int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
RMF::show_frames(rh, std::cout);
return 0;
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}
int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
RMF_ADD_OUTPUT_FILE("rmf");
int num_frames = 0;
double noise = 0, angle_noise = 0;
int max_frames = -1;
options.add_options()(
"number-interpolated", boost::program_options::value<int>(&num_frames),
"How many frames to insert between each original frame")(
"coordinate_noise", boost::program_options::value<double>(&noise),
"How much (gaussian) noise to add to each generated coordinate.")(
"angular_noise", boost::program_options::value<double>(&angle_noise),
"How much (gaussian) noise to add to each generated quaternion.")(
"frame_limit", boost::program_options::value<int>(&max_frames),
"Limits how many frames are output, for testing.");
process_options(argc, argv);
RMF::FileConstHandle irh0 = RMF::open_rmf_file_read_only(input);
RMF::FileConstHandle irh1 = RMF::open_rmf_file_read_only(input);
RMF::FileHandle orh = RMF::create_rmf_file(output);
orh.set_producer("rmf_interpolate");
orh.set_description(std::string("Interpolation between frames of ") +
input);
RMF::clone_hierarchy(irh0, orh);
RMF::clone_static_frame(irh0, orh);
for (unsigned int j = 0; j < irh0.get_number_of_frames() - 1; ++j) {
std::cout << "Processing frame " << j << std::endl;
irh0.set_current_frame(RMF::FrameID(j));
irh1.set_current_frame(RMF::FrameID(j + 1));
orh.add_frame(irh0.get_name(RMF::FrameID(j)), RMF::FRAME);
RMF::clone_loaded_frame(irh0, orh);
if (j + 1 < irh0.get_number_of_frames()) {
interpolate_frames(num_frames, noise, angle_noise, irh0, irh1, orh);
}
if (max_frames > 0 &&
orh.get_number_of_frames() > static_cast<unsigned int>(max_frames)) {
return 1;
}
}
irh0.set_current_frame(RMF::FrameID(irh0.get_number_of_frames() - 1));
RMF::clone_loaded_frame(irh0, orh);
return 0;
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}
int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
RMF_ADD_OUTPUT_FILE("xml");
int frame = 0;
options.add_options()("frame,f", boost::program_options::value<int>(&frame),
"Frame to use, if -1 just show static data")(
"verbose,v", "Show the attribute values for each node.");
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
std::ostream* out;
std::ofstream fout;
if (!output.empty()) {
fout.open(output.c_str());
if (!fout) {
std::cerr << "Error opening file " << output << std::endl;
return 1;
}
out = &fout;
} else {
out = &std::cout;
}
RMF::Categories cs = rh.get_categories();
*out << "<?xml version=\"1.0\"?>\n";
*out << "<rmf>\n";
*out << "<description>\n";
*out << rh.get_description() << std::endl;
*out << "</description>\n";
*out << "<path>\n";
*out << input << std::endl;
*out << "</path>\n";
std::set<RMF::NodeConstHandle> seen;
rh.set_current_frame(RMF::FrameID(frame));
show_hierarchy(rh.get_root_node(), cs, seen, *out);
*out << "</rmf>\n";
return 0;
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}
int main(int argc, char **argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
for (unsigned int i = 0; i < rh.get_number_of_frames(); ++i) {
rh.set_current_frame(i);
std::string cmt = rh.get_current_frame().get_name();
if (!cmt.empty()) {
std::cout << i << ": " << cmt << std::endl;
}
}
return 0;
} catch (const std::exception &e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}
int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
process_options(argc, argv);
if (boost::algorithm::ends_with(input, ".rmf2") &&
boost::filesystem::exists(boost::filesystem::path(input) / "file")) {
boost::filesystem::rename(
boost::filesystem::path(input) / "file",
boost::filesystem::path(input) / "file.rmf2info");
std::cout << "Updated" << std::endl;
} else {
std::cout << "Nothing to do" << std::endl;
}
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
return 0;
}
int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
RMF_ADD_OUTPUT_FILE("pdb");
RMF_ADD_FRAMES;
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
std::ostream* out;
std::ofstream fout;
if (!output.empty()) {
fout.open(output.c_str());
if (!fout) {
std::cerr << "Error opening file " << output << std::endl;
return 1;
}
out = &fout;
} else {
out = &std::cout;
}
RMF::decorator::IntermediateParticleFactory ipf(rh);
RMF::decorator::AtomFactory af(rh);
RMF::decorator::ChainFactory cf(rh);
RMF::decorator::ResidueFactory rf(rh);
RMF::NodeConstHandle rn = rh.get_root_node();
for (unsigned int input_frame = start_frame, output_frame = 0;
input_frame < rh.get_number_of_frames();
input_frame += step_frame, ++output_frame) {
rh.set_current_frame(RMF::FrameID(input_frame));
*out << (boost::format("MODEL%1$9d") % (output_frame + 1)) << std::endl;
write_atoms(*out, 0, rn, ipf, af, cf, rf);
*out << "ENDMDL" << output_frame + 1 << std::endl;
}
return 0;
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}