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core::import_pose::options::RNA_MinimizerOptions Class Reference

#include <RNA_MinimizerOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_MinimizerOptions:
Inheritance graph
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Public Member Functions

 RNA_MinimizerOptions ()
 
RNA_MinimizerOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
void initialize_from_options (utility::options::OptionCollection const &opts)
 
void initialize_from_tag (utility::tag::TagCOP const &tag)
 
void parse_my_tag (utility::tag::TagCOP) override
 Initialize from the recursive "tag" structure. More...
 
std::string type () const override
 The class name (its type) for a particular instance. This function allows for better error message delivery. More...
 
void set_vary_bond_geometry (bool const &setting)
 
bool vary_bond_geometry () const
 
void set_extra_minimize_res (utility::vector1< Size > const &extra_minimize_res)
 
utility::vector1< Size > const & extra_minimize_res () const
 
void set_extra_minimize_chi_res (utility::vector1< Size > const &extra_minimize_chi_res)
 
utility::vector1< Size > const & extra_minimize_chi_res () const
 
void set_minimizer_use_coordinate_constraints (bool const &setting)
 
bool minimizer_use_coordinate_constraints () const
 
void set_min_type (std::string const &setting)
 
std::string min_type () const
 
void set_minimize_bps (bool const &setting)
 
bool minimize_bps () const
 
void set_minimize_all_protein (bool const &setting)
 
bool minimize_all_protein () const
 
void set_minimize_protein_sc (bool const &setting)
 
bool minimize_protein_sc () const
 
void set_protein_packing (bool const &setting)
 
bool protein_packing () const
 
void set_protein_pack_all (bool const &setting)
 
bool protein_pack_all () const
 
void set_protein_packing_distance (core::Real const &setting)
 
core::Real protein_packing_distance () const
 
void set_deriv_check (bool const &setting)
 
bool deriv_check () const
 
void set_skip_o2prime_trials (bool const &setting)
 
bool skip_o2prime_trials () const
 
void set_minimize_rounds (core::Size const &setting)
 
core::Size minimize_rounds () const
 
void set_use_nblist (bool const &setting)
 
bool use_nblist () const
 
void set_nblist_auto_update (bool const &setting)
 
bool nblist_auto_update () const
 
void set_max_iter (core::Size const &setting)
 
core::Size max_iter () const
 
- Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions
 RNA_BasicOptions ()
 
RNA_BasicOptionsOP clone () const
 clone the options More...
 
void initialize_from_command_line ()
 
void initialize_from_options (utility::options::OptionCollection const &opts)
 
void initialize_from_tag (utility::tag::TagCOP const &tag)
 
void set_dump_pdb (bool const setting)
 
bool dump_pdb () const
 
void set_move_first_rigid_body (bool const &setting)
 
bool move_first_rigid_body () const
 
void set_dock_into_density (bool const &setting)
 
bool dock_into_density () const
 
void set_model_with_density (bool const &setting)
 
bool model_with_density () const
 
void set_verbose (bool const &setting)
 
bool verbose () const
 

Static Public Member Functions

static void list_attributes (utility::tag::AttributeList &attlist)
 
static void list_options_read (utility::options::OptionKeyList &opts)
 
- Static Public Member Functions inherited from core::import_pose::options::RNA_BasicOptions
static void list_attributes (utility::tag::AttributeList &attlist)
 
static void list_options_read (utility::options::OptionKeyList &opts)
 

Private Attributes

core::Size minimize_rounds_
 
bool deriv_check_
 
bool skip_o2prime_trials_
 
bool vary_bond_geometry_
 
utility::vector1< core::Sizeextra_minimize_res_
 
utility::vector1< core::Sizeextra_minimize_chi_res_
 
bool minimizer_use_coordinate_constraints_
 
std::string min_type_
 
bool minimize_bps_
 
bool minimize_all_protein_
 
bool minimize_protein_sc_
 
bool protein_packing_
 
bool protein_pack_all_
 
core::Real protein_packing_distance_
 
bool use_nblist_
 
bool nblist_auto_update_
 
core::Size max_iter_
 

Constructor & Destructor Documentation

core::import_pose::options::RNA_MinimizerOptions::RNA_MinimizerOptions ( )

Member Function Documentation

RNA_MinimizerOptionsOP core::import_pose::options::RNA_MinimizerOptions::clone ( ) const

clone the options

bool core::import_pose::options::RNA_MinimizerOptions::deriv_check ( ) const
inline

References deriv_check_.

utility::vector1< Size > const& core::import_pose::options::RNA_MinimizerOptions::extra_minimize_chi_res ( ) const
inline
utility::vector1< Size > const& core::import_pose::options::RNA_MinimizerOptions::extra_minimize_res ( ) const
inline

References extra_minimize_res_.

Referenced by set_extra_minimize_res().

void core::import_pose::options::RNA_MinimizerOptions::initialize_from_command_line ( )
void core::import_pose::options::RNA_MinimizerOptions::initialize_from_options ( utility::options::OptionCollection const &  opts)
void core::import_pose::options::RNA_MinimizerOptions::initialize_from_tag ( utility::tag::TagCOP const &  tag)
void core::import_pose::options::RNA_MinimizerOptions::list_attributes ( utility::tag::AttributeList &  attlist)
static
void core::import_pose::options::RNA_MinimizerOptions::list_options_read ( utility::options::OptionKeyList &  opts)
static
core::Size core::import_pose::options::RNA_MinimizerOptions::max_iter ( ) const
inline

References max_iter_.

std::string core::import_pose::options::RNA_MinimizerOptions::min_type ( ) const
inline

References min_type_.

bool core::import_pose::options::RNA_MinimizerOptions::minimize_all_protein ( ) const
inline

References minimize_all_protein_.

bool core::import_pose::options::RNA_MinimizerOptions::minimize_bps ( ) const
inline

References minimize_bps_.

bool core::import_pose::options::RNA_MinimizerOptions::minimize_protein_sc ( ) const
inline

References minimize_protein_sc_.

core::Size core::import_pose::options::RNA_MinimizerOptions::minimize_rounds ( ) const
inline

References minimize_rounds_.

bool core::import_pose::options::RNA_MinimizerOptions::minimizer_use_coordinate_constraints ( ) const
inline
bool core::import_pose::options::RNA_MinimizerOptions::nblist_auto_update ( ) const
inline

References nblist_auto_update_.

void core::import_pose::options::RNA_MinimizerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlineoverridevirtual

Initialize from the recursive "tag" structure.

Reimplemented from core::import_pose::options::RNA_BasicOptions.

bool core::import_pose::options::RNA_MinimizerOptions::protein_pack_all ( ) const
inline

References protein_pack_all_.

bool core::import_pose::options::RNA_MinimizerOptions::protein_packing ( ) const
inline

References protein_packing_.

core::Real core::import_pose::options::RNA_MinimizerOptions::protein_packing_distance ( ) const
inline
void core::import_pose::options::RNA_MinimizerOptions::set_deriv_check ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_extra_minimize_chi_res ( utility::vector1< Size > const &  extra_minimize_chi_res)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_extra_minimize_res ( utility::vector1< Size > const &  extra_minimize_res)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_max_iter ( core::Size const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_min_type ( std::string const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_minimize_all_protein ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_minimize_bps ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_minimize_protein_sc ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_minimize_rounds ( core::Size const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_minimizer_use_coordinate_constraints ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_nblist_auto_update ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_protein_pack_all ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_protein_packing ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_protein_packing_distance ( core::Real const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_skip_o2prime_trials ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_use_nblist ( bool const &  setting)
inline
void core::import_pose::options::RNA_MinimizerOptions::set_vary_bond_geometry ( bool const &  setting)
inline
bool core::import_pose::options::RNA_MinimizerOptions::skip_o2prime_trials ( ) const
inline

References skip_o2prime_trials_.

std::string core::import_pose::options::RNA_MinimizerOptions::type ( ) const
inlineoverridevirtual

The class name (its type) for a particular instance. This function allows for better error message delivery.

Reimplemented from core::import_pose::options::RNA_BasicOptions.

bool core::import_pose::options::RNA_MinimizerOptions::use_nblist ( ) const
inline

References use_nblist_.

bool core::import_pose::options::RNA_MinimizerOptions::vary_bond_geometry ( ) const
inline

Member Data Documentation

bool core::import_pose::options::RNA_MinimizerOptions::deriv_check_
private
utility::vector1< core::Size > core::import_pose::options::RNA_MinimizerOptions::extra_minimize_chi_res_
private
utility::vector1< core::Size > core::import_pose::options::RNA_MinimizerOptions::extra_minimize_res_
private
core::Size core::import_pose::options::RNA_MinimizerOptions::max_iter_
private

Referenced by max_iter(), and set_max_iter().

std::string core::import_pose::options::RNA_MinimizerOptions::min_type_
private
bool core::import_pose::options::RNA_MinimizerOptions::minimize_all_protein_
private
bool core::import_pose::options::RNA_MinimizerOptions::minimize_bps_
private
bool core::import_pose::options::RNA_MinimizerOptions::minimize_protein_sc_
private
core::Size core::import_pose::options::RNA_MinimizerOptions::minimize_rounds_
private
bool core::import_pose::options::RNA_MinimizerOptions::minimizer_use_coordinate_constraints_
private
bool core::import_pose::options::RNA_MinimizerOptions::nblist_auto_update_
private
bool core::import_pose::options::RNA_MinimizerOptions::protein_pack_all_
private
bool core::import_pose::options::RNA_MinimizerOptions::protein_packing_
private
core::Real core::import_pose::options::RNA_MinimizerOptions::protein_packing_distance_
private
bool core::import_pose::options::RNA_MinimizerOptions::skip_o2prime_trials_
private
bool core::import_pose::options::RNA_MinimizerOptions::use_nblist_
private
bool core::import_pose::options::RNA_MinimizerOptions::vary_bond_geometry_
private

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