src/apps/public/comparative_modeling/score_aln2.cc File Reference

#include <core/types.hh>
#include <protocols/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/id/SequenceMapping.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceFactory.hh>
#include <core/sequence/CompositeSequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/CompositeScoringScheme.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/util.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <protocols/evaluation/Align_RmsdEvaluator.hh>
#include <protocols/comparative_modeling/PartialThreadingMover.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 <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.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 <basic/options/keys/run.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.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::CompositeSequenceOP > const &seqs)
std::map< std::string, core::sequence::CompositeSequenceOP >	composite_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

std::map< std::string, core::sequence::CompositeSequenceOP > composite_sequences_from_cmd_line

(

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

fn_list

)

References utility::file::file_basename(), utility::file::file_exists(), test::T200_Scoring::ii, name, runtime_assert, basic::options::OptionKeys::in::file::seq, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

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

References basic::options::OptionKeys::in::file::alignment, cm::aln_format(), basic::options::OptionKeys::chemical::chemical, composite_sequences_from_cmd_line(), utility::io::oc::cout, basic::Tracer::Debug, run::debug(), end, basic::Tracer::Error, basic::Tracer::flush_all_channels(), test::T200_Scoring::ii, src::init(), cm::min_gap_extend(), cm::min_gap_open(), in::file::native(), basic::options::option, options, poses_from_cmd_line(), save_per_residue_scores(), in::file::seq(), cm::seq_score(), basic::options::OptionKeys::relax::sequence, out::file::silent(), basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::smhybrid::ss, in::file::template_pdb(), tr, and basic::options::OptionKeys::mysql::user.

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

(

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

fn_list

)

References basic::options::OptionKeys::chemical::chemical, end, utility::file::file_basename(), utility::file::file_exists(), name, and PyMOL_demo::pose.

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

References end.

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

References test::T200_Scoring::ii, basic::options::OptionKeys::out::output, and basic::options::OptionKeys::AnchoredDesign::filters::score.