massspec/mqaminoacid.h

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#ifndef _MQAMINOACID_H_
#define _MQAMINOACID_H_

/* Copyright (c) Kyriacos Leptos and the President and Fellows of Harvard University
   Release Date: 2004-11-01
   Part of the MapQuant suite library "massspec.lib" 
*/

#define NO_OF_ELEMENTS 5
#define NO_OF_AMINOACIDS 20

enum {GLY, ALA, SER, 
      PRO, VAL, THR, 
          CYS, ILE, LEU, 
          ASN, ASP, HIS, 
          GLN, LYS, GLU, 
          MET, PHE, ARG, 
          TYR, TRP};

typedef struct
{
        char* symbol;
        const float mass;
} Element;


struct HMODEL
{
        float param[5];
};

typedef struct HMODEL HydrophobicityModel;

extern int CURR_HMODEL;

struct IonizationInfo
{
        float pKa_N;
        float pKa_C;
        float pKa_R;
};

typedef struct IonizationInfo IonizationInfo;

#define NO_HYDROPHOBICITY_MODELS 4

struct Aminoacid
{
        /* ATTRIBUTES           SYMBOLS IN TABLE FILENAMES */ 
        char name[3];   //      N
        char symbol;    //      n
        
        float mass;             //      M       :       This is the parameter for calculating 
                                        //                      the first dimension i.e MZ
        
        HydrophobicityModel hmodel[NO_HYDROPHOBICITY_MODELS];
        IonizationInfo          pKas;

        int nC;                 //      C
        int nH; 
        int nO; 
        int nN;                 //      
        int nS;                 //

}; 

typedef struct Aminoacid Aminoacid;

extern Aminoacid        aminoacid[NO_OF_AMINOACIDS];

int             Aminoacid_charToIndex(char aa);
char    Aminoacid_indexToChar(int index);

float   Aminoacid_calcMW(int i);
float   Aminoacid_calcAbsoluteMW(int i);
void    Aminoacid_fprintDelimited(FILE* fp, char delimiter);
float _calcMWFromMZ(float mz, int charge);


#endif

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