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// Copyright 2017 Global Phasing Ltd.
#include "gemmi/to_cif.hpp" // for JsonWriter
#include "gemmi/fstream.hpp" // for Ofstream
#include "gemmi/read_cif.hpp" // for read_cif_gz
#include <iostream>
#define GEMMI_PROG json2cif
#include "options.h"
#include "cifmod.h" // for apply_cif_doc_modifications, ...
namespace {
enum OptionIndex { CifStyle=AfterCifModOptions, Cif2Cif };
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:"
"\n " EXE_NAME " [options] INPUT_FILE OUTPUT_FILE"
"\n\nConvert mmJSON to mmCIF."
"\n\nOptions:" },
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
{ CifStyle, 0, "", "style", Arg::CifStyle,
" --style=STYLE \tOne of: default, pdbx (categories separated with #),"
" aligned (left-aligned columns)." },
{ Cif2Cif, 0, "", "cif2cif", Arg::None,
" --cif2cif \tRead CIF not JSON." },
CifModUsage[SkipCat],
CifModUsage[SortCif],
{ NoOp, 0, "", "", Arg::None,
"\nWhen output file is -, write to standard output." },
{ 0, 0, 0, 0, 0, 0 }
};
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
std::ios_base::sync_with_stdio(false);
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
const char* input = p.nonOption(0);
const char* output = p.nonOption(1);
namespace cif = gemmi::cif;
if (p.options[Verbose])
std::cerr << "Transcribing " << input << " to cif ..." << std::endl;
try {
cif::Document doc = p.options[Cif2Cif] ? gemmi::read_cif_gz(input)
: gemmi::read_mmjson_gz(input);
apply_cif_doc_modifications(doc, p.options);
gemmi::Ofstream os(output, &std::cout);
write_cif_to_stream(os.ref(), doc, cif_write_options(p.options[CifStyle]));
} catch (std::runtime_error& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 2;
} catch (std::invalid_argument& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 3;
}
if (p.options[Verbose])
std::cerr << "Done." << std::endl;
return 0;
}
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