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-rw-r--r--src/check_hkl.c15
-rw-r--r--src/compare_hkl.c14
-rw-r--r--src/get_hkl.c24
-rw-r--r--src/indexamajig.c16
-rw-r--r--src/partial_sim.c2
-rw-r--r--src/pattern_sim.c4
-rw-r--r--src/render_hkl.c20
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);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 20:30:45 +0000