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

#include <StepWiseRNA_RotamerGenerator.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator:
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Collaboration diagram for protocols::swa::rna::StepWiseRNA_RotamerGenerator:
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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_Inforotamer_list_
 
bool sample_chi_torsion_
 
bool include_syn_chi_
 
utility::vector1< core::Sizeforce_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 
)
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
void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_extra_rotamer_perturbations ( )
private
void protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamer_generator ( core::pose::Pose const &  pose)
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
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)
void protocols::swa::rna::StepWiseRNA_RotamerGenerator::reset ( void  )
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
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
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
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 ( )

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::allow_syn_pyrimidine_
private
int protocols::swa::rna::StepWiseRNA_RotamerGenerator::beta_bins_
private
core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::bin_size_
private
int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins1_
private
int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins2_
private
int protocols::swa::rna::StepWiseRNA_RotamerGenerator::bins3_
private
int protocols::swa::rna::StepWiseRNA_RotamerGenerator::eps_bins_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::exclude_alpha_beta_gamma_sampling_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_anti_chi_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_beta_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_epsilon_
private
utility::vector1< utility::vector1< core::Real > > protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_rotamer_perturbations_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::extra_syn_chi_
private
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
core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::group_rotamer_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::include_syn_chi_
private
BaseState protocols::swa::rna::StepWiseRNA_RotamerGenerator::lower_base_state_
private
core::Size const protocols::swa::rna::StepWiseRNA_RotamerGenerator::moving_suite_
private
utility::vector1< core::id::TorsionID > protocols::swa::rna::StepWiseRNA_RotamerGenerator::perturb_torsion_ids_
private
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
utility::vector1< Torsion_Info > protocols::swa::rna::StepWiseRNA_RotamerGenerator::rotamer_list_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_chi_torsion_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_extra_rotamers_
private
bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_lower_sugar_and_base_
private
bool const protocols::swa::rna::StepWiseRNA_RotamerGenerator::sample_upper_sugar_and_base_
private
core::Size protocols::swa::rna::StepWiseRNA_RotamerGenerator::subgroup_rotamer_
private
utility::vector1< core::id::TorsionID > protocols::swa::rna::StepWiseRNA_RotamerGenerator::torsion_ids_
private
BaseState protocols::swa::rna::StepWiseRNA_RotamerGenerator::upper_base_state_
private
bool protocols::swa::rna::StepWiseRNA_RotamerGenerator::verbose_
private

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