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core::io::StructFileRepOptions Class Reference

#include <StructFileRepOptions.hh>

Inheritance diagram for core::io::StructFileRepOptions:
Inheritance graph
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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
std::string const & core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities ( ) const
std::string const & core::io::StructFileRepOptions::check_if_residues_are_Ctermini ( ) const
std::string const & core::io::StructFileRepOptions::check_if_residues_are_Ntermini ( ) const
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
bool core::io::StructFileRepOptions::constraints_from_link_records ( ) const
bool core::io::StructFileRepOptions::do_not_autoassign_SS ( ) const
bool core::io::StructFileRepOptions::exit_if_missing_heavy_atoms ( ) const
bool core::io::StructFileRepOptions::fold_tree_io ( ) const
bool core::io::StructFileRepOptions::guarantee_no_DNA ( ) const
bool core::io::StructFileRepOptions::ignore_sugars ( ) const
bool core::io::StructFileRepOptions::ignore_unrecognized_res ( ) const
bool core::io::StructFileRepOptions::ignore_waters ( ) const
bool core::io::StructFileRepOptions::ignore_zero_occupancy ( ) const
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

  1. add a data member to the class (of course!)
  2. add an accessor for that data member (of course!)
  3. add a mutator for that data member such that it can be set programmatically
  4. add the option key to the OptionKeyList in list_options_read
  5. add a read to the (XML) Tag object in the parse_my_tag function
  6. list the XML attribute (aka "Tag option") that you read from in parse_my_tag to the provide_xml_schema function.
  7. add to operator < and operator ==
  8. 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
bool core::io::StructFileRepOptions::keep_input_protonation_state ( ) const
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
core::Real core::io::StructFileRepOptions::max_bond_length ( ) const
core::Real core::io::StructFileRepOptions::min_bond_length ( ) const
bool core::io::StructFileRepOptions::missing_dens_as_jump ( ) const
bool core::io::StructFileRepOptions::mmtf_extra_data_io ( ) const
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
bool core::io::StructFileRepOptions::no_output_cen ( ) const
bool core::io::StructFileRepOptions::normalize_to_thk ( ) const
bool core::io::StructFileRepOptions::operator< ( StructFileRepOptions const &  other) const
bool core::io::StructFileRepOptions::operator== ( StructFileRepOptions const &  other) const
bool core::io::StructFileRepOptions::output_alternate_atomids ( ) const
bool core::io::StructFileRepOptions::output_ligands_as_separate_chains ( ) const
bool core::io::StructFileRepOptions::output_only_asymmetric_unit ( ) const
bool core::io::StructFileRepOptions::output_pose_cache ( ) const
bool core::io::StructFileRepOptions::output_pose_energies_table ( ) const
bool core::io::StructFileRepOptions::output_secondary_structure ( ) const
bool core::io::StructFileRepOptions::output_torsions ( ) const
bool core::io::StructFileRepOptions::output_virtual ( ) const
bool core::io::StructFileRepOptions::output_virtual_zero_occ ( ) const
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
bool core::io::StructFileRepOptions::pdb_comments ( ) const
bool core::io::StructFileRepOptions::pdb_parents ( ) const
bool core::io::StructFileRepOptions::per_chain_renumbering ( ) const
bool core::io::StructFileRepOptions::preserve_crystinfo ( ) const
bool core::io::StructFileRepOptions::preserve_header ( ) const
bool core::io::StructFileRepOptions::randomize_missing_coords ( ) const
bool core::io::StructFileRepOptions::read_only_ATOM_entries ( ) const
bool core::io::StructFileRepOptions::remember_unrecognized_res ( ) const
bool core::io::StructFileRepOptions::remember_unrecognized_water ( ) const
bool core::io::StructFileRepOptions::renumber_pdb ( ) const
utility::vector1< std::string > const & core::io::StructFileRepOptions::residues_for_atom_name_remapping ( ) const
void core::io::StructFileRepOptions::set_auto_detect_glycan_connections ( bool const  auto_detect_glycan_connections)
void core::io::StructFileRepOptions::set_chains_whose_residues_are_separate_chemical_entities ( std::string const &  setting)
void core::io::StructFileRepOptions::set_check_if_residues_are_Ctermini ( std::string const &  check_if_residues_are_Ctermini)
void core::io::StructFileRepOptions::set_check_if_residues_are_Ntermini ( std::string const &  check_if_residues_are_Ntermini)
void core::io::StructFileRepOptions::set_connect_info_cutoff ( core::Real const &  connect_info_cutoff)
void core::io::StructFileRepOptions::set_constraints_from_link_records ( bool const  setting)
void core::io::StructFileRepOptions::set_do_not_autoassign_SS ( bool const  do_not_autoassign_SS)
void core::io::StructFileRepOptions::set_exit_if_missing_heavy_atoms ( bool const  exit_if_missing_heavy_atoms)
void core::io::StructFileRepOptions::set_fold_tree_io ( bool const  fold_tree_io)
void core::io::StructFileRepOptions::set_guarantee_no_DNA ( bool const  guarantee_no_DNA)
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)
void core::io::StructFileRepOptions::set_ignore_waters ( bool const  ignore_waters)
void core::io::StructFileRepOptions::set_ignore_zero_occupancy ( bool const  ignore_zero_occupancy)
void core::io::StructFileRepOptions::set_integration_test_mode ( bool const  setting)
void core::io::StructFileRepOptions::set_keep_input_protonation_state ( bool const  keep_input_protonation_state)
void core::io::StructFileRepOptions::set_maintain_links ( bool const  maintain_links)
void core::io::StructFileRepOptions::set_max_bond_length ( core::Real const  max_bond_length)
void core::io::StructFileRepOptions::set_min_bond_length ( core::Real const  min_bond_length)
void core::io::StructFileRepOptions::set_missing_dens_as_jump ( bool const  missing_dens_as_jump)
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)
void core::io::StructFileRepOptions::set_no_detect_pseudobonds ( bool const  setting)
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)
void core::io::StructFileRepOptions::set_output_alternate_atomids ( bool const  output_alternate_atomids)
void core::io::StructFileRepOptions::set_output_ligands_as_separate_chains ( bool const  output_ligands_as_separate_chains)
void core::io::StructFileRepOptions::set_output_only_asymmetric_unit ( bool const  output_only_asymmetric_unit)
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)
void core::io::StructFileRepOptions::set_output_secondary_structure ( bool const  output_secondary_structure)
void core::io::StructFileRepOptions::set_output_torsions ( bool const  output_torsions)
void core::io::StructFileRepOptions::set_output_virtual ( bool const  output_virtual)
void core::io::StructFileRepOptions::set_output_virtual_zero_occ ( bool const  output_virtual_zero_occ)
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)
void core::io::StructFileRepOptions::set_preserve_crystinfo ( bool const  preserve_crystinfo)
void core::io::StructFileRepOptions::set_preserve_header ( bool const  preserve_header)
void core::io::StructFileRepOptions::set_randomize_missing_coords ( bool const  randomize_missing_coords)
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)
void core::io::StructFileRepOptions::set_remember_unrecognized_water ( bool const  remember_unrecognized_water)
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)
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)
void core::io::StructFileRepOptions::set_suppress_zero_occ_pdb_output ( bool const  setting)
void core::io::StructFileRepOptions::set_use_pdb_format_HETNAM_records ( bool const  setting)
void core::io::StructFileRepOptions::set_write_all_connect_info ( bool const  setting)
void core::io::StructFileRepOptions::set_write_glycan_pdb_codes ( bool const  write_glycan_pdb_codes)
void core::io::StructFileRepOptions::set_write_pdb_link_records ( bool const  setting)
void core::io::StructFileRepOptions::set_write_pdb_parametric_info ( bool const  setting)
void core::io::StructFileRepOptions::set_write_pdb_title_section_records ( bool const  setting)
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
bool core::io::StructFileRepOptions::skip_connect_info ( ) const
bool core::io::StructFileRepOptions::suppress_zero_occ_pdb_output ( ) const
std::string core::io::StructFileRepOptions::type ( ) const
virtual
bool core::io::StructFileRepOptions::use_pdb_format_HETNAM_records ( ) const
bool core::io::StructFileRepOptions::write_all_connect_info ( ) const
bool core::io::StructFileRepOptions::write_glycan_pdb_codes ( ) const
bool core::io::StructFileRepOptions::write_pdb_link_records ( ) const
bool core::io::StructFileRepOptions::write_pdb_parametric_info ( ) const
bool core::io::StructFileRepOptions::write_pdb_title_section_records ( ) const
bool core::io::StructFileRepOptions::write_seqres_records ( ) const

References write_seqres_records_.

Member Data Documentation

bool core::io::StructFileRepOptions::auto_detect_glycan_connections_
private
std::string core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities_
private
std::string core::io::StructFileRepOptions::check_if_residues_are_Ctermini_
private
std::string core::io::StructFileRepOptions::check_if_residues_are_Ntermini_
private
core::Real core::io::StructFileRepOptions::connect_info_cutoff_
private
bool core::io::StructFileRepOptions::constraints_from_link_records_
private
bool core::io::StructFileRepOptions::do_not_autoassign_SS_
private
bool core::io::StructFileRepOptions::exit_if_missing_heavy_atoms_
private
bool core::io::StructFileRepOptions::fold_tree_io_
private
bool core::io::StructFileRepOptions::guarantee_no_DNA_
private
bool core::io::StructFileRepOptions::ignore_sugars_
private
bool core::io::StructFileRepOptions::ignore_unrecognized_res_
private
bool core::io::StructFileRepOptions::ignore_waters_
private
bool core::io::StructFileRepOptions::ignore_zero_occupancy_
private
bool core::io::StructFileRepOptions::integration_test_mode_
private
bool core::io::StructFileRepOptions::keep_input_protonation_state_
private
bool core::io::StructFileRepOptions::maintain_links_
private
core::Real core::io::StructFileRepOptions::max_bond_length_
private
core::Real core::io::StructFileRepOptions::min_bond_length_
private
bool core::io::StructFileRepOptions::missing_dens_as_jump_
private
bool core::io::StructFileRepOptions::mmtf_extra_data_io_
private
bool core::io::StructFileRepOptions::no_chainend_ter_
private
bool core::io::StructFileRepOptions::no_detect_pseudobonds_
private
bool core::io::StructFileRepOptions::no_output_cen_
private
bool core::io::StructFileRepOptions::normalize_to_thk_
private
bool core::io::StructFileRepOptions::output_alternate_atomids_
private
bool core::io::StructFileRepOptions::output_ligands_as_separate_chains_
private
bool core::io::StructFileRepOptions::output_only_asymmetric_unit_
private
bool core::io::StructFileRepOptions::output_pose_cache_data_
private
bool core::io::StructFileRepOptions::output_pose_energies_table_
private
bool core::io::StructFileRepOptions::output_secondary_structure_
private
bool core::io::StructFileRepOptions::output_torsions_
private
bool core::io::StructFileRepOptions::output_virtual_
private
bool core::io::StructFileRepOptions::output_virtual_zero_occ_
private
std::string core::io::StructFileRepOptions::pdb_author_
private
bool core::io::StructFileRepOptions::pdb_comments_
private
bool core::io::StructFileRepOptions::pdb_parents_
private
bool core::io::StructFileRepOptions::per_chain_renumbering_
private
bool core::io::StructFileRepOptions::preserve_crystinfo_
private
bool core::io::StructFileRepOptions::preserve_header_
private
bool core::io::StructFileRepOptions::randomize_missing_coords_
private
bool core::io::StructFileRepOptions::read_only_ATOM_entries_
private
bool core::io::StructFileRepOptions::remember_unrecognized_res_
private
bool core::io::StructFileRepOptions::remember_unrecognized_water_
private
bool core::io::StructFileRepOptions::renumber_pdb_
private
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
bool core::io::StructFileRepOptions::skip_connect_info_
private
bool core::io::StructFileRepOptions::suppress_zero_occ_pdb_output_
private
bool core::io::StructFileRepOptions::use_pdb_format_HETNAM_records_
private
bool core::io::StructFileRepOptions::write_all_connect_info_
private
bool core::io::StructFileRepOptions::write_glycan_pdb_codes_
private
bool core::io::StructFileRepOptions::write_pdb_link_records_
private
bool core::io::StructFileRepOptions::write_pdb_parametric_info_
private
bool core::io::StructFileRepOptions::write_pdb_title_section_records_
private
bool core::io::StructFileRepOptions::write_seqres_records_
private

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