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);
}
}
}
Hierarchy create_protein(Model *m, std::string name, double resolution,
const Ints db) {
Hierarchy root = Hierarchy::setup_particle(new Particle(m));
Domain::setup_particle(root, IntRange(db.front(), db.back()));
for (unsigned int i = 1; i < db.size(); ++i) {
std::ostringstream oss;
oss << name << "-" << i - 1;
Hierarchy cur = create_protein(
m, oss.str(), resolution, db[i] - db[i - 1], db[i - 1],
atom::get_volume_from_mass(
atom::get_mass_from_number_of_residues(db[i] - db[i - 1])),
false);
root.add_child(cur);
}
Molecule::setup_particle(root);
root->set_name(name);
return root;
}