apps::pilot::frankdt Namespace Reference

Classes
class	concatenate_poses
	concatenates poses together end-to-end while transforming them to avoid chainbreaks More...
class	SmartSEWINGTester
	testing app for SEWING file IO More...
class	steric_fusion_scan
	concatenates poses together end-to-end while transforming them to avoid chainbreaks More...
class	MakeSegmentFile
	an app to make segment files More...
class	segment_file_generator
	a generator of smart sewing segment files More...
struct	SecondaryStruct
struct	Motif

Typedefs
typedef utility::pointer::shared_ptr< concatenate_poses >	concatenate_posesOP
typedef utility::pointer::shared_ptr< concatenate_poses const >	concatenate_posesCOP
typedef utility::pointer::shared_ptr< SmartSEWINGTester >	SmartSEWINGTesterOP
typedef utility::pointer::shared_ptr< SmartSEWINGTester const >	SmartSEWINGTesterCOP
typedef utility::pointer::shared_ptr< steric_fusion_scan >	steric_fusion_scanOP
typedef utility::pointer::shared_ptr< steric_fusion_scan const >	steric_fusion_scanCOP
typedef utility::pointer::shared_ptr< MakeSegmentFile >	MakeSegmentFileOP
typedef utility::pointer::shared_ptr< MakeSegmentFile const >	MakeSegmentFileCOP
typedef utility::pointer::shared_ptr< segment_file_generator >	segment_file_generatorOP
typedef utility::pointer::shared_ptr< segment_file_generator const >	segment_file_generatorCOP

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

Typedef Documentation

concatenate_posesCOP

typedef utility::pointer::shared_ptr< concatenate_poses const > apps::pilot::frankdt::concatenate_posesCOP

concatenate_posesOP

typedef utility::pointer::shared_ptr< concatenate_poses > apps::pilot::frankdt::concatenate_posesOP

MakeSegmentFileCOP

typedef utility::pointer::shared_ptr< MakeSegmentFile const > apps::pilot::frankdt::MakeSegmentFileCOP

MakeSegmentFileOP

typedef utility::pointer::shared_ptr< MakeSegmentFile > apps::pilot::frankdt::MakeSegmentFileOP

segment_file_generatorCOP

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

segment_file_generatorOP

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

SmartSEWINGTesterCOP

typedef utility::pointer::shared_ptr< SmartSEWINGTester const > apps::pilot::frankdt::SmartSEWINGTesterCOP

SmartSEWINGTesterOP

typedef utility::pointer::shared_ptr< SmartSEWINGTester > apps::pilot::frankdt::SmartSEWINGTesterOP

steric_fusion_scanCOP

typedef utility::pointer::shared_ptr< steric_fusion_scan const > apps::pilot::frankdt::steric_fusion_scanCOP

steric_fusion_scanOP

typedef utility::pointer::shared_ptr< steric_fusion_scan > apps::pilot::frankdt::steric_fusion_scanOP

Function Documentation

check_for_chain_breaks()

void apps::pilot::frankdt::check_for_chain_breaks

(

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

pdb_segments

)

References TR.

check_motifs()

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

(

utility::vector1< Motif >

motifs

)

References enumerate_junctions::bool, invalid_motif(), lt(), reverse_motif(), and set().

compare_segment_to_motif()

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(), create_a3b_hbs::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().

copy_set_to_vector()

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

(

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

copy_set

)

dssp_code_matches()

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

Referenced by compare_segment_to_motif().

import_motifs()

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_, getline(), ObjexxFCL::is_any_of(), line, apps::pilot::frankdt::SecondaryStruct::max_, apps::pilot::frankdt::SecondaryStruct::min_, motif_file, basic::options::OptionKeys::motifs::motif_filename, apps::pilot::frankdt::Motif::motif_string_, 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.

invalid_motif()

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

References utility_exit_with_message.

Referenced by check_motifs().

lt()

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

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by check_motifs(), and localtime().

main()

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

References argv, binding_partner, component_file_name, basic::options::OptionKeys::in::file::fold_tree, getline(), create_a3b_hbs::i, immobile_domain, basic::init(), numeric::HomogeneousTransform< T >::inverse(), line, option, output_filename, numeric::HomogeneousTransform< T >::point(), pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::mp::assembly::poses, residue, numeric::HomogeneousTransform< T >::rotation_matrix(), subloop_histogram::size, numeric::interpolation::to_string(), TR, value, and basic::options::OptionKeys::in::file::xyz.

Referenced by main().

reverse_motif()

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_, reverse(), apps::pilot::frankdt::Motif::secondary_structs_, and utility::to_string().

Referenced by check_motifs().

store_segment_motif_match()

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.

write_segments_to_file()

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

References evaluate_beta_mutants::file, and TR.