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;
FitResult::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::kernel::Particles ps = rec_particles_;
ps.insert(ps.end(), lig_particles_.begin(), lig_particles_.end());
// transform
for (IMP::kernel::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::kernel::ParticlesTemp pst = ps;
IMP::atom::write_pdb(pst, out_file2);
out_file2.close();
}
}
void read_pdb_ca_atoms(const std::string file_name, IMP::kernel::Particles& particles) {
IMP::kernel::Model *model = new IMP::kernel::Model();
IMP::atom::Hierarchy mhd = IMP::atom::read_pdb(file_name, model,
new IMP::atom::CAlphaPDBSelector(), true, true);
particles=IMP::get_as<IMP::kernel::Particles>(get_by_type(mhd, IMP::atom::ATOM_TYPE));
std::cout << "Number of CA atom particles " << particles.size() << std::endl;
}
void EMFit::read_pdb_atoms(IMP::kernel::Model* model,
const std::string file_name,
IMP::kernel::Particles& particles) {
IMP::atom::Hierarchy mhd = IMP::atom::read_pdb(
file_name, model, new IMP::atom::NonWaterNonHydrogenPDBSelector(), true,
true);
particles = get_by_type(mhd, IMP::atom::ATOM_TYPE);
std::cout << "Number of atom particles " << particles.size() << std::endl;
}
float EMFit::compute_volume(const IMP::kernel::Particles& particles) {
IMP::saxs::FormFactorTable* ft = IMP::saxs::get_default_form_factor_table();
float volume = 0.0;
float c = (4.0 / 3.0) * IMP::algebra::PI;
for (unsigned int pindex = 0; pindex < particles.size(); pindex++) {
float radius = ft->get_radius(particles[pindex]);
// volume = 4/3 * pi * r^3
volume += c * radius * radius * radius;
// add radius to particle. it is needed later for sampled density map
IMP::core::XYZR::setup_particle(particles[pindex], radius);
}
return volume;
}
void transform(IMP::kernel::Particles& ps, IMP::algebra::Transformation3D& t) {
for(IMP::kernel::Particles::iterator it = ps.begin(); it != ps.end(); it++) {
IMP::core::XYZ d(*it);
d.set_coordinates(t * d.get_coordinates());
}
}