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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:
Inheritance graph
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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...
 

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_
 

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
bool core::import_pose::ImportPoseOptions::centroid ( ) const
bool core::import_pose::ImportPoseOptions::fold_tree_io ( ) const
void core::import_pose::ImportPoseOptions::init_from_options ( utility::options::OptionCollection const &  options)
private
void core::import_pose::ImportPoseOptions::list_options_read ( utility::options::OptionKeyList &  read_options)
static
bool core::import_pose::ImportPoseOptions::membrane ( ) const
core::Real core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier ( ) const
core::Real core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier ( ) const
core::Real core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier ( ) const
bool core::import_pose::ImportPoseOptions::no_optH ( ) const
bool core::import_pose::ImportPoseOptions::operator< ( ImportPoseOptions const &  other) const
bool core::import_pose::ImportPoseOptions::operator== ( ImportPoseOptions const &  other) const
bool core::import_pose::ImportPoseOptions::pack_missing_sidechains ( ) const
void core::import_pose::ImportPoseOptions::parse_my_tag ( utility::tag::TagCOP  tag)
overridevirtual
bool core::import_pose::ImportPoseOptions::read_fold_tree ( ) const
core::chemical::TypeSetMode core::import_pose::ImportPoseOptions::residue_type_set_mode ( ) const
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)
void core::import_pose::ImportPoseOptions::set_metal_bond_dist_constraint_multiplier ( core::Real  invalue)
void core::import_pose::ImportPoseOptions::set_metal_bond_LJ_multiplier ( core::Real  invalue)
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_mode ( core::chemical::TypeSetMode  residue_type_set_mode)
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)
bool core::import_pose::ImportPoseOptions::set_up_metal_bonds ( ) const
bool core::import_pose::ImportPoseOptions::set_up_metal_constraints ( ) const
bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree ( ) const
std::string core::import_pose::ImportPoseOptions::type ( ) const
overridevirtual

Reimplemented from core::io::StructFileRepOptions.

Member Data Documentation

bool core::import_pose::ImportPoseOptions::centroid_
private
bool core::import_pose::ImportPoseOptions::fold_tree_io_
private
bool core::import_pose::ImportPoseOptions::membrane_
private
core::Real core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier_
private
core::Real core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier_
private
core::Real core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier_
private
bool core::import_pose::ImportPoseOptions::no_optH_
private
bool core::import_pose::ImportPoseOptions::pack_missing_sidechains_
private
bool core::import_pose::ImportPoseOptions::read_fold_tree_
private
core::chemical::TypeSetMode core::import_pose::ImportPoseOptions::residue_type_set_mode_
private
bool core::import_pose::ImportPoseOptions::set_up_metal_bonds_
private
bool core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree_
private

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