Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::io::pdb::FileDataOptions Class Reference

#include <file_data_options.hh>

Inheritance diagram for core::io::pdb::FileDataOptions:
Inheritance graph
[legend]
Collaboration diagram for core::io::pdb::FileDataOptions:
Collaboration graph
[legend]

Public Member Functions

 FileDataOptions ()
 
virtual ~FileDataOptions ()
 
virtual void parse_my_tag (utility::tag::TagPtr tag)
 
virtual std::string type () const
 
std::string check_if_residues_are_Ntermini () const
 
std::string check_if_residues_are_Ctermini () const
 
bool exit_if_missing_heavy_atoms () const
 
bool ignore_unrecognized_res () const
 
bool ignore_waters () const
 
bool ignore_zero_occupancy () const
 
bool keep_input_protonation_state () const
 
bool preserve_header () const
 
bool randomize_missing_coords () const
 
bool remember_unrecognized_res () const
 
bool remember_unrecognized_water () const
 
std::string const & chains_whose_residues_are_separate_chemical_entities () const
 
void set_check_if_residues_are_Ntermini (std::string check_if_residues_are_Ntermini)
 
void set_check_if_residues_are_Ctermini (std::string check_if_residues_are_Ctermini)
 
void set_exit_if_missing_heavy_atoms (bool exit_if_missing_heavy_atoms)
 
void set_ignore_unrecognized_res (bool ignore_unrecognized_res)
 
void set_ignore_waters (bool ignore_waters)
 
void set_ignore_zero_occupancy (bool ignore_zero_occupancy)
 
void set_keep_input_protonation_state (bool keep_input_protonation_state)
 
void set_preserve_header (bool preserve_header)
 
void set_randomize_missing_coords (bool randomize_missing_coords)
 
void set_remember_unrecognized_res (bool remember_unrecognized_res)
 
void set_remember_unrecognized_water (bool remember_unrecognized_water)
 
void set_chains_whose_residues_are_separate_chemical_entities (std::string const &setting)
 

Private Member Functions

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

Private Attributes

std::string check_if_residues_are_Ntermini_
 
std::string check_if_residues_are_Ctermini_
 
bool exit_if_missing_heavy_atoms_
 
bool ignore_unrecognized_res_
 
bool ignore_waters_
 
bool ignore_zero_occupancy_
 
bool keep_input_protonation_state_
 
bool preserve_header_
 
bool randomize_missing_coords_
 
bool remember_unrecognized_res_
 
bool remember_unrecognized_water_
 
std::string chains_whose_residues_are_separate_chemical_entities_
 

Detailed Description

Definition at line 34 of file file_data_options.hh.

Constructor & Destructor Documentation

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

Definition at line 32 of file file_data_options.cc.

References init_from_options().

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

Definition at line 34 of file file_data_options.cc.

Member Function Documentation

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

Definition at line 71 of file file_data_options.cc.

References chains_whose_residues_are_separate_chemical_entities_.

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

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

Definition at line 61 of file file_data_options.cc.

References check_if_residues_are_Ctermini_.

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

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

Definition at line 60 of file file_data_options.cc.

References check_if_residues_are_Ntermini_.

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

bool core::io::pdb::FileDataOptions::exit_if_missing_heavy_atoms ( ) const

Definition at line 62 of file file_data_options.cc.

References exit_if_missing_heavy_atoms_.

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

bool core::io::pdb::FileDataOptions::ignore_unrecognized_res ( ) const

Definition at line 63 of file file_data_options.cc.

References ignore_unrecognized_res_.

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

bool core::io::pdb::FileDataOptions::ignore_waters ( ) const

Definition at line 64 of file file_data_options.cc.

References ignore_waters_.

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

bool core::io::pdb::FileDataOptions::ignore_zero_occupancy ( ) const

Definition at line 65 of file file_data_options.cc.

References ignore_zero_occupancy_.

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

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

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

Definition at line 112 of file file_data_options.cc.

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

Referenced by FileDataOptions().

bool core::io::pdb::FileDataOptions::keep_input_protonation_state ( ) const

Definition at line 66 of file file_data_options.cc.

References keep_input_protonation_state_.

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

void core::io::pdb::FileDataOptions::parse_my_tag ( utility::tag::TagPtr  tag)
virtual

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

Definition at line 36 of file file_data_options.cc.

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

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

bool core::io::pdb::FileDataOptions::preserve_header ( ) const

Definition at line 67 of file file_data_options.cc.

References preserve_header_.

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

bool core::io::pdb::FileDataOptions::randomize_missing_coords ( ) const

Definition at line 68 of file file_data_options.cc.

References randomize_missing_coords_.

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

bool core::io::pdb::FileDataOptions::remember_unrecognized_res ( ) const

Definition at line 69 of file file_data_options.cc.

References remember_unrecognized_res_.

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

bool core::io::pdb::FileDataOptions::remember_unrecognized_water ( ) const

Definition at line 70 of file file_data_options.cc.

References remember_unrecognized_water_.

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

void core::io::pdb::FileDataOptions::set_chains_whose_residues_are_separate_chemical_entities ( std::string const &  setting)

Definition at line 108 of file file_data_options.cc.

References chains_whose_residues_are_separate_chemical_entities(), and chains_whose_residues_are_separate_chemical_entities_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_check_if_residues_are_Ctermini ( std::string  check_if_residues_are_Ctermini)

Definition at line 78 of file file_data_options.cc.

References check_if_residues_are_Ctermini(), and check_if_residues_are_Ctermini_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_check_if_residues_are_Ntermini ( std::string  check_if_residues_are_Ntermini)

Definition at line 76 of file file_data_options.cc.

References check_if_residues_are_Ntermini(), and check_if_residues_are_Ntermini_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_exit_if_missing_heavy_atoms ( bool  exit_if_missing_heavy_atoms)

Definition at line 81 of file file_data_options.cc.

References exit_if_missing_heavy_atoms(), and exit_if_missing_heavy_atoms_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_unrecognized_res ( bool  ignore_unrecognized_res)

Definition at line 84 of file file_data_options.cc.

References ignore_unrecognized_res(), and ignore_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_waters ( bool  ignore_waters)

Definition at line 87 of file file_data_options.cc.

References ignore_waters(), and ignore_waters_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_ignore_zero_occupancy ( bool  ignore_zero_occupancy)

Definition at line 90 of file file_data_options.cc.

References ignore_zero_occupancy(), and ignore_zero_occupancy_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_keep_input_protonation_state ( bool  keep_input_protonation_state)

Definition at line 93 of file file_data_options.cc.

References keep_input_protonation_state(), and keep_input_protonation_state_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_preserve_header ( bool  preserve_header)

Definition at line 96 of file file_data_options.cc.

References preserve_header(), and preserve_header_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_randomize_missing_coords ( bool  randomize_missing_coords)

Definition at line 99 of file file_data_options.cc.

References randomize_missing_coords(), and randomize_missing_coords_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_remember_unrecognized_res ( bool  remember_unrecognized_res)

Definition at line 102 of file file_data_options.cc.

References remember_unrecognized_res(), and remember_unrecognized_res_.

Referenced by init_from_options(), and parse_my_tag().

void core::io::pdb::FileDataOptions::set_remember_unrecognized_water ( bool  remember_unrecognized_water)

Definition at line 105 of file file_data_options.cc.

References remember_unrecognized_water(), and remember_unrecognized_water_.

Referenced by init_from_options(), and parse_my_tag().

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

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

Definition at line 55 of file file_data_options.cc.

Member Data Documentation

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

Definition at line 95 of file file_data_options.hh.

Referenced by chains_whose_residues_are_separate_chemical_entities(), and set_chains_whose_residues_are_separate_chemical_entities().

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

Definition at line 84 of file file_data_options.hh.

Referenced by check_if_residues_are_Ctermini(), and set_check_if_residues_are_Ctermini().

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

Definition at line 83 of file file_data_options.hh.

Referenced by check_if_residues_are_Ntermini(), and set_check_if_residues_are_Ntermini().

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

Definition at line 85 of file file_data_options.hh.

Referenced by exit_if_missing_heavy_atoms(), and set_exit_if_missing_heavy_atoms().

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

Definition at line 86 of file file_data_options.hh.

Referenced by ignore_unrecognized_res(), and set_ignore_unrecognized_res().

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

Definition at line 87 of file file_data_options.hh.

Referenced by ignore_waters(), and set_ignore_waters().

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

Definition at line 88 of file file_data_options.hh.

Referenced by ignore_zero_occupancy(), and set_ignore_zero_occupancy().

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

Definition at line 89 of file file_data_options.hh.

Referenced by keep_input_protonation_state(), and set_keep_input_protonation_state().

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

Definition at line 90 of file file_data_options.hh.

Referenced by preserve_header(), and set_preserve_header().

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

Definition at line 91 of file file_data_options.hh.

Referenced by randomize_missing_coords(), and set_randomize_missing_coords().

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

Definition at line 92 of file file_data_options.hh.

Referenced by remember_unrecognized_res(), and set_remember_unrecognized_res().

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

Definition at line 93 of file file_data_options.hh.

Referenced by remember_unrecognized_water(), and set_remember_unrecognized_water().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:26:41 for Rosetta 3.5 by   doxygen 1.8.4