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// Copyright 2020 Global Phasing Ltd.
//
// Reindex merged or unmerged MTZ file.
#include <cstdio>
#include <cstring> // for strpbrk
#include <algorithm>
#include <iostream> // for cerr
#include <gemmi/mtz.hpp>
#include <gemmi/gz.hpp> // for MaybeGzipped
#include <gemmi/version.hpp> // for GEMMI_VERSION
#define GEMMI_PROG reindex
#include "options.h"
using std::fprintf;
namespace {
enum OptionIndex { Hkl=4, NoHistory, NoSort, Asu };
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:\n " EXE_NAME " [options] INPUT_MTZ OUTPUT_MTZ"
"\nOptions:"},
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
{ Hkl, 0, "", "hkl", Arg::Required,
" --hkl=OP \tReindexing transform as triplet (e.g. k,h,-l)." },
{ NoHistory, 0, "", "no-history", Arg::None,
" --no-history \tDo not add 'Reindexed with...' line to mtz HISTORY." },
{ NoSort, 0, "", "no-sort", Arg::None,
" --no-sort \tDo not reorder reflections." },
{ Asu, 0, "", "asu", Arg::AsuChoice,
" --asu=ccp4|tnt \tWrite merged data in CCP4 (default) or TNT ASU." },
{ NoOp, 0, "", "", Arg::None,
"\nInput file can be gzipped." },
{ 0, 0, 0, 0, 0, 0 }
};
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
bool verbose = p.options[Verbose];
const char* input_path = p.nonOption(0);
const char* output_path = p.nonOption(1);
if (!p.options[Hkl] && !p.options[Asu]) {
fprintf(stderr, "Specify transform with option --hkl\n");
return 1;
}
try {
std::string from_line = "From gemmi-reindex " GEMMI_VERSION;
gemmi::Op op;
if (p.options[Hkl]) {
std::string hkl_arg = p.options[Hkl].arg;
op = gemmi::parse_triplet(hkl_arg);
if (std::strpbrk(hkl_arg.c_str(), "xyzabcXYZABC"))
gemmi::fail("specify OP in terms of h, k and l");
if (op.tran != gemmi::Op::Tran{{0, 0, 0}})
gemmi::fail("reindexing operator should not have a translation");
gemmi::cat_to(from_line, " with [", hkl_arg, ']');
}
gemmi::Mtz mtz;
if (verbose) {
fprintf(stderr, "Reading %s ...\n", input_path);
mtz.warnings = &std::cerr;
}
mtz.read_input(gemmi::MaybeGzipped(input_path), true);
if (p.options[Hkl])
mtz.reindex(op, &std::cerr);
if (mtz.is_merged()) {
bool tnt_asu = false;
if (p.options[Asu] && p.options[Asu].arg[0] == 't')
tnt_asu = true;
mtz.ensure_asu(tnt_asu);
}
if (!p.options[NoSort])
mtz.sort();
if (!p.options[NoHistory])
mtz.history.emplace(mtz.history.begin(), from_line);
if (verbose)
fprintf(stderr, "Writing %s ...\n", output_path);
mtz.write_to_file(output_path);
} catch (std::runtime_error& e) {
fprintf(stderr, "ERROR: %s\n", e.what());
return 1;
}
return 0;
}
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