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 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;
}