aa.c File Reference

#include "../headers/aa.h"

Go to the source code of this file.

Functions
char *	get_aa_name3 (const int index)
int	get_aa_index (const char *name)
float	get_aa_mw (const char *name)
float	get_aa_volume_score (const char *name)
float	get_aa_hydrophobicity_score (const char *name)
int	get_aa_charge (const char *name)
int	get_aa_polarity (const char *name)
int	get_aa_func_grp (const char *name)
float	get_volume_score_from_idx (int aa_index)
float	get_hydrophobicity_score_from_idx (int aa_index)
int	get_charge_from_idx (int aa_index)
int	get_polarity_from_idx (int aa_index)
int	get_func_grp_from_idx (int aa_index)
Variables
static const s_amino_a	ST_aa [20]

---

Function Documentation

int get_aa_charge

(

const char *

name

)

## FUNCTION: get_aa_charge

## SPECIFICATION: Return the charge score of given amino acid

## PARAMETRES: const char *name: Amno acid name (3 letter code representation)

## RETURN: charge (positiv, negativ, neutral, see header for more details), 0 if aa not found in the tab

Definition at line 258 of file aa.c.

References s_amino_a::charge, and get_aa_index().

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].charge ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return 0 ;
}

int get_aa_func_grp

(

const char *

name

)

## FUNCTION: get_func_grp_from_idx

## SPECIFICATION: Return the functional group type of the given amino acid

## PARAMETRES: @ const char *name: Amno acid name (3 letter code representation)

## RETURN: int: functional group id

Definition at line 314 of file aa.c.

References s_amino_a::func_grp, and get_aa_index().

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].func_grp ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return -1 ;
}

float get_aa_hydrophobicity_score

(

const char *

name

)

## FUNCTION: get_aa_hydrophobicity_score

## SPECIFICATION: Return the hydrophobicity score of given amino acid

## PARAMETRES: @ const char *name: Amno acid name (3 letter code representation)

## RETURN: float: hydrophobicity score, -1 if aa not found in the tab

Definition at line 229 of file aa.c.

References get_aa_index(), and s_amino_a::hydrophobicity.

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].hydrophobicity ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return -1.0 ;
}

int get_aa_index

(

const char *

name

)

## FUNCTION: get_aa_index

## SPECIFICATION: Return the index of AA given in argument (3letter code representation) in the static AA tab.

## PARAMETRES: @ const char *name: Amno acid name (3 letter code representation)

## RETURN: int: index of the given amino acid, -1 if not found in the tab

Definition at line 140 of file aa.c.

References M_NB_AA.

Referenced by get_aa_charge(), get_aa_func_grp(), get_aa_hydrophobicity_score(), get_aa_mw(), get_aa_polarity(), and get_aa_volume_score().

{
        int i,
                aa_index = -1 ;

        for(i = 0 ; i < M_NB_AA ; i++) {
                if(toupper(name[0]) == ST_aa[i].name3[0] && toupper(name[1]) == ST_aa[i].name3[1] 
                && toupper(name[2]) == ST_aa[i].name3[2]   ) {
                        aa_index = i ;
                        break ;
                }
        }

        return aa_index ;
}

float get_aa_mw

(

const char *

name

)

## FUNCTION: get_aa_mw

## SPECIFICATION: Return the molecular weight of AA given in argument

## PARAMETRES: @ const int index: Index of the AA in the tab

## RETURN: float: Molecular weight if the index is valid, NULL if not.

Definition at line 173 of file aa.c.

References get_aa_index(), and s_amino_a::mw.

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].mw ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return -1.0 ;
}

char* get_aa_name3

(

const int

index

)

## FUNCTION: get_aa_name3

## SPECIFICATION: Return the name of AA given in argument (index in the static table)

## PARAMETRES: @ const int index: Index of the AA in the tab

## RETURN: char *: Name if index is valid, NULL if not.

Definition at line 117 of file aa.c.

References s_amino_a::name3.

Referenced by dpocket(), and mdpocket_characterize().

{
        if(index < M_NB_AA && index >= 0) {
                return (char*)ST_aa[index].name3 ;
        }
        return NULL ;
}

int get_aa_polarity

(

const char *

name

)

## FUNCTION: get_aa_polarity

## SPECIFICATION: Return the polarity score of given amino acid

## PARAMETRES: @ const char *name: Amno acid name (3 letter code representation)

## RETURN: int polarity (polar, apolar), 0 if aa not found in the tab

Definition at line 286 of file aa.c.

References get_aa_index(), and s_amino_a::polarity.

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].polarity ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return -1 ;
}

float get_aa_volume_score

(

const char *

name

)

## FUNCTION: get_aa_volume_score

## SPECIFICATION: Return the volume score of given amino acid (very approximative...)

## PARAMETRES: @ const char *name: Amno acid name (3 letter code representation)

## RETURN: float: volume score, -1 if aa not found in the tab

Definition at line 201 of file aa.c.

References get_aa_index(), and s_amino_a::volume.

{
        int aa_index = get_aa_index(name) ;

        if(aa_index != -1) {
                return ST_aa[aa_index].volume ;
        }/*
        else {
                fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
        }*/

        return -1.0 ;
}

int get_charge_from_idx

(

int

aa_index

)

## FUNCTION: get_charge_from_idx

## SPECIFICATION: Return the charge score of given amino acid

## PARAMETRES: @ int aa_index: Index of the amino acid in the tab

## RETURN: int charge (positiv, negativ, neutral, see header for more details), 0 if aa not found in the tab

Definition at line 399 of file aa.c.

References s_amino_a::charge.

Referenced by set_aa_desc().

{
        if(aa_index < M_NB_AA && aa_index >= 0){
                return ST_aa[aa_index].charge ;
        }/*
        else {
                fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
        }*/

        return 0 ;
}

int get_func_grp_from_idx

(

int

aa_index

)

## FUNCTION: get_func_grp_from_idx

## SPECIFICATION: Return the functional group type of the given amino acid

## PARAMETRES: @ int aa_index: Index of the amino acid in the tab

## RETURN: int: functional group id

Definition at line 451 of file aa.c.

References s_amino_a::func_grp.

{
        if(aa_index < M_NB_AA && aa_index >= 0) {
                return ST_aa[aa_index].func_grp ;
        }/*
        else {
                fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
        }*/

        return -1 ;
}

float get_hydrophobicity_score_from_idx

(

int

aa_index

)

## FUNCTION: get_hydrophobicity_score_from_idx

## SPECIFICATION: Return the hydrophobicity score of given amino acid

## PARAMETRES: @ int aa_index: Index of the amino acid in the tab

## RETURN: float hydrophobicity score, -1 if aa not found in the tab

Definition at line 372 of file aa.c.

References s_amino_a::hydrophobicity.

Referenced by set_aa_desc().

{
        if(aa_index < M_NB_AA && aa_index >= 0) {
                return ST_aa[aa_index].hydrophobicity ;
        }/*
        else {
                fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
        }*/

        return -1.0 ;
}

int get_polarity_from_idx

(

int

aa_index

)

## FUNCTION: get_polarity_from_idx

## SPECIFICATION: Return the polarity score of given amino acid

## PARAMETRES: @ int aa_index: Index of the amino acid in the tab

## RETURN: int: polarity (polar, apolar), -1 if aa not found in the tab

Definition at line 425 of file aa.c.

References s_amino_a::polarity.

Referenced by set_aa_desc().

{
        if(aa_index < M_NB_AA && aa_index >= 0) {
                return ST_aa[aa_index].polarity ;
        }/*
        else {
                fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
        }*/

        return -1 ;
}

float get_volume_score_from_idx

(

int

aa_index

)

## FUNCTION: get_volume_score_from_idx

## SPECIFICATION: Return the volume score of given amino acid

## PARAMETRES: @ int aa_index: Index of the amino acid in the tab

## RETURN: float: volume score, -1 if aa not found in the tab

Definition at line 346 of file aa.c.

References s_amino_a::volume.

Referenced by set_aa_desc().

{
        if(aa_index < M_NB_AA && aa_index >= 0){
                return ST_aa[aa_index].volume ;
        }/*
        else {
                fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
        }*/

        return -1.0 ;
}

---

Variable Documentation

const s_amino_a ST_aa[20] [static]

Initial value:

 
{
        
        { "ALA", 'A',  89.0, 2.0,  41.0,  0, 0, 2 },
        { "ARG", 'R', 174.0, 7.0, -14.0,  1, 1, 5 },
        { "ASN", 'N', 132.0, 3.0, -28.0,  0, 1, 3 },
        { "ASP", 'D', 133.0, 3.0, -55.0, -1, 1, 3 },
        { "CYS", 'C', 121.0, 3.0,  49.0,  0, 0, 6 },
        { "GLN", 'Q', 146.0, 4.0, -10.0,  0, 1, 3 },
        { "GLU", 'E', 147.0, 4.0, -31.0, -1, 1, 3 },
        { "GLY", 'G',  75.0, 1.0,   0.0,  0, 0, 2 },
        { "HIS", 'H', 155.0, 4.0,   8.0,  1, 1, 1 },
        { "ILE", 'I', 131.0, 5.0,  99.0,  0, 0, 2 },
        { "LEU", 'L', 131.0, 5.0,  97.0,  0, 0, 2 },
        { "LYS", 'K', 146.0, 6.0, -23.0,  1, 1, 5 },
        { "MET", 'M', 149.0, 5.0,  74.0,  0, 0, 5 },
        { "PHE", 'F', 165.0, 6.0, 100.0,  0, 0, 1 },
        { "PRO", 'P', 115.0, 3.0, -46.0,  0, 0, 2 },
        { "SER", 'S', 105.0, 2.0,  -5.0,  0, 1, 4 },
        { "THR", 'T', 119.0, 3.0,  13.0,  0, 1, 4 },
        { "TRP", 'W', 204.0, 8.0,  97.0,  0, 1, 1 },
        { "TYR", 'Y', 181.0, 7.0,  63.0,  0, 1, 1 },
        { "VAL", 'V', 117.0, 4.0,  76.0,  0, 0, 2 }
}

Several amino-acid properties, taken from: http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm

Hydrophobicity taken from : http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/PolyAmino_Acids/Reference_Chart.html

Monera & al. Journal of Protein Science 1, 319-329 (1995)

Molecular weight taken from: http://www.expasy.ch/tools/pscale/Molecularweight.html

Definition at line 78 of file aa.c.