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residue_io.cc File Reference

helper methods for ResidueType input/output More...

#include <core/chemical/residue_io.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/ResidueProperties.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/residue_support.hh>
#include <core/chemical/Atom.hh>
#include <core/chemical/util.hh>
#include <core/chemical/Bond.hh>
#include <core/chemical/Elements.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/MMAtomType.hh>
#include <core/chemical/rotamers/RotamerLibrarySpecificationFactory.hh>
#include <core/chemical/rotamers/RotamerLibrarySpecification.hh>
#include <core/chemical/rotamers/DunbrackRotamerLibrarySpecification.hh>
#include <core/chemical/rotamers/PDBRotamerLibrarySpecification.hh>
#include <core/chemical/rotamers/NCAARotamerLibrarySpecification.hh>
#include <core/chemical/rings/RingSaturationType.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.fwd.hh>
#include <core/kinematics/Stub.hh>
#include <basic/database/open.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <numeric/conversions.hh>
#include <numeric/constants.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <boost/graph/graphviz.hpp>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <sstream>

Classes

class  core::chemical::GraphvizPropertyWriter
 Callback class for write_graphviz - outputs properties for the nodes and edges. More...
 

Namespaces

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

Functions

static basic::Tracer core::chemical::tr ("core.chemical")
 
MutableResidueTypeOP core::chemical::read_topology_file (std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set)
 function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set More...
 
MutableResidueTypeOP core::chemical::read_topology_file (utility::io::izstream &istream, chemical::ResidueTypeSetCOP rsd_type_set)
 function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
 
MutableResidueTypeOP core::chemical::read_topology_file (std::istream &istream, std::string const &filename,chemical::ResidueTypeSetCOP rsd_type_set)
 function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
 
MutableResidueTypeOP 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)
 function to convert params files into ResidueType objects (repackages string filename into istream) More...
 
MutableResidueTypeOP core::chemical::read_topology_file (std::istream &data, std::string const &filename,chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types)
 main function to convert params files into ResidueType objects More...
 
void core::chemical::write_topology_file (ResidueType const &rsd, std::string filename="")
 writes a .params file from a given ResidueType object More...
 
void core::chemical::write_graphviz (ResidueType const &rsd, std::ostream &out, bool header)
 Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanitory message will be printed first. More...
 
void core::chemical::write_graphviz (MutableResidueType const &rsd, std::ostream &out, bool header)
 
void core::chemical::set_up_mapfile_reassignments_from_commandline (ResidueTypeBaseOP rsd)
 Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides. More...
 
void core::chemical::setup_atom_type_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, std::string > &atom_type_reassignments)
 
void core::chemical::setup_atomic_charge_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, Real > &atomic_charge_reassignments)
 
void core::chemical::setup_icoor_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, utility::vector1< std::string > > &icoor_reassignments)
 
void core::chemical::apply_symm_gly_corrections (std::string const &child_atom, core::Real &phi, core::Real &, core::Real &d, std::string &, std::string &, std::string &torsion_atom)
 Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
 

Detailed Description

helper methods for ResidueType input/output

Author
Phil Bradley