Changes in src/molecule.hpp [c67ff9:4d2b33]

File:

• src/molecule.hpp (modified) (9 diffs)

src/molecule.hpp

@@ -21 +21 @@
 #include <vector>
 
+#include <boost/iterator/transform_iterator.hpp>
+
 #include <string>
 
-#include "AtomIdSet.hpp"
 #include "Atom/AtomSet.hpp"
 #include "CodePatterns/Cacheable.hpp"
 #include "CodePatterns/Observer/Observable.hpp"
+#include "CodePatterns/Observer/ObservedIterator.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
@@ -33 +35 @@
 #include "IdPool_policy.hpp"
 #include "IdPool.hpp"
-#include "Shapes/Shape.hpp"
 #include "types.hpp"
+
+// TODO: Was is the include of MoleculeDescriptor_impl.hpp doing in molecule.hpp
+#include "Descriptors/MoleculeDescriptor_impl.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -50 +54 @@
 class MoleculeLeafClass;
 class MoleculeListClass;
-class MoleculeUnittest;
+class periodentafel;
 class RealSpaceMatrix;
 class Vector;
+class Shape;
+
+/******************************** Some definitions for easier reading **********************************/
+
+struct FromIdToAtom :
+  public std::unary_function<atom *, atomId_t>
+{
+    atom * operator()(atomId_t id) const {
+     return World::getInstance().getAtom(AtomById(id));
+    }
+};
 
 /************************************* Class definitions ****************************************/
@@ -61 +76 @@
 class molecule : public Observable
 {
-  //!> grant unit test access
-  friend class MoleculeUnittest;
-  //!> function may access cstor
   friend molecule *NewMolecule();
-  //!> function may access dstor
   friend void DeleteMolecule(molecule *);
 
 public:
-  typedef AtomIdSet::atomIdSet atomIdSet;
-  typedef AtomIdSet::iterator iterator;
-  typedef AtomIdSet::const_iterator const_iterator;
+  typedef std::set<atomId_t> atomIdSet;
+  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::iterator, atom *, atomId_t> iterator;
+  typedef boost::transform_iterator<FromIdToAtom, atomIdSet::const_iterator, const atom *, atomId_t const &> const_iterator;
 
   int MDSteps; //!< The number of MD steps in Trajectories
@@ -86 +97 @@
   Cacheable<int> BondCount; //!< number of atoms, brought up-to-date by doCountBonds()
   moleculeId_t id;
-  AtomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
+  atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
   IdPool<atomId_t, uniqueId> atomIdPool;  //!< pool of internal ids such that way may guarantee uniqueness
 
@@ -114 +125 @@
   World::AtomComposite getAtomSet() const;
 
-  // simply pass on all functions to AtomIdSet
-  iterator begin() {
-    return atomIds.begin();
-  }
-  const_iterator begin() const
-  {
-    return atomIds.begin();
-  }
-  iterator end()
-  {
-    return atomIds.end();
-  }
-  const_iterator end() const
-  {
-    return atomIds.end();
-  }
-  bool empty() const
-  {
-    return atomIds.empty();
-  }
-  size_t size() const
-  {
-    return atomIds.size();
-  }
-  const_iterator find(atom * key) const
-  {
-    return atomIds.find(key);
-  }
-
-  /** Returns the set of atomic ids contained in this molecule.
-   *
-   * @return set of atomic ids
-   */
-  const atomIdSet & getAtomIds() const {
-    return atomIds.getAtomIds();
-  }
-
-  std::pair<iterator, bool> insert(atom * const key);
-
+  iterator begin();
+  const_iterator begin() const;
+  iterator end();
+  const_iterator end() const;
+  bool empty() const;
+  size_t size() const;
+  const_iterator find(atom * key) const;
+  pair<iterator, bool> insert(atom * const key);
   bool containsAtom(atom* key);
 
@@ -165 +145 @@
    */
   const_iterator erase(const_iterator loc);
-
   /** Erase an atom from the list.
    * \note This should only be called by atom::removeFromMolecule(),
@@ -198 +177 @@
 
 public:
-
-  /** Function to create a bounding spherical shape for the currently associated atoms.
-   *
-   */
-  Shape getBoundingShape() const;
 
   /// remove atoms from molecule.
@@ -255 +229 @@
   bond * CopyBond(atom *left, atom *right, bond *CopyBond);
 
-  molecule *CopyMolecule(const Vector &offset = zeroVec) const;
+  molecule *CopyMolecule() const;
   molecule* CopyMoleculeFromSubRegion(const Shape&) const;