!=pos->checksum){
+          ost << "!!!Chunk was corrupted!!!" << endl;
+          corrupted=true;
+        }
+    }
+    if(corrupted){
+      ost << "\n!!!Memory corruption detected!!!" << endl;
     }
   }

src/Helpers/MemDebug.hpp

@@ -61 +61 @@
    */
   void getState();
+  void dumpMemory(std::ostream&);
 
   void _ignore(void*);
@@ -100 +101 @@
 
 #else
+
+#include <iosfwd>
+
 // memory debugging was disabled
 
 namespace Memory {
-  inline void getState(){}
+  inline void getState(){};
+
+  inline void dumpMemory(std::ostream&){};
 
   template <typename T>

src/Helpers/helpers.hpp

@@ -194 +194 @@
 };
 
+/************ struct to contain simple enumerations ***************/
+template <class C>
+struct enumeration{
+  enumeration() : max(0) {}
+  enumeration(unsigned int i) : max(i) {}
+  enumeration(const enumeration &src) :
+    there(src.there),
+    back(src.back),
+    max(src.max)
+  {}
+  enumeration &operator=(const enumeration &src){
+    /* no self-assignment check needed */
+    there = src.there;
+    back = src.back;
+    max = src.max;
+    return *this;
+  }
+  void add(const C &value){
+    if(!there.count(value)){
+      there[value]=max;
+      back[max++]=value;
+    }
+  }
+  unsigned int getMax() const{
+    return max;
+  }
+
+  map<C,unsigned int> there;
+  map<unsigned int,C> back;
+private:
+  unsigned int max;
+};
+
+/***** A counter to generate sequential numbers *******************/
+struct counter{
+  inline counter() : count(0){};
+  inline counter(int i) : count(i){};
+  inline unsigned int operator()(){
+    return count++;
+  }
+private:
+  unsigned int count;
+};
+
+template <class C,class ForwardIterator>
+enumeration<C> enumerate(ForwardIterator first,ForwardIterator last){
+  enumeration<C> res;
+  for_each(first,last,bind1st(mem_fun(&enumeration<C>::add),&res));
+  return res;
+}
+
 #endif /*HELPERS_HPP_*/

src/LinearAlgebra/Makefile.am

@@ -71 +71 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(LINALGSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

src/LinearAlgebra/linearsystemofequations.hpp

@@ -6 +6 @@
  */
 
-using namespace std;
+#ifndef LINEARSYSTEMSOFEQUATIONS_HPP
+#define LINEARSYSTEMSOFEQUATIONS_HPP
 
 /*********************************************** includes ***********************************/
@@ -55 +56 @@
   bool IsSymmetric;
 };
+
+#endif /* LINEARSYSTEMSOFEQUATIONS_HPP */

src/Makefile.am

@@ -4 +4 @@
 SUBDIRS = Actions Exceptions Helpers LinearAlgebra Parser UIElements
 
-                        
 ATOMSOURCE = \
   atom.cpp \
@@ -73 +72 @@
   Shapes/Shape.hpp \
   Shapes/ShapeOps.hpp
+
   
-
-QTUIMOC_HEADER = UIElements/QT4/QTDialog.hpp \
-        UIElements/QT4/QTMainWindow.hpp \
-        UIElements/Menu/QT4/QTMenu.hpp \
-        UIElements/Views/QT4/QTWorldView.hpp \
-        UIElements/Views/QT4/GLMoleculeView.hpp \
-        UIElements/Views/QT4/QTMoleculeView.hpp \
-        UIElements/Views/QT4/QTStatusBar.hpp
- 
-QTUIMOC_TARGETS = QTMainWindow.moc.cpp \
-        QTMenu.moc.cpp\
-        QTDialog.moc.cpp \
-        QTWorldView.moc.cpp \
-        GLMoleculeView.moc.cpp \
-        QTMoleculeView.moc.cpp \
-        QTStatusBar.moc.cpp
-
 DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
   Descriptors/AtomIdDescriptor.cpp \
@@ -113 +96 @@
   Descriptors/MoleculePtrDescriptor.hpp \
   Descriptors/MoleculeSelectionDescriptor.cpp
+
+
+QTUIMOC_HEADER = UIElements/QT4/QTDialog.hpp \
+        UIElements/QT4/QTMainWindow.hpp \
+        UIElements/Menu/QT4/QTMenu.hpp \
+        UIElements/Views/QT4/QTWorldView.hpp \
+        UIElements/Views/QT4/GLMoleculeView.hpp \
+        UIElements/Views/QT4/QTMoleculeView.hpp \
+        UIElements/Views/QT4/QTStatusBar.hpp
                                   
-QTUISOURCE = ${QTUIMOC_TARGETS} \
+QTUISOURCE = allmocs.moc.cpp \
         UIElements/QT4/QTMainWindow.cpp \
         UIElements/QT4/QTDialog.cpp \
@@ -136 +128 @@
   ${SHAPESOURCE} \
   ${DESCRIPTORSOURCE} \
-  ${HELPERSOURCE} \
   bond.cpp \
   bondgraph.cpp \
@@ -229 +220 @@
 ## from each source file.  Note that it is not necessary to list header files
 ## which are already listed elsewhere in a _HEADERS variable assignment.
-libMolecuilder_@MOLECUILDER_API_VERSION@_la_SOURCES = ${MOLECUILDERSOURCE}  $(srcdir)/version.c
+libMolecuilder_@MOLECUILDER_API_VERSION@_la_SOURCES = ${MOLECUILDERSOURCE} $(srcdir)/version.c
 
 ## Instruct libtool to include ABI version information in the generated shared
@@ -264 +255 @@
 noinst_LIBRARIES = libmenu.a
 bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
+EXTRA_PROGRAMS = unity
 
 molecuilderdir = ${bindir}
@@ -292 +284 @@
 molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
 molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
+
+unity_SOURCES = unity.cpp
+unity_LDADD = $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
+
 molecuildergui_LDADD = \
         UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
@@ -329 +325 @@
 # Therfore `%'-rules do not seem to work
 #Quick fix to get it done otherwise
-${QTUIMOC_TARGETS}: ${QTUIMOC_HEADER}
+allmocs.moc.cpp: ${QTUIMOC_HEADER}
+        echo "" > allmocs.moc.cpp;\
         list='$(QTUIMOC_HEADER)'; for header in $$list; do \
         echo "Making mocfile for $$header"; \
@@ -335 +332 @@
         $(MOC) $(srcdir)/$$header -o $$target \
         || eval $$failcom; \
+        echo "#include \"$$target\"" >> allmocs.moc.cpp; \
         done;
 
-MOSTLYCLEANFILES = ${QTUIMOC_TARGETS}
-        
 #EXTRA_DIST = ${molecuilder_DATA}
 
@@ -357 +353 @@
 
 
+unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
+        echo "" >  unity.cpp; \
+        list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done; \
+        subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
+                olddir=$$PWD;\
+                cd $$directory && make unity.cpp;\
+                cd $$olddir;\
+                echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
+        done;\
+        echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
+        echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;
+
+MOSTLYCLEANFILES = allmocs.moc.cpp unity.cpp 
+        

src/Parser/Makefile.am

@@ -66 +66 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(PARSERSOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

src/Parser/TremoloParser.cpp

@@ -21 +21 @@
 
 using namespace std;
-using namespace boost;
 
 /**

src/UIElements/Makefile.am

@@ -118 +118 @@
 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
 
+unity.cpp:
+        echo "" >  unity.cpp; \
+        list='$(UISOURCE)'; for file in $$list; do \
+          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
+        done;
+        
+MOSTLYCLEANFILES = unity.cpp

src/UIElements/QT4/QTDialog.cpp

@@ -7 +7 @@
 
 #include "UIElements/QT4/QTDialog.hpp"
+
+#include <boost/lexical_cast.hpp>
 
 #include <string>

src/UIElements/TextUI/TextDialog.cpp

@@ -28 +28 @@
 #include "LinearAlgebra/Matrix.hpp"
 #include "Box.hpp"
+
+#include <boost/lexical_cast.hpp>
 
 using namespace std;
@@ -523 +525 @@
     }
   }
+  return true;
 }
 

src/UIElements/TextUI/TextWindow.cpp

@@ -25 +25 @@
 #include "Views/StreamStringView.hpp"
 #include "Views/MethodStringView.hpp"
-#include "Helpers/MemDebug.hpp"
 
 #include "defs.hpp"

src/World.cpp

@@ -32 +32 @@
 
 using namespace std;
+
+const unsigned int MAX_POOL_FRAGMENTATION=20;
+const unsigned int MAX_FRAGMENTATION_SKIPS=100;
 
 /******************************* getter and setter ************************/
@@ -718 +721 @@
   delete cell_size;
   delete molecules_deprecated;
-  delete periode;
-  delete configuration;
-  delete Thermostats;
   MoleculeSet::iterator molIter;
   for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
@@ -731 +731 @@
   }
   atoms.clear();
+  delete periode;
+  delete configuration;
+  delete Thermostats;
 }
 

src/atom.cpp

@@ -19 +19 @@
 
 #include <iomanip>
+#include <iostream>
 
 /************************************* Functions for class atom *************************************/
@@ -109 +110 @@
 };
 
+bool atom::isFather(const atom *ptr){
+  return ptr==father;
+}
+
 /** Checks whether atom is within the given box.
  * \param offset offset to box origin
@@ -161 +166 @@
   * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
+bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
 {
   AtomNo[type->Z]++;  // increment number
   if (out != NULL) {
-    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+    cout << "Looking for atom with element " << *type << endl;
+    ASSERT(elementLookup.there.find(type)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
+    *out << "Ion_Type" << elementLookup.there.find(type)->second << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
     *out << x[0] << "\t" << x[1] << "\t" << x[2];
     *out << "\t" << FixedIon;

src/atom.hpp

@@ -52 +52 @@
 
   bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
-  bool OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
+  bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
   bool OutputXYZLine(ofstream *out) const;
   bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
@@ -61 +61 @@
 
   void EqualsFather ( const atom *ptr, const atom **res ) const;
+  bool isFather(const atom *ptr);
   void CorrectFather();
   atom *GetTrueFather();

src/builder.cpp

@@ -110 +110 @@
 }
 
+void dumpMemory(){
+  ofstream ost("molecuilder.memdump");
+  Memory::dumpMemory(ost);
+}
+
 int main(int argc, char **argv)
 {
   // while we are non interactive, we want to abort from asserts
-  //ASSERT_DO(Assert::Abort);
+  ASSERT_DO(Assert::Abort);
+  ASSERT_HOOK(dumpMemory);
   string line;
   char **Arguments = NULL;
@@ -127 +133 @@
   // need to init the history before any action is created
   ActionHistory::init();
-
-  // In the interactive mode, we can leave the user the choice in case of error
-  ASSERT_DO(Assert::Ask);
 
   // from this moment on, we need to be sure to deeinitialize in the correct order
@@ -155 +158 @@
       UIFactory::makeUserInterface("CommandLine");
     } else {
+      // In the interactive mode, we can leave the user the choice in case of error
+      ASSERT_DO(Assert::Ask);
       #ifdef USE_GUI_QT
         DoLog(0) && (Log() << Verbose(0) << "Setting UI to QT4." << endl);

src/defs.hpp

@@ -84 +84 @@
 #define MOLECUILDER_NAME "Molecuilder"
 
-const unsigned int MAX_POOL_FRAGMENTATION=20;
-const unsigned int MAX_FRAGMENTATION_SKIPS=100;
+const extern unsigned int MAX_POOL_FRAGMENTATION;
+const extern unsigned int MAX_FRAGMENTATION_SKIPS;
 
 #endif /*DEFS_HPP_*/

src/element.cpp

@@ -26 +26 @@
         next(NULL),
         sort(NULL),
-        No(-1),
         Valence(0),
         NoValenceOrbitals(0)
@@ -70 +69 @@
   return string(symbol);
 }
+
+std::string element::getName() const{
+  return string(name);
+}
+
+std::ostream &operator<<(std::ostream &ost,const element &elem){
+  ost << elem.getName() << "(" << elem.getNumber() << ")";
+  return ost;
+}

src/element.hpp

@@ -41 +41 @@
     element *next;  //!< next element in list
     int *sort;      //!< sorc criteria
-    int No;         //!< number of element set on periodentafel::Output()
     double Valence;   //!< number of valence electrons for this element
     int NoValenceOrbitals;  //!< number of valence orbitals, used for determining bond degree in molecule::CreateConnectmatrix()
@@ -53 +52 @@
   atomicNumber_t getNumber() const;
   std::string getSymbol() const;
+  std::string getName() const;
 
   //> print element entries to screen
@@ -61 +61 @@
 };
 
+std::ostream &operator<<(std::ostream&,const element&);
 
 #endif /* ELEMENT_HPP_ */

src/molecule.cpp

@@ -151 +151 @@
 molecule::const_iterator molecule::erase( const_iterator loc )
 {
+  OBSERVE;
   molecule::const_iterator iter = loc;
   iter--;
@@ -156 +157 @@
   atomIds.erase( atom->getId() );
   atoms.remove( atom );
+  formula-=atom->type;
   atom->removeFromMolecule();
   return iter;
@@ -162 +164 @@
 molecule::const_iterator molecule::erase( atom * key )
 {
+  OBSERVE;
   molecule::const_iterator iter = find(key);
   if (iter != end()){
     atomIds.erase( key->getId() );
     atoms.remove( key );
+    formula-=key->type;
     key->removeFromMolecule();
   }
@@ -183 +187 @@
 pair<molecule::iterator,bool> molecule::insert ( atom * const key )
 {
+  OBSERVE;
   pair<atomIdSet::iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
     atoms.push_back(key);
+    formula+=key->type;
     return pair<iterator,bool>(molecule::iterator(--end()),res.second);
   } else {
@@ -233 +239 @@
   if (pointer != NULL) {
     atom *walker = pointer->clone();
+    formula += walker->type;
     walker->setName(pointer->getName());
     walker->nr = last_atom++;  // increase number within molecule
@@ -619 +626 @@
 {
   molecule *copy = World::getInstance().createMolecule();
-  atom *LeftAtom = NULL, *RightAtom = NULL;
 
   // copy all atoms
-  ActOnCopyWithEachAtom ( &molecule::AddCopyAtom, copy );
+  for_each(atoms.begin(),atoms.end(),bind1st(mem_fun(&molecule::AddCopyAtom),copy));
 
   // copy all bonds
-  bond *Binder = NULL;
-  bond *NewBond = NULL;
   for(molecule::iterator AtomRunner = begin(); AtomRunner != end(); ++AtomRunner)
     for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
       if ((*BondRunner)->leftatom == *AtomRunner) {
-        Binder = (*BondRunner);
+        bond *Binder = (*BondRunner);
 
         // get the pendant atoms of current bond in the copy molecule
-        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->leftatom, (const atom **)&LeftAtom );
-        copy->ActOnAllAtoms( &atom::EqualsFather, (const atom *)Binder->rightatom, (const atom **)&RightAtom );
-
-        NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
+        atomSet::iterator leftiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->leftatom));
+        atomSet::iterator rightiter=find_if(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::isFather),Binder->rightatom));
+        ASSERT(leftiter!=atoms.end(),"No original left atom for bondcopy found");
+        ASSERT(leftiter!=atoms.end(),"No original right atom for bondcopy found");
+        atom *LeftAtom = *leftiter;
+        atom *RightAtom = *rightiter;
+
+        bond *NewBond = copy->AddBond(LeftAtom, RightAtom, Binder->BondDegree);
         NewBond->Cyclic = Binder->Cyclic;
         if (Binder->Cyclic)
@@ -643 +651 @@
       }
   // correct fathers
-  ActOnAllAtoms( &atom::CorrectFather );
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::CorrectFather));
 
   // copy values
@@ -852 +860 @@
  * \param *out output stream
  */
-bool molecule::Output(ofstream * const output)
-{
-  int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
-
-  for (int i=0;i<MAX_ELEMENTS;++i) {
-    AtomNo[i] = 0;
-    ElementNo[i] = 0;
-  }
+bool molecule::Output(ostream * const output)
+{
   if (output == NULL) {
     return false;
   } else {
+    int AtomNo[MAX_ELEMENTS];
+    memset(AtomNo,0,(MAX_ELEMENTS-1)*sizeof(*AtomNo));
+    enumeration<const element*> elementLookup = formula.enumerateElements();
+    for(map<const element*,unsigned int>::iterator iter=elementLookup.there.begin();
+        iter!=elementLookup.there.end();++iter){
+      cout << "Enumerated element " << *iter->first << " with number " << iter->second << endl;
+    }
     *output << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
-    SetIndexedArrayForEachAtomTo ( ElementNo, &element::Z, &AbsoluteValue, 1);
-    int current=1;
-    for (int i=0;i<MAX_ELEMENTS;++i) {
-      if (ElementNo[i] == 1)
-        ElementNo[i] = current++;
-    }
-    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
+    for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputArrayIndexed,_1,output,elementLookup,AtomNo,(const char*)0));
     return true;
   }
@@ -913 +916 @@
 {
   DoLog(2) && (Log() << Verbose(2) << endl << "From Contents of ListOfBonds, all non-hydrogen atoms:" << endl);
-  ActOnAllAtoms (&atom::OutputBondOfAtom );
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::OutputBondOfAtom));
   DoLog(0) && (Log() << Verbose(0) << endl);
 };
@@ -936 +939 @@
     for (int step=0;step<MDSteps;step++) {
       *output << getAtomCount() << "\n\tCreated by molecuilder, step " << step << ", on " << ctime(&now);
-      ActOnAllAtoms( &atom::OutputTrajectoryXYZ, output, step );
+      for_each(atoms.begin(),atoms.end(),boost::bind(&atom::OutputTrajectoryXYZ,_1,output,step));
     }
     return true;
@@ -953 +956 @@
     now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     *output << getAtomCount() << "\n\tCreated by molecuilder on " << ctime(&now);
-    ActOnAllAtoms( &atom::OutputXYZLine, output );
+    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputXYZLine),output));
     return true;
   } else

src/molecule.hpp

@@ -341 +341 @@
 
   // Output routines.
-  bool Output(ofstream * const output);
+  bool Output(std::ostream * const output);
   bool OutputTrajectories(ofstream * const output);
   void OutputListOfBonds() const;

src/unittests/ActionSequenceTest.cpp

@@ -243 +243 @@
 
   CPPUNIT_ASSERT_EQUAL(true,wasCalled1->wasCalled());
-  CPPUNIT_ASSERT_EQUAL(true,wasCalled1->wasCalled());
+  CPPUNIT_ASSERT_EQUAL(true,wasCalled2->wasCalled());
 
   ActionHistory::getInstance().undoLast();
 
   CPPUNIT_ASSERT_EQUAL(false,wasCalled1->wasCalled());
-  CPPUNIT_ASSERT_EQUAL(false,wasCalled1->wasCalled());
-
-}
-
-
+  CPPUNIT_ASSERT_EQUAL(false,wasCalled2->wasCalled());
+
+}
+
+

src/unittests/FormulaUnittest.cpp

@@ -185 +185 @@
   }
   {
+    Formula formula("CH2(COOH)2");
+    CPPUNIT_ASSERT_EQUAL(formula["H"],(unsigned int)4);
+    CPPUNIT_ASSERT_EQUAL(formula["O"],(unsigned int)4);
+    CPPUNIT_ASSERT_EQUAL(formula["C"],(unsigned int)3);
+    CPPUNIT_ASSERT_EQUAL(formula["Na"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["He"],(unsigned int)0);
+  }
+  {
+    Formula formula("K4[Fe(CN)6]");
+    CPPUNIT_ASSERT_EQUAL(formula["H"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["O"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["C"],(unsigned int)6);
+    CPPUNIT_ASSERT_EQUAL(formula["Na"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["He"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["K"],(unsigned int)4);
+    CPPUNIT_ASSERT_EQUAL(formula["Fe"],(unsigned int)1);
+    CPPUNIT_ASSERT_EQUAL(formula["N"],(unsigned int)6);
+  }
+  {
+    Formula formula("[CrCl3(H2O)3]");
+    CPPUNIT_ASSERT_EQUAL(formula["H"],(unsigned int)6);
+    CPPUNIT_ASSERT_EQUAL(formula["O"],(unsigned int)3);
+    CPPUNIT_ASSERT_EQUAL(formula["C"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["Na"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["He"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["Cr"],(unsigned int)1);
+    CPPUNIT_ASSERT_EQUAL(formula["Cl"],(unsigned int)3);
+  }
+  {
+    Formula formula("Mg3[Fe(CN)6]2");
+    CPPUNIT_ASSERT_EQUAL(formula["H"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["O"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["C"],(unsigned int)12);
+    CPPUNIT_ASSERT_EQUAL(formula["Na"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["He"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["Mg"],(unsigned int)3);
+    CPPUNIT_ASSERT_EQUAL(formula["Fe"],(unsigned int)2);
+    CPPUNIT_ASSERT_EQUAL(formula["N"],(unsigned int)12);
+  }
+  {
+    Formula formula("Na[Fe((HO2CCH2)2NCH2CH2N(CH2CO2H)2)]");
+    CPPUNIT_ASSERT_EQUAL(formula["H"],(unsigned int)16);
+    CPPUNIT_ASSERT_EQUAL(formula["O"],(unsigned int)8);
+    CPPUNIT_ASSERT_EQUAL(formula["C"],(unsigned int)10);
+    CPPUNIT_ASSERT_EQUAL(formula["Na"],(unsigned int)1);
+    CPPUNIT_ASSERT_EQUAL(formula["He"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["Mg"],(unsigned int)0);
+    CPPUNIT_ASSERT_EQUAL(formula["Fe"],(unsigned int)1);
+    CPPUNIT_ASSERT_EQUAL(formula["N"],(unsigned int)2);
+  }
+  {
     CPPUNIT_ASSERT_THROW(Formula formula("74107"),ParseError);
     CPPUNIT_ASSERT_THROW(Formula formula("  "),ParseError);
@@ -192 +243 @@
     CPPUNIT_ASSERT_THROW(Formula formula("1NaCl"),ParseError);
     CPPUNIT_ASSERT_THROW(Formula formula("Mag"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("AgCl)"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("(Na"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("(Mag)"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("MgCl2)"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("((MgCl2)"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2))"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2]"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("[MgCl2)"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("N(aCl"),ParseError);
+    CPPUNIT_ASSERT_THROW(Formula formula("Na()Cl"),ParseError);
   }
 

src/unittests/Makefile.am

@@ -64 +64 @@
 UILIBS = ../UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la  
 
-
 TESTSOURCES = \
   ActOnAllUnitTest.cpp \

src/unittests/ShapeUnittest.cpp

@@ -16 +16 @@
 #endif /*HAVE_TESTRUNNER*/
 
+#include "LinearAlgebra/Vector.hpp"
 #include "Shapes/Shape.hpp"
-#include "LinearAlgebra/Vector.hpp"
 
 // Registers the fixture into the 'registry'

test_all.sh

@@ -111 +111 @@
   echo "Making";
   if [ $noprocs -gt 1 ]; then
-    make -j$noprocs all install >>$logfile 2>&1;
-  else
-    make all install >>$logfile 2>&1;
+    make -j$noprocs all >>$logfile 2>&1;
+  else
+    make all >>$logfile 2>&1;
   fi
 }

tests/Tesselations/Makefile.am

@@ -1 @@
-TESTS = 1_2-dimethoxyethane.test \
-1_2-dimethylbenzene.test \
-2-methylcyclohexanone.test \
-benzene.test \
-cholesterol.test \
-cycloheptane.test \
-dimethyl_bromomalonate.test \
-glucose.test \
-heptan.test \
-isoleucine.test \
-neohexane.test \
-N_N-dimethylacetamide.test \
-proline.test \
-putrescine.test \
-tartaric_acid.test
+TESTS = \
+        1_2-dimethoxyethane.test \
+        1_2-dimethylbenzene.test \
+        2-methylcyclohexanone.test \
+        benzene.test \
+        cholesterol.test \
+        cycloheptane.test \
+        dimethyl_bromomalonate.test \
+        glucose.test \
+        isoleucine.test \
+        neohexane.test \
+        N_N-dimethylacetamide.test \
+        proline.test \
+        putrescine.test \
+        tartaric_acid.test
+
+#       heptan.test