Changes in / [4917cc4:daa714]

Files:

• src/Actions/ActionRegistry.cpp (modified) (1 diff)
• src/Actions/ActionRegistry.hpp (modified) (1 diff)
• src/Actions/AnalysisAction/MolecularVolumeAction.cpp (added)
• src/Actions/AnalysisAction/MolecularVolumeAction.hpp (added)
• src/Actions/AnalysisAction/PairCorrelationAction.cpp (added)
• src/Actions/AnalysisAction/PairCorrelationAction.hpp (added)
• src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (added)
• src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (added)
• src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (added)
• src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (added)
• src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (added)
• src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (added)
• src/Actions/AtomAction/AddAction.cpp (added)
• src/Actions/AtomAction/AddAction.hpp (added)
• src/Actions/AtomAction/ChangeElementAction.cpp (added)
• src/Actions/AtomAction/ChangeElementAction.hpp (added)
• src/Actions/AtomAction/RemoveAction.cpp (added)
• src/Actions/AtomAction/RemoveAction.hpp (added)
• src/Actions/CmdAction/BondLengthTableAction.cpp (added)
• src/Actions/CmdAction/BondLengthTableAction.hpp (added)
• src/Actions/CmdAction/ElementDbAction.cpp (added)
• src/Actions/CmdAction/ElementDbAction.hpp (added)
• src/Actions/CmdAction/FastParsingAction.cpp (added)
• src/Actions/CmdAction/FastParsingAction.hpp (added)
• src/Actions/CmdAction/HelpAction.cpp (modified) (1 diff)
• src/Actions/CmdAction/VerboseAction.cpp (added)
• src/Actions/CmdAction/VerboseAction.hpp (added)
• src/Actions/CmdAction/VersionAction.cpp (modified) (1 diff)
• src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (added)
• src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (added)
• src/Actions/FragmentationAction/FragmentationAction.cpp (added)
• src/Actions/FragmentationAction/FragmentationAction.hpp (added)
• src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (added)
• src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (added)
• src/Actions/MapOfActions.cpp (added)
• src/Actions/MapOfActions.hpp (added)
• src/Actions/MoleculeAction/BondFileAction.cpp (added)
• src/Actions/MoleculeAction/BondFileAction.hpp (added)
• src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) (3 diffs)
• src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) (1 diff)
• src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (added)
• src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (added)
• src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (added)
• src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (added)
• src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (added)
• src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (added)
• src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (added)
• src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (added)
• src/Actions/MoleculeAction/SaveBondsAction.cpp (added)
• src/Actions/MoleculeAction/SaveBondsAction.hpp (added)
• src/Actions/MoleculeAction/SaveTemperatureAction.cpp (added)
• src/Actions/MoleculeAction/SaveTemperatureAction.hpp (added)
• src/Actions/MoleculeAction/SuspendInWaterAction.cpp (added)
• src/Actions/MoleculeAction/SuspendInWaterAction.hpp (added)
• src/Actions/MoleculeAction/TranslateAction.cpp (added)
• src/Actions/MoleculeAction/TranslateAction.hpp (added)
• src/Actions/MoleculeAction/VerletIntegrationAction.cpp (added)
• src/Actions/MoleculeAction/VerletIntegrationAction.hpp (added)
• src/Actions/ParserAction/LoadXyzAction.cpp (modified) (1 diff)
• src/Actions/ParserAction/SaveXyzAction.cpp (modified) (1 diff)
• src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (added)
• src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (added)
• src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (added)
• src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (added)
• src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (added)
• src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (added)
• src/Actions/WorldAction/BoundInBoxAction.cpp (added)
• src/Actions/WorldAction/BoundInBoxAction.hpp (added)
• src/Actions/WorldAction/CenterInBoxAction.cpp (added)
• src/Actions/WorldAction/CenterInBoxAction.hpp (added)
• src/Actions/WorldAction/CenterOnEdgeAction.cpp (added)
• src/Actions/WorldAction/CenterOnEdgeAction.hpp (added)
• src/Actions/WorldAction/ChangeBoxAction.cpp (added)
• src/Actions/WorldAction/ChangeBoxAction.hpp (added)
• src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (added)
• src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (added)
• src/Actions/WorldAction/RepeatBoxAction.cpp (added)
• src/Actions/WorldAction/RepeatBoxAction.hpp (added)
• src/Actions/WorldAction/ScaleBoxAction.cpp (added)
• src/Actions/WorldAction/ScaleBoxAction.hpp (added)
• src/Actions/WorldAction/SetDefaultNameAction.cpp (added)
• src/Actions/WorldAction/SetDefaultNameAction.hpp (added)
• src/Actions/WorldAction/SetGaussianBasisAction.cpp (added)
• src/Actions/WorldAction/SetGaussianBasisAction.hpp (added)
• src/CommandLineParser.cpp (modified) (2 diffs)
• src/CommandLineParser.hpp (modified) (1 diff)
• src/Legacy/oldmenu.cpp (modified) (3 diffs)
• src/Makefile.am (modified) (6 diffs)
• src/Parser/XyzParser.cpp (modified) (1 diff)
• src/UIElements/CommandLineDialog.cpp (modified) (8 diffs)
• src/UIElements/CommandLineDialog.hpp (modified) (5 diffs)
• src/UIElements/CommandLineWindow.cpp (modified) (7 diffs)
• src/UIElements/CommandLineWindow.hpp (modified) (2 diffs)
• src/UIElements/Dialog.cpp (modified) (4 diffs)
• src/UIElements/Dialog.hpp (modified) (6 diffs)
• src/UIElements/TextDialog.cpp (modified) (7 diffs)
• src/UIElements/TextDialog.hpp (modified) (5 diffs)
• src/UIElements/TextWindow.cpp (modified) (1 diff)
• src/World.cpp (modified) (1 diff)
• src/World.hpp (modified) (1 diff)
• src/bondgraph.hpp (modified) (1 diff)
• src/builder.cpp (modified) (10 diffs)
• src/molecule.hpp (modified) (1 diff)
• src/unittests/MapofActionsTest.cpp (added)
• src/unittests/MapofActionsTest.hpp (added)
• tests/Tesselations/defs.in (modified) (1 diff)

src/Actions/ActionRegistry.cpp

@@ -43 +43 @@
 }
 
+void ActionRegistry::unregisterAction(Action* action){
+  actionMap.erase(action->getName());
+}
+
 std::map<const std::string,Action*>::iterator ActionRegistry::getBeginIter()
 {

src/Actions/ActionRegistry.hpp

@@ -22 +22 @@
   Action* getActionByName(const std::string);
   void registerAction(Action*);
+  void unregisterAction(Action*);
 
   std::map<const std::string,Action*>::iterator getBeginIter();

src/Actions/CmdAction/HelpAction.cpp

@@ -16 +16 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
+#include "Actions/MapOfActions.hpp"
 
 const char CommandLineHelpAction::NAME[] = "help";

src/Actions/CmdAction/VersionAction.cpp

@@ -16 +16 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
+#include "Actions/MapOfActions.hpp"
 
 const char CommandLineVersionAction::NAME[] = "version";

src/Actions/MoleculeAction/ChangeNameAction.cpp

@@ -15 +15 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
+#include "Actions/MapOfActions.hpp"
 
 #include "atom.hpp"
@@ -35 +36 @@
 const char MoleculeChangeNameAction::NAME[] = "Change filename of Molecule";
 
-MoleculeChangeNameAction::MoleculeChangeNameAction(MoleculeListClass *_molecules) :
-  Action(NAME),
-  molecules(_molecules)
+MoleculeChangeNameAction::MoleculeChangeNameAction() :
+  Action(NAME)
 {}
 
@@ -48 +48 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  dialog->queryMolecule("Enter index of molecule: ",&mol,molecules);
+  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
   dialog->queryString("Enter name: ",&filename);
 

src/Actions/MoleculeAction/ChangeNameAction.hpp

@@ -16 +16 @@
 class MoleculeChangeNameAction : public Action {
 public:
-  MoleculeChangeNameAction(MoleculeListClass*);
+  MoleculeChangeNameAction();
   virtual ~MoleculeChangeNameAction();
 

src/Actions/ParserAction/LoadXyzAction.cpp

@@ -16 +16 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
+#include "Actions/MapOfActions.hpp"
 
 #include "atom.hpp"

src/Actions/ParserAction/SaveXyzAction.cpp

@@ -16 +16 @@
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/Dialog.hpp"
+#include "Actions/MapOfActions.hpp"
 
 #include "atom.hpp"

src/CommandLineParser.cpp

@@ -36 +36 @@
 void CommandLineParser::Parse()
 {
-  po::store(po::command_line_parser(argc,argv).options(cmdline_options).run(), vm);
-  po::store(po::command_line_parser(argc,argv).options(visible).run(), vm);
+  po::store(po::command_line_parser(argc,argv).options(cmdline_options).options(visible).positional(inputfile).run(), vm);
   ifstream input;
   input.open("example.cfg");
@@ -45 +44 @@
   po::notify(vm);
 }
+
+
 
 /** States whether there are command line arguments.

src/CommandLineParser.hpp

@@ -34 +34 @@
   po::options_description config;
   po::options_description hidden;
+  po::positional_options_description inputfile;
 
   po::options_description visible;

src/Legacy/oldmenu.cpp

@@ -35 +35 @@
 #include "Menu/DisplayMenuItem.hpp"
 #include "Menu/SubMenuItem.hpp"
+#include "Actions/MapOfActions.hpp"
 #include "Actions/MethodAction.hpp"
 #include "Actions/ErrorAction.hpp"
@@ -908 +909 @@
   molecule *srcmol = NULL, *destmol = NULL;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  dialog->queryMolecule("Enter index of destination molecule: ",&destmol, molecules);
-  dialog->queryMolecule("Enter index of source molecule to add from: ",&srcmol, molecules);
+  dialog->queryMolecule("molecule-by-id",&destmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
+  dialog->queryMolecule("molecule-by-id",&srcmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   if(dialog->display()) {
     molecules->SimpleAdd(srcmol, destmol);
@@ -922 +923 @@
   molecule *srcmol = NULL, *destmol = NULL;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  dialog->queryMolecule("Enter index of matrix molecule (the variable one): ",&srcmol,molecules);
-  dialog->queryMolecule("Enter index of molecule to merge into (the fixed one): ",&destmol,molecules);
+  dialog->queryMolecule("molecule-by-id",&destmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
+  dialog->queryMolecule("molecule-by-id",&srcmol, MapOfActions::getInstance().getDescription("molecule-by-id"));
   if(dialog->display()) {
     molecules->EmbedMerge(destmol, srcmol);

src/Makefile.am

@@ -50 +50 @@
 
 ACTIONSSOURCE = Actions/Action.cpp \
+  ${ANALYSISACTIONSOURCE} \
   ${ATOMACTIONSOURCE} \
   ${CMDACTIONSOURCE} \
@@ -56 +57 @@
   ${PARSERACTIONSOURCE} \
   ${TESSELATIONACTIONSOURCE} \
+  ${WORLDACTIONSOURCE} \
   Actions/ActionHistory.cpp \
   Actions/ActionRegistry.cpp \
@@ -62 +64 @@
   Actions/MakroAction.cpp \
   Actions/ManipulateAtomsProcess.cpp \
+  Actions/MapOfActions.cpp \
   Actions/MethodAction.cpp \
   Actions/Process.cpp
 
 ACTIONSHEADER = Actions/Action.hpp \
+  ${ANALYSISACTIONHEADER} \
   ${ATOMACTIONHEADER} \
   ${CMDACTIONHEADER} \
@@ -72 +76 @@
   ${PARSERACTIONHEADER} \
   ${TESSELATIONACTIONHEADER} \
+  ${WORLDACTIONHEADER} \
   Actions/ActionHistory.hpp \
   Actions/ActionRegistry.hpp \
@@ -80 +85 @@
   Actions/MakroAction.hpp \
   Actions/ManipulateAtomsProcess.hpp \
+  Actions/MapOfActions.hpp \
   Actions/MethodAction.hpp \
   Actions/Process.hpp
   
-ATOMACTIONSOURCE =
-#  Actions/AtomAction/SomeAction.cpp               
-ATOMACTIONHEADER =
-#  Actions/AtomAction/SomeAction.hpp
+ANALYSISACTIONSOURCE = \
+  Actions/AnalysisAction/MolecularVolumeAction.cpp \
+  Actions/AnalysisAction/PairCorrelationAction.cpp \
+  Actions/AnalysisAction/PairCorrelationToPointAction.cpp \
+  Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp \
+  Actions/AnalysisAction/PrincipalAxisSystemAction.cpp
+ANALYSISACTIONHEADER = \
+  Actions/AnalysisAction/MolecularVolumeAction.hpp \
+  Actions/AnalysisAction/PairCorrelationAction.hpp \
+  Actions/AnalysisAction/PairCorrelationToPointAction.hpp \
+  Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp \
+  Actions/AnalysisAction/PrincipalAxisSystemAction.hpp
+
+ATOMACTIONSOURCE = \
+  Actions/AtomAction/AddAction.cpp \
+  Actions/AtomAction/ChangeElementAction.cpp \
+  Actions/AtomAction/RemoveAction.cpp
+ATOMACTIONHEADER = \
+  Actions/AtomAction/AddAction.hpp \
+  Actions/AtomAction/ChangeElementAction.hpp \
+  Actions/AtomAction/RemoveAction.cpp
 
 CMDACTIONSOURCE = \
+  Actions/CmdAction/BondLengthTableAction.cpp \
+  Actions/CmdAction/ElementDbAction.cpp \
+  Actions/CmdAction/FastParsingAction.cpp \
   Actions/CmdAction/HelpAction.cpp \
+  Actions/CmdAction/VerboseAction.cpp \
   Actions/CmdAction/VersionAction.cpp
 CMDACTIONHEADER = \
+  Actions/CmdAction/BondLengthTableAction.hpp \
+  Actions/CmdAction/ElementDbAction.hpp \
+  Actions/CmdAction/FastParsingAction.hpp \
   Actions/CmdAction/HelpAction.hpp \
+  Actions/CmdAction/VerboseAction.hpp \
   Actions/CmdAction/VersionAction.hpp
 
-FRAGMENTATIONACTIONSOURCE = 
-#  Actions/FragmentationAction/SomeAction.cpp               
-FRAGMENTATIONACTIONHEADER =
-#  Actions/FragmentationAction/SomeAction.hpp
+FRAGMENTATIONACTIONSOURCE = \
+  Actions/FragmentationAction/DepthFirstSearchAction.cpp \
+  Actions/FragmentationAction/FragmentationAction.cpp \
+  Actions/FragmentationAction/SubgraphDissectionAction.cpp               
+FRAGMENTATIONACTIONHEADER = \
+  Actions/FragmentationAction/DepthFirstSearchAction.hpp \
+  Actions/FragmentationAction/FragmentationAction.hpp \
+  Actions/FragmentationAction/SubgraphDissectionAction.hpp
 
 MOLECULEACTIONSOURCE = \
-  Actions/MoleculeAction/ChangeNameAction.cpp
+  Actions/MoleculeAction/BondFileAction.cpp \
+  Actions/MoleculeAction/ChangeNameAction.cpp \
+  Actions/MoleculeAction/FillWithMoleculeAction.cpp \
+  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
+  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
+  Actions/MoleculeAction/SaveAdjacencyAction.cpp \
+  Actions/MoleculeAction/SaveBondsAction.cpp \
+  Actions/MoleculeAction/SaveTemperatureAction.cpp \
+  Actions/MoleculeAction/SuspendInWaterAction.cpp \
+  Actions/MoleculeAction/TranslateAction.cpp \
+  Actions/MoleculeAction/VerletIntegrationAction.cpp
 MOLECULEACTIONHEADER = \
-  Actions/MoleculeAction/ChangeNameAction.hpp
+  Actions/MoleculeAction/BondFileAction.hpp \
+  Actions/MoleculeAction/ChangeNameAction.hpp \
+  Actions/MoleculeAction/FillWithMoleculeAction.hpp \
+  Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
+  Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
+  Actions/MoleculeAction/SaveAdjacencyAction.hpp \
+  Actions/MoleculeAction/SaveBondsAction.hpp \
+  Actions/MoleculeAction/SaveTemperatureAction.hpp \
+  Actions/MoleculeAction/SuspendInWaterAction.hpp \
+  Actions/MoleculeAction/TranslateAction.hpp \
+  Actions/MoleculeAction/VerletIntegrationAction.hpp
                  
 PARSERACTIONSOURCE = \
@@ -112 +167 @@
   Actions/ParserAction/SaveXyzAction.hpp
 
-TESSELATIONACTIONSOURCE =
-#  Actions/TesselationAction/SomeAction.cpp               
-TESSELATIONACTIONHEADER =
-#  Actions/TesselationAction/SomeAction.hpp
+TESSELATIONACTIONSOURCE = \
+  Actions/TesselationAction/ConvexEnvelopeAction.cpp \
+  Actions/TesselationAction/NonConvexEnvelopeAction.cpp               
+TESSELATIONACTIONHEADER = \
+  Actions/TesselationAction/ConvexEnvelopeAction.hpp \
+  Actions/TesselationAction/NonConvexEnvelopeAction.hpp
+
+WORLDACTIONSOURCE = \
+  Actions/WorldAction/AddEmptyBoundaryAction.cpp \
+  Actions/WorldAction/BoundInBoxAction.cpp \
+  Actions/WorldAction/CenterInBoxAction.cpp \
+  Actions/WorldAction/CenterOnEdgeAction.cpp \
+  Actions/WorldAction/ChangeBoxAction.cpp \
+  Actions/WorldAction/RemoveSphereOfAtomsAction.cpp \
+  Actions/WorldAction/RepeatBoxAction.cpp \
+  Actions/WorldAction/ScaleBoxAction.cpp \
+  Actions/WorldAction/SetDefaultNameAction.cpp \
+  Actions/WorldAction/SetGaussianBasisAction.cpp               
+WORLDACTIONHEADER = \
+  Actions/WorldAction/AddEmptyBoundaryAction.hpp \
+  Actions/WorldAction/BoundInBoxAction.hpp \
+  Actions/WorldAction/CenterInBoxAction.hpp \
+  Actions/WorldAction/CenterOnEdgeAction.hpp \
+  Actions/WorldAction/ChangeBoxAction.hpp \
+  Actions/WorldAction/RemoveSphereOfAtomsAction.hpp \
+  Actions/WorldAction/RepeatBoxAction.hpp \
+  Actions/WorldAction/ScaleBoxAction.hpp \
+  Actions/WorldAction/SetDefaultNameAction.hpp \
+  Actions/WorldAction/SetGaussianBasisAction.hpp
+
+
 
 PARSERSOURCE = \

src/Parser/XyzParser.cpp

@@ -59 +59 @@
 
   vector<atom*> atoms = World::getInstance().getAllAtoms();
-  for(vector<atom*>::iterator it = atoms.begin(); it < atoms.end(); it++) {
+  for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
     *file << fixed << (*it)->getType()->symbol << "\t" << (*it)->x[0] << "\t" << (*it)->x[1] << "\t" << (*it)->x[2] << endl;
   }

src/UIElements/CommandLineDialog.cpp

@@ -10 +10 @@
 #include <iostream>
 
+#include <Descriptors/AtomDescriptor.hpp>
+#include <Descriptors/AtomIdDescriptor.hpp>
 #include <Descriptors/MoleculeDescriptor.hpp>
 #include <Descriptors/MoleculeIdDescriptor.hpp>
 #include "UIElements/CommandLineDialog.hpp"
 
+#include "element.hpp"
 #include "periodentafel.hpp"
-#include "atom.hpp"
 #include "CommandLineParser.hpp"
 #include "defs.hpp"
-#include "molecule.hpp"
 #include "log.hpp"
+#include "periodentafel.hpp"
 #include "verbose.hpp"
 #include "World.hpp"
 
+#include "atom.hpp"
+#include "element.hpp"
+#include "molecule.hpp"
+#include "vector.hpp"
+
 using namespace std;
 
@@ -43 +50 @@
 }
 
+void CommandLineDialog::queryBoolean(const char* title, bool* target, string _description){
+  registerQuery(new BooleanCommandLineQuery(title,target, _description));
+}
+
 void CommandLineDialog::queryDouble(const char* title, double* target, string _description){
   registerQuery(new DoubleCommandLineQuery(title,target, _description));
@@ -51 +62 @@
 }
 
-void CommandLineDialog::queryMolecule(const char* title, molecule **target, MoleculeListClass *molecules, string _description) {
-  registerQuery(new MoleculeCommandLineQuery(title,target,molecules, _description));
+void CommandLineDialog::queryAtom(const char* title, atom **target, string _description) {
+  registerQuery(new AtomCommandLineQuery(title,target, _description));
+}
+
+void CommandLineDialog::queryMolecule(const char* title, molecule **target, string _description) {
+  registerQuery(new MoleculeCommandLineQuery(title,target, _description));
 }
 
 void CommandLineDialog::queryVector(const char* title, Vector *target,const double *const cellSize, bool check, string _description) {
   registerQuery(new VectorCommandLineQuery(title,target,cellSize,check, _description));
+}
+
+void CommandLineDialog::queryBox(const char* title, double ** const cellSize, string _description) {
+  registerQuery(new BoxCommandLineQuery(title,cellSize,_description));
 }
 
@@ -90 +109 @@
 }
 
+CommandLineDialog::BooleanCommandLineQuery::BooleanCommandLineQuery(string title,bool *_target, string _description) :
+    Dialog::BooleanQuery(title,_target, _description)
+{}
+
+CommandLineDialog::BooleanCommandLineQuery::~BooleanCommandLineQuery() {}
+
+bool CommandLineDialog::BooleanCommandLineQuery::handle() {
+  bool badInput = false;
+  char input = ' ';
+  do{
+    badInput = false;
+    Log() << Verbose(0) << getTitle();
+    cin >> input;
+    if ((input == 'y' ) || (input == 'Y')) {
+      tmp = true;
+    } else if ((input == 'n' ) || (input == 'N')) {
+      tmp = false;
+    } else {
+      badInput=true;
+      cin.clear();
+      cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+      Log() << Verbose(0) << "Input was not of [yYnN]!" << endl;
+    }
+  } while(badInput);
+  // clear the input buffer of anything still in the line
+  cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+  return true;
+}
+
 CommandLineDialog::StringCommandLineQuery::StringCommandLineQuery(string title,string *_target, string _description) :
     Dialog::StringQuery(title,_target, _description)
@@ -118 +166 @@
 }
 
-CommandLineDialog::MoleculeCommandLineQuery::MoleculeCommandLineQuery(string title, molecule **_target, MoleculeListClass *_molecules, string _description) :
-    Dialog::MoleculeQuery(title,_target,_molecules, _description)
+CommandLineDialog::AtomCommandLineQuery::AtomCommandLineQuery(string title, atom **_target, string _description) :
+    Dialog::AtomQuery(title,_target, _description)
+{}
+
+CommandLineDialog::AtomCommandLineQuery::~AtomCommandLineQuery() {}
+
+bool CommandLineDialog::AtomCommandLineQuery::handle() {
+  int IdxOfAtom = -1;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    IdxOfAtom = CommandLineParser::getInstance().vm[getTitle()].as<int>();
+    tmp = World::getInstance().getAtom(AtomById(IdxOfAtom));
+    return true;
+  } else
+    return false;
+}
+
+CommandLineDialog::MoleculeCommandLineQuery::MoleculeCommandLineQuery(string title, molecule **_target, string _description) :
+    Dialog::MoleculeQuery(title,_target, _description)
 {}
 
@@ -146 +210 @@
     temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
     assert((temp.size() == 3) && "Vector from command line does not have three components.");
-    tmp = new Vector;
     for (int i=0;i<NDIM;i++)
       tmp->at(i) = temp[i];
@@ -155 +218 @@
 
 
+CommandLineDialog::BoxCommandLineQuery::BoxCommandLineQuery(string title, double ** const _cellSize, string _description) :
+    Dialog::BoxQuery(title,_cellSize, _description)
+{}
+
+CommandLineDialog::BoxCommandLineQuery::~BoxCommandLineQuery()
+{}
+
+bool CommandLineDialog::BoxCommandLineQuery::handle() {
+  vector<double> temp;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
+    assert((temp.size() == 6) && "Symmetric box matrix from command line does not have six components.");
+    for (int i=0;i<6;i++)
+      tmp[i] = temp[i];
+    return true;
+  } else
+    return false;
+}
+
 CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, const element **target, string _description) :
     Dialog::ElementQuery(title,target, _description)
@@ -163 +245 @@
 
 bool CommandLineDialog::ElementCommandLineQuery::handle() {
-  int Z = -1;
-  if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    Z = CommandLineParser::getInstance().vm[getTitle()].as<int>();
+  // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
+  int Z;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    vector<int> AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
+    vector<int>::iterator ElementRunner = AllElements.begin();
+    Z = *ElementRunner;
+    // TODO: So far, this does not really erase the element in the parsed list.
+    AllElements.erase(ElementRunner);
     tmp = World::getInstance().getPeriode()->FindElement(Z);
     return true;

src/UIElements/CommandLineDialog.hpp

@@ -10 +10 @@
 
 #include <string>
+
+class atom;
+class element;
+class molecule;
+class Vector;
 
 #include "UIElements/Dialog.hpp"
@@ -24 +29 @@
   virtual void queryEmpty(const char *, std::string = "");
   virtual void queryInt(const char *, int *, std::string = "");
+  virtual void queryBoolean(const char *, bool *, std::string = "");
   virtual void queryString(const char*, std::string *, std::string = "");
   virtual void queryDouble(const char*, double*, std::string = "");
-  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*, std::string = "");
+  virtual void queryAtom(const char*,atom**, std::string = "");
+  virtual void queryMolecule(const char*,molecule**,std::string = "");
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
+  virtual void queryBox(const char*,double ** const, std::string = "");
   virtual void queryElement(const char*,const element **, std::string = "");
 
@@ -46 +54 @@
   };
 
+  class BooleanCommandLineQuery : public Dialog::BooleanQuery {
+  public:
+    BooleanCommandLineQuery(std::string title, bool *_target, std::string _description = "");
+    virtual ~BooleanCommandLineQuery();
+    virtual bool handle();
+  };
+
   class DoubleCommandLineQuery : public Dialog::DoubleQuery {
   public:
@@ -60 +75 @@
   };
 
+  class AtomCommandLineQuery : public Dialog::AtomQuery {
+  public:
+    AtomCommandLineQuery(std::string title, atom **_target, std::string _description = "");
+    virtual ~AtomCommandLineQuery();
+    virtual bool handle();
+  };
+
   class MoleculeCommandLineQuery : public Dialog::MoleculeQuery {
   public:
-    MoleculeCommandLineQuery(std::string title, molecule **_target, MoleculeListClass *_molecules, std::string _description = "");
+    MoleculeCommandLineQuery(std::string title, molecule **_target, std::string _description = "");
     virtual ~MoleculeCommandLineQuery();
     virtual bool handle();
@@ -71 +93 @@
     VectorCommandLineQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check, std::string _description = "");
     virtual ~VectorCommandLineQuery();
+    virtual bool handle();
+  };
+
+  class BoxCommandLineQuery : public Dialog::BoxQuery {
+  public:
+    BoxCommandLineQuery(std::string title,double ** const _cellSize, std::string _description = "");
+    virtual ~BoxCommandLineQuery();
     virtual bool handle();
   };

src/UIElements/CommandLineWindow.cpp

@@ -12 +12 @@
 
 #include "Actions/ActionRegistry.hpp"
+#include "Actions/AnalysisAction/PairCorrelationAction.hpp"
+#include "Actions/AnalysisAction/PairCorrelationToPointAction.hpp"
+#include "Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp"
+#include "Actions/AtomAction/AddAction.hpp"
+#include "Actions/AtomAction/ChangeElementAction.hpp"
+#include "Actions/AtomAction/RemoveAction.hpp"
+#include "Actions/CmdAction/BondLengthTableAction.hpp"
+#include "Actions/CmdAction/ElementDbAction.hpp"
+#include "Actions/CmdAction/FastParsingAction.hpp"
 #include "Actions/CmdAction/HelpAction.hpp"
+#include "Actions/CmdAction/VerboseAction.hpp"
 #include "Actions/CmdAction/VersionAction.hpp"
+#include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
+#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
+#include "Actions/MoleculeAction/BondFileAction.hpp"
+#include "Actions/MoleculeAction/ChangeNameAction.hpp"
+#include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"
+#include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
+#include "Actions/MoleculeAction/SaveAdjacencyAction.hpp"
+#include "Actions/MoleculeAction/SaveBondsAction.hpp"
+#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
+#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
 #include "Actions/ParserAction/LoadXyzAction.hpp"
 #include "Actions/ParserAction/SaveXyzAction.hpp"
+#include "Actions/TesselationAction/ConvexEnvelopeAction.hpp"
+#include "Actions/TesselationAction/NonConvexEnvelopeAction.hpp"
+#include "Actions/WorldAction/AddEmptyBoundaryAction.hpp"
+#include "Actions/WorldAction/BoundInBoxAction.hpp"
+#include "Actions/WorldAction/CenterInBoxAction.hpp"
+#include "Actions/WorldAction/CenterOnEdgeAction.hpp"
+#include "Actions/WorldAction/ChangeBoxAction.hpp"
+#include "Actions/WorldAction/RemoveSphereOfAtomsAction.hpp"
+#include "Actions/WorldAction/RepeatBoxAction.hpp"
+#include "Actions/WorldAction/ScaleBoxAction.hpp"
+#include "Actions/WorldAction/SetDefaultNameAction.hpp"
+#include "Actions/WorldAction/SetGaussianBasisAction.hpp"
 #include "CommandLineParser.hpp"
 
@@ -26 +58 @@
 {
   // create and register all command line callable actions
+  populateAnalysisActions();
   populateAtomActions();
   populateCmdActions();
@@ -32 +65 @@
   populateParserActions();
   populateTesselationActions();
+  populateWorldActions();
 
   // Add status indicators etc...
@@ -39 +73 @@
 CommandLineWindow::~CommandLineWindow()
 {
+  // go through all possible actions
+  for(std::map<const std::string,Action*>::iterator ActionRunner = ActionRegistry::getInstance().getBeginIter(); ActionRegistry::getInstance().getBeginIter() != ActionRegistry::getInstance().getEndIter(); ActionRunner = ActionRegistry::getInstance().getBeginIter()) {
+    ActionRegistry::getInstance().unregisterAction(ActionRunner->second);
+    delete(ActionRunner->second);
+  }
+
   delete statusIndicator;
 }
@@ -52 +92 @@
 }
 
+void CommandLineWindow::populateAnalysisActions()
+{
+  new AnalysisPairCorrelationAction();
+  new AnalysisPairCorrelationToPointAction();
+  new AnalysisPairCorrelationToSurfaceAction();
+}
+
 void CommandLineWindow::populateAtomActions()
 {
+  new AtomAddAction();
+  new AtomChangeElementAction();
+  new AtomRemoveAction();
 }
 
 void CommandLineWindow::populateCmdActions()
 {
+  new CommandLineBondLengthTableAction();
+  new CommandLineElementDbAction();
+  new CommandLineFastParsingAction();
   new CommandLineHelpAction();
+  new CommandLineVerboseAction();
   new CommandLineVersionAction();
 }
@@ -64 +118 @@
 void CommandLineWindow::populateFragmentationActions()
 {
+  new FragmentationDepthFirstSearchAction();
 }
 
 void CommandLineWindow::populateMoleculeActions()
 {
+  new MoleculeBondFileAction();
+  new MoleculeChangeNameAction();
+  new MoleculeFillWithMoleculeAction();
+  new MoleculeLinearInterpolationofTrajectoriesAction();
+  new MoleculeSaveAdjacencyAction();
+  new MoleculeSaveBondsAction();
+  new MoleculeSaveTemperatureAction();
+  new MoleculeVerletIntegrationAction();
 }
 
@@ -78 +141 @@
 void CommandLineWindow::populateTesselationActions()
 {
+  new TesselationConvexEnvelopeAction();
+  new TesselationNonConvexEnvelopeAction();
 }
 
+void CommandLineWindow::populateWorldActions()
+{
+  new WorldAddEmptyBoundaryAction();
+  new WorldBoundInBoxAction();
+  new WorldCenterInBoxAction();
+  new WorldCenterOnEdgeAction();
+  new WorldChangeBoxAction();
+  new WorldRemoveSphereOfAtomsAction();
+  new WorldRepeatBoxAction();
+  new WorldScaleBoxAction();
+  new WorldSetDefaultNameAction();
+  new WorldSetGaussianBasisAction();
+}

src/UIElements/CommandLineWindow.hpp

@@ -23 +23 @@
 private:
   // populaters
+  void populateAnalysisActions();
   void populateAtomActions();
   void populateCmdActions();
@@ -29 +30 @@
   void populateParserActions();
   void populateTesselationActions();
+  void populateWorldActions();
 
   CommandLineStatusIndicator *statusIndicator;

src/UIElements/Dialog.cpp

@@ -10 +10 @@
 #include "UIElements/Dialog.hpp"
 
+#include "atom.hpp"
+#include "element.hpp"
+#include "molecule.hpp"
 #include "vector.hpp"
 
@@ -88 +91 @@
 }
 
+// Int Queries
+
+Dialog::BooleanQuery::BooleanQuery(string title,bool *_target, std::string description) :
+    Query(title, description), target(_target)
+{}
+
+Dialog::BooleanQuery::~BooleanQuery() {}
+
+void Dialog::BooleanQuery::setResult() {
+  *target = tmp;
+}
+
 // String Queries
 
@@ -113 +128 @@
 
 
-// Molecule Queries
-
-Dialog::MoleculeQuery::MoleculeQuery(string title, molecule **_target, MoleculeListClass *_molecules, std::string _description) :
+// Atom Queries
+
+Dialog::AtomQuery::AtomQuery(string title, atom **_target, std::string _description) :
     Query(title, _description),
     tmp(0),
-    molecules(_molecules),
+    target(_target)
+
+{}
+
+Dialog::AtomQuery::~AtomQuery() {}
+
+void Dialog::AtomQuery::setResult() {
+  *target = tmp;
+}
+
+// Molecule Queries
+
+Dialog::MoleculeQuery::MoleculeQuery(string title, molecule **_target, std::string _description) :
+    Query(title, _description),
+    tmp(0),
     target(_target)
 
@@ -147 +176 @@
 void Dialog::VectorQuery::setResult() {
   *target = *tmp;
+}
+
+// Box Queries
+
+Dialog::BoxQuery::BoxQuery(std::string title, double ** const _cellSize, std::string _description) :
+  Query(title, _description),
+  target(_cellSize)
+{
+    tmp = new double[6];
+}
+
+Dialog::BoxQuery::~BoxQuery()
+{
+  delete[] tmp;
+}
+
+void Dialog::BoxQuery::setResult() {
+  for (int i=0;i<6;i++)
+    *target[i] = tmp[i];
 }
 

src/UIElements/Dialog.hpp

@@ -12 +12 @@
 #include<list>
 
-class MoleculeListClass;
+class atom;
+class element;
 class molecule;
 class Vector;
-class element;
 
 class Dialog
@@ -24 +24 @@
 
   virtual void queryEmpty(const char *, std::string = "")=0;
+  virtual void queryBoolean(const char *, bool *, std::string = "")=0;
   virtual void queryInt(const char *, int *, std::string = "")=0;
   virtual void queryDouble(const char*,double *, std::string = "")=0;
   virtual void queryString(const char*, std::string *, std::string = "")=0;
-  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*, std::string = "")=0;
+  virtual void queryAtom(const char*,atom**,std::string = "")=0;
+  virtual void queryMolecule(const char*,molecule**, std::string = "")=0;
   virtual void queryVector(const char*,Vector *,const double *const,bool, std::string = "")=0;
+  virtual void queryBox(const char*,double ** const, std::string = "")=0;
   virtual void queryElement(const char*,const element **, std::string = "")=0;
 
@@ -69 +72 @@
 
   //Specialized classes for certain types. GUI-Types are not specialized at this time
+  class BooleanQuery : public Query {
+  public:
+    BooleanQuery(std::string title,bool *_target, std::string _description = "");
+    virtual ~BooleanQuery();
+    virtual bool handle()=0;
+    virtual void setResult();
+  protected:
+    bool tmp;
+  private:
+    bool *target;
+  };
+
   class IntQuery : public Query {
   public:
@@ -105 +120 @@
   };
 
-
   class MoleculeQuery : public Query {
   public:
-    MoleculeQuery(std::string title, molecule **_target, MoleculeListClass *_molecules, std::string _description = "");
+    MoleculeQuery(std::string title, molecule **_target, std::string _description = "");
     virtual ~MoleculeQuery();
     virtual bool handle()=0;
@@ -114 +128 @@
   protected:
     molecule *tmp;
-    MoleculeListClass *molecules;
   private:
     molecule **target;
+  };
+
+  class AtomQuery : public Query {
+  public:
+    AtomQuery(std::string title, atom **_target, std::string _description = "");
+    virtual ~AtomQuery();
+    virtual bool handle()=0;
+    virtual void setResult();
+  protected:
+    atom *tmp;
+  private:
+    atom **target;
   };
 
@@ -131 +156 @@
     private:
       Vector *target;
+  };
+
+  class BoxQuery : public Query {
+  public:
+      BoxQuery(std::string title,double ** const _cellSize, std::string _description = "");
+      virtual ~BoxQuery();
+      virtual bool handle()=0;
+      virtual void setResult();
+    protected:
+      double *tmp;
+    private:
+      double **target;
   };
 

src/UIElements/TextDialog.cpp

@@ -8 +8 @@
 #include <iostream>
 
+#include <Descriptors/AtomDescriptor.hpp>
+#include <Descriptors/AtomIdDescriptor.hpp>
+#include <Descriptors/MoleculeDescriptor.hpp>
+#include <Descriptors/MoleculeIdDescriptor.hpp>
 #include "UIElements/TextDialog.hpp"
 
 #include "World.hpp"
 #include "periodentafel.hpp"
-#include "atom.hpp"
-#include "molecule.hpp"
 #include "log.hpp"
 #include "verbose.hpp"
 
+#include "atom.hpp"
+#include "element.hpp"
+#include "molecule.hpp"
+#include "vector.hpp"
+
 using namespace std;
 
@@ -33 +40 @@
 }
 
+void TextDialog::queryBoolean(const char* title, bool* target, string description){
+  registerQuery(new BooleanTextQuery(title,target,description));
+}
+
 void TextDialog::queryInt(const char* title, int* target, string description){
   registerQuery(new IntTextQuery(title,target,description));
@@ -45 +56 @@
 }
 
-void TextDialog::queryMolecule(const char* title, molecule **target, MoleculeListClass *molecules, string description) {
-  registerQuery(new MoleculeTextQuery(title,target,molecules,description));
+void TextDialog::queryAtom(const char* title, atom **target, string description) {
+  registerQuery(new AtomTextQuery(title,target,description));
+}
+
+void TextDialog::queryMolecule(const char* title, molecule **target, string description) {
+  registerQuery(new MoleculeTextQuery(title,target,description));
 }
 
 void TextDialog::queryVector(const char* title, Vector *target,const double *const cellSize, bool check, string description) {
   registerQuery(new VectorTextQuery(title,target,cellSize,check,description));
+}
+
+void TextDialog::queryBox(const char* title,double ** const cellSize, string description) {
+  registerQuery(new BoxTextQuery(title,cellSize,description));
 }
 
@@ -94 +113 @@
 }
 
+TextDialog::BooleanTextQuery::BooleanTextQuery(string title, bool * _target, std::string _description) :
+    Dialog::BooleanQuery(title,_target,_description)
+{}
+
+TextDialog::BooleanTextQuery::~BooleanTextQuery() {}
+
+bool TextDialog::BooleanTextQuery::handle() {
+  bool badInput = false;
+  char input = ' ';
+  do{
+    badInput = false;
+    Log() << Verbose(0) << getTitle();
+    cin >> input;
+    if ((input == 'y' ) || (input == 'Y')) {
+      tmp = true;
+    } else if ((input == 'n' ) || (input == 'N')) {
+      tmp = false;
+    } else {
+      badInput=true;
+      cin.clear();
+      cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+      Log() << Verbose(0) << "Input was not of [yYnN]!" << endl;
+    }
+  } while(badInput);
+  // clear the input buffer of anything still in the line
+  cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+  return true;
+}
+
 TextDialog::StringTextQuery::StringTextQuery(string title,string *_target, std::string _description) :
     Dialog::StringQuery(title,_target,_description)
@@ -129 +177 @@
 }
 
-TextDialog::MoleculeTextQuery::MoleculeTextQuery(string title, molecule **_target, MoleculeListClass *_molecules, std::string _description) :
-    Dialog::MoleculeQuery(title,_target,_molecules,_description)
+TextDialog::AtomTextQuery::AtomTextQuery(string title, atom **_target, std::string _description) :
+    Dialog::AtomQuery(title,_target,_description)
+{}
+
+TextDialog::AtomTextQuery::~AtomTextQuery() {}
+
+bool TextDialog::AtomTextQuery::handle() {
+  int idxOfAtom=0;
+  bool badInput = false;
+  do{
+    badInput = false;
+    Log() << Verbose(0) << getTitle();
+    cin >> idxOfAtom;
+    if(cin.fail()){
+      badInput = true;
+      cin.clear();
+      cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+      Log() << Verbose(0) << "Input was not a number!" << endl;
+      continue;
+    }
+
+    tmp = World::getInstance().getAtom(AtomById(idxOfAtom));
+    if(!tmp && idxOfAtom!=-1){
+      Log() << Verbose(0) << "Invalid Atom Index" << endl;
+      badInput = true;
+    }
+
+  } while(badInput);
+  cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
+  return (idxOfAtom!=-1);
+}
+
+TextDialog::MoleculeTextQuery::MoleculeTextQuery(string title, molecule **_target, std::string _description) :
+    Dialog::MoleculeQuery(title,_target,_description)
 {}
 
@@ -150 +230 @@
     }
 
-    tmp = molecules->ReturnIndex(idxOfMol);
+    tmp = World::getInstance().getMolecule(MoleculeById(idxOfMol));
     if(!tmp && idxOfMol!=-1){
       Log() << Verbose(0) << "Invalid Molecule Index" << endl;
@@ -183 +263 @@
 }
 
+TextDialog::BoxTextQuery::BoxTextQuery(std::string title, double ** const _cellSize, std::string _description) :
+    Dialog::BoxQuery(title,_cellSize,_description)
+{}
+
+TextDialog::BoxTextQuery::~BoxTextQuery()
+{}
+
+bool TextDialog::BoxTextQuery::handle() {
+  Log() << Verbose(0) << getTitle();
+
+  std::string coords[6] = {"xx","xy","xz", "yy", "yz", "zz"};
+  for (int i=0;i<6;i++) {
+    Log() << Verbose(0) << coords[i] << ": ";
+    cin >> tmp[i];
+  }
+  return true;
+}
 
 TextDialog::ElementTextQuery::ElementTextQuery(std::string title, const element **target, std::string _description) :

src/UIElements/TextDialog.hpp

@@ -13 +13 @@
 #include "UIElements/Dialog.hpp"
 
+class atom;
+class element;
+class molecule;
+class Vector;
+
 class TextDialog : public Dialog
 {
@@ -20 +25 @@
 
   virtual void queryEmpty(const char *, std::string = "");
+  virtual void queryBoolean(const char *, bool *, std::string = "");
   virtual void queryInt(const char *, int *, std::string = "");
   virtual void queryString(const char*, std::string *, std::string = "");
   virtual void queryDouble(const char*, double*, std::string = "");
-  virtual void queryMolecule(const char*,molecule**,MoleculeListClass*, std::string = "");
+  virtual void queryAtom(const char*,atom**,std::string = "");
+  virtual void queryMolecule(const char*,molecule**,std::string = "");
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
+  virtual void queryBox(const char*,double ** const, std::string = "");
   virtual void queryElement(const char*,const element **, std::string = "");
 
@@ -33 +41 @@
     EmptyTextQuery(std::string title, std::string _description = NULL);
     virtual ~EmptyTextQuery();
+    virtual bool handle();
+  };
+
+  class BooleanTextQuery : public Dialog::BooleanQuery {
+  public:
+    BooleanTextQuery(std::string title, bool *_target, std::string _description = NULL);
+    virtual ~BooleanTextQuery();
     virtual bool handle();
   };
@@ -57 +72 @@
   };
 
+  class AtomTextQuery : public Dialog::AtomQuery {
+  public:
+    AtomTextQuery(std::string title, atom **_target, std::string _description = NULL);
+    virtual ~AtomTextQuery();
+    virtual bool handle();
+  };
+
   class MoleculeTextQuery : public Dialog::MoleculeQuery {
   public:
-    MoleculeTextQuery(std::string title, molecule **_target, MoleculeListClass *_molecules, std::string _description = NULL);
+    MoleculeTextQuery(std::string title, molecule **_target, std::string _description = NULL);
     virtual ~MoleculeTextQuery();
     virtual bool handle();
@@ -68 +90 @@
     VectorTextQuery(std::string title,Vector *_target,const double *const _cellSize,bool _check, std::string _description = NULL);
     virtual ~VectorTextQuery();
+    virtual bool handle();
+  };
+
+  class BoxTextQuery : public Dialog::BoxQuery {
+  public:
+    BoxTextQuery(std::string title,double ** const _cellSize, std::string _description = NULL);
+    virtual ~BoxTextQuery();
     virtual bool handle();
   };

src/UIElements/TextWindow.cpp

@@ -144 +144 @@
   new ActionMenuItem('l',"load molecule from xyz file",editMoleculesMenu,loadMoleculeAction);
 
-  Action *changeFilenameAction = new MoleculeChangeNameAction(molecules);
+  Action *changeFilenameAction = new MoleculeChangeNameAction();
   new ActionMenuItem('n',"change molecule's name",editMoleculesMenu,changeFilenameAction);
 

src/World.cpp

@@ -58 +58 @@
 std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
   return descriptor.findAll();
+}
+
+std::vector<molecule*> World::getAllMolecules(){
+  return getAllMolecules(AllMolecules());
 }
 

src/World.hpp

@@ -115 +115 @@
    */
   std::vector<molecule*> getAllMolecules(MoleculeDescriptor descriptor);
+  std::vector<molecule*> getAllMolecules();
 
   /**

src/bondgraph.hpp

@@ -27 +27 @@
 
 class molecule;
-class periodentafel;
+class BondedParticle;
 class MatrixContainer;
 

src/builder.cpp

@@ -77 +77 @@
 #include "Actions/ActionRegistry.hpp"
 #include "Actions/ActionHistory.hpp"
+#include "Actions/MapOfActions.hpp"
 #include "Actions/MethodAction.hpp"
 #include "Actions/MoleculeAction/ChangeNameAction.hpp"
@@ -1480 +1481 @@
 
 /** Parses the command line options.
+ * Note that this function is from now on transitional. All commands that are not passed
+ * here are handled by CommandLineParser and the actions of CommandLineUIFactory.
  * \param argc argument count
  * \param **argv arguments array
@@ -1487 +1490 @@
  * \param *ConfigFileName pointer to config file name in **argv
  * \param *PathToDatabases pointer to db's path in **argv
+ * \param &ArgcList list of arguments that we do not parse here
  * \return exit code (0 - successful, all else - something's wrong)
  */
-static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,\
-                                   config& configuration, char *&ConfigFileName)
+static int ParseCommandLineOptions(int argc, char **argv, MoleculeListClass *&molecules, periodentafel *&periode,
+                                   config& configuration, char *&ConfigFileName, list<int> &ArgcList)
 {
   Vector x,y,z,n;  // coordinates for absolute point in cell volume
@@ -1508 +1512 @@
   molecule *mol = NULL;
   string BondGraphFileName("\n");
-  int verbosity = 0;
   strncpy(configuration.databasepath, LocalPath, MAXSTRINGSIZE-1);
 
@@ -1522 +1525 @@
           case 'H':
           case '?':
-            DoLog(0) && (Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl);
-            DoLog(0) && (Log() << Verbose(0) << "Usage: " << argv[0] << "[config file] [-{acefpsthH?vfrp}] [further arguments]" << endl);
-            DoLog(0) && (Log() << Verbose(0) << "or simply " << argv[0] << " without arguments for interactive session." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-a Z x1 x2 x3\tAdd new atom of element Z at coordinates (x1,x2,x3)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-A <source>\tCreate adjacency list from bonds parsed from 'dbond'-style file." <<endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-b xx xy xz yy yz zz\tCenter atoms in domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-B xx xy xz yy yz zz\tBound atoms by domain with given symmetric matrix of (xx,xy,xz,yy,yz,zz)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-c x1 x2 x3\tCenter atoms in domain with a minimum distance to boundary of (x1,x2,x3)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-C <type> [params] <output> <bin output> <BinWidth> <BinStart> <BinEnd>\tPair Correlation analysis." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-d x1 x2 x3\tDuplicate cell along each axis by given factor." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-D <bond distance>\tDepth-First-Search Analysis of the molecule, giving cycles and tree/back edges." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-e <file>\tSets the databases path to be parsed (default: ./)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-E <id> <Z>\tChange atom <id>'s element to <Z>, <id> begins at 0." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-f <dist> <order>\tFragments the molecule in BOSSANOVA manner (with/out rings compressed) and stores config files in same dir as config (return code 0 - fragmented, 2 - no fragmentation necessary)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-F <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-J\t<path> Store adjacency per atom to file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-M <basis>\tSetting basis to store to MPQC config files." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-n\tFast parsing (i.e. no trajectories are looked for)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-N <radius> <file>\tGet non-convex-envelope." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-o <out>\tGet volume of the convex envelope (and store to tecplot file)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-O\tCenter atoms in origin." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-p <file>\tParse given xyz file and create raw config file from it." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-P <file>\tParse given forces file and append as an MD step to config file via Verlet." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-r <id>\t\tRemove an atom with given id." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-R <id> <radius>\t\tRemove all atoms out of sphere around a given one." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-s x1 x2 x3\tScale all atom coordinates by this vector (x1,x2,x3)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-S <file> Store temperatures from the config file in <file>." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-t x1 x2 x3\tTranslate all atoms by this vector (x1,x2,x3)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-T x1 x2 x3\tTranslate periodically all atoms by this vector (x1,x2,x3)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-u rho\tsuspend in water solution and output necessary cell lengths, average density rho and repetition." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-v\t\tsets verbosity (more is more)." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-V\t\tGives version information." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-X\t\tset default name of a molecule." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "Note: config files must not begin with '-' !" << endl);
-            return (1);
+            ArgcList.push_back(argptr-1);
+            return(1);
             break;
           case 'v':
-            while (argv[argptr-1][verbosity+1] == 'v') {
-              verbosity++;
-            }
-            setVerbosity(verbosity);
-            DoLog(0) && (Log() << Verbose(0) << "Setting verbosity to " << verbosity << "." << endl);
+            ArgcList.push_back(argptr-1);
+            return(1);
             break;
           case 'V':
-            DoLog(0) && (Log() << Verbose(0) << argv[0] << " " << VERSIONSTRING << endl);
-            DoLog(0) && (Log() << Verbose(0) << "Build your own molecule position set." << endl);
-            return (1);
+            ArgcList.push_back(argptr-1);
+            ArgcList.push_back(argptr);
+            argptr++;
             break;
           case 'B':
@@ -2515 +2475 @@
 
 void cleanUp(){
-  UIFactory::purgeInstance();
   World::purgeInstance();
   Log() << Verbose(0) <<  "Maximum of allocated memory: "
@@ -2524 +2483 @@
   logger::purgeInstance();
   errorLogger::purgeInstance();
+  UIFactory::purgeInstance();
+  MapOfActions::purgeInstance();
   CommandLineParser::purgeInstance();
   ActionRegistry::purgeInstance();
@@ -2536 +2497 @@
     ofstream output;
     string line;
+    char **Arguments = NULL;
+    int ArgcSize = 0;
+    bool ArgumentsCopied = false;
 
     cout << ESPACKVersion << endl;
@@ -2543 +2507 @@
     ActionHistory::init();
 
+    // Parse command line options and if present create respective UI
     {
-      // Parse command line options and if present create respective UI
-      CommandLineParser::getInstance().generic.add_options()
-          ("help,h", "produce help message")
-          ("version,v", "show version")
-          ("parse-xyz,p", po::value< vector<string> >(), "parse xyz file into World")
-          ;
-      CommandLineParser::getInstance().Run(argc,argv);
-      if (!CommandLineParser::getInstance().isEmpty())
+      list<int> ArgcList;
+      ArgcList.push_back(0); // push back program!
+      ArgcList.push_back(1); // push back config file name
+      char ConfigFileName[MAXSTRINGSIZE];
+      // handle arguments by ParseCommandLineOptions()
+      ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), (char *&)ConfigFileName, ArgcList);
+      // copy all remaining arguments to a new argv
+      Arguments = Malloc<char *>(ArgcList.size(), "main - **Arguments");
+      cout << "The following arguments are handled by CommandLineParser: ";
+      for (list<int>::iterator ArgcRunner = ArgcList.begin(); ArgcRunner != ArgcList.end(); ++ArgcRunner) {
+        Arguments[ArgcSize] = Malloc<char>(strlen(argv[*ArgcRunner])+2, "main - *Arguments[]");
+        strcpy(Arguments[ArgcSize], argv[*ArgcRunner]);
+        cout << " " << argv[*ArgcRunner];
+        ArgcSize++;
+      }
+      cout << endl;
+      ArgumentsCopied = true;
+      // handle remaining arguments by CommandLineParser
+      MapOfActions::getInstance().AddOptionsToParser();
+      CommandLineParser::getInstance().Run(ArgcSize,Arguments);
+      if (!CommandLineParser::getInstance().isEmpty()) {
+        DoLog(0) && (Log() << Verbose(0) << "Setting UI to CommandLine." << endl);
         UIFactory::makeUserInterface(UIFactory::CommandLine);
-      else
+      } else {
+        DoLog(0) && (Log() << Verbose(0) << "Setting UI to Text." << endl);
         UIFactory::makeUserInterface(UIFactory::Text);
+      }
     }
 
@@ -2569 +2550 @@
         Log() << Verbose(0) << "Saving of elements.db failed." << endl;
 
+  // free the new argv
+  if (ArgumentsCopied) {
+    for (int i=0; i<ArgcSize;i++)
+      Free(&Arguments[i]);
+    Free(&Arguments);
+  }
+
   cleanUp();
-
   Memory::getState();
   return (0);

src/molecule.hpp

@@ -35 +35 @@
 #include "Patterns/Observer.hpp"
 #include "Patterns/Cacheable.hpp"
+
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 
 /****************************************** forward declarations *****************************/

tests/Tesselations/defs.in

@@ -62 +62 @@
         #cat stderr
         #cat stdout
-        diff ${FILENAME}.dat ../@srcdir@/$mol/$2/${FILENAME}-$mol.dat 2>diffstderr >diffstdout || exitcode=$?
+        grep -E "^[0-9]* [0-9]* [0-9]*$" ../../../../../molecuilder/tests/Tesselations/$mol/$2/${FILENAME}-$mol.dat | sort -n >reference-triangles.dat
+        grep -E "^[0-9]* [0-9]* [0-9]*$" ${FILENAME}.dat | sort -n >new-triangles.dat
+        diff reference-triangles.dat new-triangles.dat 2>diffstderr >diffstdout || exitcode=$?
         #echo "Diff done with exitcode $exitcode."
         #cat diffstderr