void do_all_fitting(const std::string param_filename,
const std::string chimera_filename)
{
std::string protein_filename,surface_filename;
std::string density_filename;
std::string output_filename;
float spacing,resolution,dens_threshold;
int cn_symm_deg,dn_symm_deg;
int num_sols_to_fit;
internal::Parameters params(param_filename.c_str());
num_sols_to_fit=params.get_number_of_solution_to_fit();
output_filename=params.get_output_filename();
protein_filename = params.get_unit_pdb_fn();
density_filename = params.get_density_map_filename();
resolution=params.get_density_map_resolution();
spacing=params.get_density_map_spacing();
dens_threshold=params.get_density_map_threshold();
cn_symm_deg=params.get_cn_symm();
dn_symm_deg=params.get_dn_symm();
algebra::Vector3D origin = params.get_density_origin();
std::string symm_ref_output = output_filename;
symm_ref_output+=".symm.ref";
std::cout<<"============= parameters ============"<<std::endl;
std::cout<<"parameters filename : " << param_filename <<std::endl;
std::cout<<"density filename : " << density_filename <<std::endl;
std::cout<<"resolution : " << resolution <<std::endl;
std::cout<<"spacing : " << spacing <<std::endl;
std::cout<<"threshold : " << dens_threshold <<std::endl;
std::cout<<"symmetry degree (cn,dn): " << cn_symm_deg<<","
<<dn_symm_deg <<std::endl;
std::cout<<"number of solutions to fit : " << num_sols_to_fit <<std::endl;
std::cout<<"origin : (" << origin[0] << "," << origin[1] <<","
<< origin[2] << ")" << std::endl;
std::cout<<"output filename : " <<output_filename<<std::endl;
std::cout<<"====================================="<<std::endl;
//load the density
base::PointerMember<em::DensityMap> dmap =
em::read_map(density_filename, new em::MRCReaderWriter());
dmap->get_header_writable()->set_resolution(resolution);
dmap->update_voxel_size(spacing);
algebra::Vector3D v = dmap->get_origin();
dmap->set_origin(origin[0], origin[1], origin[2]);
CnSymmAxisDetector symm_map(cn_symm_deg, dmap, dens_threshold, 0.0);
params.set_density_non_symm_axis_length(
symm_map.get_non_symmetry_axis_length()*
symm_map.get_non_symmetry_axis_length()/4);
//generate the assemblies
std::cout<<"======= Sampling symmetric assemblies"<<std::endl;
multifit::FittingSolutionRecords recs = build_symmetric_assemblies(params);
multifit::write_fitting_solutions("intermediate_asmb_sols.out",recs);
// multifit::FittingSolutionRecords recs
// = multifit::read_fitting_solutions("intermediate_asmb_sols.out");
// multifit::FittingSolutionRecords pca_pruned_asmb_sols =
// prune_by_pca(param_filename,recs,2);
// std::cout<<"======= Write pruned intermediate assemblies"<<std::endl;
// multifit::write_fitting_solutions("pruned_intermediate_asmb_sols.out",
// pca_pruned_asmb_sols);
//load the protein
IMP_NEW(kernel::Model, mdl, ());
atom::Hierarchy asmb;
atom::Hierarchies mhs;
//atom::CAlphaPDBSelector sel;
for (int i=0;i<1;i++){//dn_symm_deg;i++) {
for (int j=0;j<cn_symm_deg;j++) {
atom::Hierarchy h = atom::read_pdb(protein_filename,mdl);
atom::Chain c= atom::get_chain(atom::Residue(
atom::get_residue(atom::Atom(core::get_leaves(h)[0]))));
c.set_id(char(65+i*cn_symm_deg+j));
atom::setup_as_rigid_body(h);
mhs.push_back(h);
}}
multifit::FittingSolutionRecords fitted_recs = fit_models_to_density(
dmap,mhs,
recs,params,num_sols_to_fit,false);
std::sort(fitted_recs.begin(), fitted_recs.end(),
sort_by_cc());
std::fstream out;
int i=0;
for(multifit::FittingSolutionRecords::iterator it = fitted_recs.begin();
it != fitted_recs.end(); it++){
it->show();
std::stringstream ss;
ss<<params.get_solution_model_filename()<<"."<<i++<<".pdb";
transform_cn_assembly(mhs,it->get_dock_transformation());
for(unsigned int j=0;j<mhs.size();j++){
core::transform(core::RigidBody(mhs[j]),
it->get_fit_transformation());
}
atom::write_pdb(mhs,ss.str());
for(unsigned int j=0;j<mhs.size();j++){
core::transform(core::RigidBody(mhs[j]),
it->get_fit_transformation().get_inverse());
}
it->set_solution_filename(ss.str());
transform_cn_assembly(mhs, it->get_dock_transformation().get_inverse());
}
multifit::write_fitting_solutions(output_filename.c_str(),fitted_recs);
write_in_symmref_format(fitted_recs, symm_ref_output);
if (chimera_filename != "") {
write_in_chimera_format(fitted_recs, chimera_filename);
}
}
IMPCNMULTIFIT_BEGIN_NAMESPACE
Floats get_rmsd_for_models(const std::string param_filename,
const std::string trans_filename,
const std::string ref_filename, int start_model,
int end_model) {
std::string protein_filename, surface_filename;
int cn_symm_deg;
std::cout << "============= parameters ============" << std::endl;
std::cout << "params filename : " << param_filename << std::endl;
std::cout << "trans filename : " << trans_filename << std::endl;
std::cout << "ref filename : " << ref_filename << std::endl;
std::cout << "start index to rmsd : " << start_model << std::endl;
std::cout << "end index to rmsd : " << end_model << std::endl;
std::cout << "=====================================" << std::endl;
internal::Parameters params(param_filename.c_str());
protein_filename = params.get_unit_pdb_fn();
cn_symm_deg = params.get_cn_symm();
IMP_NEW(Model, mdl, ());
atom::Hierarchy asmb_ref;
atom::Hierarchies mhs;
// read the monomer
core::XYZs model_xyzs;
for (int i = 0; i < cn_symm_deg; i++) {
atom::Hierarchy h =
atom::read_pdb(protein_filename, mdl, new atom::CAlphaPDBSelector());
atom::Chain c = atom::get_chain(
atom::Residue(atom::get_residue(atom::Atom(core::get_leaves(h)[0]))));
c.set_id(std::string(1, char(65 + i)));
atom::add_radii(h);
atom::create_rigid_body(h);
mhs.push_back(h);
Particles leaves = core::get_leaves(h);
for (Particles::iterator it = leaves.begin(); it != leaves.end();
it++) {
model_xyzs.push_back(core::XYZ(*it));
}
}
// read the transformations
multifit::FittingSolutionRecords recs =
multifit::read_fitting_solutions(trans_filename.c_str());
// read the reference structure
asmb_ref = atom::read_pdb(ref_filename, mdl, new atom::CAlphaPDBSelector());
atom::Hierarchies ref_chains =
atom::Hierarchies(atom::get_by_type(asmb_ref, atom::CHAIN_TYPE));
std::cout << "number of records:" << recs.size() << std::endl;
Floats rmsd;
std::ofstream out;
out.open("rmsd.output");
if (end_model < 0 || end_model >= static_cast<int>(recs.size())) {
end_model = recs.size() - 1;
}
for (int i = start_model; i >= 0 && i <= end_model; ++i) {
algebra::Transformation3D t1 = recs[i].get_dock_transformation();
algebra::Transformation3D t2 = recs[i].get_fit_transformation();
algebra::Transformation3D t2_inv = t1.get_inverse();
transform_cn_assembly(mhs, t1);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j]
.set_coordinates(t2.get_transformed(model_xyzs[j].get_coordinates()));
}
std::cout << mhs.size() << "," << ref_chains.size() << std::endl;
Float cn_rmsd = get_cn_rmsd(mhs, ref_chains);
out << " trans:" << i << " rmsd: " << cn_rmsd
<< " cc: " << 1. - recs[i].get_fitting_score() << std::endl;
rmsd.push_back(cn_rmsd);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j].set_coordinates(
t2_inv.get_transformed(model_xyzs[j].get_coordinates()));
}
/* std::stringstream ss;
ss<<"asmb_"<<i<<".pdb";
atom::write_pdb(mhs,ss.str());*/
transform_cn_assembly(mhs, t1.get_inverse());
}
out.close();
return rmsd;
}
