/// \brief Save the specified coord to the specified Boost Property Tree ptree
///
/// \relates coord
void cath::geom::save_to_ptree(ptree &arg_ptree, ///< The ptree to which the coord should be saved
const coord &arg_coord ///< The coord to be saved
) {
arg_ptree.put( "x", arg_coord.get_x() );
arg_ptree.put( "y", arg_coord.get_y() );
arg_ptree.put( "z", arg_coord.get_z() );
}
/// \brief TODOCUMENT
///
/// \relates pdb_atom
ostream & cath::file::write_pdb_file_entry(ostream &arg_os, ///< TODOCUMENT
const residue_id &arg_res_id, ///< TODOCUMENT
const pdb_atom &arg_pdb_atom ///< TODOCUMENT
) {
// Sanity check the inputs
if ( arg_res_id.get_residue_name().is_null() ) {
BOOST_THROW_EXCEPTION(invalid_argument_exception("Empty residue_name in cath::write_pdb_file_entry()"));
}
// Grab the necessary data
const coord atom_coord = arg_pdb_atom.get_coord();
const string residue_name_with_insert_or_space = make_residue_name_string_with_insert_or_space(
arg_res_id.get_residue_name()
);
// Output the entry to a temporary ostringstream
// (to avoid needlessly messing around with the formatting options of the ostream)
ostringstream atom_ss;
// Comments with PDB format documentation
// (http://www.wwpdb.org/documentation/format33/sect9.html#ATOM)
atom_ss << left;
atom_ss << setw( 6 ) << arg_pdb_atom.get_record_type(); // 1 - 6 Record name "ATOM " or "HETATM"
atom_ss << right;
atom_ss << setw( 5 ) << arg_pdb_atom.get_atom_serial(); // 7 - 11 Integer serial Atom serial number.
atom_ss << " ";
atom_ss << setw( 4 ) << arg_pdb_atom.get_element_type_untrimmed(); // 13 - 16 Atom name Atom name.
atom_ss << arg_pdb_atom.get_alt_locn(); // 17 Character altLoc Alternate location indicator.
atom_ss << get_amino_acid_code( arg_pdb_atom ); // 18 - 20 Residue name resName Residue name.
atom_ss << " ";
atom_ss << arg_res_id.get_chain_label(); // 22 Character chainID Chain identifier.
// 23 - 26 Integer resSeq Residue sequence number.
atom_ss << setw( 5 ) << residue_name_with_insert_or_space; // 27 AChar iCode Code for insertion of residues.
atom_ss << " ";
atom_ss << fixed << setprecision( 3 );
atom_ss << setw( 8 ) << atom_coord.get_x(); // 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms.
atom_ss << setw( 8 ) << atom_coord.get_y(); // 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms.
atom_ss << setw( 8 ) << atom_coord.get_z(); // 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms.
atom_ss << fixed << setprecision( 2 );
atom_ss << setw( 6 ) << arg_pdb_atom.get_occupancy(); // 55 - 60 Real(6.2) occupancy Occupancy.
atom_ss << setw( 6 ) << arg_pdb_atom.get_temp_factor(); // 61 - 66 Real(6.2) tempFactor Temperature factor.
// 77 - 78 LString(2) element Element symbol, right-justified.
// 79 - 80 LString(2) charge Charge on the atom.
// Output the result to the ostream and return it
arg_os << atom_ss.str();
return arg_os;
}