ResidueType CHARMMParameters::parse_residue_line(const String &line,
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() < 3) {
IMP_THROW("Invalid RESI line: " << line, ValueException);
}
String curr_residue =
get_residue_name(split_results[1], translate_names_to_pdb);
if (ResidueType::get_key_exists(curr_residue)) {
return ResidueType(curr_residue);
} else {
// assume charmm is correct
return ResidueType(ResidueType::add_key(curr_residue));
}
}
Particle *residue_particle(Model *m, int residue_index, char ins_code,
const std::string &residue_type) {
Particle* p = new Particle(m);
std::string rn = residue_type;
boost::trim(rn);
if (rn.empty()) {
rn = "UNK";
}
ResidueType residue_name = ResidueType(rn);
// residue decorator
Residue::setup_particle(p, residue_name, residue_index, (int)ins_code);
p->set_name(residue_name.get_string());
return p;
}
double get_volume_from_residue_type(ResidueType rt) {
typedef std::pair<ResidueType, double> RP;
static const RP radii[] = {
RP(ResidueType("ALA"), 2.516), RP(ResidueType("ARG"), 3.244),
RP(ResidueType("ASN"), 2.887), RP(ResidueType("ASP"), 2.866),
RP(ResidueType("CYS"), 2.710), RP(ResidueType("GLN"), 3.008),
RP(ResidueType("GLU"), 2.997), RP(ResidueType("GLY"), 2.273),
RP(ResidueType("HIS"), 3.051), RP(ResidueType("ILE"), 3.047),
RP(ResidueType("LEU"), 3.052), RP(ResidueType("LYS"), 3.047),
RP(ResidueType("MET"), 3.068), RP(ResidueType("PHE"), 3.259),
RP(ResidueType("PRO"), 2.780), RP(ResidueType("SER"), 2.609),
RP(ResidueType("THR"), 2.799), RP(ResidueType("TRP"), 3.456),
RP(ResidueType("TYR"), 3.318), RP(ResidueType("VAL"), 2.888)};
static const boost::unordered_map<ResidueType, double> radii_map(
radii, radii + sizeof(radii) / sizeof(RP));
if (radii_map.find(rt) == radii_map.end()) {
IMP_THROW("Can't approximate volume of non-standard residue " << rt,
ValueException);
}
double r = radii_map.find(rt)->second;
IMP_INTERNAL_CHECK(r > 0, "Read garbage r for " << rt);
return algebra::get_volume(
algebra::Sphere3D(algebra::get_zero_vector_d<3>(), r));
}
