protocols::peptide_deriver::PeptideDeriverPoseOutputter Class Reference

outputs poses at different points of the Peptiderive protocol, according to the given set of options More...

#include <PeptideDeriverPoseOutputter.hh>

Inheritance diagram for protocols::peptide_deriver::PeptideDeriverPoseOutputter:

Public Member Functions
	PeptideDeriverPoseOutputter (bool const is_dump_best_peptide_pose, bool const is_dump_prepared_pose, bool const is_dump_cyclic_poses, core::scoring::ScoreFunctionCOP scorefxn)
	PeptideDeriverPoseOutputter (PeptideDeriverPoseOutputter const &src)
	~PeptideDeriverPoseOutputter () override
PeptideDeriverPoseOutputterOP	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 &pose) 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, std::string const &) 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	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...
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...
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 Member Functions
void	output_pose (core::pose::Pose &pose, std::string const &pose_name)
	output a post to the given file More...

Private Attributes
bool	is_dump_best_peptide_pose_
bool	is_dump_prepared_pose_
bool	is_dump_cyclic_poses_
char	current_receptor_chain_letter_
char	current_partner_chain_letter_
core::Size	current_peptide_length_
core::pose::PoseOP	current_chain_pair_pose_
bool	is_chain_pair_new_
core::scoring::ScoreFunctionCOP	scorefxn_

Detailed Description

outputs poses at different points of the Peptiderive protocol, according to the given set of options

Constructor & Destructor Documentation

protocols::peptide_deriver::PeptideDeriverPoseOutputter::PeptideDeriverPoseOutputter	(	bool const	is_dump_best_peptide_pose,
		bool const	is_dump_prepared_pose,
		bool const	is_dump_cyclic_poses,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

Parameters

is_dump_best_peptide_pose	flag to output the best (in terms of linea/cyclic isc) poses. Max. 4 poses per chain per.
is_dump_prepared_pose	flag to output each chain-pair pose as Peptiderive sees it
is_dump_cyclic_poses	flag to output each modeled cyclic peptide (

See also

basic::options::OptionKeys::peptide_deriver::optimize_cyclic_threshold)

Parameters

scorefxn

score function to score the pose with before outputting

protocols::peptide_deriver::PeptideDeriverPoseOutputter::PeptideDeriverPoseOutputter

(

PeptideDeriverPoseOutputter const &

src

)

References is_dump_best_peptide_pose_, is_dump_cyclic_poses_, is_dump_prepared_pose_, and scorefxn_.

protocols::peptide_deriver::PeptideDeriverPoseOutputter::~PeptideDeriverPoseOutputter ( )

overridedefault

Member Function Documentation

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::begin_receptor_partner_pair ( char const  receptor_chain_letter, char const  partner_chain_letter, core::Real  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_chain_pair_pose_, current_partner_chain_letter_, current_receptor_chain_letter_, is_chain_pair_new_, is_dump_prepared_pose_, output_pose(), and protocols::kinmatch::str().

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

inlineoverridevirtual

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

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

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

overridevirtual

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

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

References current_chain_pair_pose_, and is_chain_pair_new_.

PeptideDeriverPoseOutputterOP protocols::peptide_deriver::PeptideDeriverPoseOutputter::clone

(

)

const

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::end_receptor_partner_pair ( )

inlineoverridevirtual

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

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::end_structure ( )

inlineoverridevirtual

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

Implements protocols::peptide_deriver::PeptideDeriverOutputter.

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::output_pose ( core::pose::Pose &  pose, std::string const &  pose_name  )

private

output a post to the given file

References core::io::pdb::dump_pdb(), protocols::jd2::jd2_used(), and protocols::jd2::output_intermediate_pose().

Referenced by begin_receptor_partner_pair(), and peptide_entry().

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::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 current_partner_chain_letter_, current_peptide_length_, current_receptor_chain_letter_, protocols::peptide_deriver::ET_BEST_CYCLIC, protocols::peptide_deriver::ET_BEST_LINEAR, protocols::peptide_deriver::ET_GENERAL, is_dump_best_peptide_pose_, is_dump_cyclic_poses_, output_pose(), protocols::kinmatch::str(), and protocols::TR().

void protocols::peptide_deriver::PeptideDeriverPoseOutputter::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 current_peptide_length_.

Member Data Documentation

core::pose::PoseOP protocols::peptide_deriver::PeptideDeriverPoseOutputter::current_chain_pair_pose_

private

Referenced by begin_receptor_partner_pair(), and chain_pair_pose_prepared().

char protocols::peptide_deriver::PeptideDeriverPoseOutputter::current_partner_chain_letter_

private

Referenced by begin_receptor_partner_pair(), and peptide_entry().

core::Size protocols::peptide_deriver::PeptideDeriverPoseOutputter::current_peptide_length_

private

Referenced by peptide_entry(), and peptide_length().

char protocols::peptide_deriver::PeptideDeriverPoseOutputter::current_receptor_chain_letter_

private

Referenced by begin_receptor_partner_pair(), and peptide_entry().

bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_chain_pair_new_

private

Referenced by begin_receptor_partner_pair(), and chain_pair_pose_prepared().

bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_best_peptide_pose_

private

Referenced by peptide_entry(), and PeptideDeriverPoseOutputter().

bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_cyclic_poses_

private

Referenced by peptide_entry(), and PeptideDeriverPoseOutputter().

bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_prepared_pose_

private

Referenced by begin_receptor_partner_pair(), and PeptideDeriverPoseOutputter().

core::scoring::ScoreFunctionCOP protocols::peptide_deriver::PeptideDeriverPoseOutputter::scorefxn_

private

Referenced by PeptideDeriverPoseOutputter().

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

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