ResidueTypeSet.cc File Reference

ResidueTypeSet class. More...

#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/residue_io.hh>
#include <core/chemical/adduct_util.hh>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <fstream>
#include <string>
#include <sstream>
#include <set>
#include <algorithm>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/pH.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/chemical/orbitals/AssignOrbitals.hh>
#include <boost/foreach.hpp>
#include <utility/vector1.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::chemical

Variables
static basic::Tracer	core::chemical::tr ("core.chemical.ResidueTypeSet")

Detailed Description

ResidueTypeSet class.

This class is responsible for iterating through the sets of residue types, including, but not limited to, amino acids, nucleic acids, peptoid residues, and monosaccharides. It first reads through a file that contains the location of residue types in the database. At the beginning of that file are the atom types, mm atom types, element sets, and orbital types that will be used. The sets are all for fa_standard. If a new type of atom are added for residues, this is where they would be added. Once it assigns the types, it then reads in extra residue params that are passed through the command line. Finally, patches are applied to all residues added.

Author

Phil Bradley Steven Combs - these comments