SimpleExcludedVolume create_simple_excluded_volume_on_molecules(
atom::Hierarchies const &mhs)
{
IMP_CHECK_CODE(size_t mhs_size = mhs.size());
IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be given");
kernel::ParticlesTemp ps;
for ( size_t i=0; i<mhs.size(); ++i )
{
kernel::ParticlesTemp leaves= IMP::atom::get_leaves(mhs[i]);
ps.insert(ps.end(), leaves.begin(), leaves.end());
}
/****** Set the restraint ******/
IMP_NEW(container::ListSingletonContainer, lsc, (ps));
IMP_NEW(core::ExcludedVolumeRestraint, evr, (lsc));
/****** Add restraint to the model ******/
//Model *mdl = mhs[0].get_particle()->get_model();
//mdl->add_restraint(evr);
/****** Return a SimpleExcludedVolume object ******/
return SimpleExcludedVolume(evr);
}
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];
}
}
