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// Copyright 2017 Global Phasing Ltd.
#include <iostream>
#include "gemmi/cifdoc.hpp" // for Document
#include "gemmi/to_json.hpp" // for JsonWriter
#include "gemmi/fstream.hpp" // for Ofstream
#include "gemmi/read_cif.hpp" // for read_cif_gz
#define GEMMI_PROG cif2json
#include "options.h"
#include "cifmod.h" // for apply_cif_doc_modifications, ...
namespace {
namespace cif = gemmi::cif;
struct ConvArg: public Arg {
static option::ArgStatus NumbChoice(const option::Option& option, bool msg) {
return Arg::Choice(option, msg, {"quote", "nosu", "mix"});
}
};
enum OptionIndex { Comcifs=AfterCifModOptions, Mmjson, Bare, Numb, CifDot, };
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:"
"\n " EXE_NAME " [options] INPUT_FILE OUTPUT_FILE"
"\n\nConvert CIF file (any CIF files, including mmCIF) to JSON."
"\nThe output can be COMCIFS CIF-JSON (-c), mmJSON (-m),"
"\nor a custom JSON flavor (default)."
"\n\nGeneral options:" },
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
{ NoOp, 0, "", "", Arg::None, "\nJSON output options:" },
{ Comcifs, 0, "c", "comcifs", Arg::None,
" -c, --comcifs \tConform to the COMCIFS CIF-JSON standard draft." },
{ Mmjson, 0, "m", "mmjson", Arg::None,
" -m, --mmjson \tCompatible with mmJSON from PDBj." },
{ Bare, 0, "", "bare-tags", Arg::None,
" --bare-tags \tOutput tags without the first underscore." },
{ Numb, 0, "", "numb", ConvArg::NumbChoice,
" --numb=quote|nosu|mix \tConvert the CIF numb type to one of:"
"\v quote - string in quotes,"
"\v nosu - number without s.u.,"
"\v mix (default) - quote only numbs with s.u." },
{ CifDot, 0, "", "dot", Arg::Required,
" --dot=STRING \tJSON representation of CIF's '.' (default: null)." },
{ NoOp, 0, "", "", Arg::None, "\nModifications:" },
CifModUsage[SkipCat],
CifModUsage[SortCif],
{ NoOp, 0, "", "", Arg::None,
"\nWhen output file is -, write to standard output." },
{ 0, 0, 0, 0, 0, 0 }
};
void convert(const std::string& input, const std::string& output,
const std::vector<option::Option>& options) {
cif::Document doc = gemmi::read_cif_gz(input);
apply_cif_doc_modifications(doc, options);
gemmi::Ofstream os(output, &std::cout);
cif::JsonWriter writer(os.ref());
if (options[Comcifs])
writer.set_comcifs();
if (options[Mmjson])
writer.set_mmjson();
if (options[Bare])
writer.bare_tags = true;
if (options[Numb]) {
char first_letter = options[Numb].arg[0];
if (first_letter == 'q')
writer.quote_numbers = 2;
else if (first_letter == 'n')
writer.quote_numbers = 0;
}
if (options[CifDot])
writer.cif_dot = options[CifDot].arg;
writer.write_json(doc);
}
} // 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);
if (p.options[Verbose])
std::cerr << "Transcribing " << input << " to json ..." << std::endl;
try {
convert(input, output, p.options);
} 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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