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protocols::recces::sampler Namespace Reference

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

typedef utility::pointer::shared_ptr< MC_Any const > protocols::recces::sampler::MC_AnyCOP
typedef utility::pointer::shared_ptr< MC_Any > protocols::recces::sampler::MC_AnyOP
typedef utility::pointer::shared_ptr< MC_Comb > protocols::recces::sampler::MC_CombOP
typedef utility::pointer::shared_ptr< MC_Loop const > protocols::recces::sampler::MC_LoopCOP
typedef utility::pointer::shared_ptr< MC_Loop > protocols::recces::sampler::MC_LoopOP
typedef utility::pointer::weak_ptr< MC_OneTorsion > protocols::recces::sampler::MC_OneTorsionAP
typedef utility::pointer::shared_ptr< MC_OneTorsion > protocols::recces::sampler::MC_OneTorsionOP
typedef utility::pointer::shared_ptr< MC_Sampler const > protocols::recces::sampler::MC_SamplerCOP
typedef utility::pointer::shared_ptr< MC_Sampler > protocols::recces::sampler::MC_SamplerOP

Function Documentation

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 
)
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().

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().

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