BioProtein.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : The Biologist's Programming Language 
Version 1.0 (19th December 2001)
Prasad, B.V.L.S.
Contact: burrashiva@yahoo.com
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIOPROTEIN_H
#define BIOPROTEIN_H

#include "BioProteinChain.h"
#include "BioWater.h"
#include <algorithm>
/****************************************************************************
 *
 * COMMENTARY on Each Class/Concept: Hows and Whys:
 *
 * BioProtein:
 *              This  */
class BioProtein
{

        vector<BioProteinChain>chain;
        BioWater water;

public:

        BioProtein();
        ~BioProtein();

        BioProtein(const string& );

        BioProtein(const vector<BioProteinChain>& , const BioWater&);
        
        BioProtein(const vector<BioProteinChain>&);

        char getLastChainId() const ;

        BioProteinChain& getLastChain() ;

        unsigned int getNumberOfProteinChains() const ;

        unsigned int getNumberOfWaters() const ;

        void showProteinChainIds(ostream& = cout);
        void showUniqueProteinChainIds(ostream& = cout);
        void mergeProteinChainsWithDuplicateIds();
        vector<char> getProteinChainIds();
        vector<BioProteinChain> getProteinChains();
        vector<char> getUniqueProteinChainIds();
        int getNumberOfUniqueProteinChainIds();
        vector<int> getDuplicateChainIndices(char c);
        void pushProteinChain(const BioProteinChain& );

        void pushProteinChain(const unsigned long& atnumber,const string& atname, const string& resname,const char& ch,
                    const long& resnum, const float& x1, const float& y1, const float&  z1,
                      const float& oc1, const float& bf1,const string& );

        BioProteinChain& getProteinChain( const int& );
        BioProteinChain& getProteinChain( const char&);

        BioProteinChain getProteinChain(const int&, const string&  );

        void showProtein(ostream& = cout); 

        int getProteinChainIdIndex(const char& );

        void showProteinChain(const char& , ostream& = cout);
        void showProteinChain(const int& , ostream& = cout);
  void showWater(ostream& os = cout);
  BioResidue getWaterMolecule(const int& );
  BioWater getWater();
  
};

#endif