scores a fragment by its crmsd to the given reference structure More...

#include <GunnCostScore.hh>

Inheritance diagram for protocols::frag_picker::scores::GunnCostScore:

Public Member Functions
	GunnCostScore (core::Size, core::Real, bool, core::pose::PoseOP, utility::vector1< core::Size >, core::Size)
	creates a crmsd-based scoring function. More...

	~GunnCostScore () override

void	do_caching (VallChunkOP) override

void	clean_up () override

bool	score (FragmentCandidateOP, FragmentScoreMapOP) override

bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override

void	computeGunnTuples (core::pose::Pose &, core::Size, utility::vector1< GunnTuple > &)

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 Attributes
core::Size	n_atoms_

core::pose::PoseOP	reference_pose_

utility::vector1< core::Size >	frag_sizes_

core::Size	max_chunk_size_

utility::vector1 < utility::vector1< GunnTuple > >	ref_gunn_data_

utility::vector1 < utility::vector1< GunnTuple > >	chunk_gunn_data_

GunnCost	gunn_cost_

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 its crmsd to the given reference structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::GunnCostScore::GunnCostScore	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		core::pose::PoseOP	reference_pose,
		utility::vector1< core::Size >	frag_sizes,
		core::Size	max_chunk_size
	)

creates a crmsd-based scoring function.

fragments will be compared to a given pose, which should have the same number of residues a the query sequence

References chunk_gunn_data_, computeGunnTuples(), frag_sizes_, max_chunk_size_, n_atoms_, ref_gunn_data_, reference_pose_, and protocols::frag_picker::scores::trGunnScore().

protocols::frag_picker::scores::GunnCostScore::~GunnCostScore ( )

overridedefault

Member Function Documentation

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

overridevirtual

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

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

overridevirtual

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

void protocols::frag_picker::scores::GunnCostScore::computeGunnTuples	(	core::pose::Pose &	pose,
		core::Size	frag_size,
		utility::vector1< GunnTuple > &	result
	)