BioAminoAcid.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : A Programming Language for Biologist
Version 1.0 (19th December 2001)
Dr. Prasad, B.V.L.S.
Contact: prasadbvls@helixgenomics.com
Version 1.1 (23th January 2003)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIOAMINOACID_H
#define BIOAMINOACID_H


using namespace std;
#include <string>
#include <map>
#include <iostream>
#include <cstdlib>
#include <cstdio>

class BioAminoAcid
{
        //static bool isInitialised;

        string aminoAcidName_;
        string threeLetterCode_;
        char singleLetterCode_;
        int serialNumber_;
        float molWeight_;
        float dcVolume_;
        float accessibleArea_;
        float hydropathyIndex_;
        float hydrophobicity_;
        float hydrophilicity_;
        float helixCFPropensity_; // CF- ChouFasman
        float sheetCFPropensity_; // CF- ChouFasman
  float turnCFPropensity_;  // CF- ChouFasman
  float positionProbability0_;
  float positionProbability1_;
  float positionProbability2_;
  float positionProbability3_;
        float pKaAminoAcidCarboxylate_;
        float pKaAminoAcidAmine_;
        float pKaAminoAcidSideChain_;
        int numberOfCarbons_;
        int numberOfHydrogens_;
        int numberOfNitrogens_;
        int numberOfOxygens_;
        int numberOfSulphurs_;
        float gxgSurfaceArea_;
        float averageAccessibleArea_;

/*      char *singleLetterCode_;
        int *serialNumber_;
        float *molWeight_;
        float *dcVolume_;
        float *accessibleArea_;
        float *hydropathyIndex_;
        float *hydrophobicity_;
        float *hydrophilicity_;
        float *helixCFPropensity_; // CF- ChouFasman
        float *sheetCFPropensity_; // CF- ChouFasman
  float *turnCFPropensity_;  // CF- ChouFasman
  float *positionProbability0_;
  float *positionProbability1_;
  float *positionProbability2_;
  float *positionProbability3_;
        float *pKaAminoAcidCarboxylate_;
        float *pKaAminoAcidAmine_;
        float *pKaAminoAcidSideChain_;
        int *numberOfCarbons_;
        int *numberOfHydrogens_;
        int *numberOfNitrogens_;
        int *numberOfOxygens_;
        int *numberOfSulphurs_;
        float *gxgSurfaceArea_;
        float *averageAccessibleArea_;
*/
        friend bool operator >( const BioAminoAcid& , const BioAminoAcid&);
        friend bool operator <( const BioAminoAcid& , const BioAminoAcid&);
        friend bool operator ==( const BioAminoAcid& ,  const BioAminoAcid&);
        BioAminoAcid(){ }

public:
        ~BioAminoAcid();
        BioAminoAcid(const string& aan, const int& sn, const char& slc, const string& tlc, 
const float& mw, const float& dcv,const float& aca,const float& hpi,const float& hpho,const float& hphi,
const float& hcfp,const float& scfp,const float& tcfp,const float& pr0,const float&  pr1,
const float& pr2,const float& pr3,const float& pkc,const float& pkn, const float& pks, const int& nc,
const int& nh,const int& nn, const int& no, const int& ns,const float& gxg,const float& avaca):
aminoAcidName_(aan),singleLetterCode_(slc),threeLetterCode_(tlc),
serialNumber_(sn),molWeight_(mw),dcVolume_(dcv), 
accessibleArea_(aca), hydropathyIndex_(hpi),hydrophobicity_(hpho), hydrophilicity_(hphi), helixCFPropensity_(hcfp), 
sheetCFPropensity_(scfp), turnCFPropensity_(tcfp),positionProbability0_(pr0), positionProbability1_(pr1),
positionProbability2_(pr2),positionProbability3_(pr3), pKaAminoAcidCarboxylate_(pkc), pKaAminoAcidAmine_(pkn),
pKaAminoAcidSideChain_(pks), numberOfCarbons_(nc), numberOfHydrogens_(nh),
numberOfNitrogens_(nn), numberOfOxygens_(no), numberOfSulphurs_(ns),
gxgSurfaceArea_(gxg),averageAccessibleArea_(avaca){}
/*
aminoAcidName_(new string(aan)),singleLetterCode_(new char(slc)),threeLetterCode_(new string(tlc)),
serialNumber_(new int(sn)),molWeight_(new float(mw)),dcVolume_(new float(dcv)), 
accessibleArea_(new float(aca)), hydropathyIndex_(new float(hpi)),hydrophobicity_(new float(hpho)), hydrophilicity_(new float(hphi)), helixCFPropensity_(new float(hcfp)), 
sheetCFPropensity_(new float(scfp)), turnCFPropensity_(new float(tcfp)), 
positionProbability0_(new float(pr0)), positionProbability1_(new float(pr1)),
positionProbability2_(new float(pr2)),positionProbability3_(new float(pr3)), pKaAminoAcidCarboxylate_(new float(pkc)), pKaAminoAcidAmine_(new float(pkn)),
pKaAminoAcidSideChain_(new float(pks)), numberOfCarbons_(new int(nc)), numberOfHydrogens_(new int(nh)),
numberOfNitrogens_(new int(nn)), numberOfOxygens_(new int(no)), numberOfSulphurs_(new int(ns)),
gxgSurfaceArea_(new float(gxg)),averageAccessibleArea_(new float(avaca)){}
*/      
        char getSingleLetterCode() const { return singleLetterCode_; }
        string getThreeLetterCode() const { return threeLetterCode_; }
        int getSerialNumber() const { return serialNumber_; }
        float getMolecularWeight() const { return molWeight_; }
        string getAminoAcidName() const { return aminoAcidName_; }
        float getMolecularVolume() const { return dcVolume_; }

        float getAccessibleSurfaceArea() const { return accessibleArea_; }

        float getHydropathyIndex() const { return hydropathyIndex_; }
        float getHydrophobicity() const { return hydrophobicity_; }
        float getHydrophilicity() const { return hydrophilicity_; }
        float getCFHelixPropensity() const { return helixCFPropensity_; }
        float getCFSheetPropensity() const { return sheetCFPropensity_; }
  float getCFTurnPropensity() const { return turnCFPropensity_; }
  float getCFTurnPositionProbability(int position);

        float getpKaCarboxylate() const { return pKaAminoAcidCarboxylate_; }
        float getpKaAmine() const { return pKaAminoAcidAmine_; }
        float getpKaSideChain() const { return pKaAminoAcidSideChain_; }

        int getNumberOfCarbons() const { return numberOfCarbons_; }
        int getNumberOfHydrogens() const { return numberOfHydrogens_; }
        int getNumberOfNitrogens() const { return numberOfNitrogens_; }
        int getNumberOfOxygens() const { return numberOfOxygens_; }
        int getNumberOfSulphurs() const { return numberOfSulphurs_; }

        float getGXGSurfaceArea() const { return gxgSurfaceArea_; }
        float getAverageAccessibleArea() const { return averageAccessibleArea_; }
        float getAverageBuriedArea() const { return gxgSurfaceArea_ - averageAccessibleArea_; }
        float getMeanFractionalAreaLoss() const { return getAverageBuriedArea()/(gxgSurfaceArea_); }
       
};


#endif
// Amino acid volume in cubic Angstroms as given in "Protein Structure" 
// // // by Darby, N.J. and Creighton, T.E. (IRL Press, 1993)
//
// // Accessible surface areas in Angstroms squared by Miller, S., Janin, J., 
// // // Lesk, A.M., and Chothia, C. (1987) J.Mol.Biol., 196, 641
//
// // Hydrophilicity of side chains in kJ/mol by Radzicka, A., and Wolfenden, R.
// // // (1988) Biochemistry, 27, 1664 
//
// // Hydropathy index by Kyte, J., and Doolittle, R.F., (1982), J.Mol.Biol., 
// // // 157, 105-132
//
// // Hydrophobicity of side chain analogues in kJ/mol by Radzicka, A., 
// // // and Wolfenden, R. (1988) Biochemistry, 27, 1664
//