residue_io.cc File Reference

helper methods for ResidueType input/output More...

#include <core/chemical/residue_io.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/residue_support.hh>
#include <core/chemical/Atom.hh>
#include <core/chemical/Bond.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/MMAtomType.hh>
#include <platform/types.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <numeric/conversions.hh>
#include <numeric/xyz.functions.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/Bound.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/keys/AutoKey.hh>
#include <utility/keys/SmallKeyVector.hh>
#include <boost/foreach.hpp>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/Dimension.hh>
#include <ObjexxFCL/DynamicIndexRange.hh>
#include <ObjexxFCL/FArray.hh>
#include <ObjexxFCL/FArray2D.hh>

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

Functions
id::AtomID	core::chemical::atom_id_from_icoor_line (std::string const name, ResidueType const &rsd)
	helper fxn More...
AtomIndices	core::chemical::define_mainchain_atoms (ResidueTypeOP rsd)
	If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER. More...
ResidueTypeOP	core::chemical::read_topology_file (std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types,chemical::ResidueTypeSetCAP rsd_type_set)
	virtual constructor for ResidueType objects More...
ResidueTypeOP	core::chemical::read_topology_file (utility::io::izstream &data, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types, chemical::ResidueTypeSetCAP rsd_type_set)
void	core::chemical::write_topology_file (ResidueType const &rsd, std::string filename="")
	writes a .params file from a given ResidueType object More...

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

Detailed Description

helper methods for ResidueType input/output

Author

Phil Bradley