ResidueType.cc File Reference

Method definitions for ResidueType. More...

#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueSupport.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/Element.hh>
#include <core/chemical/ElementSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/MMAtomType.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.hh>
#include <core/chemical/RingConformerSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/gasteiger/GasteigerAtomTypeSet.hh>
#include <core/chemical/gasteiger/GasteigerAtomTypeData.hh>
#include <core/chemical/rna/RNA_ResidueType.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/NumericTraits.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/pH.OptionKeys.gen.hh>
#include <utility/PyAssert.hh>
#include <utility/vector1.hh>
#include <utility/graph/ring_detection.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <boost/graph/graph_utility.hpp>
#include <algorithm>

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

Functions
std::string	core::chemical::strip_whitespace (std::string const &name)
bool	core::chemical::retype_is_virtual (std::string const &element)
	Should the element be considered to be a virtual atom? More...
std::string	core::chemical::retype_get_element (VD const &vd, Atom const &a, ElementMap const &emap, AtomTypeSet const &atom_type_set)
bool	core::chemical::retype_is_aromatic (VD const &atom, ResidueGraph const &graph, ElementMap const &emap, AtomTypeSet const &atom_type_set)
	An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection. More...
std::ostream &	core::chemical::operator<< (std::ostream &output, ResidueType const &object_to_output)

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

Detailed Description

Method definitions for ResidueType.

Author

Phil Bradley Steven Combs Vikram K. Mulligan - properties for D-, beta- and other noncanonicals Jason W. Labonte (code related to lipids, carbohydrates, and other non-AAs)