core::io::pdb::FileDataOptions Class Reference

#include <file_data_options.hh>

Public Member Functions
	FileDataOptions ()
virtual	~FileDataOptions ()
virtual void	parse_my_tag (utility::tag::TagCOP tag)
virtual std::string	type () const
std::string	check_if_residues_are_Ntermini () const
std::string	check_if_residues_are_Ctermini () const
bool	exit_if_missing_heavy_atoms () const
bool	ignore_unrecognized_res () const
bool	ignore_waters () const
bool	ignore_zero_occupancy () const
bool	keep_input_protonation_state () const
bool	preserve_header () const
bool	preserve_crystinfo () const
bool	missing_dens_as_jump () const
bool	randomize_missing_coords () const
bool	remember_unrecognized_res () const
bool	remember_unrecognized_water () const
bool	write_pdb_link_records () const
std::string const &	chains_whose_residues_are_separate_chemical_entities () const
void	set_check_if_residues_are_Ntermini (std::string check_if_residues_are_Ntermini)
void	set_check_if_residues_are_Ctermini (std::string check_if_residues_are_Ctermini)
void	set_exit_if_missing_heavy_atoms (bool exit_if_missing_heavy_atoms)
void	set_ignore_unrecognized_res (bool ignore_unrecognized_res)
void	set_ignore_waters (bool ignore_waters)
void	set_ignore_zero_occupancy (bool ignore_zero_occupancy)
void	set_keep_input_protonation_state (bool keep_input_protonation_state)
void	set_preserve_header (bool preserve_header)
void	set_preserve_crystinfo (bool preserve_crystinfo)
void	set_missing_dens_as_jump (bool missing_dens_as_jump)
void	set_randomize_missing_coords (bool randomize_missing_coords)
void	set_remember_unrecognized_res (bool remember_unrecognized_res)
void	set_remember_unrecognized_water (bool remember_unrecognized_water)
void	set_write_pdb_link_records (bool setting)
void	set_chains_whose_residues_are_separate_chemical_entities (std::string const &setting)

Private Member Functions
void	init_from_options ()
	Assigns user specified values to primitive members using command line options. More...

Private Attributes
std::string	check_if_residues_are_Ntermini_
std::string	check_if_residues_are_Ctermini_
bool	exit_if_missing_heavy_atoms_
bool	ignore_unrecognized_res_
bool	ignore_waters_
bool	ignore_zero_occupancy_
bool	keep_input_protonation_state_
bool	preserve_header_
bool	preserve_crystinfo_
bool	missing_dens_as_jump_
bool	randomize_missing_coords_
bool	remember_unrecognized_res_
bool	remember_unrecognized_water_
bool	write_pdb_link_records_
std::string	chains_whose_residues_are_separate_chemical_entities_

Constructor & Destructor Documentation

core::io::pdb::FileDataOptions::FileDataOptions

(

)

References init_from_options().

core::io::pdb::FileDataOptions::~FileDataOptions ( )

virtual

Member Function Documentation

std::string const & core::io::pdb::FileDataOptions::chains_whose_residues_are_separate_chemical_entities

(

)

const

References chains_whose_residues_are_separate_chemical_entities_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_chains_whose_residues_are_separate_chemical_entities().

std::string core::io::pdb::FileDataOptions::check_if_residues_are_Ctermini

(

)

const

References check_if_residues_are_Ctermini_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_check_if_residues_are_Ctermini().

std::string core::io::pdb::FileDataOptions::check_if_residues_are_Ntermini

(

)

const

References check_if_residues_are_Ntermini_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_check_if_residues_are_Ntermini().

bool core::io::pdb::FileDataOptions::exit_if_missing_heavy_atoms

(

)

const

References exit_if_missing_heavy_atoms_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_exit_if_missing_heavy_atoms().

bool core::io::pdb::FileDataOptions::ignore_unrecognized_res

(

)

const

References ignore_unrecognized_res_.

Referenced by core::io::pdb::is_residue_type_recognized(), and set_ignore_unrecognized_res().

bool core::io::pdb::FileDataOptions::ignore_waters

(

)

const

References ignore_waters_.

Referenced by core::io::pdb::is_residue_type_recognized(), and set_ignore_waters().

bool core::io::pdb::FileDataOptions::ignore_zero_occupancy

(

)

const

References ignore_zero_occupancy_.

Referenced by set_ignore_zero_occupancy(), and core::io::pdb::FileData::update_atom_information_based_on_occupancy().

void core::io::pdb::FileDataOptions::init_from_options ( )

private

Assigns user specified values to primitive members using command line options.

References in::Ctermini, run::exit_if_missing_heavy_atoms, in::ignore_unrecognized_res, in::ignore_waters, run::ignore_zero_occupancy, pH::keep_input_protonation_state, in::missing_density_to_jump, in::Ntermini, option, in::preserve_crystinfo, run::preserve_header, run::randomize_missing_coords, in::remember_unrecognized_res, in::remember_unrecognized_water, set_chains_whose_residues_are_separate_chemical_entities(), set_check_if_residues_are_Ctermini(), set_check_if_residues_are_Ntermini(), set_exit_if_missing_heavy_atoms(), set_ignore_unrecognized_res(), set_ignore_waters(), set_ignore_zero_occupancy(), set_keep_input_protonation_state(), set_missing_dens_as_jump(), set_preserve_crystinfo(), set_preserve_header(), set_randomize_missing_coords(), set_remember_unrecognized_res(), set_remember_unrecognized_water(), set_write_pdb_link_records(), in::file::treat_residues_in_these_chains_as_separate_chemical_entities, and out::file::write_pdb_link_records.

Referenced by FileDataOptions().

bool core::io::pdb::FileDataOptions::keep_input_protonation_state

(

)

const

References keep_input_protonation_state_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_keep_input_protonation_state().

bool core::io::pdb::FileDataOptions::missing_dens_as_jump

(

)

const

References missing_dens_as_jump_.

Referenced by core::io::pdb::build_pose_as_is1(), and set_missing_dens_as_jump().

void core::io::pdb::FileDataOptions::parse_my_tag ( utility::tag::TagCOP  tag )

virtual

Implements basic::resource_manager::ResourceOptions.

Reimplemented in core::import_pose::ImportPoseOptions, and core::io::pdb::PDB_DReaderOptions.

References set_chains_whose_residues_are_separate_chemical_entities(), set_check_if_residues_are_Ctermini(), set_check_if_residues_are_Ntermini(), set_exit_if_missing_heavy_atoms(), set_ignore_unrecognized_res(), set_ignore_waters(), set_ignore_zero_occupancy(), set_keep_input_protonation_state(), set_missing_dens_as_jump(), set_preserve_crystinfo(), set_preserve_header(), set_randomize_missing_coords(), set_remember_unrecognized_res(), set_remember_unrecognized_water(), and set_write_pdb_link_records().

Referenced by core::io::pdb::PDB_DReaderOptions::parse_my_tag().

bool core::io::pdb::FileDataOptions::preserve_crystinfo

(

)

const

References preserve_crystinfo_.

Referenced by core::io::pdb::build_pose_as_is1(), core::io::pdb::FileData::init_from_pose(), and set_preserve_crystinfo().

bool core::io::pdb::FileDataOptions::preserve_header

(

)

const

References preserve_header_.

Referenced by core::io::pdb::build_pose_as_is1(), core::io::pdb::FileData::init_from_pose(), and set_preserve_header().

bool core::io::pdb::FileDataOptions::randomize_missing_coords

(

)

const

References randomize_missing_coords_.

Referenced by set_randomize_missing_coords(), and core::io::pdb::FileData::update_atom_information_based_on_occupancy().

bool core::io::pdb::FileDataOptions::remember_unrecognized_res

(

)

const

References remember_unrecognized_res_.

Referenced by core::io::pdb::is_residue_type_recognized(), and set_remember_unrecognized_res().

bool core::io::pdb::FileDataOptions::remember_unrecognized_water

(

)

const

References remember_unrecognized_water_.

Referenced by core::io::pdb::is_residue_type_recognized(), and set_remember_unrecognized_water().

void core::io::pdb::FileDataOptions::set_chains_whose_residues_are_separate_chemical_entities

(

std::string const &

setting

)

References chains_whose_residues_are_separate_chemical_entities(), and chains_whose_residues_are_separate_chemical_entities_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_check_if_residues_are_Ctermini

(

std::string

check_if_residues_are_Ctermini

)

References check_if_residues_are_Ctermini(), and check_if_residues_are_Ctermini_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_check_if_residues_are_Ntermini

(

std::string

check_if_residues_are_Ntermini

)

References check_if_residues_are_Ntermini(), and check_if_residues_are_Ntermini_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_exit_if_missing_heavy_atoms

(

bool

exit_if_missing_heavy_atoms

)

References exit_if_missing_heavy_atoms(), and exit_if_missing_heavy_atoms_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_unrecognized_res

(

bool

ignore_unrecognized_res

)

References ignore_unrecognized_res(), and ignore_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_waters

(

bool

ignore_waters

)

References ignore_waters(), and ignore_waters_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_zero_occupancy

(

bool

ignore_zero_occupancy

)

References ignore_zero_occupancy(), and ignore_zero_occupancy_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_keep_input_protonation_state

(

bool

keep_input_protonation_state

)

References keep_input_protonation_state(), and keep_input_protonation_state_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_missing_dens_as_jump

(

bool

missing_dens_as_jump

)

References missing_dens_as_jump(), and missing_dens_as_jump_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_preserve_crystinfo

(

bool

preserve_crystinfo

)

References preserve_crystinfo(), and preserve_crystinfo_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_preserve_header

(

bool

preserve_header

)

References preserve_header(), and preserve_header_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_randomize_missing_coords

(

bool

randomize_missing_coords

)

References randomize_missing_coords(), and randomize_missing_coords_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_remember_unrecognized_res

(

bool

remember_unrecognized_res

)

References remember_unrecognized_res(), and remember_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_remember_unrecognized_water

(

bool

remember_unrecognized_water

)

References remember_unrecognized_water(), and remember_unrecognized_water_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_write_pdb_link_records

(

bool

setting

)

References write_pdb_link_records_.

Referenced by init_from_options(), and parse_my_tag().

std::string core::io::pdb::FileDataOptions::type ( ) const

virtual

Implements basic::resource_manager::ResourceOptions.

Reimplemented in core::import_pose::ImportPoseOptions, and core::io::pdb::PDB_DReaderOptions.

bool core::io::pdb::FileDataOptions::write_pdb_link_records

(

)

const

References write_pdb_link_records_.

Referenced by core::io::pdb::FileData::init_from_pose().

Member Data Documentation

std::string core::io::pdb::FileDataOptions::chains_whose_residues_are_separate_chemical_entities_

private

Referenced by chains_whose_residues_are_separate_chemical_entities(), and set_chains_whose_residues_are_separate_chemical_entities().

std::string core::io::pdb::FileDataOptions::check_if_residues_are_Ctermini_

private

Referenced by check_if_residues_are_Ctermini(), and set_check_if_residues_are_Ctermini().

std::string core::io::pdb::FileDataOptions::check_if_residues_are_Ntermini_

private

Referenced by check_if_residues_are_Ntermini(), and set_check_if_residues_are_Ntermini().

bool core::io::pdb::FileDataOptions::exit_if_missing_heavy_atoms_

private

Referenced by exit_if_missing_heavy_atoms(), and set_exit_if_missing_heavy_atoms().

bool core::io::pdb::FileDataOptions::ignore_unrecognized_res_

private

Referenced by ignore_unrecognized_res(), and set_ignore_unrecognized_res().

bool core::io::pdb::FileDataOptions::ignore_waters_

private

Referenced by ignore_waters(), and set_ignore_waters().

bool core::io::pdb::FileDataOptions::ignore_zero_occupancy_

private

Referenced by ignore_zero_occupancy(), and set_ignore_zero_occupancy().

bool core::io::pdb::FileDataOptions::keep_input_protonation_state_

private

Referenced by keep_input_protonation_state(), and set_keep_input_protonation_state().

bool core::io::pdb::FileDataOptions::missing_dens_as_jump_

private

Referenced by missing_dens_as_jump(), and set_missing_dens_as_jump().

bool core::io::pdb::FileDataOptions::preserve_crystinfo_

private

Referenced by preserve_crystinfo(), and set_preserve_crystinfo().

bool core::io::pdb::FileDataOptions::preserve_header_

private

Referenced by preserve_header(), and set_preserve_header().

bool core::io::pdb::FileDataOptions::randomize_missing_coords_

private

Referenced by randomize_missing_coords(), and set_randomize_missing_coords().

bool core::io::pdb::FileDataOptions::remember_unrecognized_res_

private

Referenced by remember_unrecognized_res(), and set_remember_unrecognized_res().

bool core::io::pdb::FileDataOptions::remember_unrecognized_water_

private

Referenced by remember_unrecognized_water(), and set_remember_unrecognized_water().

bool core::io::pdb::FileDataOptions::write_pdb_link_records_

private

Referenced by set_write_pdb_link_records(), and write_pdb_link_records().

---

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

• symlinks/rosetta/src/core/io/pdb/file_data_options.hh
• symlinks/rosetta/src/core/io/pdb/file_data_options.cc