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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Collaboration 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!

Definition at line 34 of file import_pose_options.hh.

Constructor & Destructor Documentation

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

Definition at line 59 of file import_pose_options.cc.

References init_from_options().

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

virtual

Definition at line 61 of file import_pose_options.cc.

Member Function Documentation

bool core::import_pose::ImportPoseOptions::centroid ( ) const

Definition at line 80 of file import_pose_options.cc.

References centroid_.

Referenced by init_from_options(), core::import_pose::pose_from_pdb(), core::import_pose::poseOPs_from_pdbs(), and set_centroid().

bool core::import_pose::ImportPoseOptions::fold_tree_io ( ) const

Definition at line 81 of file import_pose_options.cc.

References fold_tree_io_.

Referenced by core::import_pose::read_additional_pdb_data(), and set_fold_tree_io().

void core::import_pose::ImportPoseOptions::init_from_options ( )

private

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

Definition at line 102 of file import_pose_options.cc.

References centroid(), core::pack::pack_missing_sidechains(), set_centroid(), set_fold_tree_io(), set_no_optH(), set_pack_missing_sidechains(), set_read_fold_tree(), set_residue_type_set(), set_rna(), set_skip_set_reasonable_fold_tree_(), and core::import_pose::tr().

Referenced by ImportPoseOptions().

bool core::import_pose::ImportPoseOptions::no_optH ( ) const

Definition at line 82 of file import_pose_options.cc.

References no_optH_.

Referenced by core::import_pose::build_pose_as_is2(), and set_no_optH().

bool core::import_pose::ImportPoseOptions::pack_missing_sidechains ( ) const

Definition at line 83 of file import_pose_options.cc.

References pack_missing_sidechains_.

Referenced by core::import_pose::build_pose_as_is2(), and set_pack_missing_sidechains().

void core::import_pose::ImportPoseOptions::parse_my_tag ( utility::tag::TagPtr tag)

virtual

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

Definition at line 65 of file import_pose_options.cc.

References core::io::pdb::PDB_DReaderOptions::parse_my_tag(), set_centroid(), set_fold_tree_io(), set_no_optH(), set_pack_missing_sidechains(), set_read_fold_tree(), set_residue_type_set(), set_rna(), and set_skip_set_reasonable_fold_tree_().

bool core::import_pose::ImportPoseOptions::read_fold_tree ( ) const

Definition at line 84 of file import_pose_options.cc.

References read_fold_tree_.

Referenced by core::import_pose::pose_from_pdb_stream(), and set_read_fold_tree().

std::string const & core::import_pose::ImportPoseOptions::residue_type_set ( ) const

Definition at line 88 of file import_pose_options.cc.

References residue_type_set_.

Referenced by core::import_pose::pose_from_pdb_stream(), and set_residue_type_set().

bool core::import_pose::ImportPoseOptions::rna ( ) const

Definition at line 85 of file import_pose_options.cc.

References rna_.

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

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

Definition at line 91 of file import_pose_options.cc.

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)

Definition at line 92 of file import_pose_options.cc.

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)

Definition at line 93 of file import_pose_options.cc.

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)

Definition at line 94 of file import_pose_options.cc.

References pack_missing_sidechains(), and pack_missing_sidechains_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_read_fold_tree ( bool read_fold_tree)

Definition at line 95 of file import_pose_options.cc.

References read_fold_tree(), and read_fold_tree_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_residue_type_set ( std::string const & residue_type_set)

Definition at line 99 of file import_pose_options.cc.

References residue_type_set(), and residue_type_set_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_rna ( bool rna)

Definition at line 96 of file import_pose_options.cc.

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)

Definition at line 97 of file import_pose_options.cc.

References skip_set_reasonable_fold_tree(), and skip_set_reasonable_fold_tree_.

Referenced by init_from_options(), and parse_my_tag().

bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree ( ) const

Definition at line 86 of file import_pose_options.cc.

References skip_set_reasonable_fold_tree_.

Referenced by core::import_pose::build_pose_as_is2(), and set_skip_set_reasonable_fold_tree_().

std::string core::import_pose::ImportPoseOptions::type ( ) const

virtual

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

Definition at line 63 of file import_pose_options.cc.

Member Data Documentation

bool core::import_pose::ImportPoseOptions::centroid_

private

Definition at line 72 of file import_pose_options.hh.

Referenced by centroid(), and set_centroid().

bool core::import_pose::ImportPoseOptions::fold_tree_io_

private

Definition at line 73 of file import_pose_options.hh.

Referenced by fold_tree_io(), and set_fold_tree_io().

bool core::import_pose::ImportPoseOptions::no_optH_

private

Definition at line 74 of file import_pose_options.hh.

Referenced by no_optH(), and set_no_optH().

bool core::import_pose::ImportPoseOptions::pack_missing_sidechains_

private

Definition at line 75 of file import_pose_options.hh.

Referenced by pack_missing_sidechains(), and set_pack_missing_sidechains().

bool core::import_pose::ImportPoseOptions::read_fold_tree_

private

Definition at line 76 of file import_pose_options.hh.

Referenced by read_fold_tree(), and set_read_fold_tree().

std::string core::import_pose::ImportPoseOptions::residue_type_set_

private

Definition at line 80 of file import_pose_options.hh.

Referenced by residue_type_set(), and set_residue_type_set().

bool core::import_pose::ImportPoseOptions::rna_

private

Definition at line 77 of file import_pose_options.hh.

Referenced by rna(), and set_rna().

bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree_

private

Definition at line 78 of file import_pose_options.hh.

Referenced by set_skip_set_reasonable_fold_tree_(), and skip_set_reasonable_fold_tree().

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

src/core/import_pose/import_pose_options.hh
src/core/import_pose/import_pose_options.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation