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protocols::rna::movers Namespace Reference

Classes

class  ERRASER2Protocol
 Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job. More...
 
class  ERRASER2ProtocolCreator
 
class  ErraserMinimizerMover
 
class  ErraserMinimizerMoverCreator
 
class  RNA_DeNovoOptimizer
 
class  RNA_LoopCloser
 The RNA de novo structure modeling protocol. More...
 
class  RNAIdealizeMover
 Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization. More...
 
class  RNAIdealizeMoverCreator
 
class  RNAThreadAndMinimizeMover
 Thread a new sequence over a given RNA scaffold and do a little optimization. More...
 
class  RNAThreadAndMinimizeMoverCreator
 

Typedefs

using ERRASER2ProtocolOP = utility::pointer::shared_ptr< ERRASER2Protocol >
 
using ERRASER2ProtocolCOP = utility::pointer::shared_ptr< ERRASER2Protocol const >
 
using ErraserMinimizerMoverOP = utility::pointer::shared_ptr< ErraserMinimizerMover >
 
using ErraserMinimizerMoverCOP = utility::pointer::shared_ptr< const ErraserMinimizerMover >
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoOptimizer
RNA_DeNovoOptimizerOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoOptimizer const > 
RNA_DeNovoOptimizerCOP
 
typedef
utility::pointer::shared_ptr
< RNA_LoopCloser
RNA_LoopCloserOP
 
typedef
utility::pointer::shared_ptr
< RNA_LoopCloser const > 
RNA_LoopCloserCOP
 
typedef
utility::pointer::shared_ptr
< RNAIdealizeMover
RNAIdealizeMoverOP
 
typedef
utility::pointer::shared_ptr
< RNAIdealizeMover const > 
RNAIdealizeMoverCOP
 
typedef
utility::pointer::shared_ptr
< RNAThreadAndMinimizeMover
RNAThreadAndMinimizeMoverOP
 
typedef
utility::pointer::shared_ptr
< RNAThreadAndMinimizeMover
const > 
RNAThreadAndMinimizeMoverCOP
 

Functions

static basic::Tracer TR ("apps.public.rna.erraser.erraser2")
 
utility::vector1< core::Sizeall_pose_residues (core::pose::Pose const &pose)
 
void show_accuracy_report (pose::Pose const &start_pose, std::string const &tag, core::Size const round)
 
bool atoms_have_bond_to_bonded_atoms (pose::Pose const &pose, core::Size const ai, core::Size const ii, core::Size const aj, core::Size const jj)
 
bool atoms_have_mutual_bond_to_atom (pose::Pose const &pose, core::Size const ai, core::Size const ii, core::Size const aj, core::Size const jj)
 
bool bump_check (pose::Pose const &pose, core::Size const ii)
 
utility::vector1< core::Sizedetermine_residues_to_rebuild (utility::vector1< core::Size > const &consider_rebuild_res, pose::Pose const &start_pose)
 
std::ostream & operator<< (std::ostream &os, ERRASER2Protocol const &mover)
 private methods /// More...
 
utility::vector1< core::Sizestring_to_size_vector (std::string const &sv)
 
template<typename T >
void remove_set1_elements_from_set2 (std::set< T > const &set1, std::set< T > &set2)
 
void fill_gaps_and_remove_isolated_res (std::set< core::Size > &res_list, core::Size const total_res, std::set< core::Size > &res_remove)
 
std::set< core::Sizefind_nearby_res (Pose const &pose, std::set< core::Size > res_list_current, Real const dist_cutoff)
 
void erase_if_in_any_slice (utility::vector1< std::set< core::Size > > const &res_list_sliced, core::Size const res, std::set< core::Size > &res_list_new)
 
void clean_res_list (std::set< core::Size > &res_list_new, utility::vector1< std::set< core::Size > > const &res_list_sliced)
 
void identify_chunks (Pose const &pose, utility::vector1< std::set< core::Size > > &sliced_list_final, core::Size const virtual_res_pos, core::Size const nproc)
 
core::Vector com_of_true_residues (kinematics::MoveMap const &mm, Pose const &pose)
 
std::string min_checkpoint_namer (core::Size const nstruct)
 
std::string min_log_namer (core::Size const nstruct)
 
void read_checkpoint_log (utility::vector1< core::Size > &chunk_indices, core::Size &start_idx, core::Size const nstruct)
 
void write_checkpoint (utility::vector1< core::Size > const &chunk_indices, core::Size const cur_idx, core::Size const nstruct, Pose const &pose)
 
void load_checkpoint (core::Size const nstruct, utility::vector1< core::Size > &chunk_indices, Pose &pose, core::Size &first_chunk)
 
std::ostream & operator<< (std::ostream &os, RNAIdealizeMover const &mover)
 
std::ostream & operator<< (std::ostream &os, RNAThreadAndMinimizeMover const &mover)
 

Typedef Documentation

using protocols::rna::movers::ERRASER2ProtocolCOP = typedef utility::pointer::shared_ptr< ERRASER2Protocol const >
using protocols::rna::movers::ERRASER2ProtocolOP = typedef utility::pointer::shared_ptr< ERRASER2Protocol >
typedef utility::pointer::shared_ptr< ErraserMinimizerMover const > protocols::rna::movers::ErraserMinimizerMoverCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer const > protocols::rna::movers::RNA_DeNovoOptimizerCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer > protocols::rna::movers::RNA_DeNovoOptimizerOP
typedef utility::pointer::shared_ptr< RNA_LoopCloser const > protocols::rna::movers::RNA_LoopCloserCOP
typedef utility::pointer::shared_ptr< RNA_LoopCloser > protocols::rna::movers::RNA_LoopCloserOP
typedef utility::pointer::shared_ptr< RNAIdealizeMover const > protocols::rna::movers::RNAIdealizeMoverCOP
typedef utility::pointer::shared_ptr< RNAIdealizeMover > protocols::rna::movers::RNAIdealizeMoverOP

Function Documentation

utility::vector1< core::Size > protocols::rna::movers::all_pose_residues ( core::pose::Pose const &  pose)
bool protocols::rna::movers::atoms_have_bond_to_bonded_atoms ( pose::Pose const &  pose,
core::Size const  ai,
core::Size const  ii,
core::Size const  aj,
core::Size const  jj 
)
bool protocols::rna::movers::atoms_have_mutual_bond_to_atom ( pose::Pose const &  pose,
core::Size const  ai,
core::Size const  ii,
core::Size const  aj,
core::Size const  jj 
)
bool protocols::rna::movers::bump_check ( pose::Pose const &  pose,
core::Size const  ii 
)
void protocols::rna::movers::clean_res_list ( std::set< core::Size > &  res_list_new,
utility::vector1< std::set< core::Size > > const &  res_list_sliced 
)
core::Vector protocols::rna::movers::com_of_true_residues ( kinematics::MoveMap const &  mm,
Pose const &  pose 
)
utility::vector1< core::Size > protocols::rna::movers::determine_residues_to_rebuild ( utility::vector1< core::Size > const &  consider_rebuild_res,
pose::Pose const &  start_pose 
)
void protocols::rna::movers::erase_if_in_any_slice ( utility::vector1< std::set< core::Size > > const &  res_list_sliced,
core::Size const  res,
std::set< core::Size > &  res_list_new 
)
void protocols::rna::movers::fill_gaps_and_remove_isolated_res ( std::set< core::Size > &  res_list,
core::Size const  total_res,
std::set< core::Size > &  res_remove 
)
std::set< core::Size > protocols::rna::movers::find_nearby_res ( Pose const &  pose,
std::set< core::Size res_list_current,
Real const  dist_cutoff 
)
void protocols::rna::movers::identify_chunks ( Pose const &  pose,
utility::vector1< std::set< core::Size > > &  sliced_list_final,
core::Size const  virtual_res_pos,
core::Size const  nproc 
)
void protocols::rna::movers::load_checkpoint ( core::Size const  nstruct,
utility::vector1< core::Size > &  chunk_indices,
Pose pose,
core::Size first_chunk 
)
std::string protocols::rna::movers::min_checkpoint_namer ( core::Size const  nstruct)
std::string protocols::rna::movers::min_log_namer ( core::Size const  nstruct)
std::ostream & protocols::rna::movers::operator<< ( std::ostream &  os,
RNAIdealizeMover const &  mover 
)
std::ostream & protocols::rna::movers::operator<< ( std::ostream &  os,
ERRASER2Protocol const &  mover 
)

private methods ///

References protocols::rna::movers::ERRASER2Protocol::show().

std::ostream & protocols::rna::movers::operator<< ( std::ostream &  os,
RNAThreadAndMinimizeMover const &  mover 
)
void protocols::rna::movers::read_checkpoint_log ( utility::vector1< core::Size > &  chunk_indices,
core::Size start_idx,
core::Size const  nstruct 
)
template<typename T >
void protocols::rna::movers::remove_set1_elements_from_set2 ( std::set< T > const &  set1,
std::set< T > &  set2 
)
void protocols::rna::movers::show_accuracy_report ( pose::Pose const &  start_pose,
std::string const &  tag,
core::Size const  round 
)
utility::vector1< core::Size > protocols::rna::movers::string_to_size_vector ( std::string const &  sv)
static basic::Tracer protocols::rna::movers::TR ( "apps.public.rna.erraser.erraser2"  )
static
void protocols::rna::movers::write_checkpoint ( utility::vector1< core::Size > const &  chunk_indices,
core::Size const  cur_idx,
core::Size const  nstruct,
Pose const &  pose 
)