void HierarchySaveLink::add_recursive(Model *m, kernel::ParticleIndex root,
kernel::ParticleIndex p,
kernel::ParticleIndexes rigid_bodies,
RMF::NodeHandle cur, Data &data) {
IMP_LOG_VERBOSE("Adding " << atom::Hierarchy(m, p) << std::endl);
// make sure not to double add
if (p != root) set_association(cur, m->get_particle(p));
data.save_static.setup_node(m, p, cur);
bool local_coords =
data.save_local_coordinates.setup_node(m, p, cur, rigid_bodies);
bool global_coords =
data.save_global_coordinates.setup_node(m, p, cur, rigid_bodies);
bool static_coords =
data.save_static_coordinates.setup_node(m, p, cur, rigid_bodies);
IMP_INTERNAL_CHECK(!local_coords || !global_coords,
"A particle can't have saved local and global coords");
do_setup_node(m, root, p, cur);
if (core::RigidBody::get_is_setup(m, p)) {
rigid_bodies.push_back(p);
}
for (unsigned int i = 0; i < atom::Hierarchy(m, p).get_number_of_children();
++i) {
kernel::ParticleIndex pc = atom::Hierarchy(m, p).get_child_index(i);
RMF::NodeHandle curc =
cur.add_child(get_good_name(m, pc), RMF::REPRESENTATION);
add_recursive(m, root, pc, rigid_bodies, curc, data);
}
}
void HierarchyLoadLink::create_recursive(kernel::Model *m,
kernel::ParticleIndex root,
kernel::ParticleIndex cur,
RMF::NodeConstHandle name,
kernel::ParticleIndexes rigid_bodies,
Data &data) {
set_association(name, m->get_particle(cur));
unsigned int state = get_coords_state(name, intermediate_particle_factory_,
reference_frame_factory_);
data.load_static.setup_particle(name, m, cur, rigid_bodies);
data.load_local_coordinates.setup_particle(name, state, m, cur, rigid_bodies);
data.load_static_coordinates.setup_particle(name, state, m, cur,
rigid_bodies);
data.load_global_coordinates.setup_particle(name, state, m, cur,
rigid_bodies);
if (core::RigidBody::get_is_setup(m, cur)) {
rigid_bodies.push_back(cur);
}
RMF::NodeConstHandles ch = name.get_children();
for (unsigned int i = 0; i < ch.size(); ++i) {
if (ch[i].get_type() == RMF::REPRESENTATION) {
kernel::ParticleIndex child = m->add_particle(ch[i].get_name());
atom::Hierarchy(m, cur)
.add_child(atom::Hierarchy::setup_particle(m, child));
create_recursive(m, root, child, ch[i], rigid_bodies, data);
}
}
do_setup_particle(m, root, cur, name);
}
void HierarchyLoadLink::add_link_recursive(kernel::Model *m,
kernel::ParticleIndex root,
kernel::ParticleIndex cur,
RMF::NodeConstHandle node,
kernel::ParticleIndexes rigid_bodies,
Data &data) {
IMP_USAGE_CHECK(get_good_name(m, cur) == node.get_name(),
"Names don't match");
set_association(node, m->get_particle(cur), true);
RMF::NodeConstHandles ch = node.get_children();
unsigned int state = get_coords_state(node, intermediate_particle_factory_,
reference_frame_factory_);
data.load_static.link_particle(node, m, cur, rigid_bodies);
data.load_global_coordinates.link_particle(node, state, m, cur, rigid_bodies);
// data.load_static_coordinates.link_particle(node, m, cur, rigid_bodies);
data.load_local_coordinates.link_particle(node, state, m, cur, rigid_bodies);
do_link_particle(m, root, cur, node);
if (core::RigidBody::get_is_setup(m, cur)) {
rigid_bodies.push_back(cur);
}
int child = 0;
for (unsigned int i = 0; i < ch.size(); ++i) {
if (ch[i].get_type() == RMF::REPRESENTATION) {
add_link_recursive(m, root,
atom::Hierarchy(m, cur).get_child_index(child), ch[i],
rigid_bodies, data);
++child;
}
}
}