Hierarchy create_protein(Model *m, std::string name, double resolution,
int number_of_residues, int first_residue_index,
double volume, bool ismol) {
double mass =
atom::get_mass_from_number_of_residues(number_of_residues) / 1000;
if (volume < 0) {
volume = atom::get_volume_from_mass(mass * 1000);
}
// assume a 20% overlap in the beads to make the protein not too bumpy
double overlap_frac = .2;
std::pair<int, double> nr = compute_n(volume, resolution, overlap_frac);
Hierarchy pd = Hierarchy::setup_particle(new Particle(m));
Ints residues;
for (int i = 0; i < number_of_residues; ++i) {
residues.push_back(i + first_residue_index);
}
atom::Fragment::setup_particle(pd, residues);
if (ismol) Molecule::setup_particle(pd);
pd->set_name(name);
for (int i = 0; i < nr.first; ++i) {
Particle *pc;
if (nr.first > 1) {
pc = new Particle(m);
std::ostringstream oss;
oss << name << "-" << i;
pc->set_name(oss.str());
atom::Fragment pcd = atom::Fragment::setup_particle(pc);
Ints indexes;
for (int j = i * (number_of_residues / nr.first) + first_residue_index;
j < (i + 1) * (number_of_residues / nr.first) + first_residue_index;
++j) {
indexes.push_back(j);
}
pcd.set_residue_indexes(indexes);
pd.add_child(pcd);
} else {
pc = pd;
}
core::XYZR xyzd = core::XYZR::setup_particle(pc);
xyzd.set_radius(nr.second);
atom::Mass::setup_particle(pc, mass / nr.first);
}
IMP_INTERNAL_CHECK(pd.get_is_valid(true), "Invalid hierarchy produced "
<< pd);
return pd;
}
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;
}
