GlobalResidueTypeSet.cc File Reference

GlobalResidueTypeSet class. More...

#include <core/chemical/GlobalResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSetCache.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/chemical/Metapatch.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/MergeBehaviorManager.hh>
#include <core/chemical/sdf/MolFileIOReader.hh>
#include <core/chemical/residue_io.hh>
#include <core/chemical/adduct_util.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueDatabaseIO.hh>
#include <core/chemical/Orbital.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/residue_support.hh>
#include <core/chemical/mmCIF/mmCIFParser.hh>
#include <basic/database/open.hh>
#include <basic/database/sql_utils.hh>
#include <basic/options/option.hh>
#include <utility/thread/backwards_thread_local.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/sql_database/types.hh>
#include <utility/pointer/memory.hh>
#include <fstream>
#include <string>
#include <set>
#include <algorithm>
#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 <basic/options/keys/packing.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/file/file_sys_util.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::chemical

Functions
static basic::Tracer	core::chemical::TR ("core.chemical.GlobalResidueTypeSet")
bool	core::chemical::sort_patchop_by_name (PatchOP p, PatchOP q)

Detailed Description

GlobalResidueTypeSet 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 is 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. Then, the class reads in patches. There can be an exponentially large number of possible residue types that can be built from base_residue_types and patch applications – they are created on the fly when requested by accessor functions like has_name() and get_all_types_with_variants_aa(). Later, the class can accept 'unpatchable residue types' (to which patches will not be added).

Author

Phil Bradley Steven Combs - these comments Rocco Moretti - helper functions for more efficient GlobalResidueTypeSet use Rhiju Das - 'on-the-fly' residue type generation; allowing unpatchable residue types; ResidueTypeSetCache.