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// prints torsion restraints that are part of a ring
#include <gemmi/cif.hpp>
#include <gemmi/chemcomp.hpp>
//#include <gemmi/to_cif.hpp> // for write_cif_to_stream
#include <stdio.h>
namespace cif = gemmi::cif;
using AtomId = gemmi::Restraints::AtomId;
void check_torsions(const char* file_path) {
cif::Document doc = cif::read_file(file_path);
for (cif::Block& block : doc.blocks) {
if (block.name.empty() && block.name == "comp_list")
continue;
gemmi::ChemComp cc = gemmi::make_chemcomp_from_block(block);
for (gemmi::Restraints::Torsion& tor : cc.rt.torsions) {
std::vector<AtomId> ring = cc.rt.find_shortest_path(tor.id4, tor.id1,
{tor.id2, tor.id3});
if (ring.empty())
continue;
printf("[%s] torsion %s-%s-%s-%s angle %g +/- %g period %d\n",
cc.name.c_str(),
tor.id1.atom.c_str(), tor.id2.atom.c_str(),
tor.id3.atom.c_str(), tor.id4.atom.c_str(),
tor.value, tor.esd, tor.period);
printf(" rest of the ring: %s\n",
join_str(ring, '-',
[](const AtomId& id) { return id.atom; }).c_str());
// example modifications of torsion angle and esd
tor.value += 3.5;
tor.esd = 0.3;
}
}
// writing
//std::ofstream of("output.cif");
//of << "# " << file_path << '\n';
//of << "# modified by ...\n";
//cif::write_cif_to_stream(of, doc);
//of.close();
}
int main(int argc, char* argv[]) {
for (int i = 1; i < argc; ++i)
check_torsions(argv[i]);
return 0;
}
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