protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler Class Reference

#include <StepWiseRNA_AnalyticalLoopCloseSampler.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler:

Public Member Functions
	StepWiseRNA_AnalyticalLoopCloseSampler (StepWiseRNA_JobParametersCOP &job_parameters_)
	~StepWiseRNA_AnalyticalLoopCloseSampler ()
virtual void	apply (core::pose::Pose &pose_to_visualize)
	Apply the minimizer to one pose. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	set_centroid_screen (bool const setting)
void	set_base_pairing_only_screen (bool const setting)
void	set_VDW_atr_rep_screen (bool const setting)
void	set_silent_file (std::string const &setting)
void	set_output_filename (std::string const &output_filename)
void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
void	set_fast (bool const &setting)
void	set_medium_fast (bool const &setting)
void	set_native_rmsd_screen (bool const &setting)
void	set_native_screen_rmsd_cutoff (core::Real const &setting)
void	set_verbose (bool const &setting)
void	set_o2star_screen (bool const &setting)
void	set_cluster_rmsd (core::Real const &setting)
utility::vector1 < pose_data_struct2 > &	get_pose_data_list ()
core::io::silent::SilentFileDataOP &	silent_file_data ()
void	output_pose_data_list (std::string const final_sampler_output_silent_file) const
void	set_num_pose_kept (core::Size const &num_pose_kept)
void	set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener)
void	set_distinguish_pucker (bool const &setting)
void	set_finer_sampling_at_chain_closure (bool const &setting)
void	set_PBP_clustering_at_chain_closure (bool const &setting)
void	set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)
void	set_allow_syn_pyrimidine (bool const &setting)
void	set_extra_syn_chi_rotamer (bool const &setting)
void	set_extra_anti_chi_rotamer (bool const &setting)
void	set_use_phenix_geo (bool const &setting)
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~Mover ()
virtual MoverSP	create ()
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	parse_state (SerializableState const &state)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void	save_state (SerializableState &state)
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
void	set_current_tag (std::string const &new_tag)
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
void	type (const std::string &type_in)
virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string	get_type () const
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...
virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	initialize_scorefunctions ()
void	standard_sampling (core::pose::Pose &pose, utility::vector1< pose_data_struct2 > &pose_data_list)
void	copy_suite_torsion (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const &suite_num)
void	get_base_atr_rep_score (core::pose::Pose const &pose, core::Real &base_atr_score, core::Real &base_rep_score)
bool	Full_atom_van_der_Waals_screening_REPLICATE (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)
bool	Full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::Real const &base_atr_score, core::Real &delta_rep_score, core::Real &delta_atr_score, core::Size const &gap_size, bool const &Is_internal)
void	initialize_o2star_packer_task (core::pose::Pose const &pose)
void	sample_o2star_hydrogen (core::pose::Pose &pose, core::pose::Pose &pose_with_original_HO2star_torsion)
core::Real	Pose_selection_by_full_score (utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose &current_pose, std::string const &tag)
void	Update_pose_data_list (std::string const &tag, utility::vector1< pose_data_struct2 > &pose_data_list, core::pose::Pose const &current_pose, core::Real const &current_score) const
void	cluster_pose_data_list (utility::vector1< pose_data_struct2 > &pose_data_list)
std::string	create_tag (std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const &rotamer_generator) const
std::string	create_torsion_value_string (core::Real const &torsion_value) const
std::string	create_rotamer_string (core::pose::Pose const &pose) const

Private Attributes
StepWiseRNA_JobParametersCOP	job_parameters_
core::io::silent::SilentFileDataOP	sfd_
utility::vector1 < pose_data_struct2 >	pose_data_list_
core::scoring::ScoreFunctionOP	scorefxn_
core::scoring::ScoreFunctionOP	atr_rep_screening_scorefxn_
core::scoring::ScoreFunctionOP	sampling_scorefxn_
core::scoring::ScoreFunctionOP	o2star_pack_scorefxn_
core::scoring::ScoreFunctionOP	chainbreak_scorefxn_
utility::vector1< core::Size >	working_rmsd_res_
SillyCountStruct	count_data_
std::string	silent_file_
std::string	output_filename_
core::Real const	bin_size_
core::Real const	rep_cutoff_
core::Size	num_pose_kept_
core::Size const	multiplier_
core::Real	cluster_rmsd_
bool	verbose_
bool	native_rmsd_screen_
core::Real	native_screen_rmsd_cutoff_
bool	o2star_screen_
core::pack::task::PackerTaskOP	o2star_pack_task_
bool	fast_
bool	medium_fast_
StepWiseRNA_BaseCentroidScreenerOP	base_centroid_screener_
bool	centroid_screen_
bool	base_pairing_only_screen_
bool	VDW_atr_rep_screen_
bool	distinguish_pucker_
core::Real	current_score_cutoff_
bool	finer_sampling_at_chain_closure_
bool	PBP_clustering_at_chain_closure_
bool	extra_anti_chi_rotamer_
bool	extra_syn_chi_rotamer_
bool	allow_syn_pyrimidine_
bool	use_phenix_geo_
StepWiseRNA_VDW_Bin_ScreenerOP	user_input_VDW_bin_screener_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef protocols::filters::Filters_map	Filters_map
typedef std::list< std::string >	Strings
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::StepWiseRNA_AnalyticalLoopCloseSampler

(

StepWiseRNA_JobParametersCOP &

job_parameters_)

References protocols::swa::rna::apply_full_to_sub_mapping(), job_parameters_, protocols::swa::rna::Output_is_prepend_map(), protocols::swa::rna::Output_seq_num_list(), protocols::moves::Mover::set_native_pose(), and working_rmsd_res_.

protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::~StepWiseRNA_AnalyticalLoopCloseSampler

(

)

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::apply ( core::pose::Pose &  pose_to_visualize)

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References centroid_screen_, initialize_scorefunctions(), job_parameters_, native_rmsd_screen_, native_screen_rmsd_cutoff_, o2star_screen_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_seq_num_list(), protocols::swa::rna::Output_title_text(), standard_sampling(), and VDW_atr_rep_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_pose_data_list ( utility::vector1< pose_data_struct2 > &  pose_data_list)

private

References cluster_rmsd_, current_score_cutoff_, distinguish_pucker_, protocols::swa::rna::Get_residue_pucker_state(), protocols::swa::rna::Is_same_ribose_pucker(), job_parameters_, num_pose_kept_, protocols::swa::rna::Output_boolean(), PBP_clustering_at_chain_closure_, protocols::swa::rna::phosphate_base_phosphate_rmsd(), protocols::swa::rna::print_ribose_pucker_state(), protocols::swa::rna::suite_rmsd(), and verbose_.

Referenced by Pose_selection_by_full_score(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::copy_suite_torsion ( core::pose::Pose &  pose, core::pose::Pose const &  ref_pose, core::Size const &  suite_num  )

private

References core::id::BB, core::id::CHI, core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_rotamer_string ( core::pose::Pose const &  pose) const

private

References core::conformation::Residue::chi(), create_torsion_value_string(), job_parameters_, core::conformation::Residue::mainchain_torsion(), and core::pose::Pose::residue().

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_tag ( std::string const  prestring, StepWiseRNA_RotamerGenerator_WrapperOP const &  rotamer_generator  ) const

private

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_torsion_value_string ( core::Real const &  torsion_value) const

private

Referenced by create_rotamer_string().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening ( core::pose::Pose &  current_pose_screen, core::Real const &  base_rep_score, core::Real const &  base_atr_score, core::Real &  delta_rep_score, core::Real &  delta_atr_score, core::Size const &  gap_size, bool const &  Is_internal  )

private

References atr_rep_screening_scorefxn_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, count_data_, core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, rep_cutoff_, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), VDW_atr_rep_screen_, and verbose_.

Referenced by standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening_REPLICATE ( core::pose::Pose &  current_pose_screen, core::Real const &  base_rep_score, core::Real const &  base_atr_score, core::Real &  delta_rep_score, core::Real &  delta_atr_score, core::Size const &  gap_size, bool const &  Is_internal  )

private

References atr_rep_screening_scorefxn_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, protocols::swa::rna::SillyCountStruct::both_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, count_data_, core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, protocols::swa::rna::SillyCountStruct::non_clash_ribose, protocols::swa::rna::SillyCountStruct::pass_base_centroid_screen, rep_cutoff_, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::SillyCountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), VDW_atr_rep_screen_, and verbose_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_base_atr_rep_score ( core::pose::Pose const &  pose, core::Real &  base_atr_score, core::Real &  base_rep_score  )

private

References core::pose::add_variant_type_to_pose_residue(), atr_rep_screening_scorefxn_, core::pose::Pose::dump_pdb(), core::scoring::fa_atr, core::scoring::fa_rep, job_parameters_, protocols::swa::rna::make_cut_at_moving_suite(), core::kinematics::Jump::set_translation(), and verbose_.

Referenced by standard_sampling().

virtual std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_name ( ) const

inlinevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

utility::vector1< pose_data_struct2 > & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_pose_data_list

(

)

References pose_data_list_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_o2star_packer_task ( core::pose::Pose const &  pose)

private

References protocols::swa::rna::Contain_seq_num(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::conformation::Residue::is_RNA(), job_parameters_, o2star_pack_task_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by sample_o2star_hydrogen(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_scorefunctions ( )

private

References atr_rep_screening_scorefxn_, chainbreak_scorefxn_, protocols::swa::rna::initialize_common_scorefxns(), o2star_pack_scorefxn_, sampling_scorefxn_, and scorefxn_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_pose_data_list

(

std::string const

final_sampler_output_silent_file)

const

References protocols::moves::Mover::get_native_pose(), job_parameters_, protocols::swa::rna::Output_data(), pose_data_list_, silent_file_data(), and verbose_.

Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Pose_selection_by_full_score ( utility::vector1< pose_data_struct2 > &  pose_data_list, core::pose::Pose &  current_pose, std::string const &  tag  )

private

References cluster_pose_data_list(), multiplier_, num_pose_kept_, protocols::swa::rna::sort_criteria2(), and Update_pose_data_list().

Referenced by standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sample_o2star_hydrogen ( core::pose::Pose &  pose, core::pose::Pose &  pose_with_original_HO2star_torsion  )

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::CHI, initialize_o2star_packer_task(), o2star_pack_scorefxn_, o2star_pack_task_, core::pose::Pose::residue(), core::pack::rotamer_trials(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

Referenced by standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_allow_syn_pyrimidine ( bool const &  setting)

inline

References allow_syn_pyrimidine_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_base_centroid_screener

(

StepWiseRNA_BaseCentroidScreenerOP &

screener)

References base_centroid_screener_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_base_pairing_only_screen ( bool const  setting)

inline

References base_pairing_only_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_centroid_screen ( bool const  setting)

inline

References centroid_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_cluster_rmsd

(

core::Real const &

setting)

References cluster_rmsd_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_distinguish_pucker ( bool const &  setting)

inline

References distinguish_pucker_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_extra_anti_chi_rotamer ( bool const &  setting)

inline

References extra_anti_chi_rotamer_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_extra_syn_chi_rotamer ( bool const &  setting)

inline

References extra_syn_chi_rotamer_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_fast

(

bool const &

setting)

References fast_, and num_pose_kept_.

Referenced by set_num_pose_kept().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_finer_sampling_at_chain_closure ( bool const &  setting)

inline

References finer_sampling_at_chain_closure_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_medium_fast

(

bool const &

setting)

References medium_fast_, and num_pose_kept_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_native_rmsd_screen

(

bool const &

setting)

References native_rmsd_screen_.

Referenced by set_num_pose_kept().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_native_screen_rmsd_cutoff ( core::Real const &  setting)

inline

References native_screen_rmsd_cutoff_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_num_pose_kept

(

core::Size const &

num_pose_kept)

References fast_, native_rmsd_screen_, num_pose_kept_, set_fast(), and set_native_rmsd_screen().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_o2star_screen

(

bool const &

setting)

References o2star_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_output_filename

(

std::string const &

output_filename)

References output_filename_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_PBP_clustering_at_chain_closure ( bool const &  setting)

inline

References PBP_clustering_at_chain_closure_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_scorefxn

(

core::scoring::ScoreFunctionOP const &

scorefxn)

References scorefxn_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_silent_file

(

std::string const &

setting)

References silent_file_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_use_phenix_geo ( bool const &  setting)

inline

References use_phenix_geo_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_user_input_VDW_bin_screener

(

StepWiseRNA_VDW_Bin_ScreenerOP const &

user_input_VDW_bin_screener)

References user_input_VDW_bin_screener_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_VDW_atr_rep_screen ( bool const  setting)

inline

References VDW_atr_rep_screen_.

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::set_verbose

(

bool const &

setting)

References verbose_.

core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::silent_file_data

(

)

References sfd_.

Referenced by output_pose_data_list(), and standard_sampling().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling ( core::pose::Pose &  pose, utility::vector1< pose_data_struct2 > &  pose_data_list  )

private

References core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), allow_syn_pyrimidine_, protocols::swa::rna::ANTI, protocols::rna::RNA_IdealCoord::apply(), protocols::swa::rna::RNA_LoopCloseSampler::apply(), base_centroid_screener_, protocols::swa::rna::SillyCountStruct::base_pairing_count, protocols::swa::rna::SillyCountStruct::base_stack_count, core::id::BB, protocols::swa::rna::BOTH, protocols::swa::rna::SillyCountStruct::both_count, protocols::swa::rna::SillyCountStruct::bulge_at_chain_closure_count, centroid_screen_, protocols::swa::rna::SillyCountStruct::chain_break_screening_count, protocols::swa::rna::SillyCountStruct::chain_closable_count, core::id::CHI, protocols::swa::rna::RNA_LoopCloseSampler::clear_all(), cluster_pose_data_list(), copy_suite_torsion(), count_data_, distinguish_pucker_, extra_anti_chi_rotamer_, extra_syn_chi_rotamer_, protocols::swa::rna::RNA_LoopCloseSampler::fill_pose(), finer_sampling_at_chain_closure_, Full_atom_van_der_Waals_screening(), get_base_atr_rep_score(), protocols::moves::Mover::get_native_pose(), protocols::swa::rna::SillyCountStruct::good_angle_count, protocols::swa::rna::SillyCountStruct::good_atr_rotamer_count, protocols::swa::rna::SillyCountStruct::good_bin_rep_count, protocols::swa::rna::SillyCountStruct::good_distance_count, protocols::swa::rna::SillyCountStruct::good_rep_rotamer_count, initialize_o2star_packer_task(), core::scoring::rna::is_purine(), job_parameters_, protocols::swa::rna::RNA_LoopCloseSampler::n_construct(), native_rmsd_screen_, native_screen_rmsd_cutoff_, protocols::swa::rna::NORTH, num_pose_kept_, o2star_screen_, protocols::swa::rna::Output_boolean(), protocols::swa::rna::Output_data(), protocols::swa::rna::Output_title_text(), pose_data_list_, Pose_selection_by_full_score(), core::pose::Pose::residue(), protocols::swa::rna::SillyCountStruct::rmsd_count, protocols::swa::rna::rmsd_over_residue_list(), sample_o2star_hydrogen(), scorefxn_, protocols::swa::rna::RNA_LoopCloseSampler::set_bin_size(), protocols::swa::rna::RNA_LoopCloseSampler::set_epsilon_range(), protocols::swa::rna::RNA_LoopCloseSampler::set_sample_native_torsion(), protocols::swa::rna::RNA_LoopCloseSampler::set_sample_only(), protocols::swa::rna::RNA_LoopCloseSampler::set_scorefxn(), silent_file_, silent_file_data(), protocols::swa::rna::sort_criteria2(), protocols::swa::rna::SOUTH, protocols::swa::rna::SillyCountStruct::strict_base_pairing_count, protocols::swa::rna::suite_rmsd(), protocols::swa::rna::SillyCountStruct::tot_rotamer_count, use_phenix_geo_, user_input_VDW_bin_screener_, and verbose_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Update_pose_data_list ( std::string const &  tag, utility::vector1< pose_data_struct2 > &  pose_data_list, core::pose::Pose const &  current_pose, core::Real const &  current_score  ) const

private

References current_score_cutoff_, protocols::moves::Mover::get_native_pose(), protocols::swa::rna::pose_data_struct2::pose_OP, core::scoring::rms_at_corresponding_heavy_atoms(), protocols::swa::rna::pose_data_struct2::score, core::pose::setPoseExtraScores(), protocols::swa::rna::pose_data_struct2::tag, and verbose_.

Referenced by Pose_selection_by_full_score().

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::allow_syn_pyrimidine_

private

Referenced by set_allow_syn_pyrimidine(), and standard_sampling().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::atr_rep_screening_scorefxn_

private

Referenced by Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), get_base_atr_rep_score(), and initialize_scorefunctions().

StepWiseRNA_BaseCentroidScreenerOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::base_centroid_screener_

private

Referenced by set_base_centroid_screener(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::base_pairing_only_screen_

private

Referenced by set_base_pairing_only_screen().

core::Real const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::bin_size_

private

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::centroid_screen_

private

Referenced by apply(), set_centroid_screen(), and standard_sampling().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::chainbreak_scorefxn_

private

Referenced by initialize_scorefunctions().

core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::cluster_rmsd_

private

Referenced by cluster_pose_data_list(), and set_cluster_rmsd().

SillyCountStruct protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::count_data_

private

Referenced by Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), and standard_sampling().

core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::current_score_cutoff_

private

Referenced by cluster_pose_data_list(), and Update_pose_data_list().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::distinguish_pucker_

private

Referenced by cluster_pose_data_list(), set_distinguish_pucker(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::extra_anti_chi_rotamer_

private

Referenced by set_extra_anti_chi_rotamer(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::extra_syn_chi_rotamer_

private

Referenced by set_extra_syn_chi_rotamer(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::fast_

private

Referenced by set_fast(), and set_num_pose_kept().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::finer_sampling_at_chain_closure_

private

Referenced by set_finer_sampling_at_chain_closure(), and standard_sampling().

StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::job_parameters_

private

Referenced by apply(), cluster_pose_data_list(), create_rotamer_string(), get_base_atr_rep_score(), initialize_o2star_packer_task(), output_pose_data_list(), standard_sampling(), and StepWiseRNA_AnalyticalLoopCloseSampler().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::medium_fast_

private

Referenced by set_medium_fast().

core::Size const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::multiplier_

private

Referenced by Pose_selection_by_full_score().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::native_rmsd_screen_

private

Referenced by apply(), set_native_rmsd_screen(), set_num_pose_kept(), and standard_sampling().

core::Real protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::native_screen_rmsd_cutoff_

private

Referenced by apply(), set_native_screen_rmsd_cutoff(), and standard_sampling().

core::Size protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::num_pose_kept_

private

Referenced by cluster_pose_data_list(), Pose_selection_by_full_score(), set_fast(), set_medium_fast(), set_num_pose_kept(), and standard_sampling().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_pack_scorefxn_

private

Referenced by initialize_scorefunctions(), and sample_o2star_hydrogen().

core::pack::task::PackerTaskOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_pack_task_

private

Referenced by initialize_o2star_packer_task(), and sample_o2star_hydrogen().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::o2star_screen_

private

Referenced by apply(), set_o2star_screen(), and standard_sampling().

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::output_filename_

private

Referenced by set_output_filename().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::PBP_clustering_at_chain_closure_

private

Referenced by cluster_pose_data_list(), and set_PBP_clustering_at_chain_closure().

utility::vector1< pose_data_struct2 > protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::pose_data_list_

private

Referenced by get_pose_data_list(), output_pose_data_list(), and standard_sampling().

core::Real const protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::rep_cutoff_

private

Referenced by Full_atom_van_der_Waals_screening(), and Full_atom_van_der_Waals_screening_REPLICATE().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sampling_scorefxn_

private

Referenced by initialize_scorefunctions().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::scorefxn_

private

Referenced by initialize_scorefunctions(), set_scorefxn(), and standard_sampling().

core::io::silent::SilentFileDataOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sfd_

private

Referenced by silent_file_data().

std::string protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::silent_file_

private

Referenced by set_silent_file(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::use_phenix_geo_

private

Referenced by set_use_phenix_geo(), and standard_sampling().

StepWiseRNA_VDW_Bin_ScreenerOP protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::user_input_VDW_bin_screener_

private

Referenced by set_user_input_VDW_bin_screener(), and standard_sampling().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::VDW_atr_rep_screen_

private

Referenced by apply(), Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), and set_VDW_atr_rep_screen().

bool protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::verbose_

private

Referenced by cluster_pose_data_list(), Full_atom_van_der_Waals_screening(), Full_atom_van_der_Waals_screening_REPLICATE(), get_base_atr_rep_score(), output_pose_data_list(), set_verbose(), standard_sampling(), and Update_pose_data_list().

utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::working_rmsd_res_

private

Referenced by StepWiseRNA_AnalyticalLoopCloseSampler().

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

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