BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioProtein.h
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00001 /****************************************************************************
00002 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00003 The BioBhasha : The Biologist's Programming Language 
00004 Version 1.0 (19th December 2001)
00005 Prasad, B.V.L.S.
00006 Contact: burrashiva@yahoo.com
00007 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00008 *****************************************************************************/
00009 #ifndef BIOPROTEIN_H
00010 #define BIOPROTEIN_H
00011 
00012 #include "BioProteinChain.h"
00013 #include "BioWater.h"
00014 #include <algorithm>
00015 /****************************************************************************
00016  *
00017  * COMMENTARY on Each Class/Concept: Hows and Whys:
00018  *
00019  * BioProtein:
00020  *              This  */
00021 class BioProtein
00022 {
00023 
00024         vector<BioProteinChain>chain;
00025         BioWater water;
00026 
00027 public:
00028 
00029         BioProtein();
00030         ~BioProtein();
00031 
00032         BioProtein(const string& );
00033 
00034         BioProtein(const vector<BioProteinChain>& , const BioWater&);
00035         
00036         BioProtein(const vector<BioProteinChain>&);
00037 
00038         char getLastChainId() const ;
00039 
00040         BioProteinChain& getLastChain() ;
00041 
00042         unsigned int getNumberOfProteinChains() const ;
00043 
00044         unsigned int getNumberOfWaters() const ;
00045 
00046         void showProteinChainIds(ostream& = cout);
00047         void showUniqueProteinChainIds(ostream& = cout);
00048         void mergeProteinChainsWithDuplicateIds();
00049         vector<char> getProteinChainIds();
00050         vector<BioProteinChain> getProteinChains();
00051         vector<char> getUniqueProteinChainIds();
00052         int getNumberOfUniqueProteinChainIds();
00053         vector<int> getDuplicateChainIndices(char c);
00054         void pushProteinChain(const BioProteinChain& );
00055 
00056         void pushProteinChain(const unsigned long& atnumber,const string& atname, const string& resname,const char& ch,
00057                     const long& resnum, const float& x1, const float& y1, const float&  z1,
00058                       const float& oc1, const float& bf1,const string& );
00059 
00060         BioProteinChain& getProteinChain( const int& );
00061         BioProteinChain& getProteinChain( const char&);
00062 
00063         BioProteinChain getProteinChain(const int&, const string&  );
00064 
00065         void showProtein(ostream& = cout); 
00066 
00067         int getProteinChainIdIndex(const char& );
00068 
00069         void showProteinChain(const char& , ostream& = cout);
00070         void showProteinChain(const int& , ostream& = cout);
00071   void showWater(ostream& os = cout);
00072   BioResidue getWaterMolecule(const int& );
00073   BioWater getWater();
00074   
00075 };
00076 
00077 #endif
00078 
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