protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper Class Reference

#include <StepWiseRNA_RotamerGenerator_Wrapper.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper:

Public Member Functions
	StepWiseRNA_RotamerGenerator_Wrapper (core::pose::Pose const &pose, utility::vector1< core::Size > const &moving_suite_list, bool const &sample_sugar_and_base1, bool const &sample_sugar_and_base2)
virtual	~StepWiseRNA_RotamerGenerator_Wrapper ()
bool	has_another_rotamer () const
utility::vector1< Torsion_Info >	get_next_rotamer ()
void	set_sample_extra_rotamers (bool const &setting)
void	set_fast (bool const &setting)
void	set_sample_chi_torsion (bool const &setting)
void	set_include_syn_chi (bool const include_syn_chi)
void	set_force_syn_chi_res_list (utility::vector1< core::Size > const &setting)
void	set_force_north_ribose_list (utility::vector1< core::Size > const &setting)
void	set_force_south_ribose_list (utility::vector1< core::Size > const &setting)
void	set_bin_size (core::Size const setting)
void	set_extra_epsilon (bool const setting)
void	set_extra_beta (bool const setting)
void	set_extra_anti_chi (bool const setting)
void	set_extra_syn_chi (bool const setting)
void	set_exclude_alpha_beta_gamma_sampling (bool const setting)
void	set_allow_syn_pyrimidine (bool const setting)
core::Size	group_rotamer (core::Size const list_position)
core::Size	subgroup_rotamer (core::Size const list_position)
core::Size	rotamer_generator_list_size ()
void	initialize_rotamer_generator_list ()

Private Member Functions
StepWiseRNA_RotamerGeneratorOP const	setup_rotamer_generator (core::Size const list_position)
PuckerState	Get_residue_pucker_state_internal (core::pose::Pose const &pose, Size list_position, std::string which_sugar, bool sample_sugar_pucker) const

Private Attributes
core::pose::Pose const &	pose_
utility::vector1< core::Size > const	moving_suite_list_
bool const	sample_sugar_and_base1_
bool const	sample_sugar_and_base2_
bool	sample_extra_rotamers_
bool	fast_
bool	verbose_
bool	sample_chi_torsion_
bool	include_syn_chi_
bool	Is_prepend_
utility::vector1< core::Size >	force_syn_chi_res_list_
utility::vector1< core::Size >	force_north_ribose_list_
utility::vector1< core::Size >	force_south_ribose_list_
core::Size	bin_size_
bool	extra_epsilon_
bool	extra_beta_
bool	extra_anti_chi_
bool	extra_syn_chi_
bool	exclude_alpha_beta_gamma_sampling_
bool	allow_syn_pyrimidine_
utility::vector1 < StepWiseRNA_RotamerGeneratorOP >	rotamer_generator_list_

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::StepWiseRNA_RotamerGenerator_Wrapper	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	moving_suite_list,
		bool const &	sample_sugar_and_base1,
		bool const &	sample_sugar_and_base2
	)

References protocols::swa::rna::assert_can_append(), protocols::swa::rna::assert_can_prepend(), force_north_ribose_list_, force_south_ribose_list_, force_syn_chi_res_list_, Is_prepend_, moving_suite_list_, and protocols::swa::rna::Output_seq_num_list().

protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::~StepWiseRNA_RotamerGenerator_Wrapper ( )

virtual

Member Function Documentation

utility::vector1< Torsion_Info > protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::get_next_rotamer

(

)

References has_another_rotamer(), moving_suite_list_, rotamer_generator_list_, and setup_rotamer_generator().

PuckerState protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::Get_residue_pucker_state_internal ( core::pose::Pose const &  pose, Size  list_position, std::string  which_sugar, bool  sample_sugar_pucker  ) const

private

References protocols::swa::rna::ALL, protocols::swa::rna::Contain_seq_num(), force_north_ribose_list_, force_south_ribose_list_, protocols::swa::rna::Get_residue_pucker_state(), Is_prepend_, moving_suite_list_, protocols::swa::rna::NORTH, rotamer_generator_list_, and protocols::swa::rna::SOUTH.

Referenced by setup_rotamer_generator().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::group_rotamer

(

core::Size const

list_position)

References rotamer_generator_list_.

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::has_another_rotamer

(

)

const

References rotamer_generator_list_.

Referenced by get_next_rotamer().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list

(

)

References allow_syn_pyrimidine_, protocols::swa::rna::Contain_seq_num(), exclude_alpha_beta_gamma_sampling_, extra_anti_chi_, extra_beta_, extra_epsilon_, extra_syn_chi_, force_north_ribose_list_, force_south_ribose_list_, force_syn_chi_res_list_, include_syn_chi_, Is_prepend_, moving_suite_list_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), rotamer_generator_list_, sample_extra_rotamers_, sample_sugar_and_base1_, sample_sugar_and_base2_, and setup_rotamer_generator().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::rotamer_generator_list_size ( )

inline

References rotamer_generator_list_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_allow_syn_pyrimidine ( bool const  setting)

inline

References allow_syn_pyrimidine_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_bin_size ( core::Size const  setting)

inline

References bin_size_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_exclude_alpha_beta_gamma_sampling ( bool const  setting)

inline

References exclude_alpha_beta_gamma_sampling_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_extra_anti_chi ( bool const  setting)

inline

References extra_anti_chi_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_extra_beta ( bool const  setting)

inline

References extra_beta_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_extra_epsilon ( bool const  setting)

inline

References extra_epsilon_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_extra_syn_chi ( bool const  setting)

inline

References extra_syn_chi_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_fast

(

bool const &

setting)

References fast_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_force_north_ribose_list ( utility::vector1< core::Size > const &  setting)

inline

References force_north_ribose_list_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_force_south_ribose_list ( utility::vector1< core::Size > const &  setting)

inline

References force_south_ribose_list_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_force_syn_chi_res_list ( utility::vector1< core::Size > const &  setting)

inline

References force_syn_chi_res_list_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_include_syn_chi ( bool const  include_syn_chi)

inline

References include_syn_chi_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_sample_chi_torsion ( bool const &  setting)

inline

References sample_chi_torsion_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::set_sample_extra_rotamers ( bool const &  setting)

inline

References sample_extra_rotamers_.

StepWiseRNA_RotamerGeneratorOP const protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::setup_rotamer_generator ( core::Size const  list_position)

private

References allow_syn_pyrimidine_, bin_size_, exclude_alpha_beta_gamma_sampling_, extra_anti_chi_, extra_beta_, extra_epsilon_, extra_syn_chi_, fast_, force_syn_chi_res_list_, Get_residue_pucker_state_internal(), include_syn_chi_, Is_prepend_, moving_suite_list_, protocols::swa::rna::Output_boolean(), pose_, sample_chi_torsion_, sample_extra_rotamers_, sample_sugar_and_base1_, and sample_sugar_and_base2_.

Referenced by get_next_rotamer(), and initialize_rotamer_generator_list().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::subgroup_rotamer

(

core::Size const

list_position)

References rotamer_generator_list_.

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::allow_syn_pyrimidine_

private

Referenced by initialize_rotamer_generator_list(), set_allow_syn_pyrimidine(), and setup_rotamer_generator().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::bin_size_

private

Referenced by set_bin_size(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::exclude_alpha_beta_gamma_sampling_

private

Referenced by initialize_rotamer_generator_list(), set_exclude_alpha_beta_gamma_sampling(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::extra_anti_chi_

private

Referenced by initialize_rotamer_generator_list(), set_extra_anti_chi(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::extra_beta_

private

Referenced by initialize_rotamer_generator_list(), set_extra_beta(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::extra_epsilon_

private

Referenced by initialize_rotamer_generator_list(), set_extra_epsilon(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::extra_syn_chi_

private

Referenced by initialize_rotamer_generator_list(), set_extra_syn_chi(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::fast_

private

Referenced by set_fast(), and setup_rotamer_generator().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::force_north_ribose_list_

private

Referenced by Get_residue_pucker_state_internal(), initialize_rotamer_generator_list(), set_force_north_ribose_list(), and StepWiseRNA_RotamerGenerator_Wrapper().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::force_south_ribose_list_

private

Referenced by Get_residue_pucker_state_internal(), initialize_rotamer_generator_list(), set_force_south_ribose_list(), and StepWiseRNA_RotamerGenerator_Wrapper().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::force_syn_chi_res_list_

private

Referenced by initialize_rotamer_generator_list(), set_force_syn_chi_res_list(), setup_rotamer_generator(), and StepWiseRNA_RotamerGenerator_Wrapper().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::include_syn_chi_

private

Referenced by initialize_rotamer_generator_list(), set_include_syn_chi(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::Is_prepend_

private

Referenced by Get_residue_pucker_state_internal(), initialize_rotamer_generator_list(), setup_rotamer_generator(), and StepWiseRNA_RotamerGenerator_Wrapper().

utility::vector1< core::Size > const protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::moving_suite_list_

private

Referenced by get_next_rotamer(), Get_residue_pucker_state_internal(), initialize_rotamer_generator_list(), setup_rotamer_generator(), and StepWiseRNA_RotamerGenerator_Wrapper().

core::pose::Pose const& protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::pose_

private

Referenced by setup_rotamer_generator().

utility::vector1< StepWiseRNA_RotamerGeneratorOP > protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::rotamer_generator_list_

private

Referenced by get_next_rotamer(), Get_residue_pucker_state_internal(), group_rotamer(), has_another_rotamer(), initialize_rotamer_generator_list(), rotamer_generator_list_size(), and subgroup_rotamer().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::sample_chi_torsion_

private

Referenced by set_sample_chi_torsion(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::sample_extra_rotamers_

private

Referenced by initialize_rotamer_generator_list(), set_sample_extra_rotamers(), and setup_rotamer_generator().

bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::sample_sugar_and_base1_

private

Referenced by initialize_rotamer_generator_list(), and setup_rotamer_generator().

bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::sample_sugar_and_base2_

private

Referenced by initialize_rotamer_generator_list(), and setup_rotamer_generator().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::verbose_

private

---

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

• src/protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.hh
• src/protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.cc