protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter Class Reference

outputs a Peptiderive report to a stream in a basic, easily parsable format More...

#include <PeptideDeriverBasicStreamOutputter.hh>

Inheritance diagram for protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter:

Public Member Functions
	PeptideDeriverBasicStreamOutputter (utility::io::orstream &out, std::string prefix)
	PeptideDeriverBasicStreamOutputter (PeptideDeriverBasicStreamOutputter const &src)
	~PeptideDeriverBasicStreamOutputter () override
PeptideDeriverBasicStreamOutputterOP	clone () const
void	begin_structure (core::pose::Pose const &, std::string const &) override
	called by PeptideDeriverFilter when processing of a strucuture (possibly multi-chain) starts More...
void	chain_pair_pose_prepared (core::pose::Pose const &) override
	called by PeptideDeriverFilter when a chain-pair pose is prepared (minimized and disulfide-bridge resolved) More...
void	begin_receptor_partner_pair (char const receptor_chain_letter, char const partner_chain_letter, core::Real const total_isc, std::string const &options_string) override
	called by PeptideDeriverFilter when calculation commences on a receptor-partner pair More...
void	peptide_length (core::Size const pep_length) override
	called by PeptideDeriverFilter when calculation commences for the specified peptide length this is called for every peptide length specified to PeptideDeriverFilter, per each call to PeptideDeriverOutputter::begin_receptor_partner_pair() More...
void	peptide_entry (PeptideDeriverEntryType entry_type, core::Real const total_isc, DerivedPeptideEntryCOP entry) override
	called by PeptideDeriverFilter for each 'peptide' entry that should be output. besides the peptides for each sliding window, this is being called for the 'best' peptides ( More...
void	end_receptor_partner_pair () override
	called by PeptideDeriverFilter when calculation concludes for a receptor-partner pair (for all the different peptide lengths) More...
void	end_structure () override
	called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends More...
Public Member Functions inherited from protocols::peptide_deriver::PeptideDeriverOutputter
	PeptideDeriverOutputter ()
	default constructor More...
virtual	~PeptideDeriverOutputter ()
	destructor More...
core::Real	avoid_negative_zero (core::Real const value, core::Real const threshold)

Private Attributes
utility::io::orstream *	out_p_
std::string	prefix_

Detailed Description

outputs a Peptiderive report to a stream in a basic, easily parsable format

Constructor & Destructor Documentation

protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::PeptideDeriverBasicStreamOutputter	(	utility::io::orstream &	out,
		std::string	prefix
	)

Parameters

out	an output stream to which output will be diverted should belong to the thread on which the outputter methods are called in, and outlive the outputter object.
prefix	a string prefix to prepend to each output line

References core::conformation::membrane::out, out_p_, and prefix_.

protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::PeptideDeriverBasicStreamOutputter

(

PeptideDeriverBasicStreamOutputter const &

src

)

References out_p_, and prefix_.

protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::~PeptideDeriverBasicStreamOutputter ( )

overridedefault

Member Function Documentation

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::begin_receptor_partner_pair ( char const  receptor_chain_letter, char const  partner_chain_letter, core::Real const  total_isc, std::string const &  options_string  )

overridevirtual

called by PeptideDeriverFilter when calculation commences on a receptor-partner pair

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(), and prefix_.

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::begin_structure ( core::pose::Pose const &  , std::string const &    )

overridevirtual

called by PeptideDeriverFilter when processing of a strucuture (possibly multi-chain) starts

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References prefix_.

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::chain_pair_pose_prepared ( core::pose::Pose const &  pose )

inlineoverridevirtual

called by PeptideDeriverFilter when a chain-pair pose is prepared (minimized and disulfide-bridge resolved)

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

PeptideDeriverBasicStreamOutputterOP protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::clone

(

)

const

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::end_receptor_partner_pair ( )

overridevirtual

called by PeptideDeriverFilter when calculation concludes for a receptor-partner pair (for all the different peptide lengths)

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References prefix_.

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::end_structure ( )

overridevirtual

called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References prefix_.

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_entry ( PeptideDeriverEntryType  entry_type, core::Real const  total_isc, DerivedPeptideEntryCOP  entry  )

overridevirtual

called by PeptideDeriverFilter for each 'peptide' entry that should be output. besides the peptides for each sliding window, this is being called for the 'best' peptides (

See also

PeptideDeriverEntryType)

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(), protocols::peptide_deriver::CYCLIZATION_METHOD_NAMES, protocols::peptide_deriver::NUM_CYCLIZATION_METHODS, prefix_, and protocols::kinmatch::str().

void protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_length ( core::Size const  pep_length )

overridevirtual

called by PeptideDeriverFilter when calculation commences for the specified peptide length this is called for every peptide length specified to PeptideDeriverFilter, per each call to PeptideDeriverOutputter::begin_receptor_partner_pair()

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References prefix_.

Member Data Documentation

utility::io::orstream* protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::out_p_

private

Referenced by PeptideDeriverBasicStreamOutputter().

std::string protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::prefix_

private

Referenced by begin_receptor_partner_pair(), begin_structure(), end_receptor_partner_pair(), end_structure(), peptide_entry(), peptide_length(), and PeptideDeriverBasicStreamOutputter().

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

• src/protocols/peptide_deriver/PeptideDeriverBasicStreamOutputter.hh
• src/protocols/peptide_deriver/PeptideDeriverBasicStreamOutputter.cc