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

#include <RNA_MinimizerOptions.hh>

Inheritance diagram for core::import_pose::options::RNA_MinimizerOptions:

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::Size >	extra_minimize_res_
utility::vector1< core::Size >	extra_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

References extra_minimize_chi_res_.

Referenced by set_extra_minimize_chi_res().

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

(

)

References initialize_from_options(), and core::import_pose::options::RNA_BasicOptions::initialize_from_options().

void core::import_pose::options::RNA_MinimizerOptions::initialize_from_options

(

utility::options::OptionCollection const &

opts

)

References core::import_pose::options::RNA_BasicOptions::initialize_from_options(), set_deriv_check(), set_extra_minimize_chi_res(), set_extra_minimize_res(), set_max_iter(), set_min_type(), set_minimize_all_protein(), set_minimize_bps(), set_minimize_protein_sc(), set_minimize_rounds(), set_minimizer_use_coordinate_constraints(), set_nblist_auto_update(), set_protein_pack_all(), set_protein_packing(), set_protein_packing_distance(), set_skip_o2prime_trials(), set_use_nblist(), and set_vary_bond_geometry().

Referenced by initialize_from_command_line().

void core::import_pose::options::RNA_MinimizerOptions::initialize_from_tag

(

utility::tag::TagCOP const &

tag

)

References deriv_check_, core::import_pose::options::RNA_BasicOptions::initialize_from_tag(), min_type_, minimize_all_protein_, minimize_bps_, minimize_protein_sc_, minimize_rounds_, minimizer_use_coordinate_constraints_, nblist_auto_update_, protein_pack_all_, protein_packing_, protein_packing_distance_, set_deriv_check(), set_extra_minimize_chi_res(), set_extra_minimize_res(), set_max_iter(), set_min_type(), set_minimize_all_protein(), set_minimize_bps(), set_minimize_protein_sc(), set_minimize_rounds(), set_minimizer_use_coordinate_constraints(), set_nblist_auto_update(), set_protein_pack_all(), set_protein_packing(), set_protein_packing_distance(), set_skip_o2prime_trials(), set_use_nblist(), set_vary_bond_geometry(), skip_o2prime_trials_, use_nblist_, and vary_bond_geometry_.

void core::import_pose::options::RNA_MinimizerOptions::list_attributes ( utility::tag::AttributeList &  attlist )

static

References core::import_pose::options::RNA_BasicOptions::list_attributes().

void core::import_pose::options::RNA_MinimizerOptions::list_options_read ( utility::options::OptionKeyList &  opts )

static

References core::import_pose::options::RNA_BasicOptions::list_options_read().

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

References minimizer_use_coordinate_constraints_.

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

References protein_packing_distance_.

void core::import_pose::options::RNA_MinimizerOptions::set_deriv_check ( bool const &  setting )

inline

References deriv_check_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_extra_minimize_chi_res ( utility::vector1< Size > const &  extra_minimize_chi_res )

inline

References extra_minimize_chi_res(), and extra_minimize_chi_res_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_extra_minimize_res ( utility::vector1< Size > const &  extra_minimize_res )

inline

References extra_minimize_res(), and extra_minimize_res_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_max_iter ( core::Size const &  setting )

inline

References max_iter_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_min_type ( std::string const &  setting )

inline

References min_type_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_minimize_all_protein ( bool const &  setting )

inline

References minimize_all_protein_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_minimize_bps ( bool const &  setting )

inline

References minimize_bps_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_minimize_protein_sc ( bool const &  setting )

inline

References minimize_protein_sc_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_minimize_rounds ( core::Size const &  setting )

inline

References minimize_rounds_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_minimizer_use_coordinate_constraints ( bool const &  setting )

inline

References minimizer_use_coordinate_constraints_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_nblist_auto_update ( bool const &  setting )

inline

References nblist_auto_update_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_protein_pack_all ( bool const &  setting )

inline

References protein_pack_all_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_protein_packing ( bool const &  setting )

inline

References protein_packing_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_protein_packing_distance ( core::Real const &  setting )

inline

References protein_packing_distance_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_skip_o2prime_trials ( bool const &  setting )

inline

References skip_o2prime_trials_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_use_nblist ( bool const &  setting )

inline

References use_nblist_.

Referenced by initialize_from_options(), and initialize_from_tag().

void core::import_pose::options::RNA_MinimizerOptions::set_vary_bond_geometry ( bool const &  setting )

inline

References vary_bond_geometry_.

Referenced by initialize_from_options(), and initialize_from_tag().

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

References vary_bond_geometry_.

Referenced by core::import_pose::options::RNA_DeNovoProtocolOptions::initialize_from_options().

Member Data Documentation

bool core::import_pose::options::RNA_MinimizerOptions::deriv_check_

private

Referenced by deriv_check(), initialize_from_tag(), and set_deriv_check().

utility::vector1< core::Size > core::import_pose::options::RNA_MinimizerOptions::extra_minimize_chi_res_

private

Referenced by extra_minimize_chi_res(), and set_extra_minimize_chi_res().

utility::vector1< core::Size > core::import_pose::options::RNA_MinimizerOptions::extra_minimize_res_

private

Referenced by extra_minimize_res(), and set_extra_minimize_res().

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

Referenced by initialize_from_tag(), min_type(), and set_min_type().

bool core::import_pose::options::RNA_MinimizerOptions::minimize_all_protein_

private

Referenced by initialize_from_tag(), minimize_all_protein(), and set_minimize_all_protein().

bool core::import_pose::options::RNA_MinimizerOptions::minimize_bps_

private

Referenced by initialize_from_tag(), minimize_bps(), and set_minimize_bps().

bool core::import_pose::options::RNA_MinimizerOptions::minimize_protein_sc_

private

Referenced by initialize_from_tag(), minimize_protein_sc(), and set_minimize_protein_sc().

core::Size core::import_pose::options::RNA_MinimizerOptions::minimize_rounds_

private

Referenced by initialize_from_tag(), minimize_rounds(), and set_minimize_rounds().

bool core::import_pose::options::RNA_MinimizerOptions::minimizer_use_coordinate_constraints_

private

Referenced by initialize_from_tag(), minimizer_use_coordinate_constraints(), and set_minimizer_use_coordinate_constraints().

bool core::import_pose::options::RNA_MinimizerOptions::nblist_auto_update_

private

Referenced by initialize_from_tag(), nblist_auto_update(), and set_nblist_auto_update().

bool core::import_pose::options::RNA_MinimizerOptions::protein_pack_all_

private

Referenced by initialize_from_tag(), protein_pack_all(), and set_protein_pack_all().

bool core::import_pose::options::RNA_MinimizerOptions::protein_packing_

private

Referenced by initialize_from_tag(), protein_packing(), and set_protein_packing().

core::Real core::import_pose::options::RNA_MinimizerOptions::protein_packing_distance_

private

Referenced by initialize_from_tag(), protein_packing_distance(), and set_protein_packing_distance().

bool core::import_pose::options::RNA_MinimizerOptions::skip_o2prime_trials_

private

Referenced by initialize_from_tag(), set_skip_o2prime_trials(), and skip_o2prime_trials().

bool core::import_pose::options::RNA_MinimizerOptions::use_nblist_

private

Referenced by initialize_from_tag(), set_use_nblist(), and use_nblist().

bool core::import_pose::options::RNA_MinimizerOptions::vary_bond_geometry_

private

Referenced by initialize_from_tag(), set_vary_bond_geometry(), and vary_bond_geometry().

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

• src/core/import_pose/options/RNA_MinimizerOptions.hh
• src/core/import_pose/options/RNA_MinimizerOptions.cc