void Atom::set_atom_type(AtomType t)
{
get_particle()->set_value(get_atom_type_key(), t.get_index());
Element e= get_element_for_atom_type(t);
if (e != UNKNOWN_ELEMENT) {
set_element(e);
}
}
IMPATOM_BEGIN_INTERNAL_NAMESPACE
Particle* atom_particle(Model* m, const std::string& atom_type,
Element element, bool is_hetatm,
int atom_index, int residue_index,
double x, double y, double z,
double occupancy, double temp_factor) {
AtomType atom_name;
std::string string_name = atom_type;
// determine AtomType
if (is_hetatm) {
string_name = "HET:" + string_name;
if (!get_atom_type_exists(string_name)) {
atom_name = add_atom_type(string_name, element);
} else {
atom_name = AtomType(string_name);
}
} else { // ATOM line
boost::trim(string_name);
if (string_name.empty()) {
string_name = "UNK";
}
if (!AtomType::get_key_exists(string_name)) {
IMP_LOG_VERBOSE("ATOM record type not found: \""
<< string_name << "\" in PDB file " << std::endl);
atom_name = add_atom_type(string_name, element);
} else {
atom_name = AtomType(string_name);
}
}
// new particle
Particle* p = new Particle(m);
p->add_attribute(get_pdb_index_key(), atom_index);
algebra::Vector3D v(x, y, z);
// atom decorator
Atom d = Atom::setup_particle(p, atom_name);
std::ostringstream oss;
oss << "Atom " + atom_name.get_string() << " of residue " << residue_index;
p->set_name(oss.str());
core::XYZ::setup_particle(p, v).set_coordinates_are_optimized(true);
d.set_input_index(atom_index);
d.set_occupancy(occupancy);
d.set_temperature_factor(temp_factor);
d.set_element(element);
// check if the element matches
Element e2 = get_element_for_atom_type(atom_name);
if (element != e2) {
IMP_LOG_VERBOSE(
"AtomType element and PDB line elements don't match. AtomType "
<< e2 << " vs. determined from PDB " << element << std::endl);
}
return p;
}
