void read_pdb(Model *model, const std::string file,
std::vector<std::string>& pdb_file_names,
std::vector<IMP::Particles>& particles_vec,
bool residue_level, bool heavy_atoms_only, int multi_model_pdb,
bool explicit_water) {
IMP::atom::Hierarchies mhds;
IMP::atom::PDBSelector* selector;
if (residue_level) // read CA only
selector = new IMP::atom::CAlphaPDBSelector();
else if (heavy_atoms_only) { // read without hydrogens
if (explicit_water)
selector = new IMP::atom::NonHydrogenPDBSelector();
else
selector = new IMP::atom::NonWaterNonHydrogenPDBSelector();
} else { // read with hydrogens
if (explicit_water)
selector = new IMP::atom::NonAlternativePDBSelector();
else
selector = new IMP::atom::NonWaterPDBSelector();
}
if (multi_model_pdb == 2) {
mhds = read_multimodel_pdb(file, model, selector, true);
} else {
if (multi_model_pdb == 3) {
IMP::atom::Hierarchy mhd =
IMP::atom::read_pdb(file, model, selector, false, true);
mhds.push_back(mhd);
} else {
IMP::atom::Hierarchy mhd =
IMP::atom::read_pdb(file, model, selector, true, true);
mhds.push_back(mhd);
}
}
for (unsigned int h_index = 0; h_index < mhds.size(); h_index++) {
IMP::ParticlesTemp ps =
get_by_type(mhds[h_index], IMP::atom::ATOM_TYPE);
if (ps.size() > 0) { // pdb file
std::string pdb_id = file;
if (mhds.size() > 1) {
pdb_id = trim_extension(file) + "_m" +
std::string(boost::lexical_cast<std::string>(h_index + 1)) +
".pdb";
}
pdb_file_names.push_back(pdb_id);
particles_vec.push_back(IMP::get_as<IMP::Particles>(ps));
if (mhds.size() > 1) {
IMP_LOG_TERSE(ps.size() << " atoms were read from PDB file " << file
<< " MODEL " << h_index + 1 << std::endl);
} else {
IMP_LOG_TERSE(ps.size() << " atoms were read from PDB file " << file
<< std::endl);
}
}
}
}
