#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	matches (AtomInformation const &ai) const
	Would a ResidueInformation object created by ai be equal to this one? 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)

void	rosetta_resName (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

◆ ResidueInformation() [1/2]

core::io::ResidueInformation::ResidueInformation ( )

default constructor to initialize all values

◆ ResidueInformation() [2/2]

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

Member Function Documentation

◆ append_atom()

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_split_and_merge_residues_as_necessary().

◆ append_atoms()

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.

◆ atoms()

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::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::remap_names_on_geometry(), and protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates().

◆ chainID() [1/2]

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_link_record(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), 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().

◆ chainID() [2/2]

void core::io::ResidueInformation::chainID ( char setting )

References chainID_.

◆ iCode() [1/2]

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_link_record(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), and core::io::pose_from_sfr::remap_names_on_geometry().

◆ iCode() [2/2]

void core::io::ResidueInformation::iCode ( char setting )

References iCode_.

◆ matches()

bool core::io::ResidueInformation::matches ( AtomInformation const & ai ) const

Would a ResidueInformation object created by ai be equal to this one?

References core::io::AtomInformation::chainID, chainID_, core::io::AtomInformation::iCode, iCode_, core::io::AtomInformation::resName, resName_, core::io::AtomInformation::resSeq, resSeq_, core::io::AtomInformation::terCount, and terCount_.

◆ operator!=()

bool core::io::ResidueInformation::operator!= ( ResidueInformation const & that ) const

◆ operator==()

bool core::io::ResidueInformation::operator== ( ResidueInformation const & that ) const

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

◆ rename_atom()

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().

◆ resid()

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_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), 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::PoseFromSFRBuilder::pre_process_residue_type_information().

◆ resName() [1/2]

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_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pre_process_residue_type_information(), core::io::pose_from_sfr::remap_names_on_geometry(), and ResidueInformation().

◆ resName() [2/2]

void core::io::ResidueInformation::resName ( std::string const & setting )

References atoms_, resName_, and rosetta_resName_.

◆ resSeq() [1/2]

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_link_record(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::remap_names_on_geometry(), and core::io::reorder_glycan_residues().

◆ resSeq() [2/2]

void core::io::ResidueInformation::resSeq ( int setting )

References resSeq_.

◆ rosetta_resName() [1/2]

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

References rosetta_resName_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), and core::io::pose_from_sfr::PoseFromSFRBuilder::remember_unrecognized_res().

◆ rosetta_resName() [2/2]

void core::io::ResidueInformation::rosetta_resName ( std::string const & setting )

References rosetta_resName_.

◆ segmentID() [1/2]

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(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary().

◆ segmentID() [2/2]

void core::io::ResidueInformation::segmentID ( std::string const & setting )

References segmentID_.

◆ set_temp()

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

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

◆ set_xyz()

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

References xyz_.

◆ temps()

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

References temps_.

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

◆ terCount() [1/2]

int core::io::ResidueInformation::terCount ( ) const

References terCount_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), and core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary().

◆ terCount() [2/2]

void core::io::ResidueInformation::terCount ( int setting )

References terCount_.

◆ xyz()

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_quick_and_dirty_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::remap_names_on_geometry(), core::io::pose_from_sfr::PoseFromSFRBuilder::remember_unrecognized_res(), and core::io::pose_from_sfr::score_mapping().

Member Data Documentation

◆ atoms_

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

private

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

◆ chainID_

char core::io::ResidueInformation::chainID_

private

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

◆ iCode_

char core::io::ResidueInformation::iCode_

private

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

◆ resName_

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(), matches(), operator==(), and resName().

◆ resSeq_

int core::io::ResidueInformation::resSeq_

private

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

◆ rosetta_resName_

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().

◆ segmentID_

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

private

Referenced by segmentID().

◆ temps_

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

private

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

◆ terCount_

int core::io::ResidueInformation::terCount_

private

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

◆ xyz_

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ResidueInformation() [1/2]

◆ ResidueInformation() [2/2]

Member Function Documentation

◆ append_atom()

◆ append_atoms()

◆ atoms()

◆ chainID() [1/2]

◆ chainID() [2/2]

◆ iCode() [1/2]

◆ iCode() [2/2]

◆ matches()

◆ operator!=()

◆ operator==()

◆ rename_atom()

◆ resid()

◆ resName() [1/2]

◆ resName() [2/2]

◆ resSeq() [1/2]

◆ resSeq() [2/2]

◆ rosetta_resName() [1/2]

◆ rosetta_resName() [2/2]

◆ segmentID() [1/2]

◆ segmentID() [2/2]

◆ set_temp()

◆ set_xyz()

◆ temps()

◆ terCount() [1/2]

◆ terCount() [2/2]

◆ xyz()

Member Data Documentation

◆ atoms_

◆ chainID_

◆ iCode_

◆ resName_

◆ resSeq_

◆ rosetta_resName_

◆ segmentID_

◆ temps_

◆ terCount_

◆ xyz_