void destroy(Hierarchy d) {
ParticlesTemp all;
//core::Hierarchy h=d;
core::gather(d, True(), std::back_inserter(all));
for (unsigned int i=0; i< all.size(); ++i) {
if (Bonded::particle_is_instance(all[i])) {
Bonded b(all[i]);
while (b.get_number_of_bonds() > 0) {
destroy_bond(b.get_bond(b.get_number_of_bonds()-1));
}
}
Hierarchy hc(all[i]);
while (hc.get_number_of_children() > 0) {
hc.remove_child(hc.get_child(hc.get_number_of_children()-1));
}
}
// If this Hierarchy has a parent, remove the relationship
Hierarchy parent = d.get_parent();
if (parent) {
parent.remove_child(d);
}
for (unsigned int i=0; i< all.size(); ++i) {
all[i]->get_model()->remove_particle(all[i]);
}
}
Hierarchy create_fragment(const Hierarchies &ps) {
IMP_USAGE_CHECK(!ps.empty(), "Need some particles");
Hierarchy parent = ps[0].get_parent();
unsigned int index = ps[0].get_child_index();
IMP_IF_CHECK(USAGE) {
for (unsigned int i = 0; i < ps.size(); ++i) {
IMP_USAGE_CHECK(ps[i].get_parent() == parent, "Parents don't match");
}
}
kernel::Particle *fp =
new kernel::Particle(parent.get_particle()->get_model());
Hierarchy fd = Fragment::setup_particle(fp);
for (unsigned int i = 0; i < ps.size(); ++i) {
parent.remove_child(ps[i]);
fd.add_child(ps[i]);
}
parent.add_child_at(fd, index);
return fd;
}
