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);
}
}
}
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);
}
}
}
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 << " ";
}
}
}
void write_txt(const std::string &txt_filename, const AnchorsData &ad) {
std::ofstream out;
out.open(txt_filename.c_str(), std::ios::out);
out << "|points|" << std::endl;
for (int i = 0; i < ad.get_number_of_points(); i++) {
algebra::Vector3D xyz = ad.points_[i];
out << "|" << i << "|" << xyz[0] << "|" << xyz[1] << "|" << xyz[2] << "|"
<< std::endl;
}
out << "|edges|" << std::endl;
IntPairs edges = ad.edges_;
for (IntPairs::const_iterator it = edges.begin(); it != edges.end(); it++) {
out << "|" << it->first << "|" << it->second << "|" << std::endl;
}
out.close();
}
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;
}
