Move load_molecule to sfac

1 files changed, 108 insertions, 0 deletions

diff --git a/src/sfac.c b/src/sfac.c
index 4c3dabd3..342c9615 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -162,3 +162,111 @@ double complex get_sfac(const char *n, double s, double en)
 	
 	return fq - fq0 + f1f2;
 }
+
+
+/* Load PDB file into a memory format suitable for efficient(ish) structure
+ * factor calculation */
+struct molecule *load_molecule()
+{
+	struct molecule *mol;
+	FILE *fh;
+	char line[1024];
+	char *rval;
+	int i;
+
+	mol = malloc(sizeof(struct molecule));
+	if ( mol == NULL ) return NULL;
+	mol->n_species = 0;
+
+	fh = fopen("molecule.pdb", "r");
+	if ( fh == NULL ) {
+                fprintf(stderr, "Couldn't open file\n");
+                return NULL;
+        }
+
+	do {
+
+		char el[4];
+		int j, r;
+		int done = 0;
+		float x, y, z, occ, B;
+		char *coords;
+
+		rval = fgets(line, 1023, fh);
+
+		/* 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';
+		}
+
+		coords = line + 29;
+		r = sscanf(coords, "%f %f %f %f %f", &x, &y, &z, &occ, &B);
+		if ( r != 5 ) {
+			fprintf(stderr, "WTF?\n");
+			abort();
+		}
+
+		for ( j=0; j<mol->n_species; j++ ) {
+
+			struct mol_species *spec;
+			int n;
+
+			spec = mol->species[j];
+
+			if ( strcmp(spec->species, el) != 0 ) continue;
+
+			n = mol->species[j]->n_atoms;
+
+			spec->x[n] = x;
+			spec->y[n] = y;
+			spec->z[n] = z;
+			spec->occ[n] = occ;
+			spec->B[n] = B;
+			mol->species[j]->n_atoms++;
+
+			done = 1;
+
+		}
+
+		if ( !done ) {
+
+			/* Need to create record for this species */
+			struct mol_species *spec;
+
+			spec = malloc(sizeof(struct mol_species));
+
+			memcpy(spec->species, el, 4);
+			spec->x[0] = x;
+			spec->y[0] = y;
+			spec->z[0] = z;
+			spec->occ[0] = occ;
+			spec->B[0] = B;
+			spec->n_atoms = 1;
+
+			mol->species[mol->n_species] = spec;
+			mol->n_species++;
+
+		}
+
+
+	} while ( rval != NULL );
+
+	fclose(fh);
+
+	printf("There are %i species\n", mol->n_species);
+	for ( i=0; i<mol->n_species; i++ ) {
+		printf("'%s': %i\n", mol->species[i]->species,
+		       mol->species[i]->n_atoms);
+	}
+
+	return mol;
+}