protocols::frag_picker::scores::DisulfideDistance Class Reference

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

#include <DisulfideDistance.hh>

Inheritance diagram for protocols::frag_picker::scores::DisulfideDistance:

Collaboration diagram for protocols::frag_picker::scores::DisulfideDistance:

Public Member Functions
	DisulfideDistance (Size priority, Real lowest_acceptable_value, bool use_lowest, utility::vector1< Size > disulfide_data, Size largest_fragment)
	creates a Calpha distance based scoring function. More...
void	do_caching (VallChunkOP)
void	clean_up ()
bool	score (FragmentCandidateOP, FragmentScoreMapOP)
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP)
Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
	CachingScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
Public Member Functions inherited from protocols::frag_picker::scores::FragmentScoringMethod
	FragmentScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name)
std::string &	get_score_name ()
	Returns a name of this scoring method. More...
Size	get_id ()
	Returns an integer index assigned to this scoring method by a scoring manager. More...
void	set_id (Size id)
	Sets a new integer index for this scoring method. More...
Size	get_priority ()
	Returns a priority of this scoring method. More...
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 (Real lowest_acceptable_value)
	Sets a new value of the lowest acceptable score. More...

Private Attributes
Size	n_res_
std::string	cached_scores_id_
ObjexxFCL::FArray2D_double	chunk_ca_distances_
utility::vector1< Size >	disulfide_data_
Size	largest_fragment_

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

Detailed Description

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

Definition at line 38 of file DisulfideDistance.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::DisulfideDistance::DisulfideDistance	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		utility::vector1< Size >	disulfide_data,
		Size	largest_fragment
	)

creates a Calpha distance based scoring function.

Detailed: Scores distance matches for short range disulfides (ie: within fragment)

Definition at line 44 of file DisulfideDistance.cc.

Member Function Documentation

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

virtual

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

Definition at line 76 of file DisulfideDistance.cc.

References cached_scores_id_, chunk_ca_distances_, disulfide_data_, do_caching(), protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, n_res_, score(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by score().

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

virtual

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

Definition at line 148 of file DisulfideDistance.cc.

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

virtual

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

Definition at line 52 of file DisulfideDistance.cc.

References chunk_ca_distances_, core::kinematics::distance(), largest_fragment_, and n_res_.

Referenced by cached_score().

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

virtual

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

Definition at line 72 of file DisulfideDistance.cc.

References cached_score().

Referenced by cached_score().

Member Data Documentation

std::string protocols::frag_picker::scores::DisulfideDistance::cached_scores_id_

private

Definition at line 53 of file DisulfideDistance.hh.

Referenced by cached_score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::DisulfideDistance::chunk_ca_distances_

private

Definition at line 55 of file DisulfideDistance.hh.

Referenced by cached_score(), and do_caching().

utility::vector1< Size > protocols::frag_picker::scores::DisulfideDistance::disulfide_data_

private

Definition at line 57 of file DisulfideDistance.hh.

Referenced by cached_score().

Size protocols::frag_picker::scores::DisulfideDistance::largest_fragment_

private

Definition at line 58 of file DisulfideDistance.hh.

Referenced by do_caching().

Size protocols::frag_picker::scores::DisulfideDistance::n_res_

private

Definition at line 52 of file DisulfideDistance.hh.

Referenced by cached_score(), and do_caching().

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

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