void Fragment::set_residue_indexes(kernel::Model *m, kernel::ParticleIndex pi,
Ints o) {
if (o.empty()) {
set_residue_indexes(m, pi, IntPairs());
return;
}
std::sort(o.begin(), o.end());
o.erase(std::unique(o.begin(), o.end()), o.end());
IntPairs pairs;
int begin = 0;
for (unsigned int i = 1; i < o.size(); ++i) {
if (o[i] != o[i - 1] + 1) {
pairs.push_back(IntPair(o[begin], o[i - 1] + 1));
begin = i;
}
}
pairs.push_back(IntPair(o[begin], o.back() + 1));
set_residue_indexes(m, pi, pairs);
using IMP::operator<<;
IMP_IF_CHECK(USAGE) {
for (unsigned int i = 0; i < o.size(); ++i) {
IMP_INTERNAL_CHECK(Fragment(m, pi).get_contains_residue(o[i]),
"Residue index not found after addition: "
<< o << " became " << pairs);
}
}
}
IntPairs QuadraticClosePairsFinder::get_close_pairs(
const algebra::BoundingBox3Ds &bbs) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Adding close pairs from "
<< bbs.size() << " boxes with threshold " << get_distance()
<< std::endl);
IntPairs ret;
const double d2 = get_distance() / 2.0;
for (unsigned int i = 0; i < bbs.size(); ++i) {
algebra::BoundingBox3D bi = bbs[i] + d2;
for (unsigned int j = 0; j < i; ++j) {
algebra::BoundingBox3D bj = bbs[j] + d2;
if (get_interiors_intersect(bi, bj)) {
ret.push_back(IntPair(i, j));
}
}
}
return ret;
}
IntPairs NearestNeighborsClosePairsFinder::get_close_pairs(
const algebra::BoundingBox3Ds &bas,
const algebra::BoundingBox3Ds &bbs) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Quadratic add_close_pairs called with "
<< bas.size() << " and " << bbs.size() << std::endl);
IntPairs ret;
const double d2 = get_distance() / 2.0;
for (unsigned int i = 0; i < bas.size(); ++i) {
algebra::BoundingBox3D bi = bas[i] + d2;
for (unsigned int j = 0; j < bbs.size(); ++j) {
algebra::BoundingBox3D bj = bbs[j] + d2;
if (get_interiors_intersect(bi, bj)) {
ret.push_back(IntPair(i, j));
}
}
}
return ret;
}
