Configure PDB filename for get_hkl and pattern_sim

src/get_hkl.c

@@ -41,7 +41,9 @@ static void show_help(const char *s)
 "      --zone-axis            Generate hk0 intensities only (and add\n"
 "                              Synth2D-style header.\n"
 "  -i, --intensities=<file>   Read intensities from file instead of\n"
-"                              calculating them from scratch.\n"
+"                              calculating them from scratch.  You might use\n"
+"                              this if you need to apply noise or twinning.\n"
+"  -p, --pdb=<file>           PDB file from which to get the structure.\n"
 );
 }
 
@@ -114,6 +116,7 @@ int main(int argc, char *argv[])
 	unsigned int *cts;
 	char *input = NULL;
 	signed int h, k, l;
+	char *filename = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -124,11 +127,12 @@ int main(int argc, char *argv[])
 		{"twin",               0, &config_twin,        1},
 		{"zone-axis",          0, &config_za,          1},
 		{"intensities",        1, NULL,               'i'},
+		{"pdb",                1, NULL,               'p'},
 		{0, 0, NULL, 0}
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "ht:o:i:", longopts, NULL)) != -1) {
+	while ((c = getopt_long(argc, argv, "ht:o:i:p:", longopts, NULL)) != -1) {
 
 		switch (c) {
 		case 'h' : {
@@ -151,6 +155,11 @@ int main(int argc, char *argv[])
 			break;
 		}
 
+		case 'p' : {
+			filename = strdup(optarg);
+			break;
+		}
+
 		case 0 : {
 			break;
 		}
@@ -162,10 +171,14 @@ int main(int argc, char *argv[])
 
 	}
 
-	mol = load_molecule();
+	if ( filename == NULL ) {
+		filename = strdup("molecule.pdb");
+	}
+
+	mol = load_molecule(filename);
 	cts = new_list_count();
 	if ( input == NULL ) {
-		ideal_ref = get_reflections(mol, eV_to_J(1790.0), 1/(0.6e-9), cts);
+		ideal_ref = get_reflections(mol, eV_to_J(1790.0), 1/(0.05e-9), cts);
 	} else {
 		ideal_ref = read_reflections(input, cts);
 		free(input);

src/pattern_sim.c

@@ -41,6 +41,9 @@ static void show_help(const char *s)
 "pulses of X-rays from a free electron laser.\n"
 "\n"
 " -h, --help                Display this help message.\n"
+" -p, --pdb=<file>          PDB file from which to get the unit cell.\n"
+"                            (The actual Bragg intensities come from the\n"
+"                            intensities file)\n"
 "     --simulation-details  Show technical details of the simulation.\n"
 "     --gpu                 Use the GPU to speed up the calculation.\n"
 "\n"
@@ -166,6 +169,7 @@ int main(int argc, char *argv[])
 	int config_nosfac = 0;
 	int config_gpu = 0;
 	int config_powder = 0;
+	char *filename = NULL;
 	char *grad_str = NULL;
 	GradientMethod grad;
 	int ndone = 0;    /* Number of simulations done (images or not) */
@@ -189,11 +193,12 @@ int main(int argc, char *argv[])
 		{"intensities",        1, NULL,               'i'},
 		{"powder",             0, &config_powder,      1},
 		{"gradients",          1, NULL,               'g'},
+		{"pdb",                1, NULL,               'p'},
 		{0, 0, NULL, 0}
 	};
 
 	/* Short options */
-	while ((c = getopt_long(argc, argv, "hrn:i:g:", longopts, NULL)) != -1) {
+	while ((c = getopt_long(argc, argv, "hrn:i:g:p:", longopts, NULL)) != -1) {
 
 		switch (c) {
 		case 'h' : {
@@ -221,6 +226,11 @@ int main(int argc, char *argv[])
 			break;
 		}
 
+		case 'p' : {
+			filename = strdup(optarg);
+			break;
+		}
+
 		case 0 : {
 			break;
 		}
@@ -232,6 +242,10 @@ int main(int argc, char *argv[])
 
 	}
 
+	if ( filename == NULL ) {
+		filename = strdup("molecule.pdb");
+	}
+
 	if ( config_simdetails ) {
 		show_details();
 		return 0;
@@ -282,7 +296,7 @@ int main(int argc, char *argv[])
 	image.width = 1024;
 	image.height = 1024;
 	image.lambda = ph_en_to_lambda(eV_to_J(1790.0));  /* Wavelength */
-	cell = load_cell_from_pdb("molecule.pdb");
+	cell = load_cell_from_pdb(filename);
 	image.filename = NULL;
 
 	#include "geometry-lcls.tmp"

src/sfac.c

@@ -311,7 +311,7 @@ static void centre_molecule(struct molecule *mol)
 
 /* Load PDB file into a memory format suitable for efficient(ish) structure
  * factor calculation */
-struct molecule *load_molecule()
+struct molecule *load_molecule(const char *filename)
 {
 	struct molecule *mol;
 	FILE *fh;
@@ -327,7 +327,7 @@ struct molecule *load_molecule()
 	mol->reflections = NULL;
 	mol->cell = NULL;
 
-	fh = fopen("molecule.pdb", "r");
+	fh = fopen(filename, "r");
 	if ( fh == NULL ) {
                 ERROR("Couldn't open PDB file\n");
                 return NULL;

src/sfac.h

@@ -58,7 +58,7 @@ struct molecule
 /* This is so that the water background calculation can use it */
 extern double complex get_sfac(const char *n, double s, double en);
 
-extern struct molecule *load_molecule(void);
+extern struct molecule *load_molecule(const char *filename);
 extern void free_molecule(struct molecule *mol);
 extern double *get_reflections(struct molecule *mol, double en, double res,
                                unsigned int *counts);