1 files changed, 31 insertions, 22 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 5a47254f..e0871fe7 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -32,6 +32,7 @@
 #include "detector.h"
 #include "sfac.h"
 #include "filters.h"
+#include "reflections.h"
 
 
 static void show_help(const char *s)
@@ -77,6 +78,8 @@ 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"
 );
 }
 
@@ -138,30 +141,22 @@ static struct image *get_simage(struct image *template, int alternate)
 
 	image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
 
-	image->molecule = copy_molecule(template->molecule);
-	free(image->molecule->cell);
-	image->molecule->cell = cell_new_from_cell(template->indexed_cell);
-
 	return image;
 }
 
 
-static void simulate_and_write(struct image *simage,
-                               struct gpu_context **gctx)
+static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
+                               double *intensities, UnitCell *cell)
 {
 	/* Set up GPU if necessary */
 	if ( (gctx != NULL) && (*gctx == NULL) ) {
-		*gctx = setup_gpu(0, simage, simage->molecule);
+		*gctx = setup_gpu(0, simage, intensities);
 	}
 
 	if ( (gctx != NULL) && (*gctx != NULL) ) {
-		get_diffraction_gpu(*gctx, simage, 24, 24, 40);
+		get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
 	} else {
-		get_diffraction(simage, 24, 24, 40, 0, 0);
-	}
-	if ( simage->molecule == NULL ) {
-		ERROR("Couldn't open molecule.pdb\n");
-		return;
+		get_diffraction(simage, 24, 24, 40, intensities, cell, 0);
 	}
 	record_image(simage, 0);
 
@@ -193,6 +188,9 @@ int main(int argc, char *argv[])
 	IndexingMethod indm;
 	char *indm_str = NULL;
 	struct image image;
+	UnitCell *cell;
+	double *intensities = NULL;
+	char *intfile = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -210,6 +208,7 @@ int main(int argc, char *argv[])
 		{"no-match",           0, &config_nomatch,     1},
 		{"verbose",            0, &config_verbose,     1},
 		{"alternate",          0, &config_alternate,   1},
+		{"intensities",        0, NULL,               'q'},
 		{0, 0, NULL, 0}
 	};
 
@@ -232,6 +231,11 @@ int main(int argc, char *argv[])
 			break;
 		}
 
+		case 'q' : {
+			intfile = strdup(optarg);
+			break;
+		}
+
 		case 0 : {
 			break;
 		}
@@ -257,6 +261,12 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	if ( intfile != NULL ) {
+		intensities = read_reflections(intfile);
+	} else {
+		intensities = NULL;
+	}
+
 	if ( indm_str == NULL ) {
 		STATUS("You didn't specify an indexing method, so I won't"
 		       " try to index anything.\n"
@@ -273,10 +283,9 @@ int main(int argc, char *argv[])
 	}
 	free(indm_str);
 
-	image.molecule = load_molecule();
-	if ( image.molecule == NULL ) {
-		ERROR("You must provide molecule.pdb in the working "
-		      "directory.\n");
+	cell = load_cell_from_pdb("molecule.pdb");
+	if ( cell == NULL ) {
+		ERROR("Couldn't read unit cell (from molecule.pdb)\n");
 		return 1;
 	}
 
@@ -354,7 +363,7 @@ int main(int argc, char *argv[])
 
 		/* Calculate orientation matrix (by magic) */
 		if ( config_writedrx || (indm != INDEXING_NONE) ) {
-			index_pattern(&image, indm, config_nomatch,
+			index_pattern(&image, cell, indm, config_nomatch,
 			              config_verbose);
 		}
 
@@ -376,16 +385,17 @@ int main(int argc, char *argv[])
 		/* Simulate if requested */
 		if ( config_simulate ) {
 			if ( config_gpu ) {
-				simulate_and_write(simage, &gctx);
+				simulate_and_write(simage, &gctx, intensities,
+				                   cell);
 			} else {
-				simulate_and_write(simage, NULL);
+				simulate_and_write(simage, NULL, intensities,
+				                   cell);
 			}
 		}
 
 		/* Finished with alternate image */
 		if ( simage->twotheta != NULL ) free(simage->twotheta);
 		if ( simage->data != NULL ) free(simage->data);
-		free_molecule(simage->molecule);
 		free(simage);
 
 		/* Only free cell if found */
@@ -402,7 +412,6 @@ done:
 	} while ( rval != NULL );
 
 	fclose(fh);
-	free_molecule(image.molecule);
 
 	STATUS("There were %i images.\n", n_images);
 	STATUS("%i hits were found.\n", n_hits);