#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_

Detailed Description

Definition at line 39 of file StepWiseRNA_RotamerGenerator.hh.

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
	)

Definition at line 49 of file StepWiseRNA_RotamerGenerator.cc.

References force_syn_chi_res_list_.

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

virtual

Definition at line 81 of file StepWiseRNA_RotamerGenerator.cc.

Member Function Documentation

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

private

Definition at line 267 of file StepWiseRNA_RotamerGenerator.cc.

References torsion_ids_.

Referenced by initialize_rotamers().

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

inline

Definition at line 57 of file StepWiseRNA_RotamerGenerator.hh.

References rotamer_list_.

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

Definition at line 534 of file StepWiseRNA_RotamerGenerator.cc.

References group_rotamer_.

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::has_another_rotamer ( ) const

Definition at line 112 of file StepWiseRNA_RotamerGenerator.cc.

References fast_, group_rotamer_, and rotamer_centers_.

Referenced by update_to_next_rotamer().

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

private

Definition at line 455 of file StepWiseRNA_RotamerGenerator.cc.

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)

Definition at line 86 of file StepWiseRNA_RotamerGenerator.cc.

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

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

private

Definition at line 212 of file StepWiseRNA_RotamerGenerator.cc.

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 ( )

Definition at line 542 of file StepWiseRNA_RotamerGenerator.cc.

References moving_suite_.

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

Definition at line 530 of file StepWiseRNA_RotamerGenerator.cc.

References rotamer_centers_.

PuckerState protocols::swa::rna::StepWiseRNA_RotamerGenerator::pucker_state ( std::string const which_sugar)

Definition at line 126 of file StepWiseRNA_RotamerGenerator.cc.

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 )

Definition at line 119 of file StepWiseRNA_RotamerGenerator.cc.

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

Definition at line 85 of file StepWiseRNA_RotamerGenerator.hh.

References allow_syn_pyrimidine_.

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

inline

Definition at line 73 of file StepWiseRNA_RotamerGenerator.hh.

References bin_size_.

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

inline

Definition at line 83 of file StepWiseRNA_RotamerGenerator.hh.

References exclude_alpha_beta_gamma_sampling_.

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

inline

Definition at line 79 of file StepWiseRNA_RotamerGenerator.hh.

References extra_anti_chi_.

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

inline

Definition at line 77 of file StepWiseRNA_RotamerGenerator.hh.

References extra_beta_.

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

inline

Definition at line 75 of file StepWiseRNA_RotamerGenerator.hh.

References extra_epsilon_.

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

inline

Definition at line 81 of file StepWiseRNA_RotamerGenerator.hh.

References extra_syn_chi_.

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

inline

Definition at line 65 of file StepWiseRNA_RotamerGenerator.hh.

References fast_.

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

inline

Definition at line 71 of file StepWiseRNA_RotamerGenerator.hh.

References force_syn_chi_res_list_.

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

inline

Definition at line 69 of file StepWiseRNA_RotamerGenerator.hh.

References include_syn_chi_.

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

inline

Definition at line 67 of file StepWiseRNA_RotamerGenerator.hh.

References sample_chi_torsion_.

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

inline

Definition at line 63 of file StepWiseRNA_RotamerGenerator.hh.

References sample_extra_rotamers_.

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

Definition at line 538 of file StepWiseRNA_RotamerGenerator.cc.

References subgroup_rotamer_.

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

Definition at line 106 of file StepWiseRNA_RotamerGenerator.cc.

References torsion_ids_.

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

Definition at line 162 of file StepWiseRNA_RotamerGenerator.cc.

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

Definition at line 154 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_sample_base_states(), and set_allow_syn_pyrimidine().

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

private

Definition at line 133 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 132 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 133 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamer_generator(), and initialize_rotamers().

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

private

Definition at line 133 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 133 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 133 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 153 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 151 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and set_extra_anti_chi().

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

private

Definition at line 150 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 149 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 140 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_extra_rotamer_perturbations(), and update_to_next_rotamer().

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

private

Definition at line 152 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and set_extra_syn_chi().

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

private

Definition at line 130 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by has_another_rotamer(), and set_fast().

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

private

Definition at line 148 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 142 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 147 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_sample_base_states(), and set_include_syn_chi().

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

private

Definition at line 155 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and initialize_sample_base_states().

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

private

Definition at line 120 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 139 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_extra_rotamer_perturbations(), and update_to_next_rotamer().

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

private

Definition at line 125 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers().

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

private

Definition at line 126 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers().

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

private

Definition at line 137 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 145 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by get_current_rotamer(), and update_to_next_rotamer().

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

private

Definition at line 146 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 129 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 122 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and initialize_sample_base_states().

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

private

Definition at line 123 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and initialize_sample_base_states().

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

private

Definition at line 143 of file StepWiseRNA_RotamerGenerator.hh.

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

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

private

Definition at line 136 of file StepWiseRNA_RotamerGenerator.hh.

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

Definition at line 156 of file StepWiseRNA_RotamerGenerator.hh.

Referenced by initialize_rotamers(), and initialize_sample_base_states().

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

private

Definition at line 134 of file StepWiseRNA_RotamerGenerator.hh.

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation