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-rw-r--r--src/sfac.c66
1 files changed, 49 insertions, 17 deletions
diff --git a/src/sfac.c b/src/sfac.c
index 81e381b3..3668217f 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -318,6 +318,8 @@ struct molecule *load_molecule()
char line[1024];
char *rval;
int i;
+ int nbits;
+ char **bits;
mol = malloc(sizeof(struct molecule));
if ( mol == NULL ) return NULL;
@@ -333,12 +335,11 @@ struct molecule *load_molecule()
do {
- char el[4];
+ char *el;
int j, r;
int done = 0;
float xf, yf, zf, occf, Bf;
double x, y, z, occ, B;
- char *coords;
rval = fgets(line, 1023, fh);
@@ -360,23 +361,49 @@ struct molecule *load_molecule()
/* Only interested in atoms */
if ( strncmp(line, "HETATM", 6) != 0 ) continue;
- /* The following crimes against programming style
- * were brought to you by Wizbit Enterprises, Inc. */
- if ( line[76] == ' ' ) {
- el[0] = line[77];
- el[1] = '\0';
- } else {
- el[0] = line[76];
- el[1] = line[77];
- el[2] = '\0';
- }
+ chomp(line);
+ nbits = assplode(line, " ", &bits, ASSPLODE_NONE);
+ if ( nbits == 0 ) continue;
+
+ if ( nbits == 11 ) {
+
+ /* Normal case- HETATM<space+>number<space+>stuff */
+ r = sscanf(bits[5], "%f", &xf);
+ r += sscanf(bits[6], "%f", &yf);
+ r += sscanf(bits[7], "%f", &zf);
+ r += sscanf(bits[8], "%f", &occf);
+ r += sscanf(bits[9], "%f", &Bf);
+ if ( r != 5 ) {
+ STATUS("PDB read failed (%i)\n", r);
+ for ( i=0; i<nbits; i++ ) free(bits[i]);
+ continue;
+ }
+ el = strdup(bits[10]);
+
+ } else if ( nbits == 10 ) {
+
+ /* Squished case- HETATMnumber<space+>stuff */
+ r = sscanf(bits[4], "%f", &xf);
+ r += sscanf(bits[5], "%f", &yf);
+ r += sscanf(bits[6], "%f", &zf);
+ r += sscanf(bits[7], "%f", &occf);
+ r += sscanf(bits[8], "%f", &Bf);
+ if ( r != 5 ) {
+ STATUS("PDB read failed (%i)\n", r);
+ for ( i=0; i<nbits; i++ ) free(bits[i]);
+ continue;
+ }
+ el = strdup(bits[9]);
- coords = line + 29;
- r = sscanf(coords, "%f %f %f %f %f", &xf, &yf, &zf, &occf, &Bf);
- if ( r != 5 ) {
- STATUS("I didn't understand a line in the PDB file.\n");
+ } else {
+ STATUS("Unrecognised line in the PDB file (%i)\n",
+ nbits);
+ STATUS("'%s'\n", line);
+ for ( i=0; i<nbits; i++ ) free(bits[i]);
continue;
}
+ for ( i=0; i<nbits; i++ ) free(bits[i]);
+
/* Promote to double precision */
x = xf; y = yf; z = zf; occ = occf; B = Bf;
@@ -397,6 +424,10 @@ struct molecule *load_molecule()
spec->occ[n] = occ;
spec->B[n] = B*1.0e-20; /* Convert to m^2 */
mol->species[j]->n_atoms++;
+ if ( mol->species[j]->n_atoms == MAX_ATOMS ) {
+ ERROR("Too many atoms of type '%s'!\n", el);
+ exit(1);
+ }
done = 1;
@@ -409,7 +440,7 @@ struct molecule *load_molecule()
spec = malloc(sizeof(struct mol_species));
- memcpy(spec->species, el, 4);
+ memcpy(spec->species, el, 1+strlen(el));
spec->x[0] = x*1.0e-10; /* Convert to m */
spec->y[0] = y*1.0e-10;
spec->z[0] = z*1.0e-10;
@@ -422,6 +453,7 @@ struct molecule *load_molecule()
}
+ free(el);
} while ( rval != NULL );