unalignedEvaluate.cc File Reference

This takes an alignment file, fasta file, and a silent file. It then evaluates the qualities of the loops. More...

#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <basic/Tracer.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/id/SequenceMapping.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/Func.fwd.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/electron_density/FastDensEnergy.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <utility/options/keys/BooleanOptionKey.fwd.hh>
#include <utility/options/keys/BooleanOptionKey.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <numeric/xyzVector.hh>
#include <apps/pilot/brunette/tj_util.hh>
#include <iostream>
#include <fstream>

Namespaces
	unalignedEvaluate

Functions
Real	region_density_score (Pose &pose, Pose const templatePose, SequenceAlignment aln, Size start_res, Size end_res)
Real	region_constraint_score (Pose &pose, Size start_res, Size end_res, ConstraintSetOP cstSet_)
Real	region_score (Pose &pose, Size start_res, Size end_res)
Real	region_rmsd_structures_aligned (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res)
Real	two_region_rmsd (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res, Size region2_start_res, Size region2_end_res)
Real	region_rmsd (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size start_res, Size end_res)
bool	present_in_native (Size start_res, Size end_res, SequenceAlignment native_aln)
void	score_loop (Pose &pose, Pose const &native_pose, SequenceAlignment native_aln, SequenceAlignment template_aln, Pose native_relaxed_pose, Size start_res, Size end_res, ConstraintSetOP cstSet_, ConstraintSetOP lookBackCstSet_, Pose const templatePose, std::ostream &out)
void	score_loops (Pose pose, Loops const unalignedLoops, Pose native_pose, SequenceAlignment native_alignment, SequenceAlignment template_alignment, Pose native_relaxed_pose, Pose const templatePoseData, ConstraintSetOP cstSet_, ConstraintSetOP lookBackCstSet_, std::ostream &out)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("unalignedEvaluate")
	@usage: -in:file:alignent <alignment> -in:file:s <decoy.out> -in:file:native <native pose> -in:file:fasta <fasta> -unalignedEvaluate:pair_silent_all_aln -cm:aln_format grishin -in:file:template_pdb <templates> More...
basic::options::FileOptionKey	unalignedEvaluate::relaxed_native ("unalignedEvaluate:relaxed_native")
basic::options::FileOptionKey	unalignedEvaluate::core_pdb ("unalignedEvaluate:core_pdb")
basic::options::FileOptionKey	unalignedEvaluate::lookback_csts ("unalignedEvaluate:lookback_csts")

Detailed Description

This takes an alignment file, fasta file, and a silent file. It then evaluates the qualities of the loops.

Function Documentation

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, unalignedEvaluate::core_pdb, basic::options::OptionKeys::enzdes::cstfile, test.T009_Exceptions::e, in::file::fasta(), utility::file_basename(), get_unalignedLoopsMapped(), basic::init(), gaussian-sampling::input, input_alignmentsMapped(), subloop_histogram::iterator, unalignedEvaluate::lookback_csts, in::file::native(), docking::native_pose, usec::native_sequence, out::file::o(), option, bin_torsions::output, pyrosetta.distributed.io::pose_from_file, poses_from_cmd_line_noPDBtag(), unalignedEvaluate::relaxed_native, score_loops(), basic::options::OptionKeys::relax::sequence, and in::file::template_pdb().

present_in_native()

bool present_in_native	(	Size	start_res,
		Size	end_res,
		SequenceAlignment	native_aln
	)

References indel::end_res, create_a3b_hbs::ii, basic::options::OptionKeys::relax::sequence, and indel::start_res.

Referenced by score_loop(), and score_loops().

region_constraint_score()

Real region_constraint_score	(	Pose &	pose,
		Size	start_res,
		Size	end_res,
		ConstraintSetOP	cstSet_
	)

References basic::options::OptionKeys::constraints::constraints, test.T200_Scoring::emap, indel::end_res, create_a3b_hbs::ii, beta_nonlocal::jj, beta_nonlocal::pose, oop_conformations::scorefxn, and indel::start_res.

Referenced by score_loop().

region_density_score()

Real region_density_score	(	Pose &	pose,
		Pose const	templatePose,
		SequenceAlignment	aln,
		Size	start_res,
		Size	end_res
	)

References aln, indel::end_res, create_a3b_hbs::ii, beta_nonlocal::pose, create_a3b_hbs::score, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, indel::start_res, superimpose_pose_using_aln(), and weights().

Referenced by score_loop().

region_rmsd()

Real region_rmsd	(	Pose &	mod_pose,
		Pose const &	ref_pose,
		SequenceAlignment	aln,
		Size	start_res,
		Size	end_res
	)

References aln, indel::end_res, indel::start_res, and two_region_rmsd().

Referenced by score_loop().

region_rmsd_structures_aligned()

Real region_rmsd_structures_aligned	(	Pose &	mod_pose,
		Pose const &	ref_pose,
		SequenceAlignment	aln,
		Size	start_res,
		Size	end_res
	)

References aln, indel::end_res, create_a3b_hbs::ii, basic::options::OptionKeys::relax::sequence, indel::start_res, sum(), and superimpose_pose_using_aln().

Referenced by score_loop().

region_score()

Real region_score	(	Pose &	pose,
		Size	start_res,
		Size	end_res
	)

References basic::options::OptionKeys::constraints::constraints, indel::end_res, create_a3b_hbs::ii, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and indel::start_res.

Referenced by score_loop().

score_loop()

void score_loop	(	Pose &	pose,
		Pose const &	native_pose,
		SequenceAlignment	native_aln,
		SequenceAlignment	template_aln,
		Pose	native_relaxed_pose,
		Size	start_res,
		Size	end_res,
		ConstraintSetOP	cstSet_,
		ConstraintSetOP	lookBackCstSet_,
		Pose const	templatePose,
		std::ostream &	out
	)

References indel::end_res, basic::options::OptionKeys::optE::fixed, oop_conformations::length, docking::native_pose, beta_nonlocal::pose, present_in_native(), region_constraint_score(), region_density_score(), region_rmsd(), region_rmsd_structures_aligned(), region_score(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, indel::start_res, and two_region_rmsd().

Referenced by score_loops().

score_loops()

void score_loops	(	Pose	pose,
		Loops const	unalignedLoops,
		Pose	native_pose,
		SequenceAlignment	native_alignment,
		SequenceAlignment	template_alignment,
		Pose	native_relaxed_pose,
		Pose const	templatePoseData,
		ConstraintSetOP	cstSet_,
		ConstraintSetOP	lookBackCstSet_,
		std::ostream &	out
	)

References indel::end_res, create_a3b_hbs::ii, docking::native_pose, beta_nonlocal::pose, present_in_native(), score_loop(), and indel::start_res.

Referenced by main().

two_region_rmsd()

Real two_region_rmsd	(	Pose &	mod_pose,
		Pose const &	ref_pose,
		SequenceAlignment	aln,
		Size	start_res,
		Size	end_res,
		Size	region2_start_res,
		Size	region2_end_res
	)

References aln, indel::end_res, create_a3b_hbs::ii, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and indel::start_res.

Referenced by region_rmsd(), and score_loop().

Variable Documentation

tr

basic::Tracer tr("unalignedEvaluate") ( "unalignedEvaluate"  )

static

@usage: -in:file:alignent <alignment> -in:file:s <decoy.out> -in:file:native <native pose> -in:file:fasta <fasta> -unalignedEvaluate:pair_silent_all_aln -cm:aln_format grishin -in:file:template_pdb <templates>

Author

TJ Brunette