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protocols::recces Namespace Reference

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::Realget_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

typedef utility::pointer::shared_ptr< Histogram const > protocols::recces::HistogramCOP
typedef utility::pointer::shared_ptr< Histogram > protocols::recces::HistogramOP
typedef utility::pointer::shared_ptr< RECCES_Mover const > protocols::recces::RECCES_MoverCOP
typedef utility::pointer::shared_ptr< RECCES_Mover > protocols::recces::RECCES_MoverOP

Function Documentation

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

References get_scoretypes().

void protocols::recces::fill_data ( utility::vector1< float > &  data,
core::Size const  count,
utility::vector1< float > const &  scores 
)
core::Real protocols::recces::gaussian_stdev ( core::Real const  n_rsd,
core::Real const  temp,
bool const  is_bp 
)
utility::vector1< core::scoring::ScoreType > const & protocols::recces::get_scoretypes ( )
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().

core::pose::PoseOP protocols::recces::pose_setup_from_file ( options::RECCES_Options const &  options)
core::pose::PoseOP protocols::recces::pose_setup_turner ( std::string const &  seq1,
std::string const &  seq2 
)
void protocols::recces::print_base_centroid_atoms_for_rb_entropy ( core::conformation::Residue const &  rsd,
std::string  filename_xyz 
)
core::pose::PoseOP protocols::recces::recces_pose_setup ( options::RECCES_Options const &  options)
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 
)
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 
)
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().

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

References get_scoretypes().

template<typename T >
void protocols::recces::vector2disk_in1d ( std::string const &  out_filename,
utility::vector1< T > const &  out_vector 
)
template<typename T >
void protocols::recces::vector2disk_in2d ( std::string const &  out_filename,
core::Size const  dim1,
core::Size const  dim2,
utility::vector1< T > const &  out_vector 
)