protocols::swa::rna::StepWiseRNA_RotamerGenerator Class Reference

#include <StepWiseRNA_RotamerGenerator.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator:

Public Member Functions
	StepWiseRNA_RotamerGenerator (Size const moving_suite, bool const sample_lower_sugar_and_base, bool const sample_upper_sugar_and_base, PuckerState const pucker1, PuckerState const pucker2)
virtual	~StepWiseRNA_RotamerGenerator ()
utility::vector1 < core::id::TorsionID > const &	torsion_ids () const
bool	has_another_rotamer () const
void	update_to_next_rotamer ()
utility::vector1< Torsion_Info > const &	get_current_rotamer ()
void	reset ()
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 setting)
void	set_force_syn_chi_res_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)
void	initialize_rotamer_generator (core::pose::Pose const &pose)
core::Size	num_rotamer_centers ()
core::Size const &	group_rotamer ()
core::Size const &	subgroup_rotamer ()
core::Size const &	moving_suite ()
PuckerState	pucker_state (std::string const which_sugar)

Private Member Functions
void	initialize_sample_base_states (core::pose::Pose const &pose)
void	initialize_rotamers ()
void	initialize_extra_rotamer_perturbations ()
void	add_torsion_id (core::id::TorsionID const torsion_id)

Private Attributes
core::Size const	moving_suite_
bool const	sample_lower_sugar_and_base_
bool const	sample_upper_sugar_and_base_
PuckerState const	pucker1_specified_
PuckerState const	pucker2_specified_
bool	sample_extra_rotamers_
bool	fast_
core::Size	bin_size_
int	bins1_
int	bins2_
int	bins3_
int	eps_bins_
int	beta_bins_
bool	verbose_
utility::vector1 < core::id::TorsionID >	torsion_ids_
utility::vector1 < utility::vector1< core::Real > >	rotamer_centers_
utility::vector1 < core::id::TorsionID >	perturb_torsion_ids_
utility::vector1 < utility::vector1< core::Real > >	extra_rotamer_perturbations_
core::Size	group_rotamer_
core::Size	subgroup_rotamer_
utility::vector1< Torsion_Info >	rotamer_list_
bool	sample_chi_torsion_
bool	include_syn_chi_
utility::vector1< core::Size >	force_syn_chi_res_list_
bool	extra_epsilon_
bool	extra_beta_
bool	extra_anti_chi_
bool	extra_syn_chi_
bool	exclude_alpha_beta_gamma_sampling_
bool	allow_syn_pyrimidine_
BaseState	lower_base_state_
BaseState	upper_base_state_

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_RotamerGenerator::StepWiseRNA_RotamerGenerator	(	Size const	moving_suite,
		bool const	sample_lower_sugar_and_base,
		bool const	sample_upper_sugar_and_base,
		PuckerState const	pucker1,
		PuckerState const	pucker2
	)

References force_syn_chi_res_list_.

protocols::swa::rna::StepWiseRNA_RotamerGenerator::~StepWiseRNA_RotamerGenerator ( )

virtual

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::add_torsion_id ( core::id::TorsionID const  torsion_id)

private

References torsion_ids_.

Referenced by initialize_rotamers().

utility::vector1< Torsion_Info > const& protocols::swa::rna::StepWiseRNA_RotamerGenerator::get_current_rotamer ( )

inline

References rotamer_list_.

core::Size const & protocols::swa::rna::StepWiseRNA_RotamerGenerator::group_rotamer

(

)

References group_rotamer_.

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::has_another_rotamer

(

)

const

References fast_, group_rotamer_, and rotamer_centers_.

Referenced by update_to_next_rotamer().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_extra_rotamer_perturbations ( )

private

References core::id::BB, beta_bins_, bin_size_, bins2_, bins3_, eps_bins_, exclude_alpha_beta_gamma_sampling_, extra_beta_, extra_epsilon_, extra_rotamer_perturbations_, moving_suite_, perturb_torsion_ids_, and core::io::serialization::size().

Referenced by initialize_rotamer_generator().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamer_generator

(

core::pose::Pose const &

pose)

References beta_bins_, bin_size_, bins1_, bins2_, bins3_, eps_bins_, extra_beta_, extra_epsilon_, initialize_extra_rotamer_perturbations(), initialize_rotamers(), initialize_sample_base_states(), protocols::swa::rna::Output_title_text(), and reset().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamers ( )

private

References add_torsion_id(), protocols::swa::rna::ALL, core::id::BB, beta_bins_, bin_size_, bins1_, bins2_, bins3_, core::id::CHI, eps_bins_, exclude_alpha_beta_gamma_sampling_, extra_anti_chi_, extra_beta_, extra_epsilon_, extra_syn_chi_, lower_base_state_, moving_suite_, protocols::swa::rna::NONE, protocols::swa::rna::NORTH, protocols::swa::rna::Output_boolean(), protocols::swa::rna::print_base_state(), protocols::swa::rna::print_ribose_pucker_state(), pucker1_specified_, pucker2_specified_, rotamer_centers_, sample_chi_torsion_, sample_extra_rotamers_, sample_lower_sugar_and_base_, sample_upper_sugar_and_base_, core::io::serialization::size(), torsion_ids_, upper_base_state_, and verbose_.

Referenced by initialize_rotamer_generator().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_sample_base_states ( core::pose::Pose const &  pose)

private

References allow_syn_pyrimidine_, protocols::swa::rna::ANTI, protocols::swa::rna::BOTH, protocols::swa::rna::Contain_seq_num(), force_syn_chi_res_list_, include_syn_chi_, core::scoring::rna::is_purine(), lower_base_state_, moving_suite_, protocols::swa::rna::NONE, core::pose::Pose::residue(), sample_chi_torsion_, sample_lower_sugar_and_base_, sample_upper_sugar_and_base_, protocols::swa::rna::SYN, and upper_base_state_.

Referenced by initialize_rotamer_generator().

core::Size const & protocols::swa::rna::StepWiseRNA_RotamerGenerator::moving_suite

(

)

References moving_suite_.

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::num_rotamer_centers

(

)

References rotamer_centers_.

PuckerState protocols::swa::rna::StepWiseRNA_RotamerGenerator::pucker_state

(

std::string const

which_sugar)

References core::id::BB, group_rotamer_, moving_suite_, protocols::swa::rna::NORTH, rotamer_centers_, protocols::swa::rna::SOUTH, and torsion_ids_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::reset

(

void

)

References group_rotamer_, and subgroup_rotamer_.

Referenced by initialize_rotamer_generator().

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

inline

References allow_syn_pyrimidine_.

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

inline

References bin_size_.

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

inline

References exclude_alpha_beta_gamma_sampling_.

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

inline

References extra_anti_chi_.

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

inline

References extra_beta_.

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

inline

References extra_epsilon_.

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

inline

References extra_syn_chi_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::set_fast ( bool const  setting)

inline

References fast_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::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::set_include_syn_chi ( bool const  setting)

inline

References include_syn_chi_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::set_sample_chi_torsion ( bool const  setting)

inline

References sample_chi_torsion_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::set_sample_extra_rotamers ( bool const  setting)

inline

References sample_extra_rotamers_.

core::Size const & protocols::swa::rna::StepWiseRNA_RotamerGenerator::subgroup_rotamer

(

)

References subgroup_rotamer_.

utility::vector1< core::id::TorsionID > const & protocols::swa::rna::StepWiseRNA_RotamerGenerator::torsion_ids

(

)

const

References torsion_ids_.

void protocols::swa::rna::StepWiseRNA_RotamerGenerator::update_to_next_rotamer

(

)

References extra_rotamer_perturbations_, group_rotamer_, has_another_rotamer(), protocols::swa::rna::Torsion_Info::id, perturb_torsion_ids_, rotamer_centers_, rotamer_list_, sample_extra_rotamers_, subgroup_rotamer_, torsion_ids_, protocols::swa::rna::Torsion_Info::value, and verbose_.

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::allow_syn_pyrimidine_

private

Referenced by initialize_sample_base_states(), and set_allow_syn_pyrimidine().

int protocols::swa::rna::StepWiseRNA_RotamerGenerator::beta_bins_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), and initialize_rotamers().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::bin_size_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), initialize_rotamers(), and set_bin_size().

int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins1_

private

Referenced by initialize_rotamer_generator(), and initialize_rotamers().

int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins2_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), and initialize_rotamers().

int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins3_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), and initialize_rotamers().

int protocols::swa::rna::StepWiseRNA_RotamerGenerator::eps_bins_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), and initialize_rotamers().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::exclude_alpha_beta_gamma_sampling_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamers(), and set_exclude_alpha_beta_gamma_sampling().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_anti_chi_

private

Referenced by initialize_rotamers(), and set_extra_anti_chi().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_beta_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), initialize_rotamers(), and set_extra_beta().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_epsilon_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamer_generator(), initialize_rotamers(), and set_extra_epsilon().

utility::vector1< utility::vector1< core::Real > > protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_rotamer_perturbations_

private

Referenced by initialize_extra_rotamer_perturbations(), and update_to_next_rotamer().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_syn_chi_

private

Referenced by initialize_rotamers(), and set_extra_syn_chi().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::fast_

private

Referenced by has_another_rotamer(), and set_fast().

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

private

Referenced by initialize_sample_base_states(), set_force_syn_chi_res_list(), and StepWiseRNA_RotamerGenerator().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::group_rotamer_

private

Referenced by group_rotamer(), has_another_rotamer(), pucker_state(), reset(), and update_to_next_rotamer().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::include_syn_chi_

private

Referenced by initialize_sample_base_states(), and set_include_syn_chi().

BaseState protocols::swa::rna::StepWiseRNA_RotamerGenerator::lower_base_state_

private

Referenced by initialize_rotamers(), and initialize_sample_base_states().

core::Size const protocols::swa::rna::StepWiseRNA_RotamerGenerator::moving_suite_

private

Referenced by initialize_extra_rotamer_perturbations(), initialize_rotamers(), initialize_sample_base_states(), moving_suite(), and pucker_state().

utility::vector1< core::id::TorsionID > protocols::swa::rna::StepWiseRNA_RotamerGenerator::perturb_torsion_ids_

private

Referenced by initialize_extra_rotamer_perturbations(), and update_to_next_rotamer().

PuckerState const protocols::swa::rna::StepWiseRNA_RotamerGenerator::pucker1_specified_

private

Referenced by initialize_rotamers().

PuckerState const protocols::swa::rna::StepWiseRNA_RotamerGenerator::pucker2_specified_

private

Referenced by initialize_rotamers().

utility::vector1< utility::vector1< core::Real > > protocols::swa::rna::StepWiseRNA_RotamerGenerator::rotamer_centers_

private

Referenced by has_another_rotamer(), initialize_rotamers(), num_rotamer_centers(), pucker_state(), and update_to_next_rotamer().

utility::vector1< Torsion_Info > protocols::swa::rna::StepWiseRNA_RotamerGenerator::rotamer_list_

private

Referenced by get_current_rotamer(), and update_to_next_rotamer().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_chi_torsion_

private

Referenced by initialize_rotamers(), initialize_sample_base_states(), and set_sample_chi_torsion().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_extra_rotamers_

private

Referenced by initialize_rotamers(), set_sample_extra_rotamers(), and update_to_next_rotamer().

bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_lower_sugar_and_base_

private

Referenced by initialize_rotamers(), and initialize_sample_base_states().

bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_upper_sugar_and_base_

private

Referenced by initialize_rotamers(), and initialize_sample_base_states().

core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::subgroup_rotamer_

private

Referenced by reset(), subgroup_rotamer(), and update_to_next_rotamer().

utility::vector1< core::id::TorsionID > protocols::swa::rna::StepWiseRNA_RotamerGenerator::torsion_ids_

private

Referenced by add_torsion_id(), initialize_rotamers(), pucker_state(), torsion_ids(), and update_to_next_rotamer().

BaseState protocols::swa::rna::StepWiseRNA_RotamerGenerator::upper_base_state_

private

Referenced by initialize_rotamers(), and initialize_sample_base_states().

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::verbose_

private

Referenced by initialize_rotamers(), and update_to_next_rotamer().

---

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

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