set_sequence.c

C-package of "Long Short-Term Memory" for Protein classification

/*
 * Code one Sequence
 * 
 * $Id: set_sequence.c 1272 2007-05-09 16:26:20Z mhe $
 *
*/

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

#include "lstm.h"
#include "set_sequence.h"

/*
   ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR 
   TRP TYR VAL ASX X GLX
*/
 
const static char aaChars[AAS] = {'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X'}; 

const static double aaVal[AAS] =
    { 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.5, 0.5, 0.0 };

const static int aaIdx[AAS] =
    {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22};
 

/* return position of given char in aaChars array */
int getAACharPos(char aa) {
    
    int i;
    for (i = 0; i < AAS; i++) {
        if (aaChars[i] == aa) {
            return i;
        }
    }
    if (aa == 'x' || aa == 'U') {
        return 22;
    }
    printf("Error in sequencegeneration, unknown AA Symbol\n");
    printf("AA Symbol:%c\n", aa);
    exit(-1);
    
}

/* generate a matrix of input vectors (windows) from a sequence */
void set_sequence(double **inp, int **inp_idx, char **aaSym, int length, int prot_current) {

    int i,j, starti, iter, aaCharPos;
    
    for (i = 0; i < length; i++) {
            
            starti = i - wside;
            
            /* amino coding */
            for (j = 0; j < windowsize; j++) {
                iter = starti + j;
                if (iter < 0 || iter >= length) {
                    inp[i][j] = 0;
                    inp_idx[i][j] = 0;          
                }
                else {
                    aaCharPos = getAACharPos(aaSym[prot_current][iter]);
                    inp[i][j] = aaVal[aaCharPos];
                    inp_idx[i][j] = j * AAS + aaIdx[aaCharPos];
                }
            }
        
    }
    
}