/* mmcif */

/*  Read a "component cif" file from the RCSB components library  */

#include "../cifparse/cifparse.h"

int rmmcif(char *filename, char *blockId, int *atomnum, ATOM atom[], 
        int *bondnum, BOND bond[], CONTROLINFO *cinfo, MOLINFO *minfo, int flag)
{
/*if flag =1, read in atom type, if flag ==0, do not read in atom type */

	int i, j, numatom, numbond, iblock, iCat;
    int col2, col3, col6, col7, col8;
	FILE *fpin;

	if ((fpin = fopen(filename, "r")) == NULL) {
		fprintf(stdout, "Cannot open file %s to read in rmmcif(), exit\n", 
                filename);
		exit(1);
	}
	
	initial((*cinfo).maxatom, atom, (*minfo).resname);
	numatom = 0;
	numbond = 0;

    ndb_cif_init();
    ndb_cif_read_file( fpin );

    /*  Check for target data block.  */
    iblock = -1;
    for (i = 0; i < cifFiles.numDatablock; i++) {
        if (!strcmp(blockId, cifFiles.datablocks[i].datablockName)) {
            iblock = i;
            break;
        }
    }
    if (iblock == -1) {
        fprintf(stderr, "Target data block %s is not in file\n", blockId);
        exit(1);
    }
    iCat = get_category_index(iblock, "chem_comp_atom");
    if (iCat == -1) {
        fprintf(stderr, "Target category %s is not in data block %d\n",
                "atom_site", iblock);
        exit(1);
    }
    /* fprintf(stderr, "Read %d rows in category %d\n",
            cifFiles.datablocks[iblock].categories[iCat].numRow, iCat); */

    col2 = get_column_index(iblock, iCat, "atom_id"); /* atom name */
    assert( col2 >= 0 );
    col3 = get_column_index(iblock, iCat, "comp_id"); /* res. name */
    assert( col3 >= 0 );

#define IDEAL     /* undefine to get the regular "model" coordinates */
#ifdef IDEAL
    col6 = get_column_index(iblock, iCat, "pdbx_model_Cartn_x_ideal");   /* x-coord */
    assert( col6 >= 0 );
    col7 = get_column_index(iblock, iCat, "pdbx_model_Cartn_y_ideal");   /* y-coord */
    assert( col7 >= 0 );
    col8 = get_column_index(iblock, iCat, "pdbx_model_Cartn_z_ideal");   /* z-coord */
    assert( col8 >= 0 );
#else
    col6 = get_column_index(iblock, iCat, "model_Cartn_x");   /* x-coord */
    assert( col6 >= 0 );
    col7 = get_column_index(iblock, iCat, "model_Cartn_y");   /* y-coord */
    assert( col7 >= 0 );
    col8 = get_column_index(iblock, iCat, "model_Cartn_z");   /* z-coord */
    assert( col8 >= 0 );
#endif

    /*  --- need some better error processing here!  */

    for (i = 0; i < cifFiles.datablocks[iblock].categories[iCat].numRow; i++) {

        /* check for missing coordinates; then skip this atom  */
        if( 
        strlen(cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col6]) == 0 ||
        strlen(cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col7]) == 0 ||
        strlen(cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col8]) == 0 
        ){
           /*  fprintf( stderr, "skipping %d\n", i );  */
           continue;
        }

        strcpy(atom[numatom].name,
               cifFiles.datablocks[iblock].categories[iCat].rows[i].
               columns[col2]);
        strcpy(atom[numatom].aa,
               cifFiles.datablocks[iblock].categories[iCat].rows[i].
               columns[col3]);
        atom[numatom].resno = 1;
        atom[numatom].x = atof(
          cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col6]);
        atom[numatom].y = atof(
          cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col7]);
        atom[numatom].z = atof(
          cifFiles.datablocks[iblock].categories[iCat].rows[i].columns[col8]);

        numatom++;

    }

	fclose(fpin);
	*atomnum = numatom;
	*bondnum = numbond;
/*
	if(overflow_flag == 0) {
		tmpf1 = 0;
		tmpf2 = 0;
		for(i=0;i<numatom;i++) {
			if(atom[i].charge > 0)
				tmpf1+=atom[i].charge;
			else
				tmpf2+=atom[i].charge;
		}
		printf("\nchargep is %9.4lf", tmpf1);
		printf("\nchargen is %9.4lf", tmpf2);
	}
*/
	return 0;
}

#if 0

void wmmcif(char *filename, int atomnum, ATOM atom[], int bondnum,
		   BOND bond[], AROM arom[], CONTROLINFO cinfo, MOLINFO minfo) {
	int i,j;
	int flag; 
	int bondi, bondj;
	FILE *fpout;
	if ((fpout = fopen(filename, "w")) == NULL) {
		fprintf(stdout, "Cannot open file %s to write in wmol2(), exit\n", filename);
		return;
	}
	fclose(fpout);
}

#endif