Changes in src/molecule.hpp [1f1b23:520c8b]

File:

• src/molecule.hpp (modified) (7 diffs)

src/molecule.hpp

@@ -27 +27 @@
 #include <vector>
 
+#include <string>
+
 #include "graph.hpp"
 #include "stackclass.hpp"
 #include "tesselation.hpp"
+#include "Patterns/Observer.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -80 +83 @@
  * Class incorporates number of types
  */
-class molecule : public PointCloud {
+class molecule : public PointCloud , public Observable {
   public:
     double cell_size[6];//!< cell size
@@ -99 +102 @@
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
     Vector Center;      //!< Center of molecule in a global box
+    int IndexNr;        //!< index of molecule in a MoleculeListClass
     char name[MAXSTRINGSIZE];         //!< arbitrary name
-    int IndexNr;        //!< index of molecule in a MoleculeListClass
-
+
+public:
   molecule(const periodentafel * const teil);
   virtual ~molecule();
+
+  //getter and setter
+  const std::string getName();
+  void setName(const std::string);
 
   // re-definition of virtual functions from PointCloud
@@ -269 +277 @@
   int FragmentMolecule(int Order, config *configuration);
   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path);
   bool StoreAdjacencyToFile(char *path);
   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
@@ -299 +306 @@
   bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
 
+  // Manipulation routines
+  void flipActiveFlag();
+
   private:
   int last_atom;      //!< number given to last atom
@@ -308 +318 @@
 /** A list of \a molecule classes.
  */
-class MoleculeListClass {
+class MoleculeListClass : public Observable {
   public:
     MoleculeList ListOfMolecules; //!< List of the contained molecules
@@ -327 +337 @@
   int CountAllAtoms() const;
 
+  // Methods moved here from the menus
+  // TODO: more refactoring needed on these methods
+  void flipChosen();
+  void createNewMolecule(periodentafel *periode);
+  void loadFromXYZ(periodentafel *periode);
+  void setMoleculeFilename();
+  void parseXYZIntoMolecule();
+  void eraseMolecule();
+
+
   // merging of molecules
   bool SimpleMerge(molecule *mol, molecule *srcmol);