Changes in src/molecule.hpp [273382:6cfa36]

File:

• src/molecule.hpp (modified) (13 diffs)

src/molecule.hpp

@@ -34 +34 @@
 #include "tesselation.hpp"
 #include "Patterns/Observer.hpp"
+#include "Patterns/ObservedIterator.hpp"
 #include "Patterns/Cacheable.hpp"
+
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -88 +91 @@
   friend molecule *NewMolecule();
   friend void DeleteMolecule(molecule *);
+
   public:
-    double cell_size[6];//!< cell size
+    typedef std::set<atom*> atomSet;
+    typedef ObservedIterator<atomSet> iterator;
+    typedef atomSet::const_iterator const_iterator;
+
     const periodentafel * const elemente; //!< periodic table with each element
-    atom *start;        //!< start of atom list
-    atom *end;          //!< end of atom list
-    bond *first;        //!< start of bond list
-    bond *last;         //!< end of bond list
+    // old deprecated atom handling
+    //atom *start;        //!< start of atom list
+    //atom *end;          //!< end of atom list
+    //bond *first;        //!< start of bond list
+    //bond *last;         //!< end of bond list
     int MDSteps;        //!< The number of MD steps in Trajectories
-    int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
+    //int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
     int ElementCount;       //!< how many unique elements are therein
@@ -111 +119 @@
   private:
     Cacheable<string> formula;
+    Cacheable<int>    AtomCount;
     moleculeId_t id;
+    atomSet atoms; //<!set of atoms
   protected:
+    //void CountAtoms();
+    /**
+     * this iterator type should be used for internal variables, \
+     * since it will not lock
+     */
+    typedef atomSet::iterator internal_iterator;
+
+
     molecule(const periodentafel * const teil);
     virtual ~molecule();
@@ -120 +138 @@
   //getter and setter
   const std::string getName();
+  int getAtomCount() const;
+  int doCountAtoms();
   moleculeId_t getId();
   void setId(moleculeId_t);
@@ -126 +146 @@
   std::string calcFormula();
 
+  iterator begin();
+  const_iterator begin() const;
+  iterator end();
+  const_iterator end() const;
+  bool empty() const;
+  size_t size() const;
+  const_iterator erase( const_iterator loc );
+  const_iterator erase( atom * key );
+  const_iterator find (  atom * key ) const;
+  pair<iterator,bool> insert ( atom * const key );
+  bool containsAtom(atom* key);
+
 
   // re-definition of virtual functions from PointCloud
@@ -131 +163 @@
   Vector *GetCenter() const ;
   TesselPoint *GetPoint() const ;
-  TesselPoint *GetTerminalPoint() const ;
   int GetMaxId() const;
   void GoToNext() const ;
-  void GoToPrevious() const ;
   void GoToFirst() const ;
-  void GoToLast() const ;
   bool IsEmpty() const ;
   bool IsEnd() const ;
@@ -225 +254 @@
   bool RemoveBond(bond *pointer);
   bool RemoveBonds(atom *BondPartner);
+  bool hasBondStructure();
+  unsigned int CountBonds() const;
 
   /// Find atoms.
@@ -231 +262 @@
 
   /// Count and change present atoms' coordination.
-  void CountAtoms();
   void CountElements();
   void CalculateOrbitals(class config &configuration);
@@ -248 +278 @@
   Vector * DetermineCenterOfGravity();
   Vector * DetermineCenterOfAll() const;
+  Vector * DetermineCenterOfBox() const;
   void SetNameFromFilename(const char *filename);
   void SetBoxDimension(Vector *dim);
@@ -293 +324 @@
   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);
@@ -300 +331 @@
   bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
+  bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
   void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
   /// -# BOSSANOVA
@@ -328 +360 @@
   private:
   int last_atom;      //!< number given to last atom
-  mutable atom *InternalPointer;  //!< internal pointer for PointCloud
+  mutable internal_iterator InternalPointer;  //!< internal pointer for PointCloud
 };
 
@@ -349 +381 @@
   bool StoreForcesFile(char *path, int *SortIndex);
   void insert(molecule *mol);
+  void erase(molecule *mol);
   molecule * ReturnIndex(int index);
   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);