Rosetta  2019.31
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Functions | Variables
ResidueDisorder.cc File Reference
#include <basic/options/option.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/io/izstream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/scoring/ScoreType.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>

Functions

void check_pose_size (core::Size num_res_current, core::Size num_res)
 
void check_single_chain (const core::pose::PoseOP &mypose)
 
void check_sequence (const core::pose::PoseOP &pose, const core::pose::PoseOP &pose_current)
 
void check_number_of_poses (core::Size n_poses)
 
void check_score_function (core::scoring::ScoreFunctionOP sfxn)
 
void read_in_pdbs (utility::vector1< core::pose::PoseOP > &poses, core::Size &n_poses, core::Size &num_res)
 
void calculate_average_residue_scores (const utility::vector1< core::pose::PoseOP > &poses, utility::vector1< core::Real > &average_res_scores, std::string &sequence, core::Size num_res, core::Size n_poses)
 
void caculate_order_scores (utility::vector1< core::Real > &ORDER_RES_Score, const utility::vector1< core::Real > &average_res_scores, core::Size num_res)
 
void predict_disorder (utility::vector1< std::string > &PREDICTION, const utility::vector1< core::Real > &ORDER_RES_Score, const std::string &sequence, core::Size num_res, const utility::vector1< core::Real > &cutoffs, bool terminal)
 
core::Real calculate_percent_disorder (const utility::vector1< std::string > &PREDICTION, core::Size num_res)
 
void do_terminal_opt (utility::vector1< core::Real > &cutoffs_new, core::Size num_res)
 
void output_results (core::Size num_res, const std::string &sequence, const utility::vector1< std::string > &PREDICTION, const utility::vector1< core::Real > &ORDER_RES_Score, utility::vector1< core::Real > average_res_scores)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("apps.public.analysis.ResidueDisorder")
 

Function Documentation

void caculate_order_scores ( utility::vector1< core::Real > &  ORDER_RES_Score,
const utility::vector1< core::Real > &  average_res_scores,
core::Size  num_res 
)

References basic::options::OptionKeys::frags::j.

Referenced by main().

void calculate_average_residue_scores ( const utility::vector1< core::pose::PoseOP > &  poses,
utility::vector1< core::Real > &  average_res_scores,
std::string &  sequence,
core::Size  num_res,
core::Size  n_poses 
)
core::Real calculate_percent_disorder ( const utility::vector1< std::string > &  PREDICTION,
core::Size  num_res 
)

References clean_pdb_keep_ligand::count, and TR.

Referenced by main().

void check_number_of_poses ( core::Size  n_poses)

References TR, and basic::Tracer::Warning.

Referenced by read_in_pdbs().

void check_pose_size ( core::Size  num_res_current,
core::Size  num_res 
)

References utility_exit_with_message.

Referenced by read_in_pdbs().

void check_score_function ( core::scoring::ScoreFunctionOP  sfxn)
void check_sequence ( const core::pose::PoseOP &  pose,
const core::pose::PoseOP &  pose_current 
)
void check_single_chain ( const core::pose::PoseOP &  mypose)

References utility_exit_with_message.

Referenced by read_in_pdbs().

void do_terminal_opt ( utility::vector1< core::Real > &  cutoffs_new,
core::Size  num_res 
)

Referenced by main().

int main ( int  argc,
char *  argv[] 
)
void output_results ( core::Size  num_res,
const std::string &  sequence,
const utility::vector1< std::string > &  PREDICTION,
const utility::vector1< core::Real > &  ORDER_RES_Score,
utility::vector1< core::Real >  average_res_scores 
)
void predict_disorder ( utility::vector1< std::string > &  PREDICTION,
const utility::vector1< core::Real > &  ORDER_RES_Score,
const std::string &  sequence,
core::Size  num_res,
const utility::vector1< core::Real > &  cutoffs,
bool  terminal 
)

References TR.

Referenced by main().

void read_in_pdbs ( utility::vector1< core::pose::PoseOP > &  poses,
core::Size &  n_poses,
core::Size &  num_res 
)

Variable Documentation

basic::Tracer TR("apps.public.analysis.ResidueDisorder")
static