Rosetta  2021.16
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FragmentScoreFilter.cc File Reference

This filter analyzes fragment quality. How it does so is highly customizeable, but it is reccommended that you average the RMSD of all 200 fragments picked at every position. This is also the default behavior. It requires paths to external programs like SPARKS-X and blast-pgp, depending on your method of fragment picking. More...

#include <protocols/frag_picker/FragmentScoreFilter.hh>
#include <protocols/frag_picker/FragmentScoreFilterCreator.hh>
#include <numeric>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/filters/filter_schemas.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <core/sequence/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/ResidueIndexDescription.hh>
#include <core/pose/selection.hh>
#include <core/conformation/Residue.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/TaskFactory.hh>
#include <utility/string_util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <protocols/filters/Filter.hh>
#include <basic/options/option.hh>
#include <utility/vector1.hh>
#include <sys/stat.h>
#include <fstream>
#include <utility/file/file_sys_util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/database/open.hh>
#include <basic/prof.hh>
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/scores/FragmentCrmsd.hh>
#include <protocols/frag_picker/BoundedCollector.hh>
#include <protocols/frag_picker/BestTotalScoreSelector.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::frag_picker
 

Functions

static basic::Tracer TR ("protocols.frag_picker.FragmentScoreFilter")
 
void protocols::frag_picker::convert_binary_checkpoint (std::string const &check_filename)
 
void protocols::frag_picker::run_command (std::string const &cmd)
 Run a command in a terminal. More...
 

Detailed Description

This filter analyzes fragment quality. How it does so is highly customizeable, but it is reccommended that you average the RMSD of all 200 fragments picked at every position. This is also the default behavior. It requires paths to external programs like SPARKS-X and blast-pgp, depending on your method of fragment picking.

Author
Cody Krivacic (kriva.nosp@m.cic@.nosp@m.berke.nosp@m.ley..nosp@m.edu)

Function Documentation

static basic::Tracer TR ( "protocols.frag_picker.FragmentScoreFilter"  )
static