diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/get_hkl.c | 64 |
1 files changed, 63 insertions, 1 deletions
diff --git a/src/get_hkl.c b/src/get_hkl.c index 5fb3cfb6..fa5a0d8c 100644 --- a/src/get_hkl.c +++ b/src/get_hkl.c @@ -42,6 +42,8 @@ #include "reflist-utils.h" #include "symmetry.h" #include "beam-parameters.h" +#include "cell.h" +#include "cell-utils.h" static void show_help(const char *s) @@ -54,6 +56,8 @@ static void show_help(const char *s) "\n" " -i, --input=<file> Read reflections from <file>.\n" " -y, --symmetry=<sym> The symmetry of the input reflection list.\n" +" -p, --pdb=<file> PDB file with cell parameters (needed when\n" +" using a resolution cutoff)\n" "\n" "You can add noise to the reflections with either of:\n" " --poisson Simulate Poisson samples.\n" @@ -74,6 +78,7 @@ static void show_help(const char *s) "\n" "You can restrict which reflections are written out:\n" " -t, --template=<filename> Only include reflections mentioned in file.\n" +" --cutoff-angstroms=<n> Only include reflections with d < n Angstroms.\n" "\n" "You might sometimes need to do this:\n" " --multiplicity Multiply intensities by the number of\n" @@ -370,6 +375,9 @@ int main(int argc, char *argv[]) RefList *input; double adu_per_photon = 0.0; int have_adu_per_photon = 0; + int have_cutoff_angstroms = 0; + double cutoff = 0.0; + char *pdb = NULL; /* Long options */ const struct option longopts[] = { @@ -382,14 +390,16 @@ int main(int argc, char *argv[]) {"twin", 1, NULL, 'w'}, {"expand", 1, NULL, 'e'}, {"intensities", 1, NULL, 'i'}, + {"pdb", 1, NULL, 'p'}, {"multiplicity", 0, &config_multi, 1}, {"trim-centrics", 0, &config_trimc, 1}, {"adu-per-photon", 1, NULL, 2}, + {"cutoff-angstroms", 1, NULL, 3}, {0, 0, NULL, 0} }; /* Short options */ - while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:", + while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:p:", longopts, NULL)) != -1) { switch (c) { @@ -422,11 +432,20 @@ int main(int argc, char *argv[]) expand_str = strdup(optarg); break; + case 'p' : + pdb = strdup(optarg); + break; + case 2 : adu_per_photon = strtof(optarg, NULL); have_adu_per_photon = 1; break; + case 3 : + cutoff = strtof(optarg, NULL); + have_cutoff_angstroms = 1; + break; + case 0 : break; @@ -596,6 +615,49 @@ int main(int argc, char *argv[]) } + if ( have_cutoff_angstroms ) { + + RefList *n; + Reflection *refl; + RefListIterator *iter; + UnitCell *cell; + + if ( pdb == NULL ) { + ERROR("You must provide a PDB file when using " + "--cutoff-angstroms.\n"); + return 1; + } + + cell = load_cell_from_pdb(pdb); + if ( cell == NULL ) { + ERROR("Failed to load cell from '%s'\n", pdb); + return 1; + } + free(pdb); + + n = reflist_new(); + + for ( refl = first_refl(input, &iter); + refl != NULL; + refl = next_refl(refl, iter) ) + { + signed int h, k, l; + double res; + get_indices(refl, &h, &k, &l); + res = 2.0 * resolution(cell, h, k, l); + if ( res < 1e10 / cutoff ) { + Reflection *a; + a = add_refl(n, h, k, l); + copy_data(a, refl); + } + } + + cell_free(cell); + reflist_free(input); + input = n; + + } + write_reflist(output, input); reflist_free(input); |