atom::Hierarchy create_coarse_molecule_from_molecule(
const atom::Hierarchy &mh,int num_beads,
Model *mdl,
float bead_radius,
bool add_conn_restraint) {
IMP_NEW(IMP::statistics::internal::ParticlesDataPoints, ddp,
(core::get_leaves(mh)));
IMP::statistics::internal::VQClustering vq(ddp,num_beads);
vq.run();
multifit::DataPointsAssignment assignment(ddp,&vq);
atom::Selections sel;
algebra::Vector3Ds vecs;
for (int i=0;i<num_beads;i++){
IMP::statistics::internal::Array1DD xyz =
assignment.get_cluster_engine()->get_center(i);
vecs.push_back(algebra::Vector3D(xyz[0],xyz[1],xyz[2]));
}
//todo - mass should be a parameter
atom::Hierarchy ret_prot=create_molecule(vecs,bead_radius,3,mdl);
ParticlesTemp leaves=core::get_leaves(ret_prot);
for (ParticlesTemp::iterator it = leaves.begin();it != leaves.end();it++){
sel.push_back(atom::Selection(atom::Hierarchy(*it)));
}
if (add_conn_restraint){
int k=1;//todo - make this a parameter
Restraint *r = atom::create_connectivity_restraint(sel,k);
if (r != nullptr){
mdl->add_restraint(r);}
}
return ret_prot;
}
atom::Hierarchy create_coarse_molecule_from_density(em::DensityMap *dmap,
float dens_threshold,
int num_beads,
kernel::Model *mdl,
float bead_radius) {
IMP_NEW(DensityDataPoints, ddp, (dmap, dens_threshold));
IMP_LOG_VERBOSE("initialize calculation of initial centers" << std::endl);
IMP::statistics::internal::VQClustering vq(ddp, num_beads);
vq.run();
multifit::DataPointsAssignment assignment(ddp, &vq);
algebra::Vector3Ds vecs;
for (int i = 0; i < num_beads; i++) {
IMP::statistics::internal::Array1DD xyz =
assignment.get_cluster_engine()->get_center(i);
vecs.push_back(algebra::Vector3D(xyz[0], xyz[1], xyz[2]));
}
// todo - mass should be a parameter
atom::Hierarchy ret_prot = create_molecule(vecs, bead_radius, 3, mdl);
return ret_prot;
}
