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

#include <StepWiseRNA_RotamerGenerator_Wrapper.hh>

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

Detailed Description

Definition at line 43 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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 
)

Definition at line 49 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

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

Definition at line 100 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

Member Function Documentation

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

Definition at line 325 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

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

Definition at line 238 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

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)

Definition at line 368 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

References rotamer_generator_list_.

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

Definition at line 313 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

References rotamer_generator_list_.

Referenced by get_next_rotamer().

void protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper::initialize_rotamer_generator_list ( )

Definition at line 103 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

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

Definition at line 94 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References rotamer_generator_list_.

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

Definition at line 84 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References allow_syn_pyrimidine_.

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

Definition at line 72 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References bin_size_.

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

Definition at line 82 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References exclude_alpha_beta_gamma_sampling_.

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

Definition at line 78 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References extra_anti_chi_.

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

Definition at line 76 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References extra_beta_.

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

Definition at line 74 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References extra_epsilon_.

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

Definition at line 80 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References extra_syn_chi_.

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

Definition at line 226 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

References fast_.

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

Definition at line 68 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References force_north_ribose_list_.

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

Definition at line 70 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 66 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References force_syn_chi_res_list_.

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

Definition at line 64 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References include_syn_chi_.

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

Definition at line 62 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References sample_chi_torsion_.

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

Definition at line 58 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

References sample_extra_rotamers_.

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

Definition at line 142 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

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)

Definition at line 373 of file StepWiseRNA_RotamerGenerator_Wrapper.cc.

References rotamer_generator_list_.

Member Data Documentation

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

Definition at line 130 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 124 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by set_bin_size(), and setup_rotamer_generator().

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

Definition at line 129 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 127 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

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

Definition at line 126 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

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

Definition at line 125 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

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

Definition at line 128 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

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

Definition at line 114 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by set_fast(), and setup_rotamer_generator().

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

Definition at line 121 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 122 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 120 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 117 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

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

Definition at line 118 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 110 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 109 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by setup_rotamer_generator().

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

Definition at line 131 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 116 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by set_sample_chi_torsion(), and setup_rotamer_generator().

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

Definition at line 113 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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

Definition at line 111 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by initialize_rotamer_generator_list(), and setup_rotamer_generator().

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

Definition at line 112 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

Referenced by initialize_rotamer_generator_list(), and setup_rotamer_generator().

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

Definition at line 115 of file StepWiseRNA_RotamerGenerator_Wrapper.hh.

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