diff options
Diffstat (limited to 'src/get_hkl.c')
| -rw-r--r-- | src/get_hkl.c | 43 |
1 files changed, 29 insertions, 14 deletions
diff --git a/src/get_hkl.c b/src/get_hkl.c index ac59b2e9..0e556a4e 100644 --- a/src/get_hkl.c +++ b/src/get_hkl.c @@ -70,6 +70,8 @@ static void show_help(const char *s) " -w, --twin=<sym> Generate twinned data according to the given\n" " point group.\n" " -e, --expand=<sym> Expand reflections to this point group.\n" +" --no-need-all-parts Output a twinned reflection even if not all\n" +" the necessary equivalents were present.\n" "\n" "Use this option with care, and only if you understand why it might sometimes\n" " be necessary:\n" @@ -164,7 +166,7 @@ static RefList *template_reflections(RefList *list, RefList *template) } -static RefList *twin_reflections(RefList *in, +static RefList *twin_reflections(RefList *in, int need_all_parts, const SymOpList *holo, const SymOpList *mero) { Reflection *refl; @@ -186,6 +188,7 @@ static RefList *twin_reflections(RefList *in, refl = next_refl(refl, iter) ) { double total, sigma; + int multi, nbits; signed int h, k, l; int n, j; int skip; @@ -202,7 +205,9 @@ static RefList *twin_reflections(RefList *in, total = 0.0; sigma = 0.0; + multi = 0; skip = 0; + nbits = 0; special_position(holo, m, h, k, l); n = num_equivs(holo, m); @@ -210,6 +215,8 @@ static RefList *twin_reflections(RefList *in, signed int he, ke, le; signed int hu, ku, lu; + Reflection *part; + int r; get_equiv(holo, m, j, h, k, l, &he, &ke, &le); @@ -218,30 +225,36 @@ static RefList *twin_reflections(RefList *in, * equivalent which belongs to our definition of the * asymmetric unit cell, so check them all. */ - if ( !find_equiv_in_list(in, he, ke, le, mero, - &hu, &ku, &lu) ) { - /* Don't have this reflection, so bail out */ + r = find_equiv_in_list(in, he, ke, le, mero, + &hu, &ku, &lu); + + if ( need_all_parts && !r ) { + ERROR("Twinning %i %i %i requires the %i %i %i " "reflection (or an equivalent in %s), " - "which I don't have. %i %i %i won't " - "appear in the output\n", - h, k, l, he, ke, le, symmetry_name(mero), - h, k, l); + "which I don't have.\n", + h, k, l, he, ke, le, symmetry_name(mero)); + skip = 1; break; + } - total += get_intensity(refl); - sigma += pow(get_esd_intensity(refl), 2.0); + part = find_refl(in, hu, ku, lu); + + total += get_intensity(part); + sigma += pow(get_esd_intensity(part), 2.0); + multi += get_redundancy(part); + nbits++; } if ( !skip ) { Reflection *new = add_refl(out, h, k, l); - set_intensity(new, total); - set_esd_intensity(new, sqrt(sigma)); - set_redundancy(new, 1); + set_intensity(new, total/nbits); + set_esd_intensity(new, sqrt(sigma)/nbits); + set_redundancy(new, multi); } @@ -363,6 +376,7 @@ int main(int argc, char *argv[]) int config_poisson = 0; int config_multi = 0; int config_trimc = 0; + int config_nap = 1; char *holo_str = NULL; char *mero_str = NULL; char *expand_str = NULL; @@ -398,6 +412,7 @@ int main(int argc, char *argv[]) {"pdb", 1, NULL, 'p'}, {"multiplicity", 0, &config_multi, 1}, {"trim-centrics", 0, &config_trimc, 1}, + {"no-need-all-parts", 0, &config_nap, 0}, {"adu-per-photon", 1, NULL, 2}, {"cutoff-angstroms", 1, NULL, 3}, {0, 0, NULL, 0} @@ -569,7 +584,7 @@ int main(int argc, char *argv[]) RefList *new; STATUS("Twinning from %s into %s\n", symmetry_name(mero), symmetry_name(holo)); - new = twin_reflections(input, holo, mero); + new = twin_reflections(input, config_nap, holo, mero); /* Replace old with new */ reflist_free(input); |