BALL: system.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 
00005 #ifndef BALL_KERNEL_SYSTEM_H
00006 #define BALL_KERNEL_SYSTEM_H
00007 
00008 #ifndef BALL_KERNEL_ATOM_H
00009 # include <BALL/KERNEL/atomIterator.h>
00010 #endif
00011 
00012 #ifndef BALL_KERNEL_MOLECULEITERATOR_H
00013 # include <BALL/KERNEL/moleculeIterator.h>
00014 #endif
00015 
00016 #ifndef BALL_KERNEL_PROTEINITERATOR_H
00017 # include <BALL/KERNEL/proteinIterator.h>
00018 #endif
00019 
00020 #ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H
00021 # include <BALL/KERNEL/nucleicAcidIterator.h>
00022 #endif
00023 
00024 #ifndef BALL_KERNEL_NUCLEOTIDEIDITERATOR_H
00025 # include <BALL/KERNEL/nucleotideIterator.h>
00026 #endif
00027 
00028 #define BALL_SYSTEM_DEFAULT_NAME   ""
00029 
00030 namespace BALL 
00031 {
00038   class BALL_EXPORT System
00039     : public AtomContainer
00040   {
00041     public:
00042 
00043     BALL_CREATE_DEEP(System)
00044 
00045     
00048 
00050     System();
00051   
00053     System(const System& system, bool deep = true);
00054   
00056     System(const String& name);
00057 
00059     virtual ~System();
00060 
00062 
00065 
00069     void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
00070 
00074     void persistentRead(PersistenceManager& pm);
00075 
00077 
00080 
00086     void set(const System& system, bool deep = true);
00087 
00092     System& operator = (const System& system);
00093 
00098     void get(System& system, bool deep = true) const;
00099   
00101 
00106     bool operator == (const System& system) const;
00107 
00111     bool operator != (const System& system) const;
00112 
00116 
00125     Molecule* getMolecule(Position position);
00126 
00135     const Molecule* getMolecule(Position position) const;
00136 
00145     Protein* getProtein(Position position);
00146 
00155     const Protein* getProtein(Position position) const;
00156 
00160     Size countMolecules() const;
00161 
00165     Size countFragments() const;
00166 
00170     Size countAtoms() const;
00171 
00175     Size countProteins() const;
00176 
00180     Size countChains() const;
00181 
00185     Size countSecondaryStructures() const;
00186 
00190     Size countResidues() const;
00191 
00195     Size countNucleicAcids() const;
00196 
00200     Size countNucleotides() const;
00201 
00205     void prepend(Molecule& molecule);
00206 
00210     void append(Molecule& molecule);
00211 
00215     void insert(Molecule& molecule);
00216 
00221     void insertBefore(Molecule& molecule, Composite& before);
00222 
00227     void insertAfter(Molecule& molecule, Composite& after);
00228 
00232     bool remove(Molecule& molecule);
00233 
00238     void spliceBefore(System& system);
00239 
00244     void spliceAfter(System& system);
00245 
00249     void splice(System& system);
00250 
00252     
00253     // --- EXTERNAL ITERATORS ---
00254 
00255     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Atom)
00256     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)
00257     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)
00258     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Molecule)
00259     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Protein)
00260     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
00261     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Chain)
00262     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
00263     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Nucleotide)
00264     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(NucleicAcid)
00265 
00266   };
00267 } // namespace BALL
00268 
00269 #endif // BALL_KERNEL_SYSTEM_H