indexamajig: Add --pdb option

src/indexamajig.c

@@ -77,8 +77,9 @@ static void show_help(const char *s)
 "      --no-match          Don't attempt to match the indexed cell to the\n"
 "                           model, just proceed with the one generated by the\n"
 "                           auto-indexing procedure.\n"
-"     --intensities=<file>  Specify file containing reflection intensities\n"
-"                            to use.\n"
+"     --intensities=<file> Specify file containing reflection intensities\n"
+"                           to use when simulating.\n"
+" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
 );
 }
 
@@ -194,6 +195,7 @@ int main(int argc, char *argv[])
 	double *intensities = NULL;
 	char *intfile = NULL;
 	unsigned int *counts = NULL;
+	char *pdb = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -212,11 +214,12 @@ int main(int argc, char *argv[])
 		{"verbose",            0, &config_verbose,     1},
 		{"alternate",          0, &config_alternate,   1},
 		{"intensities",        1, NULL,               'q'},
+		{"pdb",                1, NULL,               'p'},
 		{0, 0, NULL, 0}
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hi:w", longopts, NULL)) != -1) {
+	while ((c = getopt_long(argc, argv, "hi:wp:", longopts, NULL)) != -1) {
 
 		switch (c) {
 		case 'h' : {
@@ -239,6 +242,11 @@ int main(int argc, char *argv[])
 			break;
 		}
 
+		case 'p' : {
+			pdb = strdup(optarg);
+			break;
+		}
+
 		case 0 : {
 			break;
 		}
@@ -271,6 +279,10 @@ int main(int argc, char *argv[])
 		counts = NULL;
 	}
 
+	if ( pdb == NULL ) {
+		pdb = strdup("molecule.pdb");
+	}
+
 	if ( indm_str == NULL ) {
 		STATUS("You didn't specify an indexing method, so I won't"
 		       " try to index anything.\n"
@@ -287,7 +299,8 @@ int main(int argc, char *argv[])
 	}
 	free(indm_str);
 
-	cell = load_cell_from_pdb("molecule.pdb");
+	cell = load_cell_from_pdb(pdb);
+	free(pdb);
 	if ( cell == NULL ) {
 		ERROR("Couldn't read unit cell (from molecule.pdb)\n");
 		return 1;