score_aln.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.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/sequence/ScoringScheme.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/pose/Pose.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/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/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/pose/annotated_sequence.hh>
#include <utility/io/ozstream.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

main()

int main	(	int	argc,
		char *	argv[]
	)

References in::file::alignment(), aln, cm::aln_format(), argv, numeric::model_quality::calc_rms(), basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, test.T009_Exceptions::e, basic::Tracer::Error, in::file::fasta(), basic::Tracer::flush_all_channels(), utility::keys::AutoKey< O, S, C >::id(), basic::init(), subloop_histogram::iterator, cm::min_gap_extend(), cm::min_gap_open(), in::file::native(), docking::native_pose, natoms(), option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), in::file::pssm(), numeric::model_quality::rms_wrapper(), save_per_residue_scores(), cm::seq_score(), sequences_from_cmd_line(), sfd, basic::options::OptionKeys::in::file::silent, out::file::silent(), challenge::ss, in::file::template_pdb(), tr, and basic::options::OptionKeys::inout::dbms::user.

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References basic::options::OptionKeys::chemical::chemical, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

print_seq_map()

void print_seq_map	(	std::ostream &	out,
		std::map< std::string, core::sequence::SequenceOP > const &	seqs
	)

References beta_sc_scan::seq.

save_per_residue_scores()

void save_per_residue_scores	(	std::string const &	fn,
		core::sequence::SequenceAlignment const &	aln,
		core::sequence::ScoringSchemeOP	ss,
		std::string const &	aln_id
	)

References aln, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::ii, bin_torsions::output, pna::resi, create_a3b_hbs::score, legacy_score_vs_rmsd::scores, and challenge::ss.

Referenced by main().

sequences_from_cmd_line()

std::map< std::string, core::sequence::SequenceOP > sequences_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References utility::file_basename(), utility::file::file_exists(), file_exists(), and basic::options::OptionKeys::relax::sequence.

Referenced by main().