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core::import_pose::RNA_HelixAssembler Class Reference

The RNA de novo structure modeling protocol. More...

#include <RNA_HelixAssembler.hh>

Public Member Functions

 RNA_HelixAssembler ()
 Construct the protocol object. More...
 
 ~RNA_HelixAssembler ()
 Destroy the protocol object. More...
 
void apply (core::pose::Pose &pose)
 Apply the loop-rebuild protocol to the input pose. More...
 
virtual std::string get_name () const
 
void apply (core::pose::Pose &pose, std::string const &full_sequence_in)
 Apply the loop-rebuild protocol to the input pose. More...
 
void random_perturbation (bool const &setting)
 
void set_dump (bool const &setting)
 
void set_minimize_all (bool const &setting)
 
void set_scorefxn (core::scoring::ScoreFunctionOP setting)
 
void set_finish_scorefxn (core::scoring::ScoreFunctionOP setting)
 
void use_phenix_geo (bool const setting)
 
void set_model_and_remove_capping_residues (bool setting)
 
void build_helix (core::pose::Pose &pose)
 
core::pose::PoseOP build_init_pose (std::string const &seq1, std::string const &seq2)
 

Private Member Functions

void initialize_minimizer ()
 
void set_Aform_torsions (core::pose::Pose &pose, Size const &n) const
 
void build_on_base_pair (core::pose::Pose &pose, Size const &n, std::string const &seq1, std::string const &seq2) const
 
void minimize_base_step (core::pose::Pose &pose, Size const n, core::scoring::ScoreFunctionOP scorefxn) const
 
void put_constraints_on_base_step (core::pose::Pose &pose, Size const &n) const
 
void add_capping_base_pairs_to_full_sequence ()
 
void get_rid_of_capping_base_pairs (core::pose::Pose &pose)
 
void figure_out_and_remove_dangling_ends ()
 
void build_dangling_ends (core::pose::Pose &pose) const
 
void build_dangle_seq1_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const
 
void build_dangle_seq2_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const
 
void build_dangle_seq1_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const
 
void build_dangle_seq2_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const
 
core::Size get_cutpoint (core::pose::Pose const &pose) const
 
void append_Aform_residue (core::pose::Pose &pose, Size const &n, std::string const &nt) const
 
void prepend_Aform_residue (core::pose::Pose &pose, Size const &n, std::string const &nt) const
 
void perturb_torsion (core::pose::Pose &pose, utility::vector1< core::id::TorsionID > const &id_list) const
 
void minimize_append_res (core::pose::Pose &pose, Size const n) const
 
void minimize_prepend_res (core::pose::Pose &pose, Size const n) const
 
void fill_chain_info (core::pose::Pose &pose)
 
std::string get_sequence (core::Size const n)
 
void remove_first_base_pair (std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const
 
void remove_last_base_pair (std::string &full_sequence, std::map< Size, std::string > &non_standard_residues, std::string &sequence_helix1, std::string &sequence_helix2) const
 
core::conformation::ResidueOP get_residue (std::string const &nt) const
 

Private Attributes

bool dump_
 
bool random_perturbation_
 
bool minimize_all_
 
bool minimize_jump_
 
bool use_phenix_geo_
 
core::chemical::ResidueTypeSetCOP rsd_set_
 
core::chemical::rna::RNA_FittedTorsionInfo
const 
torsion_info_
 
core::Real perturb_amplitude_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP finish_scorefxn_
 
bool model_and_remove_capping_residues_
 
std::string const capping_residues_
 
core::optimization::AtomTreeMinimizerOP minimizer_
 
core::optimization::MinimizerOptionsOP minimizer_options_
 
std::string dangle_seq1_5prime_
 
std::string dangle_seq1_3prime_
 
std::string dangle_seq2_5prime_
 
std::string dangle_seq2_3prime_
 
std::string full_sequence_
 
std::map< core::Size, std::string > non_standard_residues_
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

core::import_pose::RNA_HelixAssembler::RNA_HelixAssembler ( )

Construct the protocol object.

References initialize_minimizer().

core::import_pose::RNA_HelixAssembler::~RNA_HelixAssembler ( )
default

Destroy the protocol object.

Member Function Documentation

void core::import_pose::RNA_HelixAssembler::add_capping_base_pairs_to_full_sequence ( )
private
void core::import_pose::RNA_HelixAssembler::append_Aform_residue ( core::pose::Pose pose,
Size const &  n,
std::string const &  nt 
) const
private
void core::import_pose::RNA_HelixAssembler::apply ( core::pose::Pose pose)

Apply the loop-rebuild protocol to the input pose.

Apply the RNA HelixAssembler

References core::pose::Pose::sequence().

Referenced by core::import_pose::dump_stems().

void core::import_pose::RNA_HelixAssembler::apply ( core::pose::Pose pose,
std::string const &  full_sequence_in 
)
void core::import_pose::RNA_HelixAssembler::build_dangle_seq1_3prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void core::import_pose::RNA_HelixAssembler::build_dangle_seq1_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void core::import_pose::RNA_HelixAssembler::build_dangle_seq2_3prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void core::import_pose::RNA_HelixAssembler::build_dangle_seq2_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void core::import_pose::RNA_HelixAssembler::build_dangling_ends ( core::pose::Pose pose) const
private
void core::import_pose::RNA_HelixAssembler::build_helix ( core::pose::Pose pose)
pose::PoseOP core::import_pose::RNA_HelixAssembler::build_init_pose ( std::string const &  seq1,
std::string const &  seq2 
)
void core::import_pose::RNA_HelixAssembler::build_on_base_pair ( core::pose::Pose pose,
Size const &  n,
std::string const &  seq1,
std::string const &  seq2 
) const
private
void core::import_pose::RNA_HelixAssembler::figure_out_and_remove_dangling_ends ( )
private
void core::import_pose::RNA_HelixAssembler::fill_chain_info ( core::pose::Pose pose)
private
Size core::import_pose::RNA_HelixAssembler::get_cutpoint ( core::pose::Pose const &  pose) const
private
std::string core::import_pose::RNA_HelixAssembler::get_name ( ) const
virtual
core::conformation::ResidueOP core::import_pose::RNA_HelixAssembler::get_residue ( std::string const &  nt) const
private
void core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs ( core::pose::Pose pose)
private
std::string core::import_pose::RNA_HelixAssembler::get_sequence ( core::Size const  n)
private
void core::import_pose::RNA_HelixAssembler::initialize_minimizer ( )
private

References minimizer_, and minimizer_options_.

Referenced by RNA_HelixAssembler().

void core::import_pose::RNA_HelixAssembler::minimize_append_res ( core::pose::Pose pose,
Size const  n 
) const
private
void core::import_pose::RNA_HelixAssembler::minimize_base_step ( core::pose::Pose pose,
Size const  n,
core::scoring::ScoreFunctionOP  scorefxn 
) const
private
void core::import_pose::RNA_HelixAssembler::minimize_prepend_res ( core::pose::Pose pose,
Size const  n 
) const
private
void core::import_pose::RNA_HelixAssembler::perturb_torsion ( core::pose::Pose pose,
utility::vector1< core::id::TorsionID > const &  id_list 
) const
private
void core::import_pose::RNA_HelixAssembler::prepend_Aform_residue ( core::pose::Pose pose,
Size const &  n,
std::string const &  nt 
) const
private
void core::import_pose::RNA_HelixAssembler::put_constraints_on_base_step ( core::pose::Pose pose,
Size const &  n 
) const
private
void core::import_pose::RNA_HelixAssembler::random_perturbation ( bool const &  setting)
inline

References random_perturbation_.

void core::import_pose::RNA_HelixAssembler::remove_first_base_pair ( std::string &  full_sequence,
std::map< Size, std::string > &  non_standard_residues,
std::string &  sequence_helix1,
std::string &  sequence_helix2 
) const
private
void core::import_pose::RNA_HelixAssembler::remove_last_base_pair ( std::string &  full_sequence,
std::map< Size, std::string > &  non_standard_residues,
std::string &  sequence_helix1,
std::string &  sequence_helix2 
) const
private
void core::import_pose::RNA_HelixAssembler::set_Aform_torsions ( core::pose::Pose pose,
Size const &  n 
) const
private
void core::import_pose::RNA_HelixAssembler::set_dump ( bool const &  setting)
inline

References dump_.

void core::import_pose::RNA_HelixAssembler::set_finish_scorefxn ( core::scoring::ScoreFunctionOP  setting)

References finish_scorefxn_.

void core::import_pose::RNA_HelixAssembler::set_minimize_all ( bool const &  setting)
inline

References minimize_all_.

void core::import_pose::RNA_HelixAssembler::set_model_and_remove_capping_residues ( bool  setting)
inline
void core::import_pose::RNA_HelixAssembler::set_scorefxn ( core::scoring::ScoreFunctionOP  setting)

References scorefxn_.

void core::import_pose::RNA_HelixAssembler::use_phenix_geo ( bool const  setting)

Member Data Documentation

std::string const core::import_pose::RNA_HelixAssembler::capping_residues_
private
std::string core::import_pose::RNA_HelixAssembler::dangle_seq1_3prime_
private
std::string core::import_pose::RNA_HelixAssembler::dangle_seq1_5prime_
private
std::string core::import_pose::RNA_HelixAssembler::dangle_seq2_3prime_
private
std::string core::import_pose::RNA_HelixAssembler::dangle_seq2_5prime_
private
bool core::import_pose::RNA_HelixAssembler::dump_
private

Referenced by build_helix(), and set_dump().

core::scoring::ScoreFunctionOP core::import_pose::RNA_HelixAssembler::finish_scorefxn_
private
std::string core::import_pose::RNA_HelixAssembler::full_sequence_
private
bool core::import_pose::RNA_HelixAssembler::minimize_all_
private
bool core::import_pose::RNA_HelixAssembler::minimize_jump_
private

Referenced by minimize_base_step().

core::optimization::AtomTreeMinimizerOP core::import_pose::RNA_HelixAssembler::minimizer_
private
core::optimization::MinimizerOptionsOP core::import_pose::RNA_HelixAssembler::minimizer_options_
private
bool core::import_pose::RNA_HelixAssembler::model_and_remove_capping_residues_
private
std::map< core::Size, std::string > core::import_pose::RNA_HelixAssembler::non_standard_residues_
private
core::Real core::import_pose::RNA_HelixAssembler::perturb_amplitude_
private

Referenced by perturb_torsion().

bool core::import_pose::RNA_HelixAssembler::random_perturbation_
private
core::chemical::ResidueTypeSetCOP core::import_pose::RNA_HelixAssembler::rsd_set_
private
core::scoring::ScoreFunctionOP core::import_pose::RNA_HelixAssembler::scorefxn_
private
core::chemical::rna::RNA_FittedTorsionInfo const core::import_pose::RNA_HelixAssembler::torsion_info_
private
bool core::import_pose::RNA_HelixAssembler::use_phenix_geo_
private

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