BALL: protein.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 
00005 #ifndef BALL_KERNEL_PROTEIN_H
00006 #define BALL_KERNEL_PROTEIN_H
00007 
00008 #ifndef BALL_KERNEL_CHAINITERATOR_H
00009 # include <BALL/KERNEL/chainIterator.h>
00010 #endif
00011 
00012 #ifndef BALL_KERNEL_MOLECULE_H
00013 # include <BALL/KERNEL/molecule.h>
00014 #endif
00015 
00016 #define BALL_PROTEIN_DEFAULT_ID   ""
00017 
00018 namespace BALL 
00019 {
00028   class BALL_EXPORT Protein
00029     : public Molecule
00030   {
00031     public:
00032 
00033     BALL_CREATE_DEEP(Protein)
00034 
00035     
00038       
00039     
00041     enum Property
00042     {
00043       NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES
00044     };
00045 
00047 
00050 
00052     Protein();
00053   
00055     Protein(const Protein& protein, bool deep = true);
00056   
00058     Protein(const String& name, const String& id = BALL_PROTEIN_DEFAULT_ID);
00059 
00061     virtual ~Protein();
00062   
00064     virtual void clear();
00065   
00066     /* Clears the contents of the protein and removes it from all composite structures.
00067     */
00068     virtual void destroy();
00069 
00071 
00074     
00078     void persistentWrite(PersistenceManager& pm, const char* name = 0) const;
00079 
00083     void persistentRead(PersistenceManager& pm);
00084 
00086 
00089 
00095     void set(const Protein& protein, bool deep = true);
00096 
00101     Protein& operator = (const Protein& protein);
00102 
00107     void get(Protein& protein, bool deep = true) const;
00108   
00112     void swap(Protein& protein);
00113   
00115 
00120     bool operator == (const Protein& protein) const;
00121 
00125     bool operator != (const Protein& protein) const;
00126 
00130 
00136     Chain* getChain(Position position);
00137 
00143     const Chain* getChain(Position position) const;
00144 
00150     SecondaryStructure* getSecondaryStructure(Position position);
00151 
00157     const SecondaryStructure* getSecondaryStructure(Position position) const;
00158 
00164     Residue* getResidue(Position position);
00165 
00171     const Residue* getResidue(Position position) const;
00172 
00178     Residue* getResidueByID(String residue_ID);
00179 
00185     const Residue* getResidueByID(String residue_ID) const;
00186 
00192     Residue* getNTerminal();
00193 
00199     const Residue* getNTerminal() const;
00200 
00206     Residue* getCTerminal();
00207 
00213     const Residue* getCTerminal() const;
00214 
00220     PDBAtom* getPDBAtom(Position position);
00221 
00227     const PDBAtom* getPDBAtom(Position position) const;
00228 
00232     void setID(const String& id);
00233 
00237     const String& getID() const;
00238 
00242     Size countChains() const;
00243 
00247     Size countSecondaryStructures() const;
00248 
00252     Size countResidues() const;
00253 
00257     Size countPDBAtoms() const;
00258 
00260 
00261     using Molecule::prepend;
00262     using Molecule::append;
00263     using Molecule::insert;
00264     using Molecule::insertBefore;
00265     using Molecule::insertAfter;
00266     using Molecule::remove;
00267     using Molecule::splice;
00268     using Molecule::spliceBefore;
00269     using Molecule::spliceAfter;
00270 
00274 
00279     virtual bool isValid() const;
00280 
00287     virtual void dump(std::ostream& s = std::cout, Size depth = 0) const;
00288 
00290 
00291     // --- EXTERNAL ITERATORS
00292 
00293     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Chain)
00294     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(SecondaryStructure)
00295     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(Residue)
00296     BALL_KERNEL_DEFINE_ITERATOR_CREATORS(PDBAtom)
00297 
00298     
00299     private:
00300 
00301     // --- ATTRIBUTES
00302 
00303     String id_;
00304   };
00305 } // namespace BALL
00306 
00307 #endif // BALL_KERNEL_PROTEIN_H