Changes in src/atom.hpp [1b2d30:ad2b411]

File:

• src/atom.hpp (modified) (6 diffs)

src/atom.hpp

@@ -34 +34 @@
 class Vector;
 class World;
+class molecule;
 
 /********************************************** declarations *******************************/
@@ -44 +45 @@
   friend void  DeleteAtom(atom*);
   public:
-    atom *previous; //!< previous atom in molecule list
-    atom *next;     //!< next atom in molecule list
     atom *father;   //!< In many-body bond order fragmentations points to originating atom
     int *sort;      //!< sort criteria
@@ -52 +51 @@
 
   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(ofstream * const out, const int *ElementNo, 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;
   bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
-  void OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo) const;
+  void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;
 
   void InitComponentNr();
@@ -80 +79 @@
   void setWorld(World*);
 
-  virtual atomId_t getId();
+  virtual atomId_t getId() const;
   virtual bool changeId(atomId_t newId);
 
@@ -89 +88 @@
    virtual void setId(atomId_t);
 
+   void setMolecule(molecule*);
+   void removeFromMolecule();
+
   protected:
+
     /**
      * Protected constructor to ensure construction of atoms through the world.
@@ -108 +111 @@
     virtual ~atom();
   private:
+    molecule *mol; // !< the molecule this atom belongs to
     World* world;
     atomId_t id;