protocols::frag_picker::scores::FragmentCrmsd Class Reference

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

#include <FragmentCrmsd.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentCrmsd:

Collaboration diagram for protocols::frag_picker::scores::FragmentCrmsd:

Public Member Functions
	FragmentCrmsd (Size, Real, bool, core::pose::PoseOP)
	creates a crmsd-based scoring function. More...
	FragmentCrmsd (Size, Real, bool, utility::vector1< utility::vector1< Real > >)
	creates a crmsd-based scoring function. More...
	~FragmentCrmsd ()
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 Member Functions
void	fill_CA_coords (core::pose::Pose const &, FArray2_double &, Size)

Private Attributes
std::string	cached_scores_id_
Size	n_atoms_
pose::PoseOP	reference_pose_
FArray2D_double	reference_coordinates_
FArray2D_double	chunk_coordinates_
FArray2D_double	fragment_coordinates_
FArray2D_double	frag_pos_coordinates_
FArray1D_double	weights_

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 its crmsd to the given reference structure

Definition at line 45 of file FragmentCrmsd.hh.

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		core::pose::PoseOP	reference_pose
	)

creates a crmsd-based scoring function.

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

Definition at line 61 of file FragmentCrmsd.cc.

References fill_CA_coords(), n_atoms_, reference_coordinates_, reference_pose_, and weights_.

protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		utility::vector1< utility::vector1< Real > >	xyz
	)

creates a crmsd-based scoring function.

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

Definition at line 71 of file FragmentCrmsd.cc.

References n_atoms_, reference_coordinates_, protocols::frag_picker::scores::trRmsScore(), weights_, and protocols::kinmatch::xyz().

protocols::frag_picker::scores::FragmentCrmsd::~FragmentCrmsd

(

)

Definition at line 59 of file FragmentCrmsd.cc.

Member Function Documentation

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

virtual

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

Definition at line 146 of file FragmentCrmsd.cc.

References cached_scores_id_, chunk_coordinates_, do_caching(), frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

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

virtual

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

Definition at line 179 of file FragmentCrmsd.cc.

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

virtual

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

Definition at line 135 of file FragmentCrmsd.cc.

References chunk_coordinates_.

Referenced by cached_score().

void protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords ( core::pose::Pose const &  pose, FArray2_double &  coords, Size  n_atoms  )

private

Definition at line 88 of file FragmentCrmsd.cc.

References core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::frag_picker::scores::trRmsScore(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

Referenced by FragmentCrmsd().

bool protocols::frag_picker::scores::FragmentCrmsd::score ( FragmentCandidateOP  f, FragmentScoreMapOP  empty_map  )

virtual

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

Definition at line 104 of file FragmentCrmsd.cc.

References frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Member Data Documentation

std::string protocols::frag_picker::scores::FragmentCrmsd::cached_scores_id_

private

Definition at line 64 of file FragmentCrmsd.hh.

Referenced by cached_score().

FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::chunk_coordinates_

private

Definition at line 68 of file FragmentCrmsd.hh.

Referenced by cached_score(), and do_caching().

FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::frag_pos_coordinates_

private

Definition at line 70 of file FragmentCrmsd.hh.

Referenced by cached_score(), and score().

FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::fragment_coordinates_

private

Definition at line 69 of file FragmentCrmsd.hh.

Referenced by cached_score(), and score().

Size protocols::frag_picker::scores::FragmentCrmsd::n_atoms_

private

Definition at line 65 of file FragmentCrmsd.hh.

Referenced by FragmentCrmsd().

FArray2D_double protocols::frag_picker::scores::FragmentCrmsd::reference_coordinates_

private

Definition at line 67 of file FragmentCrmsd.hh.

Referenced by cached_score(), FragmentCrmsd(), and score().

pose::PoseOP protocols::frag_picker::scores::FragmentCrmsd::reference_pose_

private

Definition at line 66 of file FragmentCrmsd.hh.

Referenced by FragmentCrmsd().

FArray1D_double protocols::frag_picker::scores::FragmentCrmsd::weights_

private

Definition at line 71 of file FragmentCrmsd.hh.

Referenced by FragmentCrmsd().

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

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