aa.h File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>

Go to the source code of this file.

Data Structures

struct  s_amino_a

Defines

#define M_NB_AA   20
#define M_ALA_IDX   0
#define M_CYS_IDX   1
#define M_ASP_IDX   2
#define M_GLU_IDX   3
#define M_PHE_IDX   4
#define M_GLY_IDX   5
#define M_HIS_IDX   6
#define M_ILE_IDX   7
#define M_LYS_IDX   8
#define M_LEU_IDX   9
#define M_MET_IDX   10
#define M_ASN_IDX   11
#define M_PRO_IDX   12
#define M_GLN_IDX   13
#define M_ARG_IDX   14
#define M_SER_IDX   15
#define M_THR_IDX   16
#define M_VAL_IDX   17
#define M_TRP_IDX   18
#define M_TYR_IDX   19

Functions

int get_aa_index (const char *name)
char * get_aa_name3 (const int index)
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)

Define Documentation

#define M_ALA_IDX   0

0 for ALA

Definition at line 44 of file aa.h.

Referenced by set_aa_desc().

#define M_ARG_IDX   14

14 for ARG

Definition at line 58 of file aa.h.

Referenced by set_aa_desc().

#define M_ASN_IDX   11

11 for ASN

Definition at line 55 of file aa.h.

Referenced by set_aa_desc().

#define M_ASP_IDX   2

2 for ASP

Definition at line 46 of file aa.h.

Referenced by set_aa_desc().

#define M_CYS_IDX   1

1 for CYS

Definition at line 45 of file aa.h.

Referenced by set_aa_desc().

#define M_GLN_IDX   13

13 for GLN

Definition at line 57 of file aa.h.

Referenced by set_aa_desc().

#define M_GLU_IDX   3

3 for GLU

Definition at line 47 of file aa.h.

Referenced by set_aa_desc().

#define M_GLY_IDX   5

5 for GLY

Definition at line 49 of file aa.h.

Referenced by set_aa_desc().

#define M_HIS_IDX   6

6 for HIS

Definition at line 50 of file aa.h.

Referenced by set_aa_desc().

#define M_ILE_IDX   7

7 for ILE

Definition at line 51 of file aa.h.

Referenced by set_aa_desc().

#define M_LEU_IDX   9

9 for LEU

Definition at line 53 of file aa.h.

Referenced by set_aa_desc().

#define M_LYS_IDX   8

8 for LYS

Definition at line 52 of file aa.h.

Referenced by set_aa_desc().

#define M_MET_IDX   10

10 for MET

Definition at line 54 of file aa.h.

Referenced by set_aa_desc().

#define M_NB_AA   20

number of amino acid macros

Definition at line 43 of file aa.h.

Referenced by get_aa_index(), and print_pocket().

#define M_PHE_IDX   4

4 for PHE

Definition at line 48 of file aa.h.

Referenced by set_aa_desc().

#define M_PRO_IDX   12

12 for PRO

Definition at line 56 of file aa.h.

Referenced by set_aa_desc().

#define M_SER_IDX   15

15 for SER

Definition at line 59 of file aa.h.

Referenced by set_aa_desc().

#define M_THR_IDX   16

16 for THR

Definition at line 60 of file aa.h.

Referenced by set_aa_desc().

#define M_TRP_IDX   18

18 for TRP

Definition at line 62 of file aa.h.

Referenced by set_aa_desc().

#define M_TYR_IDX   19

19 for TYR

Definition at line 63 of file aa.h.

Referenced by set_aa_desc().

#define M_VAL_IDX   17

17 for VAL

Definition at line 61 of file aa.h.

Referenced by set_aa_desc().

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().

00259 {
00260         int aa_index = get_aa_index(name) ;
00261 
00262         if(aa_index != -1) {
00263                 return ST_aa[aa_index].charge ;
00264         }/*
00265         else {
00266                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00267         }*/
00268 
00269         return 0 ;
00270 }

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().

00315 {
00316         int aa_index = get_aa_index(name) ;
00317 
00318         if(aa_index != -1) {
00319                 return ST_aa[aa_index].func_grp ;
00320         }/*
00321         else {
00322                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00323         }*/
00324 
00325         return -1 ;
00326 }

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.

00230 {
00231         int aa_index = get_aa_index(name) ;
00232 
00233         if(aa_index != -1) {
00234                 return ST_aa[aa_index].hydrophobicity ;
00235         }/*
00236         else {
00237                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00238         }*/
00239 
00240         return -1.0 ;
00241 }

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().

00141 {
00142         int i,
00143                 aa_index = -1 ;
00144 
00145         for(i = 0 ; i < M_NB_AA ; i++) {
00146                 if(toupper(name[0]) == ST_aa[i].name3[0] && toupper(name[1]) == ST_aa[i].name3[1] 
00147                 && toupper(name[2]) == ST_aa[i].name3[2]   ) {
00148                         aa_index = i ;
00149                         break ;
00150                 }
00151         }
00152 
00153         return aa_index ;
00154 }

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.

00174 {
00175         int aa_index = get_aa_index(name) ;
00176 
00177         if(aa_index != -1) {
00178                 return ST_aa[aa_index].mw ;
00179         }/*
00180         else {
00181                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00182         }*/
00183 
00184         return -1.0 ;
00185 }

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().

00118 {
00119         if(index < M_NB_AA && index >= 0) {
00120                 return (char*)ST_aa[index].name3 ;
00121         }
00122         return NULL ;
00123 }

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.

00287 {
00288         int aa_index = get_aa_index(name) ;
00289 
00290         if(aa_index != -1) {
00291                 return ST_aa[aa_index].polarity ;
00292         }/*
00293         else {
00294                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00295         }*/
00296 
00297         return -1 ;
00298 }

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.

00202 {
00203         int aa_index = get_aa_index(name) ;
00204 
00205         if(aa_index != -1) {
00206                 return ST_aa[aa_index].volume ;
00207         }/*
00208         else {
00209                 fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);
00210         }*/
00211 
00212         return -1.0 ;
00213 }

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().

00400 {
00401         if(aa_index < M_NB_AA && aa_index >= 0){
00402                 return ST_aa[aa_index].charge ;
00403         }/*
00404         else {
00405                 fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
00406         }*/
00407 
00408         return 0 ;
00409 }

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.

00452 {
00453         if(aa_index < M_NB_AA && aa_index >= 0) {
00454                 return ST_aa[aa_index].func_grp ;
00455         }/*
00456         else {
00457                 fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
00458         }*/
00459 
00460         return -1 ;
00461 }

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().

00373 {
00374         if(aa_index < M_NB_AA && aa_index >= 0) {
00375                 return ST_aa[aa_index].hydrophobicity ;
00376         }/*
00377         else {
00378                 fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
00379         }*/
00380 
00381         return -1.0 ;
00382 }

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().

00426 {
00427         if(aa_index < M_NB_AA && aa_index >= 0) {
00428                 return ST_aa[aa_index].polarity ;
00429         }/*
00430         else {
00431                 fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
00432         }*/
00433 
00434         return -1 ;
00435 }

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().

00347 {
00348         if(aa_index < M_NB_AA && aa_index >= 0){
00349                 return ST_aa[aa_index].volume ;
00350         }/*
00351         else {
00352                 fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);
00353         }*/
00354 
00355         return -1.0 ;
00356 }

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