#include <StructFileRepOptions.hh>

Inheritance diagram for core::io::StructFileRepOptions:

Public Member Functions
	StructFileRepOptions ()
	Constructor that takes default values from the global OptionCollection object, basic::options::option. More...

	StructFileRepOptions (utility::options::OptionCollection const &options)
	Constructor that takes default values from a provided OptionCollection object. More...

	~StructFileRepOptions () override

virtual StructFileRepOptionsOP	clone () const
	Copy this object and return an owning pointer to the copy. More...

virtual void	parse_my_tag (utility::tag::TagCOP tag)

virtual std::string	type () const

std::string const &	check_if_residues_are_Ntermini () const

std::string const &	check_if_residues_are_Ctermini () const

bool	skip_connect_info () const

core::Real	connect_info_cutoff () const

bool	do_not_autoassign_SS () const

bool	exit_if_missing_heavy_atoms () const

bool	fold_tree_io () const

bool	ignore_unrecognized_res () const

bool	ignore_sugars () const

bool	ignore_waters () const

bool	ignore_zero_occupancy () const

bool	guarantee_no_DNA () const

bool	keep_input_protonation_state () const

bool	preserve_header () const

std::string const &	pdb_author () const

bool	preserve_crystinfo () const

bool	missing_dens_as_jump () const

bool	no_chainend_ter () const

bool	no_detect_pseudobonds () const

bool	no_output_cen () const

bool	normalize_to_thk () const

bool	output_secondary_structure () const

bool	output_torsions () const

bool	output_virtual () const

bool	output_virtual_zero_occ () const

bool	output_only_asymmetric_unit () const

bool	pdb_parents () const

bool	per_chain_renumbering () const

bool	randomize_missing_coords () const

bool	remember_unrecognized_res () const

bool	remember_unrecognized_water () const

bool	renumber_pdb () const

bool	read_only_ATOM_entries () const

bool	suppress_zero_occ_pdb_output () const

bool	auto_detect_glycan_connections () const

bool	write_glycan_pdb_codes () const

bool	output_alternate_atomids () const

bool	output_ligands_as_separate_chains () const

bool	maintain_links () const

core::Real	max_bond_length () const

core::Real	min_bond_length () const

bool	use_pdb_format_HETNAM_records () const

bool	write_pdb_title_section_records () const

bool	write_pdb_link_records () const

bool	write_pdb_parametric_info () const

bool	write_all_connect_info () const

bool	write_seqres_records () const

std::string const &	chains_whose_residues_are_separate_chemical_entities () const

utility::vector1< std::string > const &	residues_for_atom_name_remapping () const

bool	pdb_comments () const

bool	show_all_fixes () const

bool	constraints_from_link_records () const

bool	output_pose_energies_table () const

bool	output_pose_cache () const

bool	integration_test_mode () const

bool	mmtf_extra_data_io () const

void	set_check_if_residues_are_Ntermini (std::string const &check_if_residues_are_Ntermini)

void	set_check_if_residues_are_Ctermini (std::string const &check_if_residues_are_Ctermini)

void	set_skip_connect_info (bool const skip_connect_info)

void	set_connect_info_cutoff (core::Real const &connect_info_cutoff)

void	set_do_not_autoassign_SS (bool const do_not_autoassign_SS)

void	set_exit_if_missing_heavy_atoms (bool const exit_if_missing_heavy_atoms)

void	set_fold_tree_io (bool const fold_tree_io)

void	set_ignore_unrecognized_res (bool const ignore_unrecognized_res)

void	set_ignore_sugars (bool const setting)

void	set_ignore_waters (bool const ignore_waters)

void	set_ignore_zero_occupancy (bool const ignore_zero_occupancy)

void	set_guarantee_no_DNA (bool const guarantee_no_DNA)

void	set_keep_input_protonation_state (bool const keep_input_protonation_state)

void	set_preserve_header (bool const preserve_header)

void	set_pdb_author (std::string const &pdb_author)

void	set_preserve_crystinfo (bool const preserve_crystinfo)

void	set_missing_dens_as_jump (bool const missing_dens_as_jump)

void	set_no_chainend_ter (bool const no_chainend_ter)

void	set_no_detect_pseudobonds (bool const setting)

void	set_no_output_cen (bool const no_output_cen)

void	set_normalize_to_thk (bool const normalize_to_thk)

void	set_output_secondary_structure (bool const output_secondary_structure)

void	set_output_torsions (bool const output_torsions)

void	set_output_virtual (bool const output_virtual)

void	set_output_virtual_zero_occ (bool const output_virtual_zero_occ)

void	set_output_only_asymmetric_unit (bool const output_only_asymmetric_unit)

void	set_pdb_parents (bool const pdb_parents)

void	set_per_chain_renumbering (bool const per_chain_renumbering)

void	set_randomize_missing_coords (bool const randomize_missing_coords)

void	set_remember_unrecognized_res (bool const remember_unrecognized_res)

void	set_remember_unrecognized_water (bool const remember_unrecognized_water)

void	set_renumber_pdb (bool const setting)

void	set_read_only_ATOM_entries (bool const setting)

void	set_suppress_zero_occ_pdb_output (bool const setting)

void	set_auto_detect_glycan_connections (bool const auto_detect_glycan_connections)

void	set_write_glycan_pdb_codes (bool const write_glycan_pdb_codes)

void	set_output_alternate_atomids (bool const output_alternate_atomids)

void	set_output_ligands_as_separate_chains (bool const output_ligands_as_separate_chains)

void	set_maintain_links (bool const maintain_links)

void	set_max_bond_length (core::Real const max_bond_length)

void	set_min_bond_length (core::Real const min_bond_length)

void	set_use_pdb_format_HETNAM_records (bool const setting)

void	set_write_pdb_title_section_records (bool const setting)

void	set_write_pdb_link_records (bool const setting)

void	set_write_pdb_parametric_info (bool const setting)

void	set_write_all_connect_info (bool const setting)

void	set_write_seqres_records (bool const setting)

void	set_chains_whose_residues_are_separate_chemical_entities (std::string const &setting)

void	set_residues_for_atom_name_remapping (utility::vector1< std::string > const &setting)

void	set_pdb_comments (bool const pdb_comments)

void	set_show_all_fixes (bool const setting)

void	set_constraints_from_link_records (bool const setting)

void	set_output_pose_energies_table (bool const setting)

void	set_output_pose_cache_data (bool const setting)

void	set_integration_test_mode (bool const setting)

void	set_mmtf_extra_data_io (bool const setting)

bool	operator== (StructFileRepOptions const &other) const

bool	operator< (StructFileRepOptions const &other) const

Static Public Member Functions
static void	list_options_read (utility::options::OptionKeyList &read_options)
	Declare the list of options that are read in the process of reading a PDB (or SDF) and converting it into a Pose. More...

static void	append_schema_attributes (utility::tag::AttributeList &attributes)
	Describe the XML Schema for this ResourceOption object. More...

Private Member Functions
void	init_from_options (utility::options::OptionCollection const &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	skip_connect_info_

core::Real	connect_info_cutoff_

bool	do_not_autoassign_SS_

bool	exit_if_missing_heavy_atoms_

bool	fold_tree_io_

bool	ignore_unrecognized_res_

bool	ignore_sugars_

bool	ignore_waters_

bool	ignore_zero_occupancy_

bool	guarantee_no_DNA_

bool	keep_input_protonation_state_

bool	preserve_header_

std::string	pdb_author_

bool	preserve_crystinfo_

bool	missing_dens_as_jump_

bool	no_chainend_ter_

bool	no_detect_pseudobonds_

bool	no_output_cen_

bool	normalize_to_thk_

bool	output_secondary_structure_

bool	output_torsions_

bool	output_virtual_

bool	output_virtual_zero_occ_

bool	output_only_asymmetric_unit_

bool	pdb_parents_

bool	per_chain_renumbering_

bool	randomize_missing_coords_

bool	remember_unrecognized_res_

bool	remember_unrecognized_water_

bool	renumber_pdb_

bool	read_only_ATOM_entries_

bool	suppress_zero_occ_pdb_output_

bool	auto_detect_glycan_connections_

bool	write_glycan_pdb_codes_

bool	output_alternate_atomids_

bool	output_ligands_as_separate_chains_

bool	maintain_links_

core::Real	max_bond_length_

core::Real	min_bond_length_

bool	use_pdb_format_HETNAM_records_

bool	write_pdb_title_section_records_

bool	write_pdb_link_records_

bool	write_pdb_parametric_info_

bool	write_all_connect_info_

bool	write_seqres_records_

std::string	chains_whose_residues_are_separate_chemical_entities_

utility::vector1< std::string >	residues_for_atom_name_remapping_
	Three letter codes of residues for which to allow atom renaming. More...

bool	pdb_comments_

bool	show_all_fixes_

bool	constraints_from_link_records_

bool	output_pose_energies_table_

bool	output_pose_cache_data_

bool	integration_test_mode_

bool	mmtf_extra_data_io_

Constructor & Destructor Documentation

core::io::StructFileRepOptions::StructFileRepOptions ( )

Constructor that takes default values from the global OptionCollection object, basic::options::option.

References init_from_options().

core::io::StructFileRepOptions::StructFileRepOptions ( utility::options::OptionCollection const & options )

Constructor that takes default values from a provided OptionCollection object.

References init_from_options().

core::io::StructFileRepOptions::~StructFileRepOptions ( )

overridedefault

Member Function Documentation

void core::io::StructFileRepOptions::append_schema_attributes ( utility::tag::AttributeList & attributes )

static

Describe the XML Schema for this ResourceOption object.

The StructFileRepOptions object can be used to initialize a Pose within the ResourceManager and elsewhere. The attributes (aka options) listed here are those read in the parse_my_tag method.

Referenced by core::io::StructFileReaderOptions::append_schema_attributes().

bool core::io::StructFileRepOptions::auto_detect_glycan_connections ( ) const

References auto_detect_glycan_connections_.

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

std::string const & core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities ( ) const

References chains_whose_residues_are_separate_chemical_entities_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::determine_separate_chemical_entity(), and set_chains_whose_residues_are_separate_chemical_entities().

std::string const & core::io::StructFileRepOptions::check_if_residues_are_Ctermini ( ) const

References check_if_residues_are_Ctermini_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::determine_check_Ctermini_for_this_chain(), and set_check_if_residues_are_Ctermini().

std::string const & core::io::StructFileRepOptions::check_if_residues_are_Ntermini ( ) const

References check_if_residues_are_Ntermini_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::determine_check_Ntermini_for_this_chain(), and set_check_if_residues_are_Ntermini().

StructFileRepOptionsOP core::io::StructFileRepOptions::clone ( ) const

virtual

Copy this object and return an owning pointer to the copy.

core::Real core::io::StructFileRepOptions::connect_info_cutoff ( ) const

References connect_info_cutoff_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and set_connect_info_cutoff().

bool core::io::StructFileRepOptions::constraints_from_link_records ( ) const

References constraints_from_link_records_.

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

bool core::io::StructFileRepOptions::do_not_autoassign_SS ( ) const

References do_not_autoassign_SS_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), and set_do_not_autoassign_SS().

bool core::io::StructFileRepOptions::exit_if_missing_heavy_atoms ( ) const

References exit_if_missing_heavy_atoms_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), and set_exit_if_missing_heavy_atoms().

bool core::io::StructFileRepOptions::fold_tree_io ( ) const

References fold_tree_io_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data(), and set_fold_tree_io().

bool core::io::StructFileRepOptions::guarantee_no_DNA ( ) const

References guarantee_no_DNA_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::convert_nucleic_acid_residue_info_to_standard(), and set_guarantee_no_DNA().

bool core::io::StructFileRepOptions::ignore_sugars ( ) const

References ignore_sugars_.

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

bool core::io::StructFileRepOptions::ignore_unrecognized_res ( ) const

References ignore_unrecognized_res_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), core::io::pose_from_sfr::PoseFromSFRBuilder::output_ignore_water_warning_once(), and set_ignore_unrecognized_res().

bool core::io::StructFileRepOptions::ignore_waters ( ) const

References ignore_waters_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), core::io::pose_from_sfr::PoseFromSFRBuilder::output_ignore_water_warning_once(), and set_ignore_waters().

bool core::io::StructFileRepOptions::ignore_zero_occupancy ( ) const

References ignore_zero_occupancy_.

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

void core::io::StructFileRepOptions::init_from_options ( utility::options::OptionCollection const & options )

private

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

Note that if you should add a new option to this function, that you should

add a data member to the class (of course!)
add an accessor for that data member (of course!)
add a mutator for that data member such that it can be set programmatically
add the option key to the OptionKeyList in list_options_read
add a read to the (XML) Tag object in the parse_my_tag function
list the XML attribute (aka "Tag option") that you read from in parse_my_tag to the provide_xml_schema function.
add to operator < and operator ==
add to init_from_options (here)

The usability of Rosetta is improved by continued vigilance of its developers to provide a well documented and accessible code, and the process of reading in structures is vital to Rosetta. Do your part and follow in the careful efforts of those who came before you.

References protocols::stepwise::screener::INTEGRATION_TEST, core::io::mmtf::pdb_comments, core::io::pose_from_sfr::randomize_missing_coords(), set_auto_detect_glycan_connections(), set_chains_whose_residues_are_separate_chemical_entities(), set_check_if_residues_are_Ctermini(), set_check_if_residues_are_Ntermini(), set_connect_info_cutoff(), set_constraints_from_link_records(), set_do_not_autoassign_SS(), set_exit_if_missing_heavy_atoms(), set_fold_tree_io(), set_guarantee_no_DNA(), set_ignore_sugars(), set_ignore_unrecognized_res(), set_ignore_waters(), set_ignore_zero_occupancy(), set_integration_test_mode(), set_keep_input_protonation_state(), set_maintain_links(), set_max_bond_length(), set_min_bond_length(), set_missing_dens_as_jump(), set_mmtf_extra_data_io(), set_no_chainend_ter(), set_no_detect_pseudobonds(), set_no_output_cen(), set_normalize_to_thk(), set_output_alternate_atomids(), set_output_ligands_as_separate_chains(), set_output_only_asymmetric_unit(), set_output_pose_cache_data(), set_output_pose_energies_table(), set_output_secondary_structure(), set_output_torsions(), set_output_virtual(), set_output_virtual_zero_occ(), set_pdb_author(), set_pdb_comments(), set_pdb_parents(), set_per_chain_renumbering(), set_preserve_crystinfo(), set_preserve_header(), set_randomize_missing_coords(), set_read_only_ATOM_entries(), set_remember_unrecognized_res(), set_remember_unrecognized_water(), set_renumber_pdb(), set_residues_for_atom_name_remapping(), set_show_all_fixes(), set_skip_connect_info(), set_suppress_zero_occ_pdb_output(), set_use_pdb_format_HETNAM_records(), set_write_all_connect_info(), set_write_glycan_pdb_codes(), set_write_pdb_link_records(), set_write_pdb_parametric_info(), set_write_pdb_title_section_records(), and set_write_seqres_records().

Referenced by StructFileRepOptions().

bool core::io::StructFileRepOptions::integration_test_mode ( ) const

References integration_test_mode_.

Referenced by core::io::mmtf::add_extra_data(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_remarks(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_title_section().

bool core::io::StructFileRepOptions::keep_input_protonation_state ( ) const

References keep_input_protonation_state_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), and set_keep_input_protonation_state().

void core::io::StructFileRepOptions::list_options_read ( utility::options::OptionKeyList & read_options )

static

Declare the list of options that are read in the process of reading a PDB (or SDF) and converting it into a Pose.

List all of the options (by option key) that are read in the init_from_options function.

References protocols::stepwise::screener::INTEGRATION_TEST, core::io::mmtf::pdb_comments, and core::io::pose_from_sfr::randomize_missing_coords().

Referenced by core::io::StructFileReaderOptions::list_options_read(), protocols::jd3::pose_outputters::mmTFPoseOutputter::list_options_read(), and protocols::jd3::pose_outputters::PDBPoseOutputter::list_options_read().

bool core::io::StructFileRepOptions::maintain_links ( ) const

References maintain_links_.

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

core::Real core::io::StructFileRepOptions::max_bond_length ( ) const

References max_bond_length_.

Referenced by core::io::determine_glycan_links(), and set_max_bond_length().

core::Real core::io::StructFileRepOptions::min_bond_length ( ) const

References min_bond_length_.

Referenced by core::io::determine_glycan_links(), and set_min_bond_length().

bool core::io::StructFileRepOptions::missing_dens_as_jump ( ) const

References missing_dens_as_jump_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), and set_missing_dens_as_jump().

bool core::io::StructFileRepOptions::mmtf_extra_data_io ( ) const

References mmtf_extra_data_io_.

Referenced by core::io::mmtf::add_extra_data().

bool core::io::StructFileRepOptions::no_chainend_ter ( ) const

References no_chainend_ter_.

Referenced by set_no_chainend_ter().

bool core::io::StructFileRepOptions::no_detect_pseudobonds ( ) const

References no_detect_pseudobonds_.

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

bool core::io::StructFileRepOptions::no_output_cen ( ) const

References no_output_cen_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), and set_no_output_cen().

bool core::io::StructFileRepOptions::normalize_to_thk ( ) const

References normalize_to_thk_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data(), and set_normalize_to_thk().

bool core::io::StructFileRepOptions::operator< ( StructFileRepOptions const & other ) const

Note: This function makes no sense. If ANY option is less than that in other, this returns true. –VKM 24 Jan 2018.

References auto_detect_glycan_connections_, chains_whose_residues_are_separate_chemical_entities_, check_if_residues_are_Ctermini_, check_if_residues_are_Ntermini_, connect_info_cutoff_, constraints_from_link_records_, do_not_autoassign_SS_, exit_if_missing_heavy_atoms_, fold_tree_io_, ignore_sugars_, ignore_unrecognized_res_, ignore_waters_, ignore_zero_occupancy_, integration_test_mode_, keep_input_protonation_state_, maintain_links_, max_bond_length_, min_bond_length_, missing_dens_as_jump_, mmtf_extra_data_io_, no_chainend_ter_, no_detect_pseudobonds_, no_output_cen_, normalize_to_thk_, output_alternate_atomids_, output_ligands_as_separate_chains_, output_only_asymmetric_unit_, output_secondary_structure_, output_torsions_, output_virtual_, output_virtual_zero_occ_, pdb_author_, pdb_comments_, pdb_parents_, per_chain_renumbering_, preserve_crystinfo_, preserve_header_, randomize_missing_coords_, remember_unrecognized_res_, remember_unrecognized_water_, renumber_pdb_, residues_for_atom_name_remapping_, show_all_fixes_, skip_connect_info_, suppress_zero_occ_pdb_output_, use_pdb_format_HETNAM_records_, write_all_connect_info_, write_glycan_pdb_codes_, write_pdb_link_records_, write_pdb_parametric_info_, write_pdb_title_section_records_, and write_seqres_records_.

bool core::io::StructFileRepOptions::operator== ( StructFileRepOptions const & other ) const

References auto_detect_glycan_connections_, chains_whose_residues_are_separate_chemical_entities_, check_if_residues_are_Ctermini_, check_if_residues_are_Ntermini_, connect_info_cutoff_, constraints_from_link_records_, do_not_autoassign_SS_, exit_if_missing_heavy_atoms_, fold_tree_io_, ignore_sugars_, ignore_unrecognized_res_, ignore_waters_, ignore_zero_occupancy_, integration_test_mode_, keep_input_protonation_state_, maintain_links_, max_bond_length_, min_bond_length_, missing_dens_as_jump_, mmtf_extra_data_io_, no_chainend_ter_, no_detect_pseudobonds_, no_output_cen_, normalize_to_thk_, output_alternate_atomids_, output_ligands_as_separate_chains_, output_only_asymmetric_unit_, output_secondary_structure_, output_torsions_, output_virtual_, output_virtual_zero_occ_, pdb_author_, pdb_comments_, pdb_parents_, per_chain_renumbering_, preserve_crystinfo_, preserve_header_, randomize_missing_coords_, remember_unrecognized_res_, remember_unrecognized_water_, renumber_pdb_, residues_for_atom_name_remapping_, show_all_fixes_, skip_connect_info_, suppress_zero_occ_pdb_output_, use_pdb_format_HETNAM_records_, write_all_connect_info_, write_glycan_pdb_codes_, write_pdb_link_records_, write_pdb_parametric_info_, write_pdb_title_section_records_, and write_seqres_records_.

bool core::io::StructFileRepOptions::output_alternate_atomids ( ) const

References output_alternate_atomids_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), and set_output_alternate_atomids().

bool core::io::StructFileRepOptions::output_ligands_as_separate_chains ( ) const

References output_ligands_as_separate_chains_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and set_output_ligands_as_separate_chains().

bool core::io::StructFileRepOptions::output_only_asymmetric_unit ( ) const

References output_only_asymmetric_unit_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and set_output_only_asymmetric_unit().

bool core::io::StructFileRepOptions::output_pose_cache ( ) const

References output_pose_cache_data_.

Referenced by core::io::mmcif::dump_cif(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose().

bool core::io::StructFileRepOptions::output_pose_energies_table ( ) const

References output_pose_energies_table_.

Referenced by core::io::mmcif::dump_cif(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose().

bool core::io::StructFileRepOptions::output_secondary_structure ( ) const

References output_secondary_structure_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and set_output_secondary_structure().

bool core::io::StructFileRepOptions::output_torsions ( ) const

References output_torsions_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data(), and set_output_torsions().

bool core::io::StructFileRepOptions::output_virtual ( ) const

References output_virtual_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::determine_atom_indices(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and set_output_virtual().

bool core::io::StructFileRepOptions::output_virtual_zero_occ ( ) const

References output_virtual_zero_occ_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), and set_output_virtual_zero_occ().

void core::io::StructFileRepOptions::parse_my_tag ( utility::tag::TagCOP tag )

virtual

Reimplemented in core::io::StructFileReaderOptions, and core::import_pose::ImportPoseOptions.

References set_auto_detect_glycan_connections(), set_chains_whose_residues_are_separate_chemical_entities(), set_check_if_residues_are_Ctermini(), set_check_if_residues_are_Ntermini(), set_connect_info_cutoff(), set_constraints_from_link_records(), set_do_not_autoassign_SS(), set_exit_if_missing_heavy_atoms(), set_fold_tree_io(), set_guarantee_no_DNA(), set_ignore_sugars(), set_ignore_unrecognized_res(), set_ignore_waters(), set_ignore_zero_occupancy(), set_integration_test_mode(), set_keep_input_protonation_state(), set_maintain_links(), set_max_bond_length(), set_min_bond_length(), set_missing_dens_as_jump(), set_mmtf_extra_data_io(), set_no_chainend_ter(), set_no_detect_pseudobonds(), set_no_output_cen(), set_normalize_to_thk(), set_output_alternate_atomids(), set_output_ligands_as_separate_chains(), set_output_only_asymmetric_unit(), set_output_secondary_structure(), set_output_torsions(), set_output_virtual(), set_output_virtual_zero_occ(), set_pdb_author(), set_pdb_comments(), set_pdb_parents(), set_per_chain_renumbering(), set_preserve_crystinfo(), set_preserve_header(), set_randomize_missing_coords(), set_remember_unrecognized_res(), set_remember_unrecognized_water(), set_renumber_pdb(), set_residues_for_atom_name_remapping(), set_show_all_fixes(), set_skip_connect_info(), set_suppress_zero_occ_pdb_output(), set_use_pdb_format_HETNAM_records(), set_write_all_connect_info(), set_write_glycan_pdb_codes(), set_write_pdb_link_records(), set_write_pdb_parametric_info(), set_write_pdb_title_section_records(), and set_write_seqres_records().

Referenced by core::io::StructFileReaderOptions::parse_my_tag().

std::string const & core::io::StructFileRepOptions::pdb_author ( ) const

References pdb_author_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_remarks(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_title_section(), and set_pdb_author().

bool core::io::StructFileRepOptions::pdb_comments ( ) const

References pdb_comments_.

Referenced by core::io::pdb::create_sfr_from_pdb_records(), and set_pdb_comments().

bool core::io::StructFileRepOptions::pdb_parents ( ) const

References pdb_parents_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_additional_pose_data(), and set_pdb_parents().

bool core::io::StructFileRepOptions::per_chain_renumbering ( ) const

References per_chain_renumbering_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and set_per_chain_renumbering().

bool core::io::StructFileRepOptions::preserve_crystinfo ( ) const

References preserve_crystinfo_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and set_preserve_crystinfo().

bool core::io::StructFileRepOptions::preserve_header ( ) const

References preserve_header_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_1_everything_but_temps(), core::io::mmcif::dump_cif(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and set_preserve_header().

bool core::io::StructFileRepOptions::randomize_missing_coords ( ) const

References randomize_missing_coords_.

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

bool core::io::StructFileRepOptions::read_only_ATOM_entries ( ) const

References read_only_ATOM_entries_.

Referenced by core::io::mmcif::create_sfr_from_cif_file_op(), and core::io::pdb::create_sfr_from_pdb_records().

bool core::io::StructFileRepOptions::remember_unrecognized_res ( ) const

References remember_unrecognized_res_.

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

bool core::io::StructFileRepOptions::remember_unrecognized_water ( ) const

References remember_unrecognized_water_.

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

bool core::io::StructFileRepOptions::renumber_pdb ( ) const

References renumber_pdb_.

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

utility::vector1< std::string > const & core::io::StructFileRepOptions::residues_for_atom_name_remapping ( ) const

References residues_for_atom_name_remapping_.

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

void core::io::StructFileRepOptions::set_auto_detect_glycan_connections ( bool const auto_detect_glycan_connections )

References auto_detect_glycan_connections(), and auto_detect_glycan_connections_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::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::StructFileRepOptions::set_check_if_residues_are_Ctermini ( std::string const & 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::StructFileRepOptions::set_check_if_residues_are_Ntermini ( std::string const & 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::StructFileRepOptions::set_connect_info_cutoff ( core::Real const & connect_info_cutoff )

References connect_info_cutoff(), and connect_info_cutoff_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_constraints_from_link_records ( bool const setting )

References constraints_from_link_records_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_do_not_autoassign_SS ( bool const do_not_autoassign_SS )

References do_not_autoassign_SS(), and do_not_autoassign_SS_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_exit_if_missing_heavy_atoms ( bool const 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::StructFileRepOptions::set_fold_tree_io ( bool const fold_tree_io )

References fold_tree_io(), and fold_tree_io_.

Referenced by init_from_options(), parse_my_tag(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::set_fold_tree_io().

void core::io::StructFileRepOptions::set_guarantee_no_DNA ( bool const guarantee_no_DNA )

References guarantee_no_DNA(), and guarantee_no_DNA_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_ignore_sugars ( bool const setting )

References ignore_sugars_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_ignore_unrecognized_res ( bool const ignore_unrecognized_res )

References ignore_unrecognized_res(), and ignore_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_ignore_waters ( bool const ignore_waters )

References ignore_waters(), and ignore_waters_.

Referenced by protocols::simple_moves::ExplicitWaterMover::init(), init_from_options(), parse_my_tag(), and protocols::simple_moves::ExplicitWaterMover::parse_my_tag().

void core::io::StructFileRepOptions::set_ignore_zero_occupancy ( bool const ignore_zero_occupancy )

References ignore_zero_occupancy(), and ignore_zero_occupancy_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_integration_test_mode ( bool const setting )

References integration_test_mode_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_keep_input_protonation_state ( bool const 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::StructFileRepOptions::set_maintain_links ( bool const maintain_links )

References maintain_links(), and maintain_links_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_max_bond_length ( core::Real const max_bond_length )

References max_bond_length(), and max_bond_length_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_min_bond_length ( core::Real const min_bond_length )

References min_bond_length(), and min_bond_length_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_missing_dens_as_jump ( bool const 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::StructFileRepOptions::set_mmtf_extra_data_io ( bool const setting )

References mmtf_extra_data_io_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_no_chainend_ter ( bool const no_chainend_ter )

References no_chainend_ter(), and no_chainend_ter_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_no_detect_pseudobonds ( bool const setting )

References no_detect_pseudobonds_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_no_output_cen ( bool const no_output_cen )

References no_output_cen(), and no_output_cen_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_normalize_to_thk ( bool const normalize_to_thk )

References normalize_to_thk(), and normalize_to_thk_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_alternate_atomids ( bool const output_alternate_atomids )

References output_alternate_atomids(), and output_alternate_atomids_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_ligands_as_separate_chains ( bool const output_ligands_as_separate_chains )

References output_ligands_as_separate_chains(), and output_ligands_as_separate_chains_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_only_asymmetric_unit ( bool const output_only_asymmetric_unit )

References output_only_asymmetric_unit(), and output_only_asymmetric_unit_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_pose_cache_data ( bool const setting )

References output_pose_cache_data_.

Referenced by init_from_options().

void core::io::StructFileRepOptions::set_output_pose_energies_table ( bool const setting )

References output_pose_energies_table_.

Referenced by init_from_options().

void core::io::StructFileRepOptions::set_output_secondary_structure ( bool const output_secondary_structure )

References output_secondary_structure(), and output_secondary_structure_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_torsions ( bool const output_torsions )

References output_torsions(), and output_torsions_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_virtual ( bool const output_virtual )

References output_virtual(), and output_virtual_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_output_virtual_zero_occ ( bool const output_virtual_zero_occ )

References output_virtual_zero_occ(), and output_virtual_zero_occ_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_pdb_author ( std::string const & pdb_author )

References pdb_author(), and pdb_author_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_pdb_comments ( bool const pdb_comments )

References pdb_comments(), and pdb_comments_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_pdb_parents ( bool const pdb_parents )

References pdb_parents(), and pdb_parents_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_per_chain_renumbering ( bool const per_chain_renumbering )

References per_chain_renumbering(), and per_chain_renumbering_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_preserve_crystinfo ( bool const preserve_crystinfo )

References preserve_crystinfo(), and preserve_crystinfo_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_preserve_header ( bool const preserve_header )

References preserve_header(), and preserve_header_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_randomize_missing_coords ( bool const randomize_missing_coords )

References randomize_missing_coords(), and randomize_missing_coords_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_read_only_ATOM_entries ( bool const setting )

References read_only_ATOM_entries_.

Referenced by init_from_options().

void core::io::StructFileRepOptions::set_remember_unrecognized_res ( bool const remember_unrecognized_res )

References remember_unrecognized_res(), and remember_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_remember_unrecognized_water ( bool const remember_unrecognized_water )

References remember_unrecognized_water(), and remember_unrecognized_water_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_renumber_pdb ( bool const setting )

References renumber_pdb_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_residues_for_atom_name_remapping ( utility::vector1< std::string > const & setting )

References residues_for_atom_name_remapping_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_show_all_fixes ( bool const setting )

References show_all_fixes_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_skip_connect_info ( bool const skip_connect_info )

References skip_connect_info(), and skip_connect_info_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_suppress_zero_occ_pdb_output ( bool const setting )

References suppress_zero_occ_pdb_output_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_use_pdb_format_HETNAM_records ( bool const setting )

References use_pdb_format_HETNAM_records_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_write_all_connect_info ( bool const setting )

References write_all_connect_info_.

Referenced by init_from_options(), parse_my_tag(), and core::io::mmtf::set_mmtf_default_options().

void core::io::StructFileRepOptions::set_write_glycan_pdb_codes ( bool const write_glycan_pdb_codes )

References write_glycan_pdb_codes(), and write_glycan_pdb_codes_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_write_pdb_link_records ( bool const setting )

References write_pdb_link_records_.

Referenced by init_from_options(), parse_my_tag(), and core::io::mmtf::set_mmtf_default_options().

void core::io::StructFileRepOptions::set_write_pdb_parametric_info ( bool const setting )

References write_pdb_parametric_info_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_write_pdb_title_section_records ( bool const setting )

References write_pdb_title_section_records_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileRepOptions::set_write_seqres_records ( bool const setting )

References write_seqres_records_.

Referenced by init_from_options(), and parse_my_tag().

bool core::io::StructFileRepOptions::show_all_fixes ( ) const

References show_all_fixes_.

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

bool core::io::StructFileRepOptions::skip_connect_info ( ) const

References skip_connect_info_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), and set_skip_connect_info().

bool core::io::StructFileRepOptions::suppress_zero_occ_pdb_output ( ) const

References suppress_zero_occ_pdb_output_.

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

std::string core::io::StructFileRepOptions::type ( ) const

virtual

Reimplemented in core::io::StructFileReaderOptions, and core::import_pose::ImportPoseOptions.

bool core::io::StructFileRepOptions::use_pdb_format_HETNAM_records ( ) const

References use_pdb_format_HETNAM_records_.

Referenced by core::io::mmtf::add_extra_data().

bool core::io::StructFileRepOptions::write_all_connect_info ( ) const

References write_all_connect_info_.

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

bool core::io::StructFileRepOptions::write_glycan_pdb_codes ( ) const

References write_glycan_pdb_codes_.

Referenced by core::io::mmtf::add_extra_data(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), and set_write_glycan_pdb_codes().

bool core::io::StructFileRepOptions::write_pdb_link_records ( ) const

References write_pdb_link_records_.

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

bool core::io::StructFileRepOptions::write_pdb_parametric_info ( ) const

References write_pdb_parametric_info_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_default_remarks(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose().

bool core::io::StructFileRepOptions::write_pdb_title_section_records ( ) const

References write_pdb_title_section_records_.

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

bool core::io::StructFileRepOptions::write_seqres_records ( ) const

References write_seqres_records_.

Member Data Documentation

bool core::io::StructFileRepOptions::auto_detect_glycan_connections_

private

Referenced by auto_detect_glycan_connections(), operator<(), operator==(), and set_auto_detect_glycan_connections().

std::string core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities_

private

Referenced by chains_whose_residues_are_separate_chemical_entities(), operator<(), operator==(), and set_chains_whose_residues_are_separate_chemical_entities().

std::string core::io::StructFileRepOptions::check_if_residues_are_Ctermini_

private

Referenced by check_if_residues_are_Ctermini(), operator<(), operator==(), and set_check_if_residues_are_Ctermini().

std::string core::io::StructFileRepOptions::check_if_residues_are_Ntermini_

private

Referenced by check_if_residues_are_Ntermini(), operator<(), operator==(), and set_check_if_residues_are_Ntermini().

core::Real core::io::StructFileRepOptions::connect_info_cutoff_

private

Referenced by connect_info_cutoff(), operator<(), operator==(), and set_connect_info_cutoff().

bool core::io::StructFileRepOptions::constraints_from_link_records_

private

Referenced by constraints_from_link_records(), operator<(), operator==(), and set_constraints_from_link_records().

bool core::io::StructFileRepOptions::do_not_autoassign_SS_

private

Referenced by do_not_autoassign_SS(), operator<(), operator==(), and set_do_not_autoassign_SS().

bool core::io::StructFileRepOptions::exit_if_missing_heavy_atoms_

private

Referenced by exit_if_missing_heavy_atoms(), operator<(), operator==(), and set_exit_if_missing_heavy_atoms().

bool core::io::StructFileRepOptions::fold_tree_io_

private

Referenced by fold_tree_io(), operator<(), operator==(), and set_fold_tree_io().

bool core::io::StructFileRepOptions::guarantee_no_DNA_

private

Referenced by guarantee_no_DNA(), and set_guarantee_no_DNA().

bool core::io::StructFileRepOptions::ignore_sugars_

private

Referenced by ignore_sugars(), operator<(), operator==(), and set_ignore_sugars().

bool core::io::StructFileRepOptions::ignore_unrecognized_res_

private

Referenced by ignore_unrecognized_res(), operator<(), operator==(), and set_ignore_unrecognized_res().

bool core::io::StructFileRepOptions::ignore_waters_

private

Referenced by ignore_waters(), operator<(), operator==(), and set_ignore_waters().

bool core::io::StructFileRepOptions::ignore_zero_occupancy_

private

Referenced by ignore_zero_occupancy(), operator<(), operator==(), and set_ignore_zero_occupancy().

bool core::io::StructFileRepOptions::integration_test_mode_

private

Referenced by integration_test_mode(), operator<(), operator==(), and set_integration_test_mode().

bool core::io::StructFileRepOptions::keep_input_protonation_state_

private

Referenced by keep_input_protonation_state(), operator<(), operator==(), and set_keep_input_protonation_state().

bool core::io::StructFileRepOptions::maintain_links_

private

Referenced by maintain_links(), operator<(), operator==(), and set_maintain_links().

core::Real core::io::StructFileRepOptions::max_bond_length_

private

Referenced by max_bond_length(), operator<(), operator==(), and set_max_bond_length().

core::Real core::io::StructFileRepOptions::min_bond_length_

private

Referenced by min_bond_length(), operator<(), operator==(), and set_min_bond_length().

bool core::io::StructFileRepOptions::missing_dens_as_jump_

private

Referenced by missing_dens_as_jump(), operator<(), operator==(), and set_missing_dens_as_jump().

bool core::io::StructFileRepOptions::mmtf_extra_data_io_

private

Referenced by mmtf_extra_data_io(), operator<(), operator==(), and set_mmtf_extra_data_io().

bool core::io::StructFileRepOptions::no_chainend_ter_

private

Referenced by no_chainend_ter(), operator<(), operator==(), and set_no_chainend_ter().

bool core::io::StructFileRepOptions::no_detect_pseudobonds_

private

Referenced by no_detect_pseudobonds(), operator<(), operator==(), and set_no_detect_pseudobonds().

bool core::io::StructFileRepOptions::no_output_cen_

private

Referenced by no_output_cen(), operator<(), operator==(), and set_no_output_cen().

bool core::io::StructFileRepOptions::normalize_to_thk_

private

Referenced by normalize_to_thk(), operator<(), operator==(), and set_normalize_to_thk().

bool core::io::StructFileRepOptions::output_alternate_atomids_

private

Referenced by operator<(), operator==(), output_alternate_atomids(), and set_output_alternate_atomids().

bool core::io::StructFileRepOptions::output_ligands_as_separate_chains_

private

Referenced by operator<(), operator==(), output_ligands_as_separate_chains(), and set_output_ligands_as_separate_chains().

bool core::io::StructFileRepOptions::output_only_asymmetric_unit_

private

Referenced by operator<(), operator==(), output_only_asymmetric_unit(), and set_output_only_asymmetric_unit().

bool core::io::StructFileRepOptions::output_pose_cache_data_

private

Referenced by output_pose_cache(), and set_output_pose_cache_data().

bool core::io::StructFileRepOptions::output_pose_energies_table_

private

Referenced by output_pose_energies_table(), and set_output_pose_energies_table().

bool core::io::StructFileRepOptions::output_secondary_structure_

private

Referenced by operator<(), operator==(), output_secondary_structure(), and set_output_secondary_structure().

bool core::io::StructFileRepOptions::output_torsions_

private

Referenced by operator<(), operator==(), output_torsions(), and set_output_torsions().

bool core::io::StructFileRepOptions::output_virtual_

private

Referenced by operator<(), operator==(), output_virtual(), and set_output_virtual().

bool core::io::StructFileRepOptions::output_virtual_zero_occ_

private

Referenced by operator<(), operator==(), output_virtual_zero_occ(), and set_output_virtual_zero_occ().

std::string core::io::StructFileRepOptions::pdb_author_

private

Referenced by operator<(), operator==(), pdb_author(), and set_pdb_author().

bool core::io::StructFileRepOptions::pdb_comments_

private

Referenced by operator<(), operator==(), pdb_comments(), and set_pdb_comments().

bool core::io::StructFileRepOptions::pdb_parents_

private

Referenced by operator<(), operator==(), pdb_parents(), and set_pdb_parents().

bool core::io::StructFileRepOptions::per_chain_renumbering_

private

Referenced by operator<(), operator==(), per_chain_renumbering(), and set_per_chain_renumbering().

bool core::io::StructFileRepOptions::preserve_crystinfo_

private

Referenced by operator<(), operator==(), preserve_crystinfo(), and set_preserve_crystinfo().

bool core::io::StructFileRepOptions::preserve_header_

private

Referenced by operator<(), operator==(), preserve_header(), and set_preserve_header().

bool core::io::StructFileRepOptions::randomize_missing_coords_

private

Referenced by operator<(), operator==(), randomize_missing_coords(), and set_randomize_missing_coords().

bool core::io::StructFileRepOptions::read_only_ATOM_entries_

private

Referenced by read_only_ATOM_entries(), and set_read_only_ATOM_entries().

bool core::io::StructFileRepOptions::remember_unrecognized_res_

private

Referenced by operator<(), operator==(), remember_unrecognized_res(), and set_remember_unrecognized_res().

bool core::io::StructFileRepOptions::remember_unrecognized_water_

private

Referenced by operator<(), operator==(), remember_unrecognized_water(), and set_remember_unrecognized_water().

bool core::io::StructFileRepOptions::renumber_pdb_

private

Referenced by operator<(), operator==(), renumber_pdb(), and set_renumber_pdb().

utility::vector1< std::string > core::io::StructFileRepOptions::residues_for_atom_name_remapping_

private

Three letter codes of residues for which to allow atom renaming.

Referenced by operator<(), operator==(), residues_for_atom_name_remapping(), and set_residues_for_atom_name_remapping().

bool core::io::StructFileRepOptions::show_all_fixes_

private

Referenced by operator<(), operator==(), set_show_all_fixes(), and show_all_fixes().

bool core::io::StructFileRepOptions::skip_connect_info_

private

Referenced by operator<(), operator==(), set_skip_connect_info(), and skip_connect_info().

bool core::io::StructFileRepOptions::suppress_zero_occ_pdb_output_

private

Referenced by operator<(), operator==(), set_suppress_zero_occ_pdb_output(), and suppress_zero_occ_pdb_output().

bool core::io::StructFileRepOptions::use_pdb_format_HETNAM_records_

private

Referenced by operator<(), operator==(), set_use_pdb_format_HETNAM_records(), and use_pdb_format_HETNAM_records().

bool core::io::StructFileRepOptions::write_all_connect_info_

private

Referenced by operator<(), operator==(), set_write_all_connect_info(), and write_all_connect_info().

bool core::io::StructFileRepOptions::write_glycan_pdb_codes_

private

Referenced by operator<(), operator==(), set_write_glycan_pdb_codes(), and write_glycan_pdb_codes().

bool core::io::StructFileRepOptions::write_pdb_link_records_

private

Referenced by operator<(), operator==(), set_write_pdb_link_records(), and write_pdb_link_records().

bool core::io::StructFileRepOptions::write_pdb_parametric_info_

private

Referenced by operator<(), operator==(), set_write_pdb_parametric_info(), and write_pdb_parametric_info().

bool core::io::StructFileRepOptions::write_pdb_title_section_records_

private

Referenced by operator<(), operator==(), set_write_pdb_title_section_records(), and write_pdb_title_section_records().

bool core::io::StructFileRepOptions::write_seqres_records_

private

Referenced by operator<(), operator==(), set_write_seqres_records(), and write_seqres_records().

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

src/core/io/StructFileRepOptions.hh
src/core/io/StructFileRepOptions.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation