CHARMMTopology *CHARMMParameters::create_topology(Hierarchy hierarchy) const {
IMP_OBJECT_LOG;
IMP_NEW(CHARMMTopology, topology, (this));
Hierarchies chains = get_by_type(hierarchy, CHAIN_TYPE);
for (Hierarchies::iterator chainit = chains.begin(); chainit != chains.end();
++chainit) {
IMP_NEW(CHARMMSegmentTopology, segment, ());
Hierarchies residues = get_by_type(*chainit, RESIDUE_TYPE);
for (Hierarchies::iterator resit = residues.begin();
resit != residues.end(); ++resit) {
ResidueType restyp = Residue(*resit).get_residue_type();
try {
IMP_NEW(CHARMMResidueTopology, residue, (get_residue_topology(restyp)));
segment->add_residue(residue);
}
catch (base::ValueException) {
// If residue type is unknown, add empty topology for this residue
IMP_WARN_ONCE(
restyp.get_string(),
"Residue type "
<< restyp
<< " was not found in "
"topology library; using empty topology for this residue",
warn_context_);
IMP_NEW(CHARMMResidueTopology, residue, (restyp));
segment->add_residue(residue);
}
}
topology->add_segment(segment);
}
// keep clang happy
bool dumped = false;
IMP_IF_LOG(VERBOSE) {
dumped = true;
warn_context_.dump_warnings();
}
if (!dumped) {
warn_context_.clear_warnings();
}
// Topology objects are not designed to be added into other containers
topology->set_was_used(true);
return topology.release();
}
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())));
}
void Residue::set_residue_type(ResidueType t) {
get_particle()->set_value(get_residue_type_key(), t.get_index());
}
