outputs a Markdown formatted Peptiderive report to a stream More...

#include <PeptideDeriverMarkdownStreamOutputter.hh>

Inheritance diagram for protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter:

Classes
class	CyclizedReportInfo

Public Member Functions
	PeptideDeriverMarkdownStreamOutputter (utility::io::orstream &out, std::string prefix)

	PeptideDeriverMarkdownStreamOutputter (PeptideDeriverMarkdownStreamOutputter const &src)

	~PeptideDeriverMarkdownStreamOutputter () override

PeptideDeriverMarkdownStreamOutputterOP	clone () const

void	begin_structure (core::pose::Pose const &pose, 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	end_structure () override
	called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends 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...

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 Types
typedef utility::pointer::shared_ptr< CyclizedReportInfo >	CyclizedReportInfoOP

typedef utility::pointer::shared_ptr< CyclizedReportInfo const >	CyclizedReportInfoCOP

Private Member Functions
void	clear_buffers ()
	clear accumulating member variables More...

Private Attributes
CyclizedReportInfoOP	cyc_report_info_set_ [NUM_CYCLIZATION_METHODS]

utility::io::orstream *	out_p_

std::string	prefix_

core::Size	current_pep_length_

core::Real	current_total_isc_

char	current_receptor_chain_letter_

char	current_partner_chain_letter_

std::string	current_sequence_

std::ostringstream	header_

std::ostringstream	best_linear_peptides_

std::ostringstream	all_peptides_

std::ostringstream	footer_

Detailed Description

outputs a Markdown formatted Peptiderive report to a stream

Member Typedef Documentation

◆ CyclizedReportInfoCOP

typedef utility::pointer::shared_ptr<CyclizedReportInfo const> protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfoCOP

private

◆ CyclizedReportInfoOP

typedef utility::pointer::shared_ptr<CyclizedReportInfo> protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfoOP

private

Constructor & Destructor Documentation

◆ PeptideDeriverMarkdownStreamOutputter() [1/2]

protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::PeptideDeriverMarkdownStreamOutputter	(	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 cyc_report_info_set_, core::conformation::membrane::out, out_p_, and prefix_.

◆ PeptideDeriverMarkdownStreamOutputter() [2/2]

protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::PeptideDeriverMarkdownStreamOutputter ( PeptideDeriverMarkdownStreamOutputter const & src )

References cyc_report_info_set_, protocols::peptide_deriver::NUM_CYCLIZATION_METHODS, out_p_, and prefix_.

◆ ~PeptideDeriverMarkdownStreamOutputter()

protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::~PeptideDeriverMarkdownStreamOutputter ( )

overridedefault

Member Function Documentation

◆ begin_receptor_partner_pair()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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 current_partner_chain_letter_, current_receptor_chain_letter_, and current_total_isc_.

◆ begin_structure()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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 all_peptides_, best_linear_peptides_, clear_buffers(), core::pose::Pose::conformation(), cyc_report_info_set_, protocols::peptide_deriver::CYCLIZATION_METHOD_NAMES, header_, core::conformation::Conformation::num_chains(), protocols::peptide_deriver::NUM_CYCLIZATION_METHODS, and prefix_.

◆ chain_pair_pose_prepared()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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.

◆ clear_buffers()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::clear_buffers ( )

private

clear accumulating member variables

References all_peptides_, best_linear_peptides_, cyc_report_info_set_, footer_, and header_.

Referenced by begin_structure(), and end_structure().

◆ clone()

PeptideDeriverMarkdownStreamOutputterOP protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::clone ( ) const

◆ end_receptor_partner_pair()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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.

◆ end_structure()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::end_structure ( )

overridevirtual

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

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References all_peptides_, best_linear_peptides_, clear_buffers(), cyc_report_info_set_, footer_, header_, and prefix_.

◆ peptide_entry()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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 all_peptides_, protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(), best_linear_peptides_, current_partner_chain_letter_, current_pep_length_, current_receptor_chain_letter_, current_total_isc_, cyc_report_info_set_, protocols::peptide_deriver::ET_BEST_CYCLIC, protocols::peptide_deriver::ET_BEST_LINEAR, protocols::peptide_deriver::ET_GENERAL, protocols::peptide_deriver::NUM_CYCLIZATION_METHODS, prefix_, and protocols::kinmatch::str().

◆ peptide_length()

void protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::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 all_peptides_, protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero(), current_partner_chain_letter_, current_pep_length_, current_receptor_chain_letter_, current_total_isc_, cyc_report_info_set_, and prefix_.