Namespaces
	rna

Classes
class	MC_Any

class	MC_Comb

class	MC_Loop

class	MC_OneTorsion

class	MC_Sampler

Typedefs
typedef utility::pointer::shared_ptr< MC_Any >	MC_AnyOP

typedef utility::pointer::shared_ptr< MC_Any const >	MC_AnyCOP

typedef utility::pointer::shared_ptr< MC_Comb >	MC_CombOP

typedef utility::pointer::shared_ptr< MC_Loop >	MC_LoopOP

typedef utility::pointer::shared_ptr< MC_Loop const >	MC_LoopCOP

typedef utility::pointer::shared_ptr< MC_OneTorsion >	MC_OneTorsionOP

typedef utility::pointer::weak_ptr< MC_OneTorsion >	MC_OneTorsionAP

typedef utility::pointer::shared_ptr< MC_Sampler >	MC_SamplerOP

typedef utility::pointer::shared_ptr< MC_Sampler const >	MC_SamplerCOP

Functions
protocols::recces::sampler::MC_CombOP	initialize_sampler (pose::Pose const &pose, options::RECCES_Options const &options, params::RECCES_Parameters const &params)

protocols::recces::sampler::MC_CombOP	get_recces_turner_sampler_from_secstruct (pose::Pose const &pose, core::Real const &a_form_range, core::pose::rna::RNA_SecStruct const &rna_secstruct)

protocols::recces::sampler::MC_CombOP	get_recces_turner_sampler_legacy (pose::Pose const &pose, core::Real const &a_form_range, params::RECCES_Parameters const &params)

protocols::recces::sampler::MC_CombOP	get_recces_turner_sampler (pose::Pose const &pose, core::Real const &a_form_range, core::pose::rna::RNA_SecStruct const &secstruct, params::RECCES_Parameters const &params)

MC_CombOP	initialize_thermal_sampler (pose::Pose const &pose, options::RECCES_Options const &options)

MC_RNA_OneJumpOP	initialize_jump_sampler (core::pose::Pose const &pose, core::Size const &num_jump, options::RECCES_Options const &options)

Typedef Documentation

◆ MC_AnyCOP

typedef utility::pointer::shared_ptr< MC_Any const > protocols::recces::sampler::MC_AnyCOP

◆ MC_AnyOP

typedef utility::pointer::shared_ptr< MC_Any > protocols::recces::sampler::MC_AnyOP

◆ MC_CombOP

typedef utility::pointer::shared_ptr< MC_Comb > protocols::recces::sampler::MC_CombOP

◆ MC_LoopCOP

typedef utility::pointer::shared_ptr< MC_Loop const > protocols::recces::sampler::MC_LoopCOP

◆ MC_LoopOP

typedef utility::pointer::shared_ptr< MC_Loop > protocols::recces::sampler::MC_LoopOP

◆ MC_OneTorsionAP

typedef utility::pointer::weak_ptr< MC_OneTorsion > protocols::recces::sampler::MC_OneTorsionAP

◆ MC_OneTorsionOP

typedef utility::pointer::shared_ptr< MC_OneTorsion > protocols::recces::sampler::MC_OneTorsionOP

◆ MC_SamplerCOP

typedef utility::pointer::shared_ptr< MC_Sampler const > protocols::recces::sampler::MC_SamplerCOP

◆ MC_SamplerOP

typedef utility::pointer::shared_ptr< MC_Sampler > protocols::recces::sampler::MC_SamplerOP

Function Documentation

◆ get_recces_turner_sampler()

protocols::recces::sampler::MC_CombOP protocols::recces::sampler::get_recces_turner_sampler	(	pose::Pose const &	pose,
		core::Real const &	a_form_range,
		core::pose::rna::RNA_SecStruct const &	secstruct,
		params::RECCES_Parameters const &	params
	)

References core::pose::rna::RNA_SecStruct::blank(), get_recces_turner_sampler_from_secstruct(), and get_recces_turner_sampler_legacy().

Referenced by initialize_sampler().

◆ get_recces_turner_sampler_from_secstruct()

protocols::recces::sampler::MC_CombOP protocols::recces::sampler::get_recces_turner_sampler_from_secstruct	(	pose::Pose const &	pose,
		core::Real const &	a_form_range,
		core::pose::rna::RNA_SecStruct const &	rna_secstruct
	)

pretty satisfactory sampler setup function. Developed to handle single-nucleotide bulge & other motifs more complex than helices.

TODO: This remains a little cryptic due to use of MC_RNA_Suite wrapper which has convenient set_sample_near_a_form functions ... would be better (and pretty easy) to create more 'atomic' MC_RNA_Sugar, MC_RNA_Chi, and MC_RNA_SuiteBB functions with set_sample_near_a_form() function. – rhiju, jan2017

References core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::pose::rna::RNA_SecStruct::in_helix(), core::pose::rna::RNA_SecStruct::in_same_helix(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RIBOSE.

Referenced by get_recces_turner_sampler().

◆ get_recces_turner_sampler_legacy()

protocols::recces::sampler::MC_CombOP protocols::recces::sampler::get_recces_turner_sampler_legacy	(	pose::Pose const &	pose,
		core::Real const &	a_form_range,
		params::RECCES_Parameters const &	params
	)

Detailed: Legacy sampler setup from Fang

Goes through some cryptic book-keeping in order to fit
   samplers into "MultiSuite" framework.

How MC_RNA_Suite samplers are grouped in some typical use cases:

Single-stranded
----------------
  1       1         2      2        3      3         4

5'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-3' | | | |

Helix

1* 1* 2* 2* 3* 3* 4* 5'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-3' | | | | | | | | 3'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-5' 8* 7* 7* 6* 6* 5* 5*

= use A-form range for sugar/chi or backbone.

3'-dangle

1* 1* 2* 2* 3* 3 4 (len1=4) 5'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-3' | | | | | | | 3'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-5' 7* 6* 6* 5* 5*

5'-dangle

1* 1* 2* 2* 3* (len1=3) 5'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-3' | | | | | | | 3'-[Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-[Backbone-Sugar]-5' 7* 6* 6* 5* 5* 4 4

TODO: Could unify with get_recces_turner_sampler_from_secstruct() if we had a silly function that could set up order of chi & bb samplers to exactly match the order created by this legacy order – and then check exact numerical trajectory with recces_turner integration test. Use of recces_turner app would trigger that reordering (or perhaps recognition that sequence is a perfect helix, perhaps with dangle in recces_turner style). Note that we should also be able to deprecate bp_res and dangle_res – and actually then deprecate RECCES_Parameters (since those are its only variables). – rhiju, 2016

References protocols::recces::params::RECCES_Parameters::bp_res(), protocols::recces::params::RECCES_Parameters::dangling_res(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::size().

Referenced by get_recces_turner_sampler().

◆ initialize_jump_sampler()

protocols::recces::sampler::rna::MC_RNA_OneJumpOP protocols::recces::sampler::initialize_jump_sampler	(	core::pose::Pose const &	pose,
		core::Size const &	num_jump,
		options::RECCES_Options const &	options
	)

References protocols::recces::options::RECCES_Options::base_pair_rmsd_cutoff(), protocols::recces::options::RECCES_Options::base_pair_rotation_mag(), and protocols::recces::options::RECCES_Options::base_pair_translation_mag().

Referenced by initialize_sampler(), and initialize_thermal_sampler().

◆ initialize_sampler()

protocols::recces::sampler::MC_CombOP protocols::recces::sampler::initialize_sampler	(	pose::Pose const &	pose,
		options::RECCES_Options const &	options,
		params::RECCES_Parameters const &	params
	)

TODO – unify recces_turner & thermal_sampler setup by making HELIX and DANGLE full_model_parameters specify recces_turner-like residues. May also want rna_secstruct setup in full_model_parameters!

Tests: rb_recces, recces_turner, & thermal_sampler integration tests: must not change.

More tests: 1. handle long helices setup with -seq & -jump_res in the middle.

long helices + KIC to improve sampling.
check compatibility of sample_jump with helix+dangling ends.
multiple dangles hanging off helix.

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

◆ initialize_thermal_sampler()

protocols::recces::sampler::MC_CombOP protocols::recces::sampler::initialize_thermal_sampler	(	pose::Pose const &	pose,
		options::RECCES_Options const &	options
	)

References protocols::recces::options::RECCES_Options::angle_range_bb(), protocols::recces::options::RECCES_Options::angle_range_chi(), protocols::recces::options::RECCES_Options::angle_range_free_bb(), protocols::recces::options::RECCES_Options::angle_range_free_chi(), core::id::CHI, core::pose::Pose::fold_tree(), core::scoring::free_res, protocols::recces::options::RECCES_Options::free_residues(), core::pose::Pose::get_self_ptr(), core::conformation::Residue::has_variant_type(), initialize_jump_sampler(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), protocols::recces::options::RECCES_Options::sample_jump(), protocols::recces::options::RECCES_Options::sample_residues(), core::pose::Pose::torsion(), core::pose::Pose::total_residue(), core::pose::TR(), and core::chemical::VIRTUAL_RIBOSE.