IMPATOM_BEGIN_INTERNAL_NAMESPACE
Particle* atom_particle(Model* m, const std::string& atom_type,
Element element, bool is_hetatm,
int atom_index, int residue_index,
double x, double y, double z,
double occupancy, double temp_factor) {
AtomType atom_name;
std::string string_name = atom_type;
// determine AtomType
if (is_hetatm) {
string_name = "HET:" + string_name;
if (!get_atom_type_exists(string_name)) {
atom_name = add_atom_type(string_name, element);
} else {
atom_name = AtomType(string_name);
}
} else { // ATOM line
boost::trim(string_name);
if (string_name.empty()) {
string_name = "UNK";
}
if (!AtomType::get_key_exists(string_name)) {
IMP_LOG_VERBOSE("ATOM record type not found: \""
<< string_name << "\" in PDB file " << std::endl);
atom_name = add_atom_type(string_name, element);
} else {
atom_name = AtomType(string_name);
}
}
// new particle
Particle* p = new Particle(m);
p->add_attribute(get_pdb_index_key(), atom_index);
algebra::Vector3D v(x, y, z);
// atom decorator
Atom d = Atom::setup_particle(p, atom_name);
std::ostringstream oss;
oss << "Atom " + atom_name.get_string() << " of residue " << residue_index;
p->set_name(oss.str());
core::XYZ::setup_particle(p, v).set_coordinates_are_optimized(true);
d.set_input_index(atom_index);
d.set_occupancy(occupancy);
d.set_temperature_factor(temp_factor);
d.set_element(element);
// check if the element matches
Element e2 = get_element_for_atom_type(atom_name);
if (element != e2) {
IMP_LOG_VERBOSE(
"AtomType element and PDB line elements don't match. AtomType "
<< e2 << " vs. determined from PDB " << element << std::endl);
}
return p;
}
void Nuisance::set_lower(Float d) {
Particle * p = get_particle();
if (! p->has_attribute(get_lower_key()))
p->add_attribute(get_lower_key(), d);
p->set_value(get_lower_key(), d);
}
void KMLProxy::run(Particles *initial_centers) {
IMP_INTERNAL_CHECK(is_init_,"The proxy was not initialized");
IMP_LOG(VERBOSE,"KMLProxy::run start \n");
//use the initial centers if provided
KMPointArray *kmc=nullptr;
if (initial_centers != nullptr) {
IMP_INTERNAL_CHECK(kcenters_ == initial_centers->size(),
"the number of initial points differs from the number of required"
<<" centers\n");
IMP_LOG(VERBOSE,"KMLProxy::run initial centers provided : \n");
kmc = allocate_points(kcenters_,atts_.size());
for (unsigned int i=0;i<kcenters_;i++){
Particle *cen=(*initial_centers)[i];
for(unsigned int j=0;j<atts_.size();j++) {
(*(*kmc)[i])[j]=cen->get_value(atts_[j]);
}
}
}
IMP_LOG(VERBOSE,"KMLProxy::run load initial guess \n");
//load the initail guess
KMFilterCenters ctrs(kcenters_, data_, kmc,damp_factor_);
//apply lloyd search
IMP_LOG(VERBOSE,"KMLProxy::run load lloyd \n");
lloyd_alg_ = new KMLocalSearchLloyd(&ctrs,&term_);
log_header();
IMP_CHECK_CODE(clock_t start = clock());
IMP_LOG(VERBOSE,"KMLProxy::run excute lloyd \n");
lloyd_alg_->execute();
IMP_LOG(VERBOSE,"KMLProxy::run analyse \n");
KMFilterCentersResults best_clusters = lloyd_alg_->get_best();
IMP_CHECK_CODE(Float exec_time = elapsed_time(start));
// print summary
IMP_LOG_WRITE(TERSE,log_summary(&best_clusters,exec_time));
IMP_LOG_WRITE(TERSE,best_clusters.show(IMP_STREAM));
IMP_INTERNAL_CHECK(kcenters_
== (unsigned int) best_clusters.get_number_of_centers(),
"The final number of centers does not match the requested one");
IMP_INTERNAL_CHECK (dim_ == (unsigned int) best_clusters.get_dim(),
"The dimension of the final clusters is wrong");
//TODO clear the centroids list
//set the centroids:
Particle *p;
IMP_LOG(VERBOSE,"KMLProxy::run load best results \n");
for (unsigned int ctr_ind = 0; ctr_ind < kcenters_; ctr_ind++) {
KMPoint *kmp = best_clusters[ctr_ind];
//create a new particle
p = new Particle(m_);
centroids_.push_back(p);
for (unsigned int att_ind = 0; att_ind < dim_; att_ind++) {
p->add_attribute(atts_[att_ind],(*kmp)[att_ind],false);
}
}
//set the assignment of particles to centers
//array of number of all points
//TODO - return this
IMP_LOG(VERBOSE,"KMLProxy::run get assignments \n");
const Ints *close_center = best_clusters.get_assignments();
IMP_LOG(VERBOSE,"KMLProxy::run get assignments 2\n");
for (int i=0;i<data_->get_number_of_points();i++) {
//std::cout<<"ps number i: " << i << " close center : "
//<< (*close_center)[i] << std::endl;
assignment_[ps_[i]]=(*close_center)[i];
}
}
