protocols::evolution::AlignmentCleanerTools Namespace Reference

Functions
static basic::Tracer	TR ("protocols.evolution.AlignmentCleanerTools")
void	thread_sequence_on_pose (core::pose::Pose &pose, std::string const &thread_seq, core::scoring::ScoreFunctionOP scorefxn)
std::tuple< std::string, std::string >	indel_motif (std::string const &aln_seq, core::Size const motif_radius, core::Size const aln_resi, std::string const &pose_ss_aln)
core::Real	indel_motif_seq_id (std::string const &motif1, std::string const &motif2)
std::string	short_ss_loop_filter (std::string ss, core::Size min_loop_length)

Function Documentation

indel_motif()

std::tuple< std::string, std::string > protocols::evolution::AlignmentCleanerTools::indel_motif	(	std::string const &	aln_seq,
		core::Size const	motif_radius,
		core::Size const	aln_resi,
		std::string const &	pose_ss_aln
	)

Referenced by protocols::evolution::AlignmentAAFinder::apply(), and protocols::evolution::AlignmentGapInserter::apply().

indel_motif_seq_id()

core::Real protocols::evolution::AlignmentCleanerTools::indel_motif_seq_id	(	std::string const &	motif1,
		std::string const &	motif2
	)

Referenced by protocols::evolution::AlignmentAAFinder::apply(), and protocols::evolution::AlignmentGapInserter::apply().

short_ss_loop_filter()

std::string protocols::evolution::AlignmentCleanerTools::short_ss_loop_filter	(	std::string	ss,
		core::Size	min_loop_length
	)

Referenced by protocols::evolution::AlignmentAAFinder::apply(), and protocols::evolution::AlignmentGapInserter::apply().

thread_sequence_on_pose()

void protocols::evolution::AlignmentCleanerTools::thread_sequence_on_pose	(	core::pose::Pose &	pose,
		std::string const &	thread_seq,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References core::pose::symmetry::is_symmetric().

Referenced by protocols::evolution::AlignmentAAFinder::apply(), and protocols::evolution::AlignmentGapInserter::apply().

TR()

static basic::Tracer protocols::evolution::AlignmentCleanerTools::TR ( "protocols.evolution.AlignmentCleanerTools"  )

static