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) {
try {
options.add_options()("frame,f",
boost::program_options::value<unsigned int>(&frame),
"Frame to use");
RMF_ADD_INPUT_FILE("rmf");
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
if (!rh.get_description().empty()) {
std::cout << "description: " << rh.get_description() << std::endl;
}
if (!rh.get_producer().empty()) {
std::cout << "producer: " << rh.get_producer() << std::endl;
}
rh.set_current_frame(RMF::FrameID(frame));
std::cout << "frames: " << rh.get_number_of_frames() << std::endl;
RMF::show_info(rh, std::cout);
RMF::decorator::AlternativesFactory af(rh);
using RMF::operator<<;
std::cout << "resolutions: " << RMF::decorator::get_resolutions(
rh.get_root_node(), RMF::PARTICLE, 0)
<< std::endl;
std::cout << "gaussian resolutions: "
<< RMF::decorator::get_resolutions(rh.get_root_node(),
RMF::GAUSSIAN_PARTICLE, 0)
<< 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");
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;
}
}
LoadLinks get_load_linkers(RMF::FileConstHandle fh) {
LoadLinks ret;
typedef std::pair<std::string, int> P;
IMP_FOREACH(P kl, known_load_linkers) {
if (fh.get_has_associated_data(kl.second)) {
ret.push_back(fh.get_associated_data<LoadLinkAssociationType>(kl.second));
}
}
IMP_LOG_VERBOSE("Found " << ret.size() << " load linkers" << std::endl);
return ret;
}
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;
}
}
IMPRMF_BEGIN_NAMESPACE
void load_frame(RMF::FileConstHandle fh, RMF::FrameID frame) {
bool except = false;
std::string what;
try {
fh.set_current_frame(frame);
IMP_FOREACH(LoadLink * ll, internal::get_load_linkers(fh)) { ll->load(fh); }
}
catch (const std::exception& e) {
except = true;
what = e.what();
}
// Work around an MSVC 2012 compiler bug (exceptions thrown within a
// catch block cannot be caught)
if (except) {
IMP_THROW(what, IOException);
}
}
void set_linker(RMF::FileConstHandle fh, unsigned int id,
LoadLinkAssociationType l) {
fh.add_associated_data(id, l);
}
bool get_has_linker(RMF::FileConstHandle fh, unsigned int id) {
return fh.get_has_associated_data(id);
}
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;
}
IMP_FOREACH(Pair pp, local_) {
IMP_LOG_VERBOSE("Loading local coordinates for "
<< m->get_particle_name(pp.second) << std::endl);
algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_));
core::RigidBodyMember(m, pp.second).set_internal_coordinates(rf);
}
IMP_FOREACH(Pair pp, global_) {
IMP_LOG_VERBOSE("Loading global coordinates for "
<< m->get_particle_name(pp.second) << std::endl);
algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_));
core::XYZ(m, pp.second).set_coordinates(rf);
}
bool get_has_associated_node(RMF::FileConstHandle nh, Object *oi) {
return nh.get_node_from_association(oi) != RMF::NodeConstHandle();
}
RMF::NodeConstHandle get_node_from_association(RMF::FileConstHandle nh,
Object *oi) {
AssociationType o(oi);
return nh.get_node_from_association(o);
}