BioProteinChain.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 BIOPROTEINCHAIN_H
#define BIOPROTEINCHAIN_H

#define FILLED_CIRCLE   1
#define PLUS            2
#define OPEN_CIRCLE     3
#define FILLED_TRIANGLE 4


#include "BioChain.h"
#include "BioPostScript.h"

using namespace std;

class BioProteinChain : public BioChain
{
           friend bool operator >(const BioProteinChain& , const BioProteinChain&);
              friend bool operator <(const BioProteinChain& , const BioProteinChain&);
                 friend bool operator ==(const BioProteinChain& , const BioProteinChain&);

              float ri,gi,bi;
              float ro,go,bo;
              float rp,gp,bp;
              double SETCALLED;

              double startX_,startY_,size_;
              double SETAREACALLED;

 public:
        BioProteinChain();
        ~BioProteinChain(){};
        BioProteinChain(const string& );
        BioProteinChain(const string& ,const char& );
        BioProteinChain(const char& chid,const vector<BioResidue>& );
        BioProteinChain(const long& atnumber,const string& atname,const string& resname,const char& ch,
                 const long& resnumber, const float& x1, const float& y1, const float& z1,
                 const float& oc1, const float& bf1,const string& atrec);

        // CAUTION: THE ARGUMENTS EXPECT THE RESIDUE INDEX AND *NOT* RESIDUE NUMBER.......
        // PLEASE NOTE THIS....USE getResidueIndex(residue_number) FUNCTION.......... 
        // use the RETURN VALUE OF THE ABOVE FUNCTION AS ARGUMENT TO THIS FOLLOWING FUNCTION.
        
         BioProteinChain getChainSegment(const long& first, const long& last);
         BioProteinChain getChainSegment(const long& first, const long& last, const string& atname);

         BioProteinChain eraseHydrogen();
         friend ostream& operator<<(ostream& os, BioProteinChain& ip);

// The structurally near, sequentially far apart...........this is the general observation...
// The structurally nearer residues and atom information can be added together again into
// another chain..................For me, in my analysis, this speeded up the process of finding
// the process of finding the least squares plane for a set of coordinates.............
// the example: BioChain x, y, z;
// BioChain a = x+y+z; now what ever is there in these 3 BioChains is put together and returned
// to a as a chain again....................
         
   BioProteinChain operator+( BioProteinChain&);
         friend BioProteinChain operator+ ( BioResidue&, BioResidue&);
         BioProteinChain operator+ ( BioResidue&);


        //This Method Collects all the ResidueNames given in the ATOM RECORD and converts it 
        //into singleLetterCode and returns it as a Sequence. The importance of AtomSequence
        //is that the SEquence which is being returned is "NOT" from SEQRES RECORD of PDB file 
        //but from the ATOM RECORD of the PDBfile.The Residue Names should be strictly Standard
        //AminoAcid else it cannot convert to SingleLetterAminoAcid Code. It may lead to unknown
        // behavior and errors.
        
        string getSequence();
        long getSequenceLength();
        void showInFasta(ostream& os = cout);   
        

        // CAUTION: THE ARGUMENTS EXPECT THE RESIDUE INDEX AND *NOT* RESIDUE NUMBER.......
        // PLEASE NOTE THIS....USE getResidueIndex(residue_number) FUNCTION.......... 
        // use the RETURN VALUE OF THE ABOVE FUNCTION AS ARGUMENT TO THIS FOLLOWING FUNCTION.
        string getSequenceSegment(const long&, const long&);
        //
        // All the Chi[1,2,3,4,5] of all the Residues in the Chain will be shown, which can
        // be redirected to a file, if desired.

     BioProteinChain getRotatedProteinChain(const float  **arr);
   void showChiAngles(ostream& = cout);
        
  // This method is most important to structural Biologist. It shows the phi-psi-omega
  // values of all the Residues in the Chain.
   void showPhiPsiOmega(ostream&  = cout);
   void setRamaPlotColorSpec(float=96.0,float=128.99,float=170.9,float=249, float=219, float=31.98, float=0, float=0, float=0);
   
   void showRamaChandranPlot(BioPostScript& bioPostScriptObject,int type=FILLED_TRIANGLE,int pointWidth=3.2,int startX=80,int startY=250,int width=450,int height=450);
   void setProteinDisplayArea(double startx=80,double starty=250,double size=450);
   void showProteinChain(BioPostScript& obj,double width=1,double r=0, double g=0, double b=0);
   void showCAlphaTrace(BioPostScript& bioPostScriptObject,double width=1,double r=0, double g=0, double b=0);
   void showBackBone(BioPostScript &ps,double width=1,double r=255,double g=0,double b=0);

};

#endif