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>

Public Member Functions
	ImportPoseOptions ()
virtual	~ImportPoseOptions ()
virtual void	parse_my_tag (utility::tag::TagCOP 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
bool	set_up_metal_bonds () const
bool	set_up_metal_constraints () const
core::Real	metal_bond_LJ_multiplier () const
core::Real	metal_bond_dist_constraint_multiplier () const
core::Real	metal_bond_angle_constraint_multiplier () 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)
void	set_set_up_metal_bonds (bool invalue)
void	set_metal_bond_LJ_multiplier (core::Real invalue)
void	set_metal_bond_dist_constraint_multiplier (core::Real invalue)
void	set_metal_bond_angle_constraint_multiplier (core::Real invalue)
Public Member Functions inherited from core::io::pdb::PDB_DReaderOptions
	PDB_DReaderOptions ()
virtual	~PDB_DReaderOptions ()
bool	new_chain_order () const
bool	obey_ENDMDL () const
bool	read_pdb_header () const
bool	read_link_records () const
void	set_new_chain_order (bool setting)
void	set_obey_ENDMDL (bool setting)
void	set_read_pdb_header (bool setting)
void	set_read_link_records (bool setting)
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	preserve_crystinfo () const
bool	missing_dens_as_jump () const
bool	randomize_missing_coords () const
bool	remember_unrecognized_res () const
bool	remember_unrecognized_water () const
bool	write_pdb_link_records () 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_preserve_crystinfo (bool preserve_crystinfo)
void	set_missing_dens_as_jump (bool missing_dens_as_jump)
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_write_pdb_link_records (bool setting)
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_
bool	set_up_metal_bonds_
core::Real	metal_bond_LJ_multiplier_
core::Real	metal_bond_dist_constraint_multiplier_
core::Real	metal_bond_angle_constraint_multiplier_
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

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

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.

References in::auto_setup_metals, in::file::centroid, centroid(), in::file::centroid_input, inout::fold_tree_io, in::file::fullatom, in::metals_angle_constraint_multiplier, in::metals_detection_LJ_multiplier, in::metals_distance_constraint_multiplier, packing::no_optH, option, packing::pack_missing_sidechains, in::file::residue_type_set, set_centroid(), set_fold_tree_io(), set_metal_bond_angle_constraint_multiplier(), set_metal_bond_dist_constraint_multiplier(), set_metal_bond_LJ_multiplier(), set_no_optH(), set_pack_missing_sidechains(), set_read_fold_tree(), set_residue_type_set(), set_rna(), set_set_up_metal_bonds(), set_skip_set_reasonable_fold_tree(), run::skip_set_reasonable_fold_tree, core::import_pose::tr, and user.

Referenced by ImportPoseOptions().

core::Real core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier

(

)

const

References metal_bond_angle_constraint_multiplier_.

Referenced by core::import_pose::build_pose_as_is2().

core::Real core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier

(

)

const

References metal_bond_dist_constraint_multiplier_.

Referenced by core::import_pose::build_pose_as_is2().

core::Real core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier

(

)

const

References metal_bond_LJ_multiplier_.

Referenced by core::import_pose::build_pose_as_is2().

bool core::import_pose::ImportPoseOptions::no_optH

(

)

const

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

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::TagCOP  tag )

virtual

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

References core::io::pdb::PDB_DReaderOptions::parse_my_tag(), set_centroid(), set_fold_tree_io(), set_metal_bond_angle_constraint_multiplier(), set_metal_bond_dist_constraint_multiplier(), set_metal_bond_LJ_multiplier(), set_no_optH(), set_pack_missing_sidechains(), set_read_fold_tree(), set_residue_type_set(), set_rna(), set_set_up_metal_bonds(), and set_skip_set_reasonable_fold_tree().

bool core::import_pose::ImportPoseOptions::read_fold_tree

(

)

const

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

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

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_metal_bond_angle_constraint_multiplier

(

core::Real

invalue

)

References metal_bond_angle_constraint_multiplier_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_metal_bond_dist_constraint_multiplier

(

core::Real

invalue

)

References metal_bond_dist_constraint_multiplier_.

Referenced by init_from_options(), and parse_my_tag().

void core::import_pose::ImportPoseOptions::set_metal_bond_LJ_multiplier

(

core::Real

invalue

)

References metal_bond_LJ_multiplier_.

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

)

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

)

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

)

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

)

References rna(), and rna_.

Referenced by core::import_pose::build_pose(), init_from_options(), parse_my_tag(), core::import_pose::pose_from_pdb(), and core::import_pose::pose_from_pdbstring().

void core::import_pose::ImportPoseOptions::set_set_up_metal_bonds

(

bool

invalue

)

References set_up_metal_bonds_.

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

)

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::set_up_metal_bonds

(

)

const

References set_up_metal_bonds_.

Referenced by core::import_pose::build_pose_as_is2().

bool core::import_pose::ImportPoseOptions::set_up_metal_constraints

(

)

const

References metal_bond_angle_constraint_multiplier_, metal_bond_dist_constraint_multiplier_, and set_up_metal_bonds_.

Referenced by core::import_pose::build_pose_as_is2().

bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree

(

)

const

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.

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().

core::Real core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier_

private

Referenced by metal_bond_angle_constraint_multiplier(), set_metal_bond_angle_constraint_multiplier(), and set_up_metal_constraints().

core::Real core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier_

private

Referenced by metal_bond_dist_constraint_multiplier(), set_metal_bond_dist_constraint_multiplier(), and set_up_metal_constraints().

core::Real core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier_

private

Referenced by metal_bond_LJ_multiplier(), and set_metal_bond_LJ_multiplier().

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

Referenced by pack_missing_sidechains(), and set_pack_missing_sidechains().

bool core::import_pose::ImportPoseOptions::read_fold_tree_

private

Referenced by read_fold_tree(), and set_read_fold_tree().

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

private

Referenced by residue_type_set(), and set_residue_type_set().

bool core::import_pose::ImportPoseOptions::rna_

private

Referenced by rna(), and set_rna().

bool core::import_pose::ImportPoseOptions::set_up_metal_bonds_

private

Referenced by set_set_up_metal_bonds(), set_up_metal_bonds(), and set_up_metal_constraints().

bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree_

private

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:

• symlinks/rosetta/src/core/import_pose/import_pose_options.hh
• symlinks/rosetta/src/core/import_pose/import_pose_options.cc