#include <StructFileReaderOptions.hh>

Inheritance diagram for core::io::StructFileReaderOptions:

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

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

	~StructFileReaderOptions () override

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

std::string	type () const override

bool	new_chain_order () const

bool	obey_ENDMDL () const

bool	read_pdb_header () const

bool	glycam_pdb_format () const

bool	mmtf_extra_data_io () const

void	set_new_chain_order (bool setting)

void	set_obey_ENDMDL (bool setting)

void	set_read_pdb_header (bool setting)

void	set_glycam_pdb_format (bool setting)

void	set_mmtf_extra_data_io (bool setting)

bool	operator== (StructFileReaderOptions const &other) const

bool	operator< (StructFileReaderOptions const &other) const

Public Member Functions inherited from core::io::StructFileRepOptions
	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...

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)

Static Public Member Functions inherited from core::io::StructFileRepOptions
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
bool	new_chain_order_

bool	obey_ENDMDL_

bool	read_pdb_header_

bool	glycam_pdb_format_

bool	mmtf_extra_data_io_

Constructor & Destructor Documentation

core::io::StructFileReaderOptions::StructFileReaderOptions ( )

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

References init_from_options().

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

Constructor that takes default values from a provided OptionCollection object.

References init_from_options().

core::io::StructFileReaderOptions::~StructFileReaderOptions ( )

overridedefault

Member Function Documentation

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

static

References core::io::StructFileRepOptions::append_schema_attributes().

Referenced by core::import_pose::ImportPoseOptions::append_schema_attributes().

bool core::io::StructFileReaderOptions::glycam_pdb_format ( ) const

References glycam_pdb_format_.

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

private

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

References set_glycam_pdb_format(), set_mmtf_extra_data_io(), set_new_chain_order(), set_obey_ENDMDL(), and set_read_pdb_header().

Referenced by StructFileReaderOptions().

void core::io::StructFileReaderOptions::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.

References core::io::StructFileRepOptions::list_options_read().

Referenced by core::import_pose::ImportPoseOptions::list_options_read().

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

References mmtf_extra_data_io_.

bool core::io::StructFileReaderOptions::new_chain_order ( ) const

References new_chain_order_.

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

bool core::io::StructFileReaderOptions::obey_ENDMDL ( ) const

References obey_ENDMDL_.

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

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

References glycam_pdb_format_, mmtf_extra_data_io_, new_chain_order_, obey_ENDMDL_, and read_pdb_header_.

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

References glycam_pdb_format_, mmtf_extra_data_io_, new_chain_order_, obey_ENDMDL_, and read_pdb_header_.

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

overridevirtual

Reimplemented from core::io::StructFileRepOptions.

References core::io::StructFileRepOptions::parse_my_tag(), set_glycam_pdb_format(), set_mmtf_extra_data_io(), set_new_chain_order(), set_obey_ENDMDL(), and set_read_pdb_header().

Referenced by core::import_pose::ImportPoseOptions::parse_my_tag().

bool core::io::StructFileReaderOptions::read_pdb_header ( ) const

References read_pdb_header_.

Referenced by core::io::mmcif::create_sfr_from_cif_file_op(), and core::io::mmtf::create_sfrs_from_mmtf_filename().

void core::io::StructFileReaderOptions::set_glycam_pdb_format ( bool setting )

References glycam_pdb_format_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileReaderOptions::set_mmtf_extra_data_io ( bool setting )

References mmtf_extra_data_io_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileReaderOptions::set_new_chain_order ( bool setting )

References new_chain_order_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileReaderOptions::set_obey_ENDMDL ( bool setting )

References obey_ENDMDL_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::StructFileReaderOptions::set_read_pdb_header ( bool setting )

References read_pdb_header_.

Referenced by init_from_options(), and parse_my_tag().

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

overridevirtual

Reimplemented from core::io::StructFileRepOptions.

Member Data Documentation

bool core::io::StructFileReaderOptions::glycam_pdb_format_

private

Referenced by glycam_pdb_format(), operator<(), operator==(), and set_glycam_pdb_format().

bool core::io::StructFileReaderOptions::mmtf_extra_data_io_

private

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

bool core::io::StructFileReaderOptions::new_chain_order_

private

Referenced by new_chain_order(), operator<(), operator==(), and set_new_chain_order().

bool core::io::StructFileReaderOptions::obey_ENDMDL_

private

Referenced by obey_ENDMDL(), operator<(), operator==(), and set_obey_ENDMDL().

bool core::io::StructFileReaderOptions::read_pdb_header_

private

Referenced by operator<(), operator==(), read_pdb_header(), and set_read_pdb_header().

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

src/core/io/StructFileReaderOptions.hh
src/core/io/StructFileReaderOptions.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation