void Fragment::set_residue_indexes(kernel::Model *m, kernel::ParticleIndex pi,
const IntPairs &ris) {
Ints begins(ris.size());
Ints ends(ris.size());
for (unsigned int i = 0; i < ris.size(); ++i) {
begins[i] = ris[i].first;
ends[i] = ris[i].second;
IMP_USAGE_CHECK(ris[i].first < ris[i].second,
"Bad range for residue indexes");
}
if (begins.size() > 0) {
if (m->get_has_attribute(get_begins_key(), pi)) {
m->set_attribute(get_begins_key(), pi, begins);
m->set_attribute(get_ends_key(), pi, ends);
} else {
m->add_attribute(get_begins_key(), pi, begins);
m->add_attribute(get_ends_key(), pi, ends);
}
} else {
if (m->get_has_attribute(get_begins_key(), pi)) {
m->remove_attribute(get_begins_key(), pi);
m->remove_attribute(get_ends_key(), pi);
}
}
}
bool Fragment::get_contains_residue(int ri) const {
IntPairs all = get_residue_index_ranges();
for (unsigned int i = 0; i < all.size(); ++i) {
if (ri >= all[i].first && ri < all[i].second) return true;
}
return false;
}
Ints Fragment::get_residue_indexes() const {
IntPairs ranges = get_residue_index_ranges();
Ints ret;
for (unsigned int i = 0; i < ranges.size(); ++i) {
for (int j = ranges[i].first; j < ranges[i].second; ++j) {
ret.push_back(j);
}
}
return ret;
}
IMPATOM_BEGIN_NAMESPACE
void Fragment::show(std::ostream &out) const {
out << "Fragment: ";
IntPairs ps = get_residue_index_ranges();
for (unsigned int i = 0; i < ps.size(); ++i) {
if (ps[i].first != ps[i].second - 1) {
out << "[" << ps[i].first << ", " << ps[i].second << ") ";
} else {
out << ps[i].first << " ";
}
}
}
