Changes in src/molecule.hpp [24a5e0:8ab0407]

File:

• src/molecule.hpp (modified) (8 diffs)

src/molecule.hpp

@@ -27 +27 @@
 #include <vector>
 
-#include <string>
-
-#include "defs.hpp"
 #include "graph.hpp"
 #include "stackclass.hpp"
 #include "tesselation.hpp"
-#include "Patterns/Observer.hpp"
-#include "Patterns/Cacheable.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -85 +80 @@
  * Class incorporates number of types
  */
-class molecule : public PointCloud , public Observable {
-  friend molecule *NewMolecule();
-  friend void DeleteMolecule(molecule *);
+class molecule : public PointCloud {
   public:
     double cell_size[6];//!< cell size
@@ -106 +99 @@
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
     Vector Center;      //!< Center of molecule in a global box
+    char name[MAXSTRINGSIZE];         //!< arbitrary name
     int IndexNr;        //!< index of molecule in a MoleculeListClass
-    char name[MAXSTRINGSIZE];         //!< arbitrary name
-
-  private:
-    Cacheable<string> formula;
-    moleculeId_t id;
-  protected:
-    molecule(const periodentafel * const teil);
-    virtual ~molecule();
-
-
-public:
-  //getter and setter
-  const std::string getName();
-  moleculeId_t getId();
-  void setId(moleculeId_t);
-  void setName(const std::string);
-  const std::string getFormula();
-  std::string calcFormula();
-
+
+  molecule(const periodentafel * const teil);
+  virtual ~molecule();
 
   // re-definition of virtual functions from PointCloud
@@ -291 +269 @@
   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 StoreBondsToFile(char *path, char *filename);
+  bool StoreAdjacencyToFile(char *path, char *filename);
   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
   bool ParseOrderAtSiteFromFile(char *path);
@@ -321 +299 @@
   bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
 
-  // Manipulation routines
-  void flipActiveFlag();
-
   private:
   int last_atom;      //!< number given to last atom
@@ -329 +304 @@
 };
 
-molecule *NewMolecule();
-void DeleteMolecule(molecule* mol);
-
 #include "molecule_template.hpp"
 
 /** A list of \a molecule classes.
  */
-class MoleculeListClass : public Observable {
+class MoleculeListClass {
   public:
     MoleculeList ListOfMolecules; //!< List of the contained molecules
     int MaxIndex;
 
-  MoleculeListClass(World *world);
+  MoleculeListClass();
   ~MoleculeListClass();
 
@@ -350 +322 @@
   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
   int NumberOfActiveMolecules();
-  void Enumerate(ostream *out);
+  void Enumerate(ofstream *out);
   void Output(ofstream *out);
   void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
   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
@@ -374 +336 @@
 
   private:
-  World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
 };