Exemple #1
0
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;
}
Exemple #2
0
void CHARMMParameters::parse_atom_line(const String& line,
                                       ResidueType curr_res_type,
                                       CHARMMResidueTopologyBase *residue,
                                       bool translate_names_to_pdb)
{
  Strings split_results;
  boost::split(split_results, line, boost::is_any_of(" \t"),
               boost::token_compress_on);
  if(split_results.size() < 4) return; // ATOM line has at least 4 fields

  CHARMMAtomTopology atom(get_atom_name(split_results[1], residue,
                                        translate_names_to_pdb));
  atom.set_charmm_type(split_results[2]);
  atom.set_charge(atof(split_results[3].c_str()));
  residue->add_atom(atom);

  AtomType imp_atom_type;
  std::string imp_atom_name = atom.get_name();
  // really need Residue.get_is_protein() and friends here
  if (curr_res_type.get_index() >= HOH.get_index()) {
    imp_atom_name = "HET:" + imp_atom_name;
  }
  if (AtomType::get_key_exists(imp_atom_name)) {
     imp_atom_type = AtomType(imp_atom_name);
  } else {
     imp_atom_type= add_atom_type(imp_atom_name,
                                  get_element_for_type(split_results[2],
                                                       atom_type_to_element_));
  }
  // save in map
  if(atom_res_type_2_force_field_atom_type_.find(curr_res_type) ==
     atom_res_type_2_force_field_atom_type_.end()) {
    atom_res_type_2_force_field_atom_type_[curr_res_type] = AtomTypeMap();
  }
  atom_res_type_2_force_field_atom_type_[curr_res_type].insert(
           std::make_pair(imp_atom_type,
                          std::make_pair(atom.get_charmm_type(),
                                         atom.get_charge())));
}