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core::import_pose::ImportPoseOptions Class Reference

This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data! More...

#include <import_pose_options.hh>

Inheritance diagram for core::import_pose::ImportPoseOptions:
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Public Member Functions

 ImportPoseOptions ()
 
virtual ~ImportPoseOptions ()
 
virtual void parse_my_tag (utility::tag::TagPtr tag)
 
virtual std::string type () const
 
bool centroid () const
 
bool fold_tree_io () const
 
bool no_optH () const
 
bool pack_missing_sidechains () const
 
bool read_fold_tree () const
 
bool rna () const
 
bool skip_set_reasonable_fold_tree () const
 
std::string const & residue_type_set () const
 
void set_centroid (bool centroid)
 
void set_fold_tree_io (bool fold_tree_io)
 
void set_no_optH (bool no_optH)
 
void set_pack_missing_sidechains (bool pack_missing_sidechains)
 
void set_read_fold_tree (bool read_fold_tree)
 
void set_rna (bool rna)
 
void set_skip_set_reasonable_fold_tree_ (bool skip_set_reasonable_fold_tree)
 
void set_residue_type_set (std::string const &residue_type_set)
 
- Public Member Functions inherited from core::io::pdb::PDB_DReaderOptions
 PDB_DReaderOptions ()
 
virtual ~PDB_DReaderOptions ()
 
bool new_chain_order () const
 
bool obey_ENDMDL () const
 
void set_new_chain_order (bool new_chain_order)
 
void set_obey_ENDMDL (bool obey_ENDMDL)
 
- Public Member Functions inherited from core::io::pdb::FileDataOptions
 FileDataOptions ()
 
virtual ~FileDataOptions ()
 
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

bool centroid_
 
bool fold_tree_io_
 
bool no_optH_
 
bool pack_missing_sidechains_
 
bool read_fold_tree_
 
bool rna_
 
bool skip_set_reasonable_fold_tree_
 
std::string residue_type_set_
 

Detailed Description

This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data!

Constructor & Destructor Documentation

core::import_pose::ImportPoseOptions::ImportPoseOptions ( )

References init_from_options().

core::import_pose::ImportPoseOptions::~ImportPoseOptions ( )
virtual

Member Function Documentation

bool core::import_pose::ImportPoseOptions::centroid ( ) const
bool core::import_pose::ImportPoseOptions::fold_tree_io ( ) const
void core::import_pose::ImportPoseOptions::init_from_options ( )
private
bool core::import_pose::ImportPoseOptions::no_optH ( ) const
bool core::import_pose::ImportPoseOptions::pack_missing_sidechains ( ) const
void core::import_pose::ImportPoseOptions::parse_my_tag ( utility::tag::TagPtr  tag)
virtual
bool core::import_pose::ImportPoseOptions::read_fold_tree ( ) const
std::string const & core::import_pose::ImportPoseOptions::residue_type_set ( ) const
bool core::import_pose::ImportPoseOptions::rna ( ) const

References rna_.

Referenced by core::import_pose::pose_from_pdb(), and set_rna().

void core::import_pose::ImportPoseOptions::set_centroid ( bool  centroid)

References centroid(), and centroid_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_fold_tree_io ( bool  fold_tree_io)

References fold_tree_io(), and fold_tree_io_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_no_optH ( bool  no_optH)

References no_optH(), and no_optH_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_pack_missing_sidechains ( bool  pack_missing_sidechains)
void core::import_pose::ImportPoseOptions::set_read_fold_tree ( bool  read_fold_tree)
void core::import_pose::ImportPoseOptions::set_residue_type_set ( std::string const &  residue_type_set)
void core::import_pose::ImportPoseOptions::set_rna ( bool  rna)

References rna(), and rna_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_skip_set_reasonable_fold_tree_ ( bool  skip_set_reasonable_fold_tree)
bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree ( ) const
std::string core::import_pose::ImportPoseOptions::type ( ) const
virtual

Reimplemented from core::io::pdb::PDB_DReaderOptions.

Member Data Documentation

bool core::import_pose::ImportPoseOptions::centroid_
private

Referenced by centroid(), and set_centroid().

bool core::import_pose::ImportPoseOptions::fold_tree_io_
private

Referenced by fold_tree_io(), and set_fold_tree_io().

bool core::import_pose::ImportPoseOptions::no_optH_
private

Referenced by no_optH(), and set_no_optH().

bool core::import_pose::ImportPoseOptions::pack_missing_sidechains_
private
bool core::import_pose::ImportPoseOptions::read_fold_tree_
private
std::string core::import_pose::ImportPoseOptions::residue_type_set_
private
bool core::import_pose::ImportPoseOptions::rna_
private

Referenced by rna(), and set_rna().

bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree_
private

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