an abstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class. More...

#include <PeptideDeriverOutputter.hh>

Inheritance diagram for protocols::peptide_deriver::PeptideDeriverOutputter:

[legend]

Public Member Functions
	PeptideDeriverOutputter ()
	default constructor More...

virtual	~PeptideDeriverOutputter ()
	destructor More...

virtual void	begin_structure (core::pose::Pose const &, std::string const &)=0
	called by PeptideDeriverFilter when processing of a strucuture (possibly multi-chain) starts More...

virtual void	chain_pair_pose_prepared (core::pose::Pose const &pose)=0
	called by PeptideDeriverFilter when a chain-pair pose is prepared (minimized and disulfide-bridge resolved) More...

virtual 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)=0
	called by PeptideDeriverFilter when calculation commences on a receptor-partner pair More...

virtual void	peptide_length (core::Size const pep_length)=0
	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...

virtual void	peptide_entry (PeptideDeriverEntryType entry_type, core::Real const total_isc, DerivedPeptideEntryCOP entry)=0
	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...

virtual void	end_receptor_partner_pair ()=0
	called by PeptideDeriverFilter when calculation concludes for a receptor-partner pair (for all the different peptide lengths) More...

virtual void	end_structure ()=0
	called by PeptideDeriverFilter when processing of a strucuture (all chain-pairs considered) ends More...

core::Real	avoid_negative_zero (core::Real const value, core::Real const threshold)

Detailed Description

an abstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class.

Constructor & Destructor Documentation

protocols::peptide_deriver::PeptideDeriverOutputter::PeptideDeriverOutputter ( )

default

default constructor

protocols::peptide_deriver::PeptideDeriverOutputter::~PeptideDeriverOutputter ( )

virtualdefault

destructor

Member Function Documentation

core::Real protocols::peptide_deriver::PeptideDeriverOutputter::avoid_negative_zero	(	core::Real const	value,
		core::Real const	threshold
	)

Referenced by protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::begin_receptor_partner_pair(), protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_entry(), protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::peptide_entry(), and protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::peptide_length().

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

pure virtual

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

Implemented in protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverOutputterContainer, and protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter.

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().

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

pure virtual

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

Implemented in protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverOutputterContainer, and protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter.

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

pure virtual

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

Implemented in protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverOutputterContainer, and protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter.

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().

virtual void protocols::peptide_deriver::PeptideDeriverOutputter::end_receptor_partner_pair ( )

pure virtual

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

Implemented in protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter, and protocols::peptide_deriver::PeptideDeriverOutputterContainer.

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().

virtual void protocols::peptide_deriver::PeptideDeriverOutputter::end_structure ( )

pure virtual

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

Implemented in protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter, protocols::peptide_deriver::PeptideDeriverOutputterContainer, and protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter.

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

pure virtual

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)

Implemented in protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter, and protocols::peptide_deriver::PeptideDeriverOutputterContainer.

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().

virtual void protocols::peptide_deriver::PeptideDeriverOutputter::peptide_length ( core::Size const pep_length )

pure virtual

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()

Implemented in protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter, protocols::peptide_deriver::PeptideDeriverPoseOutputter, protocols::peptide_deriver::PeptideDeriverOutputterContainer, and protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter.

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().

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

src/protocols/peptide_deriver/PeptideDeriverOutputter.hh
src/protocols/peptide_deriver/PeptideDeriverOutputter.cc

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation