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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:
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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_poseflag to output the best (in terms of linea/cyclic isc) poses. Max. 4 poses per chain per.
is_dump_prepared_poseflag to output each chain-pair pose as Peptiderive sees it
is_dump_cyclic_posesflag to output each modeled cyclic peptide (
See also
basic::options::OptionKeys::peptide_deriver::optimize_cyclic_threshold)
Parameters
scorefxnscore function to score the pose with before outputting
protocols::peptide_deriver::PeptideDeriverPoseOutputter::PeptideDeriverPoseOutputter ( PeptideDeriverPoseOutputter const &  src)
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
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
void protocols::peptide_deriver::PeptideDeriverPoseOutputter::peptide_entry ( PeptideDeriverEntryType  entry_type,
core::Real const  total_isc,
DerivedPeptideEntryCOP  entry 
)
overridevirtual
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
char protocols::peptide_deriver::PeptideDeriverPoseOutputter::current_partner_chain_letter_
private
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
bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_chain_pair_new_
private
bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_best_peptide_pose_
private
bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_cyclic_poses_
private
bool protocols::peptide_deriver::PeptideDeriverPoseOutputter::is_dump_prepared_pose_
private
core::scoring::ScoreFunctionCOP protocols::peptide_deriver::PeptideDeriverPoseOutputter::scorefxn_
private

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