Rosetta  2020.28
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score_aln.cc File Reference
#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/rms_util.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <protocols/comparative_modeling/PartialThreadingMover.hh>
#include <protocols/comparative_modeling/coord_util.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <numeric/model_quality/rms.hh>
#include <map>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/annotated_sequence.hh>
#include <utility/io/ozstream.hh>
#include <ObjexxFCL/format.hh>

Functions

std::map< std::string,
core::pose::Pose
poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
 
void print_seq_map (std::ostream &out, std::map< std::string, core::sequence::SequenceOP > const &seqs)
 
std::map< std::string,
core::sequence::SequenceOP > 
sequences_from_cmd_line (utility::vector1< std::string > const &fn_list)
 
void save_per_residue_scores (std::string const &fn, core::sequence::SequenceAlignment const &aln, core::sequence::ScoringSchemeOP ss, std::string const &aln_id)
 
int main (int argc, char *argv[])
 

Detailed Description

Author
James Thompson

Function Documentation

int main ( int  argc,
char *  argv[] 
)
std::map< std::string, core::pose::Pose > poses_from_cmd_line ( utility::vector1< std::string > const &  fn_list)
void print_seq_map ( std::ostream &  out,
std::map< std::string, core::sequence::SequenceOP > const &  seqs 
)
void save_per_residue_scores ( std::string const &  fn,
core::sequence::SequenceAlignment const &  aln,
core::sequence::ScoringSchemeOP  ss,
std::string const &  aln_id 
)
std::map< std::string, core::sequence::SequenceOP > sequences_from_cmd_line ( utility::vector1< std::string > const &  fn_list)