AminoAcidScore

This class serves for a score calculation of sequence of amino acid pairs. The score can be based on the PAM250 or BLOSUM62 matrix or any other user defined score matrix.

Quick Index

KEYWORD

AUTHORS

CHANGES LOG

USAGE

Class Summary

class AminoAcidScore

{

public:
class	ScoreMatrix ;
float	score(int i,int j)const ;
float	minValue()const ;
float	maxValue()const ;
void	normDiagonal()
void	reverseValueDiagonal()
class	Hydrophobic;
class	PAM250;
class	BLOSUM62;
template< class TMolecule,class TMatch> float	calcScore( const TMolecule& pdbModel, const TMolecule& pdbTarget, const Match& match, const ScoreMatrix& m_scoreMtrx)const
protected:

}; // AminoAcidScore

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KEYWORD

Atom, Match, ScoreMatrix

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AUTHORS

Yuval Inbar (inbaryuv@post.tau.ac.il) Maxim Shatsky (maxshats@post.tau.ac.il)

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CHANGES LOG

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USAGE

Before calculating the score of two matched amino acid sequences,the user should define a score matrix.This is a 20x20 (more exact MAX_AA x MAX_AA, to allow GAP, OTHER) matrix M when M[i,j] which defines a value for AminoAcid_i against AminoAcid_j (0<=i,j<=19). The amino acids are indexed in the following way (see AminoAcid class for enum RESIDUE_INDEX): ARG,LYS,GLU,GLN,ASP,ASN,PRO,GLY,SER, THR,HIS,ALA,ILE,LEU,VAL,PHE,CYS,MET,TYR,TRP. (ARG=0,...,TRP=19) It means that M[3,0]=M[GLN,ARG] (to map amino acid to proper index see AminoAcid class) . There is a predefined PAM250 score matrix AminoAcidScore::PAM250 ,someone can use it as a template for creating another score matrix.

 
 vector<Atom> vModel;
 vector<Atom> vTarget;
 //...
 //fill atom information into vectors vModel,vTarget  
 //...
 vector<Match*> vMatches; 
 //..
 //find some matches 
 //...

 AminoAcidScore::PAM250 pam250; //define score matrix
 AminoAcidScore seqScore;

 //calculate and output PAM250 score for each found match. 
 for(int i=0;i < vMatches.size();i++){
  float score=seqScore.calcScore(vModel,
                          vTarget,
                          *vMatches[i],
                          pam250);
  score=score/vMatches[i].size(); //normolize the score
  cout<<score<<endl;
 }

Function calcScore is a template that is defined by 2 classes: ,class TMatch>. For example: TMolecule=vector<Atom>, TMatch=Match.

Class TMolecule should support the following:

 Molecule<Atom> pdbRec;
 pdbRec[int index].residueType(); //this function returns one-letter abbreviation of amino acid residue.

Class TMatch should support the following:

 Match match;
 match[i].model; //returns index in  pdbRec
 match[i].scene; //returns index in  pdbRec

If one wishes to create its own score matrix just see how PAM250 class is defined.

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class ScoreMatrix ;

ScoreMatrix class defines the score for each pair of amino acid residues

  class ScoreMatrix{
  protected:
    float m_fScore[MAX_AA][MAX_AA];
    float m_fMax;
    float m_fMin;

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float score(int i,int j)const ;

Returns the score

    float score(int i,int j)const                        
;

Function is currently defined inline.

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float minValue()const ;

Returns min score value

    float minValue()const                ;

Function is currently defined inline.

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float maxValue()const ;

Return max score value

    float maxValue()const                ;

Function is currently defined inline.

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void normDiagonal()

sets all diagonal elements to sum(a_ii)/20 usefull for computing conservation score.

    void normDiagonal()

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void reverseValueDiagonal()

reverses the value of diagonal elements, i.e. the higest value becomes the lowest value. usefull for computing conservation score.

    void reverseValueDiagonal()

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class Hydrophobic;

Extends ScoreMatrix. The score is defined in the following way: Hydrophobic matched with Hydrophobic receives 1. Hydrophilic matched with Hydrophilic receives 1. Otherwise -1.

  class Hydrophobic:public ScoreMatrix{
  public:
    ////Constructor. Complexity O(400).
    Hydrophobic();
  };

Function is currently defined inline.

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class PAM250;

Extends ScoreMatrix. The score is defined as in PAM250 matrix.

  class PAM250:public ScoreMatrix{
  public:
    ////Constructor. Complexity O(400).
    PAM250();
  };

Function is currently defined inline.

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class BLOSUM62;

Extends ScoreMatrix. The score is defined as in BLOSUM62 matrix.

  class BLOSUM62:public ScoreMatrix{
  public:
    ////Constructor. Complexity O(400).
    BLOSUM62();
  };

Function is currently defined inline.

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template< class TMolecule,class TMatch> float calcScore( const TMolecule& pdbModel, const TMolecule& pdbTarget, const Match& match, const ScoreMatrix& m_scoreMtrx)const

Returns the score of two matched sequences.Complexity O(match.size()).

  template< class TMolecule,class TMatch>
  float calcScore( const TMolecule& pdbModel,
                   const TMolecule& pdbTarget,
		   const Match& match,
                   const ScoreMatrix& m_scoreMtrx)const

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All Members

public:
class	ScoreMatrix ;
float	score(int i,int j)const ;
float	minValue()const ;
float	maxValue()const ;
void	normDiagonal()
void	reverseValueDiagonal()
class	Hydrophobic;
class	PAM250;
class	BLOSUM62;
template< class TMolecule,class TMatch> float	calcScore( const TMolecule& pdbModel, const TMolecule& pdbTarget, const Match& match, const ScoreMatrix& m_scoreMtrx)const
protected:

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Ancestors

Class does not inherit from any other class.

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Descendants

Class is not inherited by any others.

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Generated from source by the Cocoon utilities on Sun Nov 15 13:35:25 2009 .

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