filterAlignments.cc File Reference

#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/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 <map>
#include <iostream>
#include <fstream>

Namespaces
	filterAlignments

Functions
SequenceAlignment	filterNonCore (SequenceAlignment inptAln, SequenceAlignment partialThreadAln, Size startRes, Size endRes, Pose partialThreadPose, vector1< core::pose::PoseOP > poses)
SequenceAlignment	filterCore (SequenceAlignment inptAln, SequenceAlignment coreAln)
SequenceAlignment	combineIdenticalLengthAln (vector1< SequenceAlignment > subsetAlns)
SequenceAlignment	filterAlignment (SequenceAlignment inptAln, SequenceAlignment coreAln, protocols::loops::LoopsOP unconvergedLoops, Pose partialThreadPose, vector1< core::pose::PoseOP > poses)
vector1< SequenceAlignment >	filterAllAlignments (map< string, SequenceAlignment > alignDataMapped, SequenceAlignment coreAln, protocols::loops::LoopsOP unconvergedLoops, map< string, Pose > partialThreadsMapped, vector1< core::pose::PoseOP > poses)
void	output_alignments (vector1< SequenceAlignment > alns, std::ostream &out)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("filterAlignments")
	@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	filterAlignments::core_pdb ("filterAlignments:core_pdb")

Function Documentation

combineIdenticalLengthAln()

SequenceAlignment combineIdenticalLengthAln

(

vector1< SequenceAlignment >

subsetAlns

)

References create_a3b_hbs::ii, and beta_nonlocal::jj.

Referenced by filterAlignment().

filterAlignment()

SequenceAlignment filterAlignment	(	SequenceAlignment	inptAln,
		SequenceAlignment	coreAln,
		protocols::loops::LoopsOP	unconvergedLoops,
		Pose	partialThreadPose,
		vector1< core::pose::PoseOP >	poses
	)

References combineIdenticalLengthAln(), utility::io::oc::cout, indel::end_res, filterCore(), filterNonCore(), create_a3b_hbs::ii, basic::options::OptionKeys::mp::assembly::poses, and indel::start_res.

Referenced by filterAllAlignments().

filterAllAlignments()

vector1<SequenceAlignment> filterAllAlignments	(	map< string, SequenceAlignment >	alignDataMapped,
		SequenceAlignment	coreAln,
		protocols::loops::LoopsOP	unconvergedLoops,
		map< string, Pose >	partialThreadsMapped,
		vector1< core::pose::PoseOP >	poses
	)

References utility::io::oc::cout, filterAlignment(), subloop_histogram::iterator, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

filterCore()

SequenceAlignment filterCore	(	SequenceAlignment	inptAln,
		SequenceAlignment	coreAln
	)

References create_a3b_hbs::ii.

Referenced by filterAlignment().

filterNonCore()

SequenceAlignment filterNonCore	(	SequenceAlignment	inptAln,
		SequenceAlignment	partialThreadAln,
		Size	startRes,
		Size	endRes,
		Pose	partialThreadPose,
		vector1< core::pose::PoseOP >	poses
	)

References utility::io::oc::cout, create_a3b_hbs::ii, subloop_histogram::iterator, basic::options::OptionKeys::mp::assembly::poses, region_rmsd(), average_rmsds::rmsd, and round().

Referenced by filterAlignment().

main()

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

References out::file::alignment(), argv, basic::options::OptionKeys::chemical::chemical, filterAlignments::core_pdb, test.T009_Exceptions::e, in::file::fasta(), utility::file_basename(), filterAllAlignments(), generate_partial_threads(), basic::init(), gaussian-sampling::input, input_alignmentsMapped(), option, output_alignments(), pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::mp::assembly::poses, poses_from_cmd_line(), basic::options::OptionKeys::relax::sequence, and in::file::template_pdb().

output_alignments()

void output_alignments	(	vector1< SequenceAlignment >	alns,
		std::ostream &	out
	)

References create_a3b_hbs::ii.

Referenced by main().

Variable Documentation

tr

basic::Tracer tr("filterAlignments") ( "filterAlignments"  )

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