ModelObjectsTemp TransformationAndReflectionSymmetry::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ModelObjectsTemp ret(2 * pis.size());
for (unsigned int i = 0; i < pis.size(); ++i) {
ret[2 * i + 0] = m->get_particle(pis[i]);
ret[2 * i + 0] = Reference(m, pis[i]).get_reference_particle();
}
return ret;
}
ModelObjectsTemp AngleSingletonScore::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pi) const {
kernel::ModelObjectsTemp ret(4 * pi.size());
for (unsigned int i = 0; i < pi.size(); ++i) {
Angle ad(m, pi[i]);
ret[4 * i + 0] = ad.get_particle(0);
ret[4 * i + 1] = ad.get_particle(1);
ret[4 * i + 2] = ad.get_particle(2);
ret[4 * i + 3] = m->get_particle(pi[i]);
}
return ret;
}
ParticleIndexPairs GridClosePairsFinder::get_close_pairs(
kernel::Model *m, const kernel::ParticleIndexes &ca,
const kernel::ParticleIndexes &cb) const {
IMP_OBJECT_LOG;
set_was_used(true);
kernel::ParticleIndexPairs out;
internal::ParticleIndexHelper::fill_close_pairs(
internal::ParticleIndexHelper::get_particle_set(ca.begin(), ca.end(), 0),
internal::ParticleIndexHelper::get_particle_set(cb.begin(), cb.end(), 1),
internal::ParticleIndexTraits(m, get_distance()),
internal::ParticleIndexPairSink(m, access_pair_filters(), out));
return out;
}
ParticleIndexPairs GridClosePairsFinder::get_close_pairs(
kernel::Model *m, const kernel::ParticleIndexes &c) const {
IMP_OBJECT_LOG;
set_was_used(true);
IMP_LOG_TERSE("Rebuilding NBL with Grid and cutoff " << get_distance()
<< std::endl);
kernel::ParticleIndexPairs out;
internal::ParticleIndexHelper::fill_close_pairs(
internal::ParticleIndexHelper::get_particle_set(c.begin(), c.end(), 0),
internal::ParticleIndexTraits(m, get_distance()),
internal::ParticleIndexPairSink(m, access_pair_filters(), out));
return out;
}
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 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::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;
}
}
}
ParticleIndexPairs QuadraticClosePairsFinder::get_close_pairs(
kernel::Model *m, const kernel::ParticleIndexes &pt) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Adding close pairs from "
<< pt.size() << " particles with threshold " << get_distance()
<< std::endl);
kernel::ParticleIndexPairs ret;
for (unsigned int i = 0; i < pt.size(); ++i) {
for (unsigned int j = 0; j < i; ++j) {
if (get_are_close(m, pt[i], pt[j])) {
ret.push_back(kernel::ParticleIndexPair(pt[i], pt[j]));
}
}
}
return ret;
}
ParticleIndexPairs QuadraticClosePairsFinder::get_close_pairs(
kernel::Model *m, const kernel::ParticleIndexes &pta,
const kernel::ParticleIndexes &ptb) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Quadratic add_close_pairs called with "
<< pta.size() << " and " << ptb.size() << std::endl);
kernel::ParticleIndexPairs ret;
for (unsigned int i = 0; i < pta.size(); ++i) {
for (unsigned int j = 0; j < ptb.size(); ++j) {
if (get_are_close(m, pta[i], ptb[j])) {
ret.push_back(kernel::ParticleIndexPair(pta[i], ptb[j]));
}
}
}
return ret;
}
ModelObjectsTemp LeavesRefiner::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ModelObjectsTemp ret;
for (unsigned int i = 0; i < pis.size(); ++i) {
ret += get_all_descendants(Hierarchy(m, pis[i], traits_));
}
return ret;
}
ModelObjectsTemp TransformationSymmetry::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ModelObjectsTemp ret = IMP::kernel::get_particles(m, pis);
for (unsigned int i = 0; i < pis.size(); ++i) {
ret.push_back(Reference(m, pis[i]).get_reference_particle());
}
return ret;
}
ModelObjectsTemp DerivativesToRefined::do_get_outputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ModelObjectsTemp ret;
for (unsigned int i = 0; i < pis.size(); ++i) {
ret +=
IMP::kernel::get_particles(m, refiner_->get_refined_indexes(m, pis[i]));
}
return ret;
}
ModelObjectsTemp SoftCylinderPairScore::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ModelObjectsTemp ret(pis.size() * 3);
for (unsigned int i = 0; i < pis.size(); ++i) {
ret[3 * i + 0] = m->get_particle(pis[i]);
ret[3 * i + 1] = atom::Bond(m, pis[i]).get_bonded(0);
ret[3 * i + 2] = atom::Bond(m, pis[i]).get_bonded(1);
}
return ret;
}
void Selection::set_hierarchies(kernel::Model *m,
const kernel::ParticleIndexes &pi) {
m_ = m;
h_ = pi;
for (unsigned int i = 0; i < pi.size(); ++i) {
Hierarchy h(m_, pi[i]);
IMP_USAGE_CHECK(h.get_is_valid(true), "Hierarchy " << h
<< " is not valid.");
}
}
ModelObjectsTemp RefinedPairsPairScore::do_get_inputs(
kernel::Model *m, const kernel::ParticleIndexes &pis) const {
kernel::ParticleIndexes ps;
for (unsigned int i = 0; i < pis.size(); ++i) {
ps += get_indexes(get_set(m->get_particle(pis[i]), r_));
}
kernel::ModelObjectsTemp ret;
ret += f_->get_inputs(m, ps);
ret += r_->get_inputs(m, ps);
return ret;
}