Changes in src/World.hpp [5d880e:cf0ca1]

File:

• src/World.hpp (modified) (5 diffs)

src/World.hpp

@@ -62 +62 @@
 friend class MoleculeDescriptor_impl;
 friend class MoleculeDescriptor;
+// coupling with descriptors over selection
+friend class AtomSelectionDescriptor_impl;
+friend class MoleculeSelectionDescriptor_impl;
 
 // Actions, calculations etc associated with the World
@@ -222 +225 @@
    * All these iterators are observed to track changes.
    * There is a corresponding protected section with unobserved iterators,
-   * which ca be used internally when the extra speed is needed
+   * which can be used internally when the extra speed is needed
    */
 
@@ -239 +242 @@
   typedef SelectiveIterator<molecule*,MoleculeSet,MoleculeDescriptor>   MoleculeIterator;
 
+  /**
+   * returns an iterator over all Molecules matching a given descriptor.
+   * This iterator is observed, so don't keep it around unnecessary to
+   * avoid unintended blocking.
+   */
   MoleculeIterator getMoleculeIter(MoleculeDescriptor descr);
   MoleculeIterator getMoleculeIter();
 
   MoleculeIterator moleculeEnd();
+
+  /******** Selections of molecules and Atoms *************/
+  void clearAtomSelection();
+  void selectAtom(atom*);
+  void selectAtom(atomId_t);
+  void selectAllAtoms(AtomDescriptor);
+  void selectAtomsOfMolecule(molecule*);
+  void selectAtomsOfMolecule(moleculeId_t);
+  void unselectAtom(atom*);
+  void unselectAtom(atomId_t);
+  void unselectAllAtoms(AtomDescriptor);
+  void unselectAtomsOfMolecule(molecule*);
+  void unselectAtomsOfMolecule(moleculeId_t);
+
+  void clearMoleculeSelection();
+  void selectMolecule(molecule*);
+  void selectMolecule(moleculeId_t);
+  void selectAllMoleculess(MoleculeDescriptor);
+  void selectMoleculeOfAtom(atom*);
+  void selectMoleculeOfAtom(atomId_t);
+  void unselectMolecule(molecule*);
+  void unselectMolecule(moleculeId_t);
+  void unselectAllMoleculess(MoleculeDescriptor);
+  void unselectMoleculeOfAtom(atom*);
+  void unselectMoleculeOfAtom(atomId_t);
+
+  /******************** Iterators to selections *****************/
+  typedef AtomSet::iterator AtomSelectionIterator;
+  AtomSelectionIterator beginAtomSelection();
+  AtomSelectionIterator endAtomSelection();
+
+  typedef MoleculeSet::iterator MoleculeSelectionIterator;
+  MoleculeSelectionIterator beginMoleculeSelection();
+  MoleculeSelectionIterator endMoleculeSelection();
 
 protected:
@@ -308 +350 @@
   class ThermoStatContainer *Thermostats;
   int ExitFlag;
-public:
+private:
+
   AtomSet atoms;
-private:
+  AtomSet selectedAtoms;
   typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
-
   /**
    * stores the pool for all available AtomIds below currAtomId
@@ -324 +366 @@
 
   MoleculeSet molecules;
+  MoleculeSet selectedMolecules;
   typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
+  /**
+   * stores the pool for all available AtomIds below currAtomId
+   *
+   * The pool contains ranges of free ids in the form [bottom,top).
+   */
   moleculeIdPool_t moleculeIdPool;
   moleculeId_t currMoleculeId;