apps::pilot::frankdt Namespace Reference

Classes
struct	Motif
struct	SecondaryStruct
class	segment_file_generator
	a generator of smart sewing segment files More...

Typedefs
typedef utility::pointer::shared_ptr < segment_file_generator >	segment_file_generatorOP
typedef utility::pointer::shared_ptr < segment_file_generator const >	segment_file_generatorCOP

Functions
utility::vector1< Motif >	import_motifs (std::string motif_filename)
void	invalid_motif (std::string bad_motif, std::string error_msg)
Motif	reverse_motif (Motif const motif)
bool	lt (Motif i, Motif j)
std::set< Motif, bool(*)(Motif, Motif) >	check_motifs (utility::vector1< Motif > motifs)
void	check_for_chain_breaks (std::map< core::Size, protocols::sewing::data_storage::SmartSegmentOP > &pdb_segments)
utility::vector1< Motif >	copy_set_to_vector (std::set< Motif, bool(*)(Motif, Motif) > const copy_set)
bool	dssp_code_matches (std::string motif_dssp, std::string segment_dssp)
utility::vector1< Motif >	compare_segment_to_motif (utility::vector1< Motif > &motifs_to_match, core::Size position, protocols::sewing::data_storage::SmartSegmentOP current_segment)
protocols::sewing::hashing::SegmentVectorOP	store_segment_motif_match (protocols::sewing::data_storage::SmartSegmentOP segment, core::Size last_segment_position)
void	write_segments_to_file (protocols::sewing::hashing::SegmentVectorOP seg_vec, utility::pointer::shared_ptr< utility::io::ozstream > file)
int	main (int argc, char *argv[])

Typedef Documentation

typedef utility::pointer::shared_ptr< segment_file_generator const > apps::pilot::frankdt::segment_file_generatorCOP

typedef utility::pointer::shared_ptr< segment_file_generator > apps::pilot::frankdt::segment_file_generatorOP

Function Documentation

void apps::pilot::frankdt::check_for_chain_breaks

(

std::map< core::Size, protocols::sewing::data_storage::SmartSegmentOP > &

pdb_segments

)

References TR.

Referenced by main().

std::set< Motif, bool(*)( Motif, Motif ) > apps::pilot::frankdt::check_motifs

(

utility::vector1< Motif >

motifs

)

References invalid_motif(), lt(), and reverse_motif().

Referenced by main().

utility::vector1< Motif > apps::pilot::frankdt::compare_segment_to_motif	(	utility::vector1< Motif > &	motifs_to_match,
		core::Size	position,
		protocols::sewing::data_storage::SmartSegmentOP	current_segment
	)

References apps::pilot::frankdt::SecondaryStruct::dssp_, dssp_code_matches(), test.T150_PyMOL_Integration::i, apps::pilot::frankdt::SecondaryStruct::max_, apps::pilot::frankdt::SecondaryStruct::min_, make_symmdef_file_denovo::pos, apps::pilot::frankdt::Motif::secondary_structs_, and utility::to_string().

Referenced by main().

utility::vector1< Motif > apps::pilot::frankdt::copy_set_to_vector

(

std::set< Motif, bool(*)(Motif, Motif) > const

copy_set

)

Referenced by main().

bool apps::pilot::frankdt::dssp_code_matches	(	std::string	motif_dssp,
		std::string	segment_dssp
	)

Referenced by compare_segment_to_motif().

utility::vector1< Motif > apps::pilot::frankdt::import_motifs

(

std::string

motif_filename

)

References apps::pilot::frankdt::Motif::abv_motif_string_, apps::pilot::frankdt::SecondaryStruct::dssp_, ObjexxFCL::getline(), ObjexxFCL::is_any_of(), line, apps::pilot::frankdt::SecondaryStruct::max_, apps::pilot::frankdt::SecondaryStruct::min_, motif_file, apps::pilot::frankdt::Motif::motif_string_, basic::options::OptionKeys::mh::path::motifs, apps::pilot::frankdt::Motif::secondary_structs_, binder::split(), utility::string2Size(), utility::to_string(), TR, basic::options::OptionKeys::sc::trim, and utility_exit_with_message.

Referenced by main().

void apps::pilot::frankdt::invalid_motif	(	std::string	bad_motif,
		std::string	error_msg
	)

References utility_exit_with_message.

Referenced by check_motifs().

bool apps::pilot::frankdt::lt	(	Motif	i,
		Motif	j
	)

References apps::pilot::frankdt::Motif::motif_string_.

Referenced by check_motifs().

int apps::pilot::frankdt::main	(	int	argc,
		char *	argv[]
	)

References check_for_chain_breaks(), check_motifs(), compare_segment_to_motif(), copy_set_to_vector(), ObjexxFCL::getline(), import_motifs(), devel::init(), line, motif_file, basic::options::option, option, pdb_list_file, basic::options::OptionKeys::lh::symfragrm::pdblist, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, numeric::random::random_range(), store_segment_motif_match(), strict_dssp_changes, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, value, basic::options::OptionKeys::run::version, and write_segments_to_file().

Referenced by main().

Motif apps::pilot::frankdt::reverse_motif

(

Motif const

motif

)

References apps::pilot::frankdt::Motif::abv_motif_string_, apps::pilot::frankdt::SecondaryStruct::dssp_, apps::pilot::frankdt::SecondaryStruct::max_, apps::pilot::frankdt::SecondaryStruct::min_, apps::pilot::frankdt::Motif::motif_string_, apps::pilot::frankdt::Motif::secondary_structs_, and utility::to_string().

Referenced by check_motifs().

protocols::sewing::hashing::SegmentVectorOP apps::pilot::frankdt::store_segment_motif_match	(	protocols::sewing::data_storage::SmartSegmentOP	segment,
		core::Size	last_segment_position
	)

References utility::to_string(), and utility_exit_with_message.

Referenced by main().

void apps::pilot::frankdt::write_segments_to_file	(	protocols::sewing::hashing::SegmentVectorOP	seg_vec,
		utility::pointer::shared_ptr< utility::io::ozstream >	file
	)

References TR.

Referenced by main().