Introduce CrystFEL unit cell files

7 files changed, 47 insertions, 48 deletions

diff --git a/src/check_hkl.c b/src/check_hkl.c
index f22373b0..e10f5f29 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -57,7 +57,7 @@ static void show_help(const char *s)
 "  -h, --help                 Display this help message.\n"
 "      --version              Print CrystFEL version number and exit.\n"
 "  -y, --symmetry=<sym>       The symmetry of the input file.\n"
-"  -p, --pdb=<filename>       PDB file to use.\n"
+"  -p, --pdb=<filename>       Unit cell file to use (PDB or CrystFEL format).\n"
 "      --rmin=<res>           Low resolution cutoff (1/d in m^-1).\n"
 "      --rmax=<res>           High resolution cutoff (1/d in m^-1).\n"
 "      --lowres=<n>           Low resolution cutoff in (d in A).\n"
@@ -692,7 +692,7 @@ int main(int argc, char *argv[])
 	RefList *list;
 	Reflection *refl;
 	RefListIterator *iter;
-	char *pdb = NULL;
+	char *cellfile = NULL;
 	int rej = 0;
 	float rmin_fix = -1.0;
 	float rmax_fix = -1.0;
@@ -751,7 +751,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'p' :
-			pdb = strdup(optarg);
+			cellfile = strdup(optarg);
 			break;
 
 			case 0 :
@@ -833,13 +833,12 @@ int main(int argc, char *argv[])
 
 	file = strdup(argv[optind++]);
 
-	if ( pdb == NULL ) {
-		ERROR("You need to provide a PDB file containing"
-		       " the unit cell.\n");
+	if ( cellfile == NULL ) {
+		ERROR("You need to provide a unit cell.\n");
 		return 1;
 	}
-	cell = load_cell_from_pdb(pdb);
-	free(pdb);
+	cell = load_cell_from_file(cellfile);
+	free(cellfile);
 
 	raw_list = read_reflections(file);
 	if ( raw_list == NULL ) {
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index e10b93aa..a35e4f3b 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -89,7 +89,7 @@ static void show_help(const char *s)
 "Compare intensity lists.\n"
 "\n"
 "  -y, --symmetry=<sym>       The symmetry of both the input files.\n"
-"  -p, --pdb=<filename>       PDB file to use.\n"
+"  -p, --pdb=<filename>       Unit cell file to use.\n"
 "      --fom=<FoM>            Calculate this figure of merit  Choose from:\n"
 "                              R1I, R1F, R2, Rsplit, CC, CCstar,\n"
 "			       CCano, CRDano, Rano, Rano/Rsplit\n"
@@ -916,7 +916,7 @@ int main(int argc, char *argv[])
 	RefList *list1_raw;
 	RefList *list2_raw;
 	enum fom fom = FOM_R1I;
-	char *pdb = NULL;
+	char *cellfile = NULL;
 	float rmin_fix = -1.0;
 	float rmax_fix = -1.0;
 	double rmin, rmax;
@@ -974,7 +974,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'p' :
-			pdb = strdup(optarg);
+			cellfile = strdup(optarg);
 			break;
 
 			case 'u' :
@@ -1116,15 +1116,15 @@ int main(int argc, char *argv[])
 	afile = strdup(argv[optind++]);
 	bfile = strdup(argv[optind]);
 
-	if ( pdb == NULL ) {
-		ERROR("You must provide a PDB file with the unit cell.\n");
+	if ( cellfile == NULL ) {
+		ERROR("You must provide a unit cell.\n");
 		exit(1);
 	}
 
 	if ( shell_file == NULL ) shell_file = strdup("shells.dat");
 
-	cell = load_cell_from_pdb(pdb);
-	free(pdb);
+	cell = load_cell_from_file(cellfile);
+	free(cellfile);
 
 	list1_raw = read_reflections(afile);
 	if ( list1_raw == NULL ) {
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 3da68ef7..72b73041 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -421,7 +421,7 @@ int main(int argc, char *argv[])
 	char *cutoff_str = NULL;
 	double cutiso = 0.0;
 	float cutn1, cutn2, cutn3;
-	char *pdb = NULL;
+	char *cellfile = NULL;
 	char *reindex_str = NULL;
 	SymOpList *reindex = NULL;
 
@@ -487,7 +487,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'p' :
-			pdb = strdup(optarg);
+			cellfile = strdup(optarg);
 			break;
 
 			case 2 :
@@ -715,18 +715,18 @@ int main(int argc, char *argv[])
 		RefListIterator *iter;
 		UnitCell *cell;
 
-		if ( pdb == NULL ) {
-			ERROR("You must provide a PDB file when using "
+		if ( cellfile == NULL ) {
+			ERROR("You must provide a unit cell when using "
 			      "--cutoff-angstroms.\n");
 			return 1;
 		}
 
-		cell = load_cell_from_pdb(pdb);
+		cell = load_cell_from_file(cellfile);
 		if ( cell == NULL ) {
-			ERROR("Failed to load cell from '%s'\n", pdb);
+			ERROR("Failed to load cell from '%s'\n", cellfile);
 			return 1;
 		}
-		free(pdb);
+		free(cellfile);
 
 		n = reflist_new();
 
@@ -762,18 +762,18 @@ int main(int argc, char *argv[])
 		double csx, csy, csz;
 		double as, bs, cs;
 
-		if ( pdb == NULL ) {
-			ERROR("You must provide a PDB file when using "
+		if ( cellfile == NULL ) {
+			ERROR("You must provide a unit cell when using "
 			      "--cutoff-angstroms.\n");
 			return 1;
 		}
 
-		cell = load_cell_from_pdb(pdb);
+		cell = load_cell_from_file(cellfile);
 		if ( cell == NULL ) {
-			ERROR("Failed to load cell from '%s'\n", pdb);
+			ERROR("Failed to load cell from '%s'\n", cellfile);
 			return 1;
 		}
-		free(pdb);
+		free(cellfile);
 
 		cell_get_reciprocal(cell, &asx, &asy, &asz,
 				          &bsx, &bsy, &bsz,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 2ef98c2c..ff4b2243 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -93,8 +93,8 @@ static void show_help(const char *s)
 " -b, --beam=<file>        Get beam parameters from file (provides nominal\n"
 "                           wavelength value if no per-shot value is found in\n"
 "                           the HDF5 files.\n"
-" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
-"                           Default: 'molecule.pdb'.\n"
+" -p, --pdb=<file>         File (PDB or CrystFEL unit cell format) from which\n"
+"                           to get the unit cell.  Default: 'molecule.pdb'.\n"
 "     --basename           Remove the directory parts of the filenames.\n"
 " -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
 "     --peaks=<method>     Use 'method' for finding peaks.  Choose from:\n"
@@ -187,7 +187,7 @@ int main(int argc, char *argv[])
 	IndexingMethod *indm;
 	IndexingPrivate **ipriv;
 	char *indm_str = NULL;
-	char *pdb = NULL;
+	char *cellfile = NULL;
 	char *prefix = NULL;
 	char *speaks = NULL;
 	char *toler = NULL;
@@ -327,7 +327,7 @@ int main(int argc, char *argv[])
 			break;
 
 			case 'p' :
-			pdb = strdup(optarg);
+			cellfile = strdup(optarg);
 			break;
 
 			case 'x' :
@@ -606,13 +606,13 @@ int main(int argc, char *argv[])
 
 	add_geom_beam_stuff_to_copy_hdf5(iargs.copyme, iargs.det, iargs.beam);
 
-	if ( pdb != NULL ) {
-		iargs.cell = load_cell_from_pdb(pdb);
+	if ( cellfile != NULL ) {
+		iargs.cell = load_cell_from_file(cellfile);
 		if ( iargs.cell == NULL ) {
-			ERROR("Couldn't read unit cell (from %s)\n", pdb);
+			ERROR("Couldn't read unit cell (from %s)\n", cellfile);
 			return 1;
 		}
-		free(pdb);
+		free(cellfile);
 		STATUS("This is what I understood your unit cell to be:\n");
 		cell_print(iargs.cell);
 	} else {
diff --git a/src/partial_sim.c b/src/partial_sim.c
index d5933afd..47d8766e 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -624,7 +624,7 @@ int main(int argc, char *argv[])
 		ERROR("You need to give a PDB file with the unit cell.\n");
 		return 1;
 	}
-	cell = load_cell_from_pdb(cellfile);
+	cell = load_cell_from_file(cellfile);
 	if ( cell == NULL ) {
 		ERROR("Failed to get cell from '%s'\n", cellfile);
 		return 1;
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 0889697d..8e048b4e 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -69,7 +69,7 @@ static void show_help(const char *s)
 " -h, --help                Display this help message.\n"
 "     --version             Print CrystFEL version number and exit.\n"
 "\n"
-" -p, --pdb=<file>          PDB file from which to get the unit cell.\n"
+" -p, --pdb=<file>          File from which to get the unit cell.\n"
 "                            (The actual Bragg intensities come from the\n"
 "                            intensities file)\n"
 "     --gpu                 Use the GPU to speed up the calculation.\n"
@@ -572,7 +572,7 @@ int main(int argc, char *argv[])
 	free(beamfile);
 
 	/* Load unit cell */
-	input_cell = load_cell_from_pdb(filename);
+	input_cell = load_cell_from_file(filename);
 	if ( input_cell == NULL ) {
 		exit(1);
 	}
diff --git a/src/render_hkl.c b/src/render_hkl.c
index bdf1bbe6..1b13be66 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -3,11 +3,11 @@
  *
  * Draw pretty renderings of reflection lists
  *
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2013 Thomas White <taw@physics.org>
+ *   2010-2014 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -71,7 +71,7 @@ static void show_help(const char *s)
 "      --zone=<z>          Show the <z>th Laue zone.\n"
 "  -o, --output=<filename> Output filename.  Default: za.pdf\n"
 "      --boost=<val>       Squash colour scale by <val>.\n"
-"  -p, --pdb=<file>        PDB file from which to get the unit cell.\n"
+"  -p, --pdb=<file>        File from which to get the unit cell.\n"
 "  -y, --symmetry=<sym>    Expand reflections according to point group <sym>.\n"
 "\n"
 "  -c, --colscale=<scale>  Use the given colour scale.  Choose from:\n"
@@ -741,7 +741,7 @@ int main(int argc, char *argv[])
 	int config_sqrt = 0;
 	int config_colkey = 0;
 	int config_zawhinge = 0;
-	char *pdb = NULL;
+	char *cellfile = NULL;
 	int r = 0;
 	double boost = 1.0;
 	char *sym_str = NULL;
@@ -800,7 +800,7 @@ int main(int argc, char *argv[])
 			return 0;
 
 			case 'p' :
-			pdb = strdup(optarg);
+			cellfile = strdup(optarg);
 			break;
 
 			case 'b' :
@@ -888,8 +888,8 @@ int main(int argc, char *argv[])
 		      " any longer (I ignored it for you).\n");
 	}
 
-	if ( (pdb == NULL) && !config_colkey ) {
-		ERROR("You must specify the PDB containing the unit cell.\n");
+	if ( (cellfile == NULL) && !config_colkey ) {
+		ERROR("You must specify the unit cell.\n");
 		return 1;
 	}
 
@@ -974,9 +974,9 @@ int main(int argc, char *argv[])
 
 	infile = argv[optind];
 
-	cell = load_cell_from_pdb(pdb);
+	cell = load_cell_from_file(cellfile);
 	if ( cell == NULL ) {
-		ERROR("Couldn't load unit cell from %s\n", pdb);
+		ERROR("Couldn't load unit cell from %s\n", cellfile);
 		return 1;
 	}
 	list = read_reflections(infile);
@@ -993,7 +993,7 @@ int main(int argc, char *argv[])
 	render_za(cell, list, boost, sym, wght, colscale,
 	          rh, rk, rl, dh, dk, dl, outfile, scale_top, zone, &rings);
 
-	free(pdb);
+	free(cellfile);
 	free_symoplist(sym);
 	reflist_free(list);
 	if ( outfile != NULL ) free(outfile);