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rugnux: accept a space-group symbol for -S, not just a number

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-S now takes either a number ("92") or a Hermann-Mauguin symbol
("P43212"), resolved via gemmi find_spacegroup_by_name. Previously a
non-numeric argument was atoi'd to 0 and tripped the early space-group
validation, aborting the run.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-15 15:23:31 +02:00
co-authored by Claude Opus 4.8
parent ebe7e7ec5e
commit bd094e585f
1 changed files with 14 additions and 3 deletions
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rugnux/rugnux_cli.cpp
+14 -3
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@@ -73,7 +73,7 @@ void print_usage() {
std::cout << " --redo-rotation-spots Redo spot finding for two-pass rotation indexing" << std::endl;
std::cout << " --force-rotation-lattice <vec> Force rotation indexer with external lattice (in Angstrom) : \"a0x,a0y,a0z,a1x,a1y,a1z,a2x,a2y,a2z\" (9 floats, skips first pass)" << std::endl;
std::cout << " -X, --indexing-algorithm <txt> Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
std::cout << " -S, --space-group <num> Space group number - used for both indexing and scaling" << std::endl;
std::cout << " -S, --space-group <num|symbol> Space group number (92) or symbol (P43212) - for indexing and scaling" << std::endl;
std::cout << " -C, --unit-cell <cell> Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
std::cout << " -r, --refine <txt> Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
std::cout << " --refine-geometry[=N|off] Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default: 200) then re-indexes (lifts weak-stills indexing). Default ON for stills when a reference cell is given (-C / reference MTZ); =off disables" << std::endl;
@@ -672,9 +672,20 @@ int main(int argc, char **argv) {
case 'B':
refine_bfactor = true;
break;
case 'S':
space_group_number = atoi(optarg);
case 'S': {
// Accept a space-group number ("92") or a Hermann-Mauguin symbol ("P43212", "P 43 21 2").
char *end = nullptr;
const long as_number = strtol(optarg, &end, 10);
if (end != optarg && *end == '\0') {
space_group_number = as_number;
} else if (const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name(optarg)) {
space_group_number = sg->number;
} else {
logger.Error("Unknown space group '{}' (use a number like 92 or a symbol like P43212)", optarg);
exit(EXIT_FAILURE);
}
break;
}
case OPT_SPOT_SIGMA:
sigma_spot_finding = atof(optarg);
logger.Info("Noise threshold level for spot finding set to {:.2f} sigma", sigma_spot_finding);