RestraintsTemp RestraintCache::get_restraints() const {
IMP_OBJECT_LOG;
RestraintsTemp ret;
for (KnownRestraints::const_iterator it = known_restraints_.begin();
it != known_restraints_.end(); ++it) {
ret.push_back(it->first);
}
return ret;
}
void RestraintCache::load_cache(const ParticlesTemp &particle_ordering,
RMF::HDF5::ConstGroup group) {
ParticleIndex particle_index = get_particle_index(particle_ordering);
boost::unordered_map<RestraintID, Restraint *> index;
for (KnownRestraints::const_iterator it = known_restraints_.begin();
it != known_restraints_.end(); ++it) {
index[get_restraint_id(particle_index, it->second,
restraint_index_.find(it->first)->second)] =
it->first;
}
RestraintsTemp restraints;
for (unsigned int i = 0; i < group.get_number_of_children(); ++i) {
RMF::HDF5::ConstGroup ch = group.get_child_group(i);
int restraint_index =
ch.get_attribute<RMF::HDF5::IndexTraits>("restraint")[0];
RMF::HDF5::Indexes particle_indexes =
ch.get_attribute<RMF::HDF5::IndexTraits>("particles");
RestraintID rid(restraint_index,
ConstVector<unsigned int>(Ints(
particle_indexes.begin(), particle_indexes.end())));
Restraint *r = index.find(rid)->second;
restraints.push_back(r);
IMP_LOG_TERSE("Matching " << Showable(r) << " with " << ch.get_name()
<< std::endl);
}
Orders orders = get_orders(known_restraints_, restraints, particle_ordering);
for (unsigned int i = 0; i < group.get_number_of_children(); ++i) {
RMF::HDF5::ConstGroup ch = group.get_child_group(i);
RMF::HDF5::FloatConstDataSet1D scores =
ch.get_child_float_data_set_1d("scores");
RMF::HDF5::IntConstDataSet2D assignments =
ch.get_child_int_data_set_2d("assignments");
for (unsigned int j = 0; j < scores.get_size()[0]; ++j) {
double s = scores.get_value(RMF::HDF5::DataSetIndex1D(j));
RMF::HDF5::Ints rw = assignments.get_row(RMF::HDF5::DataSetIndex1D(j));
Ints psit(rw.begin(), rw.end());
Assignment ass = orders[i].get_subset_ordered(psit);
cache_.insert(Key(restraints[i], ass), s);
}
}
validate();
}
int main(int argc, char **argv) {
IMP::setup_from_argv(argc, argv, "An example program");
Pointer<Model> m(new Model());
ParticleIndex p0 = m->add_particle("P0");
core::XYZ d0 = core::XYZ::setup_particle(m, p0);
ParticleIndex p1 = m->add_particle("P1");
core::XYZ d1 = core::XYZ::setup_particle(m, p1);
Pointer<example::ExampleRestraint> r0 =
new example::ExampleRestraint(m, p0, 1);
Pointer<example::ExampleRestraint> r1 =
new example::ExampleRestraint(m, p1, 1);
RestraintsTemp rs;
rs.push_back(r0);
rs.push_back(r1);
d0.set_coordinates(algebra::Vector3D(0, 0, 2));
d1.set_coordinates(algebra::Vector3D(0, 0, 3));
Pointer<core::RestraintsScoringFunction> scoring_function =
new core::RestraintsScoringFunction(rs);
return 0;
}
RestraintsTemp RestraintCache::get_restraints(const Subset &s,
const Subsets &exclusions) const {
IMP_OBJECT_LOG;
RestraintsTemp ret;
for (KnownRestraints::const_iterator it = known_restraints_.begin();
it != known_restraints_.end(); ++it) {
if (s.get_contains(it->second)) {
bool excluded = false;
for (unsigned int i = 0; i < exclusions.size(); ++i) {
if (exclusions[i].get_contains(it->second)) {
excluded = true;
break;
}
}
if (!excluded) {
ret.push_back(it->first);
}
}
}
return ret;
}