Namespaces
	options

	params

	sampler

	scratch

Classes
class	Histogram

class	RECCES_Mover

Typedefs
typedef utility::pointer::shared_ptr< Histogram >	HistogramOP

typedef utility::pointer::shared_ptr< Histogram const >	HistogramCOP

typedef utility::pointer::shared_ptr< RECCES_Mover >	RECCES_MoverOP

typedef utility::pointer::shared_ptr< RECCES_Mover const >	RECCES_MoverCOP

Functions
PoseOP	recces_pose_setup (options::RECCES_Options const &options)
	TODO: Unify – read pose from file, and then fill_full_model_info_from_command_line(). More...

core::pose::PoseOP	pose_setup_turner (std::string const &seq1, std::string const &seq2)

core::pose::PoseOP	pose_setup_from_file (options::RECCES_Options const &options)

void	set_sampler_gaussian_stdev (protocols::recces::sampler::MC_CombOP sampler, core::Real const &temperature, core::pose::Pose const &pose, protocols::recces::options::RECCES_Options const &options, protocols::recces::params::RECCES_Parameters const &params)
	TODO: Unify into single function (see notes below on using MC_Sampler::find) More...

void	set_gaussian_stdevs_recces_turner_from_secstruct (protocols::recces::sampler::MC_CombOP sampler, core::Real const &temperature, core::pose::Pose const &pose, core::pose::rna::RNA_SecStruct const &rna_secstruct)

void	set_gaussian_stdevs_recces_turner_legacy (protocols::recces::sampler::MC_CombOP sampler, core::Real const &temperature, core::pose::Pose const &pose, protocols::recces::params::RECCES_Parameters const &params)

void	set_gaussian_stdevs_recces_turner (protocols::recces::sampler::MC_CombOP sampler, core::Real const &temperature, core::pose::Pose const &pose, core::pose::rna::RNA_SecStruct const &rna_secstruct, protocols::recces::params::RECCES_Parameters const &params)

core::Real	gaussian_stdev (core::Real const n_rsd, core::Real const temp, bool const is_bp)

void	set_gaussian_stdevs_thermal_sampler (protocols::recces::sampler::MC_CombOP internal_bb_sampler, protocols::recces::sampler::MC_CombOP chi_sampler, protocols::recces::sampler::rna::MC_RNA_MultiSuiteOP standard_bb_sampler, Real const &temp, core::Size const &total_rsd, core::Size const &sampled_rsd, utility::vector1< bool > const &is_free)

void	set_gaussian_stdevs_thermal_sampler (protocols::recces::sampler::MC_SamplerOP sampler, core::Real const &temperature, core::pose::Pose const &pose, protocols::recces::options::RECCES_Options const &options)

utility::vector1< core::scoring::ScoreType > const &	get_scoretypes ()

core::Size	data_dim (utility::vector1< core::scoring::ScoreType > const &score_types)

core::Size	data_dim ()

void	update_scores (utility::vector1< float > &scores, core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, utility::vector1< core::scoring::ScoreType > const &score_types)

void	update_scores (utility::vector1< float > &scores, core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn)

void	fill_data (utility::vector1< float > &data, core::Size const count, utility::vector1< float > const &scores)

void	print_base_centroid_atoms_for_rb_entropy (core::conformation::Residue const &rsd, std::string filename_xyz)

utility::vector1< core::Real >	get_torsions (utility::vector1< core::id::TorsionID > const &torsion_ids, core::pose::Pose const &pose)
	used to output torsions from pose – useful for clustering states, etc. More...

template<typename T >
void	vector2disk_in1d (std::string const &out_filename, utility::vector1< T > const &out_vector)

template<typename T >
void	vector2disk_in2d (std::string const &out_filename, core::Size const dim1, core::Size const dim2, utility::vector1< T > const &out_vector)

Typedef Documentation

◆ HistogramCOP

typedef utility::pointer::shared_ptr< Histogram const > protocols::recces::HistogramCOP

◆ HistogramOP

typedef utility::pointer::shared_ptr< Histogram > protocols::recces::HistogramOP

◆ RECCES_MoverCOP

typedef utility::pointer::shared_ptr< RECCES_Mover const > protocols::recces::RECCES_MoverCOP

◆ RECCES_MoverOP

typedef utility::pointer::shared_ptr< RECCES_Mover > protocols::recces::RECCES_MoverOP

Function Documentation

◆ data_dim() [1/2]

core::Size protocols::recces::data_dim ( )

References get_scoretypes().

◆ data_dim() [2/2]

core::Size protocols::recces::data_dim ( utility::vector1< core::scoring::ScoreType > const & score_types )

Referenced by protocols::recces::RECCES_Mover::save_data_to_disk().

◆ fill_data()

void protocols::recces::fill_data	(	utility::vector1< float > &	data,
		core::Size const	count,
		utility::vector1< float > const &	scores
	)

Referenced by protocols::recces::scratch::ThermalSamplingMover::apply(), and protocols::recces::RECCES_Mover::save_history().

◆ gaussian_stdev()

core::Real protocols::recces::gaussian_stdev	(	core::Real const	n_rsd,
		core::Real const	temp,
		bool const	is_bp
	)

Referenced by set_gaussian_stdevs_recces_turner_from_secstruct(), and set_gaussian_stdevs_recces_turner_legacy().

◆ get_scoretypes()

utility::vector1< core::scoring::ScoreType > const & protocols::recces::get_scoretypes ( )

References core::scoring::fa_atr, core::scoring::fa_elec_rna_phos_phos, core::scoring::fa_intra_rep, core::scoring::fa_rep, core::scoring::fa_stack, core::scoring::geom_sol_fast, core::scoring::hbond_sc, core::scoring::lk_nonpolar, core::scoring::rna_torsion, and core::scoring::stack_elec.

Referenced by protocols::recces::scratch::ThermalSamplingMover::apply(), data_dim(), protocols::recces::RECCES_Mover::run_sampler(), protocols::recces::RECCES_Mover::save_data_to_disk(), and update_scores().

◆ get_torsions()

utility::vector1<core::Real> protocols::recces::get_torsions	(	utility::vector1< core::id::TorsionID > const &	torsion_ids,
		core::pose::Pose const &	pose
	)

used to output torsions from pose – useful for clustering states, etc.

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

Referenced by protocols::recces::RECCES_Mover::output_torsions().

◆ pose_setup_from_file()

core::pose::PoseOP protocols::recces::pose_setup_from_file ( options::RECCES_Options const & options )

References core::pose::add_variant_type_to_pose_residue(), protocols::recces::options::RECCES_Options::block_stack(), core::chemical::BLOCK_STACK_ABOVE, core::chemical::BLOCK_STACK_BELOW, core::import_pose::FullModelPoseBuilder::build(), core::chemical::rna::default_jump_atom(), core::chemical::FA_STANDARD, core::pose::fix_up_residue_type_variants(), core::import_pose::get_pdb_and_cleanup(), protocols::recces::options::RECCES_Options::infile(), core::import_pose::FullModelPoseBuilder::initialize_further_from_options(), core::kinematics::FoldTree::new_jump(), core::import_pose::FullModelPoseBuilder::set_input_poses(), core::kinematics::FoldTree::set_jump_atoms(), core::import_pose::FullModelPoseBuilder::set_options(), core::chemical::TR(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by recces_pose_setup().

◆ pose_setup_turner()

core::pose::PoseOP protocols::recces::pose_setup_turner	(	std::string const &	seq1,
		std::string const &	seq2
	)

References core::import_pose::RNA_HelixAssembler::build_init_pose(), core::pose::get_sequence_len(), protocols::mean_field::min(), core::pose::rna::secstruct_legacy::set_rna_secstruct_legacy(), core::import_pose::RNA_HelixAssembler::use_phenix_geo(), and core::pose::rna::virtualize_5prime_phosphates().

Referenced by recces_pose_setup().

◆ print_base_centroid_atoms_for_rb_entropy()

void protocols::recces::print_base_centroid_atoms_for_rb_entropy	(	core::conformation::Residue const &	rsd,
		std::string	filename_xyz
	)

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::recces::sampler::initialize_sampler().

◆ recces_pose_setup()

core::pose::PoseOP protocols::recces::recces_pose_setup ( options::RECCES_Options const & options )

TODO: Unify – read pose from file, and then fill_full_model_info_from_command_line().

References core::pose::rna::RNA_SecStruct::base_pairs(), core::pose::rna::get_base_pairing_list(), protocols::recces::options::RECCES_Options::infile(), protocols::recces::options::RECCES_Options::legacy_turner_mode(), pose_setup_from_file(), pose_setup_turner(), protocols::recces::options::RECCES_Options::rna_secstruct(), protocols::recces::options::RECCES_Options::seq1(), protocols::recces::options::RECCES_Options::seq2(), protocols::recces::options::RECCES_Options::setup_base_pair_constraints(), core::pose::rna::setup_base_pair_constraints(), and core::chemical::TR().

◆ set_gaussian_stdevs_recces_turner()

void protocols::recces::set_gaussian_stdevs_recces_turner	(	protocols::recces::sampler::MC_CombOP	sampler,
		core::Real const &	temperature,
		core::pose::Pose const &	pose,
		core::pose::rna::RNA_SecStruct const &	rna_secstruct,
		protocols::recces::params::RECCES_Parameters const &	params
	)

References core::pose::rna::RNA_SecStruct::blank(), set_gaussian_stdevs_recces_turner_from_secstruct(), and set_gaussian_stdevs_recces_turner_legacy().

Referenced by set_sampler_gaussian_stdev().

◆ set_gaussian_stdevs_recces_turner_from_secstruct()

void protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct	(	protocols::recces::sampler::MC_CombOP	sampler,
		core::Real const &	temperature,
		core::pose::Pose const &	pose,
		core::pose::rna::RNA_SecStruct const &	rna_secstruct
	)

References core::chemical::rna::CHI, core::pose::Pose::fold_tree(), gaussian_stdev(), core::pose::rna::get_suite_torsion_ids(), core::pose::rna::RNA_SecStruct::in_helix(), core::pose::rna::RNA_SecStruct::in_same_helix(), core::kinematics::FoldTree::is_cutpoint(), core::pose::rna::RNA_SecStruct::size(), and core::pose::Pose::total_residue().

Referenced by set_gaussian_stdevs_recces_turner().

◆ set_gaussian_stdevs_recces_turner_legacy()

void protocols::recces::set_gaussian_stdevs_recces_turner_legacy	(	protocols::recces::sampler::MC_CombOP	sampler,
		core::Real const &	temperature,
		core::pose::Pose const &	pose,
		protocols::recces::params::RECCES_Parameters const &	params
	)

Detailed: Legacy stdev setting. Important to recognize helix vs. dangle.

TODO: This should be deprecated in favor of set_gaussian_stdevs_recces_turner... should be a straightforward replacement, but need to check integration tests.

References protocols::recces::params::RECCES_Parameters::bp_res(), core::chemical::rna::CHI, protocols::recces::params::RECCES_Parameters::dangling_res(), core::pose::Pose::fold_tree(), gaussian_stdev(), core::pose::rna::get_suite_torsion_ids(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::total_residue().

Referenced by set_gaussian_stdevs_recces_turner().

◆ set_gaussian_stdevs_thermal_sampler() [1/2]

void protocols::recces::set_gaussian_stdevs_thermal_sampler	(	protocols::recces::sampler::MC_CombOP	internal_bb_sampler,
		protocols::recces::sampler::MC_CombOP	chi_sampler,
		protocols::recces::sampler::rna::MC_RNA_MultiSuiteOP	standard_bb_sampler,
		Real const &	temp,
		core::Size const &	total_rsd,
		core::Size const &	sampled_rsd,
		utility::vector1< bool > const &	is_free
	)

References protocols::toolbox::MC_ONE_TORSION, and protocols::toolbox::MC_RNA_KIC.

◆ set_gaussian_stdevs_thermal_sampler() [2/2]

void protocols::recces::set_gaussian_stdevs_thermal_sampler	(	protocols::recces::sampler::MC_SamplerOP	sampler,
		core::Real const &	temperature,
		core::pose::Pose const &	pose,
		protocols::recces::options::RECCES_Options const &	options
	)

References protocols::recces::options::RECCES_Options::free_residues(), protocols::toolbox::MC_ANY, protocols::toolbox::MC_LOOP, protocols::toolbox::MC_RNA_MULTI_SUITE, protocols::recces::sampler::MC_Comb::num_rotamers(), protocols::recces::options::RECCES_Options::sample_residues(), and core::pose::Pose::size().

Referenced by set_sampler_gaussian_stdev().

◆ set_sampler_gaussian_stdev()

void protocols::recces::set_sampler_gaussian_stdev	(	protocols::recces::sampler::MC_CombOP	sampler,
		core::Real const &	temperature,
		core::pose::Pose const &	pose,
		protocols::recces::options::RECCES_Options const &	options,
		protocols::recces::params::RECCES_Parameters const &	params
	)

TODO: Unify into single function (see notes below on using MC_Sampler::find)

References protocols::recces::options::RECCES_Options::legacy_turner_mode(), protocols::recces::options::RECCES_Options::rna_secstruct(), set_gaussian_stdevs_recces_turner(), set_gaussian_stdevs_thermal_sampler(), and protocols::recces::options::RECCES_Options::thermal_sampler_mode().

Referenced by protocols::recces::RECCES_Mover::set_sampler_gaussian_stdev().

◆ update_scores() [1/2]

void protocols::recces::update_scores	(	utility::vector1< float > &	scores,
		core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn
	)