void add_NuisanceMover(Particle *p, double dp, core::MonteCarloMovers &mvs) {
// put particle in a list
Particles ps;
ps.push_back(p);
// put nuisance floatkey in a list
FloatKeys fks;
fks.push_back(FloatKey("nuisance"));
IMP_NEW(core::NormalMover, mv, (ps, fks, dp));
mvs.push_back(mv);
}
FloatKey Weight::get_weight_key(int j) {
static FloatKeys kk;
if (kk.empty()) {
for (int i = 0; i < nstates_max; ++i) {
std::stringstream out;
out << i;
kk.push_back(FloatKey("weight" + out.str()));
}
}
return kk[j];
}
base::Vector<char>
write_particles_to_buffer(const ParticlesTemp &particles,
const FloatKeys &keys) {
if (particles.empty() || keys.empty()) {
return base::Vector<char>();
}
unsigned int size= particles.size()*keys.size()*sizeof(double);
base::Vector<char> ret(size);
write_particles_to_buffer(particles, keys, &ret.front(), size);
return ret;
}
void Particle::show(std::ostream &out) const {
internal::PrefixStream preout(&out);
preout << "index: " << get_index()
<< (get_is_active() ? " (active)" : " (dead)");
preout << std::endl;
if (get_model()) {
{
FloatKeys fks = get_float_keys();
if (!fks.empty()) {
preout << "float attributes:" << std::endl;
preout.set_prefix(" ");
for (FloatKeys::const_iterator it = fks.begin(); it != fks.end();
++it) {
FloatKey k = *it;
preout << k << ": " << get_model()->get_attribute(k, id_, false);
preout << " (" << get_model()->get_derivative(k, id_, false) << ") ";
preout << (get_is_optimized(k) ? " (optimized)" : "");
preout << std::endl;
}
preout.set_prefix("");
}
}
show_attributes(get_model(), get_int_keys(), id_, "int", IdentityValue(),
preout);
show_attributes(get_model(), get_string_keys(), id_, "string",
IdentityValue(), preout);
show_attributes(
get_model(),
get_model()->internal::ParticleAttributeTable::get_attribute_keys(id_),
id_, "particle", NameValue(get_model()), preout);
show_attributes(
get_model(),
get_model()->internal::ObjectAttributeTable::get_attribute_keys(id_),
id_, "object", DirectNameValue(), preout);
show_attributes(
get_model(),
get_model()->internal::ParticlesAttributeTable::get_attribute_keys(id_),
id_, "particles", SizeValue<NameValue>(NameValue(get_model())), preout);
show_attributes(
get_model(),
get_model()->internal::ObjectsAttributeTable::get_attribute_keys(id_),
id_, "objects", SizeValue<DirectNameValue>(), preout);
show_attributes(
get_model(),
get_model()->internal::IntsAttributeTable::get_attribute_keys(id_), id_,
"ints", SizeValue<IdentityValue>(), preout);
}
}
void NormalMover::initialize(ParticleIndexes pis, FloatKeys keys,
double radius) {
pis_ = pis;
keys_ = keys;
stddev_ = radius;
originals_.resize(pis.size(), algebra::get_zero_vector_kd(keys.size()));
}
void KMLProxy::initialize(Model *m,const Particles &ps,
const FloatKeys &atts,unsigned int num_centers){
for(Particles::const_iterator it = ps.begin(); it != ps.end();it++)
{ps_.push_back(*it);}
for(FloatKeys::const_iterator it = atts.begin();
it != atts.end();it++)
{atts_.push_back(*it);}
m_ = m;
kcenters_=num_centers;
dim_=atts.size();
centroids_ = Particles();
data_ = new KMData(dim_,ps_.size());
for(unsigned int i=0;i<ps_.size(); i++) {
for(unsigned int j=0;j<atts.size();j++){
(*(*data_)[i])[j]=ps_[i]->get_value(atts[j]);
}
}
is_init_=true;
}
void
read_particles_from_buffer( const base::Vector<char> &buffer,
const ParticlesTemp &particles,
const FloatKeys &keys) {
if (particles.empty() || keys.empty()) {
return;
}
read_particles_from_buffer(&buffer.front(),
buffer.size()*sizeof(double), particles, keys);
IMP_CHECK_MODEL_PARTICLES(particles[0]->get_model());
}
FloatKeys _pass_float_keys(const FloatKeys &in) {
for (unsigned int i = 0; i < in.size(); ++i) {
std::cout << in[i] << " ";
}
return in;
}
const FloatKeys Voxel::get_keys() {
static FloatKeys keys = core::XYZ::get_xyz_keys();
keys.push_back(core::XYZR::get_radius_key());
keys.push_back(Voxel::get_density_key());
return keys;
}