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:

[legend]

Public Member Functions
	ImportPoseOptions ()
	Constructor that takes default values from the global OptionCollection object, basic::options::option. More...

	ImportPoseOptions (utility::options::OptionCollection const &options)
	Constructor that takes default values from a provided OptionCollection object. More...

	~ImportPoseOptions () override

void	parse_my_tag (utility::tag::TagCOP tag) override

std::string	type () const override

bool	centroid () const

bool	fold_tree_io () const

bool	membrane () const

bool	no_optH () const

bool	pack_missing_sidechains () const

bool	read_fold_tree () const

bool	skip_set_reasonable_fold_tree () const

core::chemical::TypeSetMode	residue_type_set_mode () 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_membrane (bool membrane)

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_skip_set_reasonable_fold_tree (bool skip_set_reasonable_fold_tree)

void	set_residue_type_set_mode (core::chemical::TypeSetMode residue_type_set_mode)

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)

bool	operator== (ImportPoseOptions const &other) const

bool	operator< (ImportPoseOptions const &other) const

Public Member Functions inherited from core::io::StructFileReaderOptions
	StructFileReaderOptions ()
	Constructor that takes default values from the global OptionCollection object, basic::options::option. More...

	StructFileReaderOptions (utility::options::OptionCollection const &options)
	Constructor that takes default values from a provided OptionCollection object. More...

	~StructFileReaderOptions () override

void	parse_my_tag (utility::tag::TagCOP tag) override

std::string	type () const override

bool	new_chain_order () const

bool	obey_ENDMDL () const

bool	read_pdb_header () const

bool	glycam_pdb_format () const

bool	mmtf_extra_data_io () const

void	set_new_chain_order (bool setting)

void	set_obey_ENDMDL (bool setting)

void	set_read_pdb_header (bool setting)

void	set_glycam_pdb_format (bool setting)

void	set_mmtf_extra_data_io (bool setting)

bool	operator== (StructFileReaderOptions const &other) const

bool	operator< (StructFileReaderOptions const &other) const

Public Member Functions inherited from core::io::StructFileRepOptions
	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...

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)

static void	append_schema_attributes (utility::tag::AttributeList &attrs)

Static Public Member Functions inherited from core::io::StructFileReaderOptions
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)

Static Public Member Functions inherited from core::io::StructFileRepOptions
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...

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 ( )

Constructor that takes default values from the global OptionCollection object, basic::options::option.

References init_from_options().

core::import_pose::ImportPoseOptions::ImportPoseOptions ( utility::options::OptionCollection const & options )

Constructor that takes default values from a provided OptionCollection object.

References init_from_options().

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

overridedefault

Member Function Documentation

void core::import_pose::ImportPoseOptions::append_schema_attributes ( utility::tag::AttributeList & attrs )

static

References core::io::StructFileReaderOptions::append_schema_attributes().

Referenced by core::import_pose::PoseResourceLoader::provide_xml_schema().

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

References centroid_.

Referenced by init_from_options(), core::import_pose::pose_from_file(), core::import_pose::poseOPs_from_files(), 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 ( utility::options::OptionCollection const & options )

private

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

References centroid(), core::pack::pack_missing_sidechains(), set_centroid(), set_fold_tree_io(), set_membrane(), 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_mode(), set_set_up_metal_bonds(), set_skip_set_reasonable_fold_tree(), core::import_pose::tr(), and core::chemical::type_set_mode_from_string().

Referenced by ImportPoseOptions().

void core::import_pose::ImportPoseOptions::list_options_read ( utility::options::OptionKeyList & read_options )

static

References core::io::StructFileReaderOptions::list_options_read(), and core::pack::pack_missing_sidechains().

Referenced by protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter::list_options_read(), protocols::jd3::full_model_inputters::PDBFullModelInputter::list_options_read(), and protocols::jd3::pose_inputters::PDBPoseInputter::list_options_read().

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

References membrane_.

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

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::operator< ( ImportPoseOptions const & other ) const

References centroid_, fold_tree_io_, membrane_, metal_bond_angle_constraint_multiplier_, metal_bond_dist_constraint_multiplier_, metal_bond_LJ_multiplier_, no_optH_, pack_missing_sidechains_, read_fold_tree_, residue_type_set_mode_, set_up_metal_bonds_, and skip_set_reasonable_fold_tree_.

bool core::import_pose::ImportPoseOptions::operator== ( ImportPoseOptions const & other ) const

References centroid_, fold_tree_io_, membrane_, metal_bond_angle_constraint_multiplier_, metal_bond_dist_constraint_multiplier_, metal_bond_LJ_multiplier_, no_optH_, pack_missing_sidechains_, read_fold_tree_, residue_type_set_mode_, set_up_metal_bonds_, and skip_set_reasonable_fold_tree_.

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 )

overridevirtual

Reimplemented from core::io::StructFileRepOptions.

References core::io::StructFileReaderOptions::parse_my_tag(), set_centroid(), set_fold_tree_io(), set_membrane(), 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_mode(), set_set_up_metal_bonds(), set_skip_set_reasonable_fold_tree(), and core::chemical::type_set_mode_from_string().

Referenced by core::import_pose::PoseResourceLoader::create_resource().

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

References read_fold_tree_.

Referenced by protocols::jd3::pose_inputters::PDBPoseInputter::pose_from_input_source(), core::import_pose::pose_from_pdbstring(), and set_read_fold_tree().

core::chemical::TypeSetMode core::import_pose::ImportPoseOptions::residue_type_set_mode ( ) const

References residue_type_set_mode_.

Referenced by core::import_pose::pose_from_file(), core::import_pose::pose_from_pdb_stream(), core::import_pose::poseOPs_from_files(), and set_residue_type_set_mode().

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_membrane ( bool membrane )

References membrane(), and membrane_.

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_mode ( core::chemical::TypeSetMode residue_type_set_mode )

References residue_type_set_mode(), and residue_type_set_mode_.

Referenced by init_from_options(), and parse_my_tag().

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

overridevirtual

Reimplemented from core::io::StructFileRepOptions.

Member Data Documentation

bool core::import_pose::ImportPoseOptions::centroid_

private

Referenced by centroid(), operator<(), operator==(), and set_centroid().

bool core::import_pose::ImportPoseOptions::fold_tree_io_

private

Referenced by fold_tree_io(), operator<(), operator==(), and set_fold_tree_io().

bool core::import_pose::ImportPoseOptions::membrane_

private

Referenced by membrane(), operator<(), operator==(), and set_membrane().

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

private

Referenced by metal_bond_angle_constraint_multiplier(), operator<(), operator==(), 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(), operator<(), operator==(), 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(), operator<(), operator==(), and set_metal_bond_LJ_multiplier().

bool core::import_pose::ImportPoseOptions::no_optH_

private

Referenced by no_optH(), operator<(), operator==(), and set_no_optH().

bool core::import_pose::ImportPoseOptions::pack_missing_sidechains_

private

Referenced by operator<(), operator==(), pack_missing_sidechains(), and set_pack_missing_sidechains().

bool core::import_pose::ImportPoseOptions::read_fold_tree_

private

Referenced by operator<(), operator==(), read_fold_tree(), and set_read_fold_tree().

core::chemical::TypeSetMode core::import_pose::ImportPoseOptions::residue_type_set_mode_

private

Referenced by operator<(), operator==(), residue_type_set_mode(), and set_residue_type_set_mode().

bool core::import_pose::ImportPoseOptions::set_up_metal_bonds_

private

Referenced by operator<(), operator==(), 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 operator<(), operator==(), 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

Private Attributes
bool	centroid_

bool	fold_tree_io_

bool	membrane_

bool	no_optH_

bool	pack_missing_sidechains_

bool	read_fold_tree_

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_

core::chemical::TypeSetMode	residue_type_set_mode_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation