ParticlesTemp CoreCloseBipartitePairContainer
::get_input_particles() const {
ParticlesTemp ret= internal::get_input_particles(get_model(),
sc_[0],
access_pair_filters());
ParticlesTemp ret1= internal::get_input_particles(get_model(), sc_[1],
access_pair_filters());
if (covers_[0] != base::get_invalid_index<ParticleIndexTag>()) {
ret.push_back(get_model()->get_particle(covers_[0]));
ret.push_back(get_model()->get_particle(covers_[1]));
}
ret.insert(ret.end(), ret1.begin(), ret1.end());
return ret;
}
ParticleIndexPairs GridClosePairsFinder::get_close_pairs(
Model *m, const ParticleIndexes &ca,
const ParticleIndexes &cb) const {
IMP_OBJECT_LOG;
set_was_used(true);
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(
Model *m, const ParticleIndexes &c) const {
IMP_OBJECT_LOG;
set_was_used(true);
IMP_LOG_TERSE("Rebuilding NBL with Grid and cutoff " << get_distance()
<< std::endl);
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;
}
bool QuadraticClosePairsFinder::get_are_close(kernel::Model *m,
kernel::ParticleIndex a,
kernel::ParticleIndex b) const {
return internal::get_are_close(m, access_pair_filters(), a, b,
get_distance());
}
void CoreCloseBipartitePairContainer::do_before_evaluate() {
IMP_OBJECT_LOG;
if (covers_[0]==base::get_invalid_index<ParticleIndexTag>()
|| algebra::get_distance(get_model()->get_sphere(covers_[0]),
get_model()->get_sphere(covers_[1]))
< distance_ || reset_) {
if (!reset_ && were_close_ && !internal::get_if_moved(get_model(), slack_,
xyzrs_[0], rbs_[0],
constituents_,
rbs_backup_[0],
xyzrs_backup_[0])
&& !internal::get_if_moved(get_model(), slack_,
xyzrs_[1], rbs_[1], constituents_,
rbs_backup_[1], xyzrs_backup_[1])){
// all ok
} else {
// rebuild
IMP_LOG(TERSE, "Recomputing bipartite close pairs list." << std::endl);
internal::reset_moved(get_model(),
xyzrs_[0], rbs_[0], constituents_,
rbs_backup_[0], xyzrs_backup_[0]);
internal::reset_moved(get_model(),
xyzrs_[1], rbs_[1], constituents_,
rbs_backup_[1], xyzrs_backup_[1]);
ParticleIndexPairs pips;
internal::fill_list(get_model(), access_pair_filters(),
key_, 2*slack_+distance_, xyzrs_, rbs_,
constituents_, pips);
reset_=false;
update_list(pips);
}
were_close_=true;
} else {
ParticleIndexPairs none;
update_list(none);
}
IMP_IF_CHECK(base::USAGE_AND_INTERNAL) {
for (unsigned int i=0; i< sc_[0]->get_number_of_particles(); ++i) {
XYZR d0(sc_[0]->get_particle(i));
for (unsigned int j=0; j< sc_[1]->get_number_of_particles(); ++j) {
XYZR d1(sc_[1]->get_particle(j));
double dist = get_distance(d0, d1);
if (dist < .9*distance_) {
ParticleIndexPair pip(d0.get_particle_index(),
d1.get_particle_index());
bool filtered=false;
for (unsigned int i=0; i< get_number_of_pair_filters(); ++i) {
if (get_pair_filter(i)->get_value_index(get_model(), pip)) {
filtered=true;
break;
}
}
IMP_INTERNAL_CHECK(filtered|| std::find(get_access().begin(),
get_access().end(), pip)
!= get_access().end(),
"Pair " << pip
<< " not found in list with coordinates "
<< d0 << " and " << d1
<< " list is " << get_access());
}
}
}
}
}
