IMPRMF_BEGIN_INTERNAL_NAMESPACE
HierarchyLoadXYZs::HierarchyLoadXYZs(RMF::FileConstHandle f)
: reference_frame_factory_(f), ip_factory_(f) {
// backwards compat
RMF::Category cat = f.get_category("IMP");
rb_index_key_ = f.get_key(cat, "rigid body", RMF::IntTraits());
}
int main(int argc, char* argv[])
{
IMP::setup_from_argv(argc,argv,"Test score of a model");
// read input
std::string inputfile="config.ini";
// parsing input
SPBParameters mydata=get_SPBParameters(inputfile,"0");
// create a new model
IMP_NEW(Model,m,());
IMP_NEW(RestraintSet, allrs, (m, "All restraints"));
// List of particles for layer restraint
IMP_NEW(container::ListSingletonContainer,CP_ps,(m));
IMP_NEW(container::ListSingletonContainer,IL2_ps,(m));
// List of MonteCarloMovers for MC, not used here
core::MonteCarloMovers mvs;
//
// ISD PARTICLES
//
std::map<std::string,IMP::Pointer<Particle> > ISD_ps=
add_ISD_particles(m,allrs,mydata,mvs);
// create list of particles from map
Particles ISD_ps_list;
std::map<std::string, IMP::Pointer<Particle> >::iterator itr;
for(itr = ISD_ps.begin(); itr != ISD_ps.end(); ++itr){
ISD_ps_list.push_back((*itr).second);
}
//
// PROTEIN REPRESENTATION
//
atom::Hierarchies all_mol=
create_representation(m,allrs,mydata,CP_ps,IL2_ps,mvs,
ISD_ps["SideXY"],ISD_ps["SideZ"],0);
//
// CREATING RESTRAINTS
//
std::map< std::string, IMP::Pointer<RestraintSet> > rst_map=
spb_assemble_restraints(m,allrs,mydata,all_mol,CP_ps,IL2_ps,ISD_ps);
//
// CREATE LIST TO LINK TO RMF
//
atom::Hierarchies hhs;
for(unsigned int i=0;i<all_mol.size();++i){
atom::Hierarchies hs=all_mol[i].get_children();
for(unsigned int j=0;j<hs.size();++j) {hhs.push_back(hs[j]);}
}
// print statistics
// open rmf for coordinates
RMF::FileConstHandle rhc =
RMF::open_rmf_file_read_only(argv[1]);
// read various info
RMF::Category my_kc_read = rhc.get_category("my data");
RMF::FloatKey my_key0_read = rhc.get_key<RMF::FloatTag>(my_kc_read,"my score");
// linking hierarchies
rmf::link_hierarchies(rhc, hhs);
// number of frames
unsigned int nframes=rhc.get_number_of_frames();
// open rmf for ISD particles
RMF::FileConstHandle rhc_ISD =
RMF::open_rmf_file_read_only(argv[2]);
// linking particles
rmf::link_particles(rhc_ISD, ISD_ps_list);
// number of frames
unsigned int nframes_ISD=rhc_ISD.get_number_of_frames();
// check number of frames are the same
if(nframes!=nframes_ISD) {exit(1);}
// cycle on frames
for(unsigned int imc = 0; imc < nframes; imc++){
// load coordinates
rmf::load_frame(rhc,RMF::FrameID(imc));
//rhc.set_current_frame(RMF::FrameID(imc));
// and ISD particles
//rhc_ISD.set_current_frame(RMF::FrameID(imc));
rmf::load_frame(rhc_ISD,RMF::FrameID(imc));
// get score and REM index
Float score = (rhc.get_root_node()).get_value(my_key0_read);
// do the scoring here
//
double totalscore = allrs->evaluate(false);
std::cout << "Stored score" << score <<
" Calculated score " <<totalscore <<std::endl;
// get all the restraints in the model
for(unsigned i=0;i<allrs->get_number_of_restraints();++i) {
IMP::Pointer<IMP::Restraint> rst=dynamic_cast<
IMP::Restraint*>(allrs->get_restraint(i));
std::cout<< rst->get_name() << " " << rst->get_score() <<std::endl;
}
for(unsigned i=0;i<rst_map["FRET_R"]->get_number_of_restraints();++i){
IMP::Pointer<isd::FretRestraint> rst=
dynamic_cast<isd::FretRestraint*>(
rst_map["FRET_R"]->get_restraint(i));
std::string name = rst->get_name();
Float fmod = rst->get_model_fretr();
Float fmod_err = rst->get_standard_error();
Float fexp = rst->get_experimental_value();
printf("TimeStep %10d Name %30s Model %6.3f",imc,name.c_str(),fmod);
printf("Model_Error %6.3f Exp %6.3f\n",fmod_err,fexp);
}
break;
}
// close RMFs
rhc = RMF::FileHandle();
rhc_ISD = RMF::FileHandle();
return 0;
}