core::io::ResidueInformation Class Reference

#include <ResidueInformation.hh>

Public Member Functions
	ResidueInformation ()
	default constructor to initialize all values More...
	ResidueInformation (AtomInformation const &ai)
	Initialize the resName/chainID/etc. data from an atom, but do not add the atom to the atoms_ array. More...
bool	operator== (ResidueInformation const &that) const
bool	operator!= (ResidueInformation const &that) const
std::string const &	resName () const
char	chainID () const
int	resSeq () const
char	iCode () const
int	terCount () const
std::string const &	segmentID () const
std::string const &	rosetta_resName () const
void	resName (std::string const &setting)
void	chainID (char setting)
void	resSeq (int setting)
void	iCode (char setting)
void	terCount (int setting)
void	set_xyz (std::string const &atomname, Vector const &vect)
void	set_temp (std::string const &atomname, core::Real const &val)
void	segmentID (std::string const &setting)
utility::vector1 < AtomInformation > const &	atoms () const
void	append_atom (AtomInformation const &atoms)
void	rename_atom (std::string const &orig_name, std::string const &new_name)
void	append_atoms (ResidueInformation const &source)
std::map< std::string, Vector > const &	xyz () const
	A convenience accessor for the coordinates. More...
std::map< std::string, core::Real > const &	temps () const
std::string	resid () const
	Returns a short, printable designation for this residue. More...

Private Attributes
std::string	resName_
	For now, all member names have the same names as fields in PDB standard. More...
char	chainID_
int	resSeq_
char	iCode_
int	terCount_
utility::vector1< AtomInformation >	atoms_
std::map< std::string, Vector >	xyz_
std::map< std::string, core::Real >	temps_
std::string	segmentID_
std::string	rosetta_resName_
	Some Residues have a different three letter code in Rosetta versus the PDB. Store that here. More...

Detailed Description

Subset of data from "ATOM" lines that is shared by all atoms in a residue.
This class is used for temporary storage of information during Pose building and "unbuilding".

Constructor & Destructor Documentation

core::io::ResidueInformation::ResidueInformation

(

)

default constructor to initialize all values

core::io::ResidueInformation::ResidueInformation

(

AtomInformation const &

ai

)

Initialize the resName/chainID/etc. data from an atom, but do not add the atom to the atoms_ array.

References resName(), and core::io::AtomInformation::resName.

Member Function Documentation

void core::io::ResidueInformation::append_atom

(

AtomInformation const &

atoms

)

References atoms_, core::io::AtomInformation::name, core::io::AtomInformation::temperature, temps_, core::io::AtomInformation::x, xyz_, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_merge_residues_as_necessary().

void core::io::ResidueInformation::append_atoms

(

ResidueInformation const &

source

)

Append all the atoms from the source residue, updating their resName so that they all have the same resName, and so that the xyz_ and temps_ maps are updated.

References atoms_, core::io::AtomInformation::name, core::io::AtomInformation::resName, resName_, core::io::AtomInformation::temperature, temps_, core::io::AtomInformation::x, xyz_, core::io::AtomInformation::y, and core::io::AtomInformation::z.

utility::vector1< AtomInformation > const & core::io::ResidueInformation::atoms

(

)

const

References atoms_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), core::io::pose_from_sfr::remap_names_on_geometry(), and protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates().

char core::io::ResidueInformation::chainID

(

)

const

References chainID_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_HELIXInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_SHEETInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini(), and core::io::pose_from_sfr::remap_names_on_geometry().

void core::io::ResidueInformation::chainID

(

char

setting

)

References chainID_.

char core::io::ResidueInformation::iCode

(

)

const

References iCode_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_HELIXInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_SHEETInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), and core::io::pose_from_sfr::remap_names_on_geometry().

void core::io::ResidueInformation::iCode

(

char

setting

)

References iCode_.

bool core::io::ResidueInformation::operator!=

(

ResidueInformation const &

that

)

const

bool core::io::ResidueInformation::operator==

(

ResidueInformation const &

that

)

const

References chainID_, iCode_, resName_, resSeq_, and terCount_.

void core::io::ResidueInformation::rename_atom	(	std::string const &	orig_name,
		std::string const &	new_name
	)

References atoms_, temps_, and xyz_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard().

std::string core::io::ResidueInformation::resid

(

)

const

Returns a short, printable designation for this residue.

References chainID_, iCode_, and resSeq_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pass_4_redo_termini().

std::string const & core::io::ResidueInformation::resName

(

)

const

References resName_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_HELIXInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_SHEETInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::remap_names_on_geometry(), and ResidueInformation().

void core::io::ResidueInformation::resName

(

std::string const &

setting

)

References atoms_, resName_, and rosetta_resName_.

int core::io::ResidueInformation::resSeq

(

)

const

References resSeq_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_HELIXInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_SHEETInformation(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_from_sfr::remap_names_on_geometry(), and core::io::reorder_glycan_residues().

void core::io::ResidueInformation::resSeq

(

int

setting

)

References resSeq_.

std::string const & core::io::ResidueInformation::rosetta_resName

(

)

const

References rosetta_resName_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types().

std::string const & core::io::ResidueInformation::segmentID

(

)

const

References segmentID_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information().

void core::io::ResidueInformation::segmentID

(

std::string const &

setting

)

References segmentID_.

void core::io::ResidueInformation::set_temp	(	std::string const &	atomname,
		core::Real const &	val
	)

References temps_, and protocols::hybridization::val.

void core::io::ResidueInformation::set_xyz	(	std::string const &	atomname,
		Vector const &	vect
	)

References xyz_.

std::map< std::string, core::Real > const & core::io::ResidueInformation::temps

(

)

const

References temps_.

int core::io::ResidueInformation::terCount

(

)

const

References terCount_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information().

void core::io::ResidueInformation::terCount

(

int

setting

)

References terCount_.

std::map< std::string, Vector > const & core::io::ResidueInformation::xyz

(

)

const

A convenience accessor for the coordinates.

References xyz_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::remap_names_on_geometry(), and core::io::pose_from_sfr::score_mapping().

Member Data Documentation

utility::vector1< AtomInformation > core::io::ResidueInformation::atoms_

private

Referenced by append_atom(), append_atoms(), atoms(), rename_atom(), and resName().

char core::io::ResidueInformation::chainID_

private

Referenced by chainID(), operator==(), and resid().

char core::io::ResidueInformation::iCode_

private

Referenced by iCode(), operator==(), and resid().

std::string core::io::ResidueInformation::resName_

private

For now, all member names have the same names as fields in PDB standard.

Referenced by append_atoms(), operator==(), and resName().

int core::io::ResidueInformation::resSeq_

private

Referenced by operator==(), resid(), and resSeq().

std::string core::io::ResidueInformation::rosetta_resName_

private

Some Residues have a different three letter code in Rosetta versus the PDB. Store that here.

Referenced by resName(), and rosetta_resName().

std::string core::io::ResidueInformation::segmentID_

private

Referenced by segmentID().

std::map< std::string, core::Real > core::io::ResidueInformation::temps_

private

Referenced by append_atom(), append_atoms(), rename_atom(), set_temp(), and temps().

int core::io::ResidueInformation::terCount_

private

Referenced by operator==(), and terCount().

std::map< std::string, Vector > core::io::ResidueInformation::xyz_

private

Referenced by append_atom(), append_atoms(), rename_atom(), set_xyz(), and xyz().

---

The documentation for this class was generated from the following files:

• src/core/io/ResidueInformation.hh
• src/core/io/ResidueInformation.cc