protocols::frag_picker::scores::CSScore Class Reference

scores a fragment by the root mean square deviation of Phi and Psi angles. More...

#include <CSScore.hh>

Inheritance diagram for protocols::frag_picker::scores::CSScore:

Public Member Functions
	CSScore (core::Size, core::Real, bool, CSTalosIO &)
	creates a Phi-Psi-based scoring function. More...
void	do_caching (VallChunkOP) override
void	clean_up () override
bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
	FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
std::string &	get_score_name ()
	Returns a name of this scoring method. More...
core::Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...
void	set_id (core::Size id)
	Sets a new integer index for this scoring method. More...
core::Size	get_priority ()
	Returns a priority of this scoring method. More...
core::Real	get_min_allowed_score ()
	Returns the lowest acceptable score value for this scoring method. More...
bool	get_use_lowest ()
	Returns the boolean choice on using the above lowest acceptable score value. More...
void	set_min_allowed_score (core::Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Private Member Functions
void	read_talos_phi_psi (std::string const &)

Private Attributes
utility::io::ozstream	outfile_
	Print debugging informations about a score for a given fragment. More...
utility::vector1< utility::vector1< std::pair< core::Size, core::Real > > >	target_shifts_
utility::vector1< utility::vector1< std::pair< core::Real, core::Real > > >	scores_
std::string	cached_scores_id_
utility::vector1< bool >	existing_data_

Additional Inherited Members
Protected Attributes inherited from protocols::frag_picker::scores::FragmentScoringMethod
core::Size	id_
core::Size	priority_
std::string	name_
core::Real	lowest_acceptable_value_
bool	use_lowest_

Detailed Description

scores a fragment by the root mean square deviation of Phi and Psi angles.

Constructor & Destructor Documentation

CSScore()

protocols::frag_picker::scores::CSScore::CSScore	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		CSTalosIO &	reader
	)

creates a Phi-Psi-based scoring function.

Phi-Psi angles from a fragment will be compared to relevant angles in a given pose, which should have the same number of residues a the query sequence

References protocols::frag_picker::CS2ndShift::shifts(), target_shifts_, and protocols::frag_picker::scores::trCSScore().

Member Function Documentation

cached_score()

bool protocols::frag_picker::scores::CSScore::cached_score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

overridevirtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References cached_scores_id_, do_caching(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, scores_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by score().

clean_up()

void protocols::frag_picker::scores::CSScore::clean_up ( )

overridevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

do_caching()

void protocols::frag_picker::scores::CSScore::do_caching ( VallChunkOP  current_chunk )

overridevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

References core::pose::motif::a(), protocols::match::upstream::b, cached_scores_id_, scores_, target_shifts_, and protocols::frag_picker::scores::trCSScore().

Referenced by cached_score().

read_talos_phi_psi()

void protocols::frag_picker::scores::CSScore::read_talos_phi_psi ( std::string const &  )

private

score()

bool protocols::frag_picker::scores::CSScore::score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

overridevirtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References cached_score().

Member Data Documentation

cached_scores_id_

std::string protocols::frag_picker::scores::CSScore::cached_scores_id_

private

Referenced by cached_score(), and do_caching().

existing_data_

utility::vector1<bool> protocols::frag_picker::scores::CSScore::existing_data_

private

outfile_

utility::io::ozstream protocols::frag_picker::scores::CSScore::outfile_

private

Print debugging informations about a score for a given fragment.

scores_

utility::vector1< utility::vector1< std::pair< core::Real, core::Real> > > protocols::frag_picker::scores::CSScore::scores_

private

Referenced by cached_score(), and do_caching().

target_shifts_

utility::vector1< utility::vector1< std::pair< core::Size, core::Real > > > protocols::frag_picker::scores::CSScore::target_shifts_

private

Referenced by CSScore(), and do_caching().

---

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

• src/protocols/frag_picker/scores/CSScore.hh
• src/protocols/frag_picker/scores/CSScore.cc