void EMFit::output(std::string out_file_name, std::string out_pdb_file_name) {
std::ofstream out_file(out_file_name.c_str());
out_file << "receptorPdb (str) " << rec_file_name_ << std::endl;
out_file << "ligandPdb (str) " << lig_file_name_ << std::endl;
EM3DFitResult::print_header(out_file);
out_file.setf(std::ios::fixed, std::ios::floatfield);
out_file.setf(std::ios::right, std::ios::adjustfield);
IMP::algebra::Vector3Ds lig_points;
IMP::saxs::get_coordinates(lig_particles_, lig_points);
for (unsigned int i = 0; i < fit_results_.size(); i++) {
out_file << fit_results_[i] << std::endl;
}
out_file.close();
if (fit_results_.size() == 1) { // output PDB
IMP::algebra::Transformation3D tr = fit_results_[0].get_map_trans();
IMP::Particles ps = rec_particles_;
ps.insert(ps.end(), lig_particles_.begin(), lig_particles_.end());
// transform
for (IMP::Particles::iterator it = ps.begin(); it != ps.end();
it++) {
IMP::core::XYZ d(*it);
d.set_coordinates(tr * d.get_coordinates());
}
// output
std::ofstream out_file2(out_pdb_file_name.c_str());
IMP::ParticlesTemp pst = ps;
IMP::atom::write_pdb(pst, out_file2);
out_file2.close();
}
}
void transform(IMP::Particles& ps, IMP::algebra::Transformation3D& t) {
for(IMP::Particles::iterator it = ps.begin(); it != ps.end(); it++) {
IMP::core::XYZ d(*it);
d.set_coordinates(t * d.get_coordinates());
}
}