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protocols::stepwise::legacy::modeler::rna Namespace Reference

Classes

class  Cluster_Member
 
class  RNA_AnalyticLoopCloser
 The RNA de novo structure modeling protocol. More...
 
class  SlicedPoseWorkingParameters
 
class  StepWiseRNA_Clusterer
 
class  StepWiseRNA_PoseSelection
 
class  StepWiseRNA_PoseSetup
 
class  StepWiseWorkingParametersSetup
 

Typedefs

typedef
utility::pointer::shared_ptr
< RNA_AnalyticLoopCloser
RNA_AnalyticLoopCloserOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_Minimizer > 
StepWiseRNA_MinimizerOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_Minimizer const > 
StepWiseRNA_MinimizerCOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_PoseSelection
StepWiseRNA_PoseSelectionOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_PoseSelection
const > 
StepWiseRNA_PoseSelectionCOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_PoseSetup
StepWiseRNA_PoseSetupOP
 
typedef
utility::pointer::shared_ptr
< StepWiseRNA_PoseSetup const > 
StepWiseRNA_PoseSetupCOP
 
typedef
utility::pointer::shared_ptr
< util > 
utilOP
 
typedef
utility::pointer::shared_ptr
< util const > 
utilCOP
 

Functions

void apply_chi_cst (core::pose::Pose &pose, core::pose::Pose const &ref_pose)
 
std::string get_working_directory ()
 
utility::vector1< core::Sizeget_fixed_res (core::Size const nres)
 
bool is_nonempty_input_silent_file (std::string const &input_silent_file, std::string const &exit_key_string)
 
utility::vector1< core::Sizeget_input_res (core::Size const nres, std::string const &pose_num)
 
utility::vector1< std::string > get_silent_file_tags ()
 
core::scoring::ScoreFunctionOP create_scorefxn ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP setup_simple_full_length_rna_working_parameters ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP setup_rna_working_parameters (bool check_for_previously_closed_cutpoint_with_input_pose)
 
void setup_copy_DOF_input (StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)
 
StepWiseRNA_PoseSetupOP setup_pose_setup_class (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters, bool const copy_DOF)
 
bool get_tag_and_silent_file_for_struct (std::string &swa_silent_file, std::string &out_tag, core::Size const &n, bool const &multiple_shots, std::string const &silent_file)
 
void ensure_directory_for_out_silent_file_exists ()
 
bool check_can_prepend (utility::vector1< core::Size > const &seq_num_list)
 
bool check_can_append (utility::vector1< core::Size > const &seq_num_list)
 
bool pair_sort_criterion (std::pair< core::Size, core::Size > pair_one, std::pair< core::Size, core::Size > pair_two)
 
void sort_pair_list (utility::vector1< std::pair< core::Size, core::Size > > pair_list)
 
void output_pair_size (std::pair< core::Size, core::Size > const &pair_size, std::ostream &outstream)
 
void output_pair_size (utility::vector1< std::pair< core::Size, core::Size > > const &pair_size_vector, std::string const &output_string, std::ostream &outstream, core::Size const spacing)
 
void output_is_prepend_map (std::string const &tag, std::map< core::Size, bool > const &my_map, core::Size const max_seq_num, std::ostream &outstream, core::Size const tag_spacing)
 
void output_bool_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)
 
void output_bool_list (std::string const &tag, utility::vector1< bool > const &bool_list, std::ostream &outstream, core::Size const spacing)
 
void output_size_list (std::string const &tag, utility::vector1< core::Size > const &size_list, std::ostream &outstream, core::Size const spacing)
 
void output_fold_tree_info (kinematics::FoldTree const &fold_tree, std::string const &pose_name, std::ostream &outstream)
 
void output_fold_tree_info (pose::Pose const &pose, std::string pose_name, std::ostream &outstream)
 
core::Real full_length_rmsd_over_residue_list (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< core::Size > const &residue_list, std::string const &full_sequence, bool const verbose, bool const ignore_virtual_atom)
 
void print_backbone_torsions (pose::Pose const &pose, core::Size const five_prime_chainbreak)
 
core::Size setup_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
 
void remove_chain_break_jump_point (core::pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
 
core::Size setup_bulge_jump_point (pose::Pose &pose, core::Size const &moving_base, core::Size const &reference_base, bool const verbose)
 
void apply_rotamer (pose::Pose &pose, utility::vector1< Torsion_Info > const &rotamer_list)
 
bool is_same_sugar_pucker (core::pose::Pose const &current_pose, core::pose::Pose const &cluster_center_pose, core::Size const seq_num)
 
void setup_simple_fold_tree (core::pose::Pose &pose)
 
void import_pose_from_silent_file (core::pose::Pose &import_pose, std::string const &silent_file, std::string const &input_tag)
 
std::string get_tag_from_pdb_filename (std::string const &pdb_filename)
 
void print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersCOP const &const_WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)
 
void print_WorkingParameters_info (working_parameters::StepWiseWorkingParametersOP const &WP, std::string const &WP_name, std::ostream &outstream, bool const is_simple_full_length_WP)
 
void set_nucleotide_to_A_form (pose::Pose &pose, core::Size const seq_num)
 
std::string path_basename (std::string const &full_path)
 

Variables

StepWiseRNA_CountStruct local_count_data
 

Typedef Documentation

typedef utility::pointer::shared_ptr< StepWiseRNA_Minimizer const > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_MinimizerCOP
typedef utility::pointer::shared_ptr< StepWiseRNA_Minimizer > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_MinimizerOP
typedef utility::pointer::shared_ptr< util const > protocols::stepwise::legacy::modeler::rna::utilCOP
typedef utility::pointer::shared_ptr< util > protocols::stepwise::legacy::modeler::rna::utilOP

Function Documentation

void protocols::stepwise::legacy::modeler::rna::apply_chi_cst ( core::pose::Pose pose,
core::pose::Pose const &  ref_pose 
)
void protocols::stepwise::legacy::modeler::rna::apply_rotamer ( pose::Pose pose,
utility::vector1< Torsion_Info > const &  rotamer_list 
)
bool protocols::stepwise::legacy::modeler::rna::check_can_append ( utility::vector1< core::Size > const &  seq_num_list)
bool protocols::stepwise::legacy::modeler::rna::check_can_prepend ( utility::vector1< core::Size > const &  seq_num_list)
core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::create_scorefxn ( )
void protocols::stepwise::legacy::modeler::rna::ensure_directory_for_out_silent_file_exists ( )

References TR().

core::Real protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< core::Size > const &  residue_list,
std::string const &  full_sequence,
bool const  verbose,
bool const  ignore_virtual_atom 
)
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::get_fixed_res ( core::Size const  nres)
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::get_input_res ( core::Size const  nres,
std::string const &  pose_num 
)
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::get_silent_file_tags ( )
bool protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct ( std::string &  swa_silent_file,
std::string &  out_tag,
core::Size const &  n,
bool const &  multiple_shots,
std::string const &  silent_file 
)
std::string protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename ( std::string const &  pdb_filename)
std::string protocols::stepwise::legacy::modeler::rna::get_working_directory ( )

References GetCurrentDir.

void protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file ( core::pose::Pose import_pose,
std::string const &  silent_file,
std::string const &  input_tag 
)
bool protocols::stepwise::legacy::modeler::rna::is_nonempty_input_silent_file ( std::string const &  input_silent_file,
std::string const &  exit_key_string 
)

References TR().

bool protocols::stepwise::legacy::modeler::rna::is_same_sugar_pucker ( core::pose::Pose const &  current_pose,
core::pose::Pose const &  cluster_center_pose,
core::Size const  seq_num 
)
void protocols::stepwise::legacy::modeler::rna::output_bool_list ( std::string const &  tag,
utility::vector1< core::Size > const &  size_list,
std::ostream &  outstream,
core::Size const  spacing 
)
void protocols::stepwise::legacy::modeler::rna::output_bool_list ( std::string const &  tag,
utility::vector1< bool > const &  bool_list,
std::ostream &  outstream,
core::Size const  spacing 
)
void protocols::stepwise::legacy::modeler::rna::output_fold_tree_info ( kinematics::FoldTree const &  fold_tree,
std::string const &  pose_name,
std::ostream &  outstream 
)
void protocols::stepwise::legacy::modeler::rna::output_fold_tree_info ( pose::Pose const &  pose,
std::string  pose_name,
std::ostream &  outstream 
)
void protocols::stepwise::legacy::modeler::rna::output_is_prepend_map ( std::string const &  tag,
std::map< core::Size, bool > const &  my_map,
core::Size const  max_seq_num,
std::ostream &  outstream,
core::Size const  tag_spacing 
)
void protocols::stepwise::legacy::modeler::rna::output_pair_size ( std::pair< core::Size, core::Size > const &  pair_size,
std::ostream &  outstream 
)
void protocols::stepwise::legacy::modeler::rna::output_pair_size ( utility::vector1< std::pair< core::Size, core::Size > > const &  pair_size_vector,
std::string const &  output_string,
std::ostream &  outstream,
core::Size const  spacing 
)

References core::sequence::left.

void protocols::stepwise::legacy::modeler::rna::output_size_list ( std::string const &  tag,
utility::vector1< core::Size > const &  size_list,
std::ostream &  outstream,
core::Size const  spacing 
)
bool protocols::stepwise::legacy::modeler::rna::pair_sort_criterion ( std::pair< core::Size, core::Size pair_one,
std::pair< core::Size, core::Size pair_two 
)

Referenced by sort_pair_list().

std::string protocols::stepwise::legacy::modeler::rna::path_basename ( std::string const &  full_path)
void protocols::stepwise::legacy::modeler::rna::print_backbone_torsions ( pose::Pose const &  pose,
core::Size const  five_prime_chainbreak 
)
void protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info ( working_parameters::StepWiseWorkingParametersCOP const &  const_WP,
std::string const &  WP_name,
std::ostream &  outstream,
bool const  is_simple_full_length_WP 
)
void protocols::stepwise::legacy::modeler::rna::print_WorkingParameters_info ( working_parameters::StepWiseWorkingParametersOP const &  WP,
std::string const &  WP_name,
std::ostream &  outstream,
bool const  is_simple_full_length_WP 
)
void protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point ( core::pose::Pose pose,
core::Size const  moving_res,
core::Size const  reference_res 
)
void protocols::stepwise::legacy::modeler::rna::set_nucleotide_to_A_form ( pose::Pose pose,
core::Size const  seq_num 
)
core::Size protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point ( pose::Pose pose,
core::Size const &  moving_base,
core::Size const &  reference_base,
bool const  verbose 
)
core::Size protocols::stepwise::legacy::modeler::rna::setup_chain_break_jump_point ( core::pose::Pose pose,
core::Size const  moving_res,
core::Size const  reference_res 
)
void protocols::stepwise::legacy::modeler::rna::setup_copy_DOF_input ( StepWiseRNA_PoseSetupOP stepwise_rna_pose_setup)

References get_silent_file_tags(), and TR().

Referenced by setup_pose_setup_class().

StepWiseRNA_PoseSetupOP protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class ( stepwise::modeler::working_parameters::StepWiseWorkingParametersOP working_parameters,
bool const  copy_DOF 
)
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters ( bool  check_for_previously_closed_cutpoint_with_input_pose)
void protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree ( core::pose::Pose pose)
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters ( )

Oct 28, 2011:This function is an alternative way to setup the working_parameters//////////////////////////////////////////////////// The original working_parameters was designed primarily for use during the SWA building step///////////////////////////////////////// However since then, many other other SWA and FARFAR class make use of it especially the full pose length version//////////////// Hence the original working_parameters setup has become clumbersome for most usage (containing many options and independencies)////// The new job_parameter setup function is a work in progress and will be updated as needed./////////////////////////////////////// For example right now (Oct 28, 2011), it only contains parameters needed by output_data()///////////////////////////////////////

References core::pose::rna::apply_virtual_rna_residue_variant_type(), core::chemical::FA_STANDARD, core::pose::full_model_info::full_to_sub(), get_fixed_res(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), print_WorkingParameters_info(), core::sequence::read_fasta_file_and_concatenate(), core::pose::rna::remove_bracketed(), core::pose::rna::string_to_int(), core::pose::rna::tokenize(), and TR().

void protocols::stepwise::legacy::modeler::rna::sort_pair_list ( utility::vector1< std::pair< core::Size, core::Size > >  pair_list)

Variable Documentation

protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct protocols::stepwise::legacy::modeler::rna::local_count_data