protocols::splice::SpliceSegment Class Reference

utility class and functions for dealing with sequence profiles for varying segments in Splice More...

#include <SpliceSegment.hh>

Inheritance diagram for protocols::splice::SpliceSegment:

Public Member Functions
	SpliceSegment ()
	~SpliceSegment () override
void	read_profile (std::string const &file_name, std::string const &segment_name)
void	read_many (std::string const &protein_family, std::string const &segmetn)
	read pssm More...
void	read_pdb_profile_file (std::string const &s, std::string const )
	read pssm More...
void	read_pdb_profile (std::string const &file_name)
	reads the pdb-profile match file, matching each pdb file to one profile More...
core::sequence::SequenceProfileOP	get_profile (std::string const &segment_name)
	read the pdb-profile match from a disk file More...
void	add_pdb_profile_pair (std::string const &pdb, std::string const &profile_name)
core::sequence::SequenceProfileOP	pdb_profile (std::string const &pdb_name)
	add a sequence profile More...
core::sequence::SequenceProfileOP	sequence_profile (std::string const &profile_name)
std::string	get_cluster_name_by_PDB (std::string pdbNAme)
void	add_profile (std::string const &pdb_name, core::sequence::SequenceProfileOP const prof)
std::map< std::string, std::string >	pdb_to_profile_map ()

Private Attributes
std::map< std::string, core::sequence::SequenceProfileOP >	sequence_profile_
std::map< std::string, std::string >	pdb_to_profile_map_

Detailed Description

utility class and functions for dealing with sequence profiles for varying segments in Splice

Constructor & Destructor Documentation

protocols::splice::SpliceSegment::SpliceSegment

(

)

References pdb_to_profile_map_, and sequence_profile_.

protocols::splice::SpliceSegment::~SpliceSegment ( )

overridedefault

Member Function Documentation

void protocols::splice::SpliceSegment::add_pdb_profile_pair	(	std::string const &	pdb,
		std::string const &	profile_name
	)

References pdb_to_profile_map_.

void protocols::splice::SpliceSegment::add_profile	(	std::string const &	pdb_name,
		core::sequence::SequenceProfileOP const	prof
	)

References sequence_profile_.

std::string protocols::splice::SpliceSegment::get_cluster_name_by_PDB ( std::string  pdbNAme )

inline

References pdb_to_profile_map_.

SequenceProfileOP protocols::splice::SpliceSegment::get_profile

(

std::string const &

segment_name

)

read the pdb-profile match from a disk file

References sequence_profile_.

SequenceProfileOP protocols::splice::SpliceSegment::pdb_profile

(

std::string const &

pdb_name

)

add a sequence profile

this is the most useful method, returning the sequence profile according to a pdb file name

References pdb_to_profile_map_, and sequence_profile_.

std::map< std::string, std::string> protocols::splice::SpliceSegment::pdb_to_profile_map ( )

inline

References pdb_to_profile_map_.

void protocols::splice::SpliceSegment::read_many	(	std::string const &	protein_family,
		std::string const &	segmetn
	)

read pssm

References core::pack::dunbrack::c, and read_profile().

void protocols::splice::SpliceSegment::read_pdb_profile

(

std::string const &

file_name

)

reads the pdb-profile match file, matching each pdb file to one profile

References pdb_to_profile_map_.

void protocols::splice::SpliceSegment::read_pdb_profile_file	(	std::string const &	s,
		std::string const	segment
	)

read pssm

References core::pack::dunbrack::c, and pdb_to_profile_map_.

void protocols::splice::SpliceSegment::read_profile	(	std::string const &	file_name,
		std::string const &	segment_name
	)

References sequence_profile_.

Referenced by read_many().

core::sequence::SequenceProfileOP protocols::splice::SpliceSegment::sequence_profile

(

std::string const &

profile_name

)

References sequence_profile_.

Member Data Documentation

std::map< std::string, std::string > protocols::splice::SpliceSegment::pdb_to_profile_map_

private

Referenced by add_pdb_profile_pair(), get_cluster_name_by_PDB(), pdb_profile(), pdb_to_profile_map(), read_pdb_profile(), read_pdb_profile_file(), and SpliceSegment().

std::map< std::string, core::sequence::SequenceProfileOP > protocols::splice::SpliceSegment::sequence_profile_

private

Referenced by add_profile(), get_profile(), pdb_profile(), read_profile(), sequence_profile(), and SpliceSegment().

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The documentation for this class was generated from the following files:

• src/protocols/splice/SpliceSegment.hh
• src/protocols/splice/SpliceSegment.cc