BALL: system.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // $Id: system.h,v 1.38 2005/10/23 12:02:20 oliver Exp $
00005 //
00006 
00007 #ifndef BALL_KERNEL_SYSTEM_H
00008 #define BALL_KERNEL_SYSTEM_H
00009 
00010 #ifndef BALL_KERNEL_ATOM_H
00011 # include <BALL/KERNEL/atomIterator.h>
00012 #endif
00013 
00014 #ifndef BALL_KERNEL_MOLECULEITERATOR_H
00015 # include <BALL/KERNEL/moleculeIterator.h>
00016 #endif
00017 
00018 #ifndef BALL_KERNEL_PROTEINITERATOR_H
00019 # include <BALL/KERNEL/proteinIterator.h>
00020 #endif
00021 
00022 #ifndef BALL_KERNEL_NUCLEICACIDITERATOR_H
00023 # include <BALL/KERNEL/nucleicAcidIterator.h>
00024 #endif
00025 
00026 #ifndef BALL_KERNEL_NUCLEOTIDEIDITERATOR_H
00027 # include <BALL/KERNEL/nucleotideIterator.h>
00028 #endif
00029 
00030 #define BALL_SYSTEM_DEFAULT_NAME   ""
00031 
00032 namespace BALL 
00033 {
00040   class BALL_EXPORT System
00041     : public AtomContainer
00042   {
00043     public:
00044 
00045     BALL_CREATE_DEEP(System)
00046 
00047     
00050 
00052     System();
00053   
00055     System(const System& system, bool deep = true);
00056   
00058     System(const String& name);
00059 
00061     virtual ~System();
00062 
00064 
00067 
00071     void persistentWrite(PersistenceManager& pm, const char* name = 0) const
00072       throw(Exception::GeneralException);
00073 
00077     void persistentRead(PersistenceManager& pm)
00078       throw(Exception::GeneralException);
00079 
00081 
00084 
00090     void set(const System& system, bool deep = true);
00091 
00096     System& operator = (const System& system);
00097 
00102     void get(System& system, bool deep = true) const;
00103   
00105 
00110     bool operator == (const System& system) const;
00111 
00115     bool operator != (const System& system) const;
00116 
00120 
00126     Molecule* getMolecule(Position position);
00127 
00133     const Molecule* getMolecule(Position position) const;
00134 
00138     Size countMolecules() const;
00139 
00143     Size countFragments() const;
00144 
00148     Size countAtoms() const;
00149 
00153     Size countProteins() const;
00154 
00158     Size countChains() const;
00159 
00163     Size countSecondaryStructures() const;
00164 
00168     Size countResidues() const;
00169 
00173     Size countNucleicAcids() const;
00174 
00178     Size countNucleotides() const;
00179 
00183     void prepend(Molecule& molecule);
00184 
00188     void append(Molecule& molecule);
00189 
00193     void insert(Molecule& molecule);
00194 
00199     void insertBefore(Molecule& molecule, Composite& before);
00200 
00205     void insertAfter(Molecule& molecule, Composite& after);
00206 
00210     bool remove(Molecule& molecule);
00211 
00216     void spliceBefore(System& system);
00217 
00222     void spliceAfter(System& system);
00223 
00227     void splice(System& system);
00228 
00230     
00231     // --- EXTERNAL ITERATORS ---
00232 
00233     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Atom)
00234     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(AtomContainer)
00235     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Fragment)
00236     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Molecule)
00237     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Protein)
00238     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
00239     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Chain)
00240     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
00241     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Nucleotide)
00242     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(NucleicAcid)
00243 
00244   };
00245 } // namespace BALL
00246 
00247 #endif // BALL_KERNEL_SYSTEM_H