std::string InputOutputException::get_message(ModelObject *o) const {
std::ostringstream oss;
switch (get_entity()) {
case DERIVATIVE:
if (o->get_model()->get_stage() == BEFORE_EVALUATING) {
oss << "Derivatives cannot be read before evaluating.";
break;
}
default:
switch (get_operation()) {
case GET:
oss << "Not in input list.";
break;
case SET:
case ADD:
case REMOVE:
oss << "Not in output list.";
break;
default:
// should not exist
oss << "Unknown read/write error";
}
break;
};
oss << " Violating object: \"" << o->get_name() << "\".";
if (particle_index_ >= 0) {
oss << " Attribute " << get_key_name() << " of particle \""
<< o->get_model()
->get_particle(ParticleIndex(get_particle_index()))
->get_name() << "\" with id " << get_particle_index();
} else {
oss << "Container \"" << container_name_ << "\".";
}
return oss.str();
}
void RestraintCache::save_cache(const kernel::ParticlesTemp &particle_ordering,
const kernel::RestraintsTemp &restraints,
RMF::HDF5::Group group,
unsigned int max_entries) {
RMF::HDF5::FloatDataSet1Ds scores;
RMF::HDF5::IntDataSet2Ds assignments;
base::map<kernel::Restraint *, int> restraint_index;
ParticleIndex particle_index = get_particle_index(particle_ordering);
Orders orders = get_orders(known_restraints_, restraints, particle_ordering);
// create data sets for restraints
for (unsigned int i = 0; i < restraints.size(); ++i) {
kernel::Restraint *r = restraints[i];
RestraintID rid =
get_restraint_id(particle_index, known_restraints_.find(r)->second,
restraint_index_.find(r)->second);
RMF::HDF5::Group g = group.add_child_group(r->get_name());
g.set_attribute<RMF::HDF5::IndexTraits>(
"restraint", RMF::HDF5::Indexes(1, rid.get_restraint_index()));
g.set_attribute<RMF::HDF5::IndexTraits>(
"particles", RMF::HDF5::Indexes(rid.get_particle_indexes().begin(),
rid.get_particle_indexes().end()));
scores.push_back(g.add_child_data_set<RMF::HDF5::FloatTraits, 1>("scores"));
assignments.push_back(
g.add_child_data_set<RMF::HDF5::IntTraits, 2>("assignments"));
restraint_index[r] = i;
}
// finally start saving them
unsigned int count = 0;
for (Cache::ContentIterator it = cache_.contents_begin();
it != cache_.contents_end(); ++it) {
int ri = restraint_index.find(it->key.get_restraint())->second;
Ints ord = orders[ri].get_list_ordered(it->key.get_assignment());
double score = it->value;
RMF::HDF5::DataSetIndexD<2> asz = assignments[ri].get_size();
RMF::HDF5::DataSetIndexD<1> row(asz[0]);
asz[1] = ord.size();
++asz[0];
assignments[ri].set_size(asz);
assignments[ri].set_row(row, RMF::HDF5::Ints(ord.begin(), ord.end()));
RMF::HDF5::DataSetIndexD<1> ssz = scores[ri].get_size();
RMF::HDF5::DataSetIndexD<1> nsz = ssz;
++nsz[0];
scores[ri].set_size(nsz);
scores[ri].set_value(ssz, score);
++count;
if (count > max_entries) break;
}
}
void RestraintCache::load_cache(const kernel::ParticlesTemp &particle_ordering,
RMF::HDF5::ConstGroup group) {
ParticleIndex particle_index = get_particle_index(particle_ordering);
base::map<RestraintID, kernel::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;
}
kernel::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,
base::ConstVector<unsigned int>(Ints(
particle_indexes.begin(), particle_indexes.end())));
kernel::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();
}
IMPCORE_END_INTERNAL_NAMESPACE
IMPCORE_BEGIN_NAMESPACE
void RigidBody::normalize_rotation() {
double &q0 = get_model()->access_attribute(
internal::rigid_body_data().quaternion_[0], get_particle_index());
double &q1 = get_model()->access_attribute(
internal::rigid_body_data().quaternion_[1], get_particle_index());
double &q2 = get_model()->access_attribute(
internal::rigid_body_data().quaternion_[2], get_particle_index());
double &q3 = get_model()->access_attribute(
internal::rigid_body_data().quaternion_[3], get_particle_index());
algebra::VectorD<4> v(q0, q1, q2, q3);
// IMP_LOG_TERSE( "Rotation was " << v << std::endl);
double sm = v.get_squared_magnitude();
if (sm < .001) {
v = algebra::VectorD<4>(1, 0, 0, 0);
// IMP_LOG_TERSE( "Rotation is " << v << std::endl);
q0 = 1;
q1 = 0;
q2 = 0;
q3 = 0;
} else if (std::abs(sm - 1.0) > .01) {
v = v.get_unit_vector();
// IMP_LOG_TERSE( "Rotation is " << v << std::endl);
q0 = v[0];
q1 = v[1];
q2 = v[2];
q3 = v[3];
}
// evil hack
get_model()->set_attribute(internal::rigid_body_data().torque_[0],
get_particle_index(), 0);
get_model()->set_attribute(internal::rigid_body_data().torque_[1],
get_particle_index(), 0);
get_model()->set_attribute(internal::rigid_body_data().torque_[2],
get_particle_index(), 0);
}