protocols::frag_picker::scores::FragmentChunkCrms Class Reference

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

#include <FragmentChunkCrms.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentChunkCrms:

Public Member Functions
	FragmentChunkCrms (core::Size, core::Real, bool, std::string, core::pose::PoseOP, ObjexxFCL::FArray1D_int &)
	creates a tmscore-based scoring function. More...
	~FragmentChunkCrms () override
bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
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	fill_bb_coords (core::pose::Pose const &, ObjexxFCL::FArray2_double &, core::Size)
void	fill_bb_coords (core::pose::Pose const &, ObjexxFCL::FArray2_double &, ObjexxFCL::FArray1D_int &)

Private Attributes
std::string	cached_scores_id_
core::Size	n_atoms_
core::pose::PoseOP	reference_pose_
core::pose::PoseOP	fragment_pose_
ObjexxFCL::FArray2D_double	reference_coordinates_
ObjexxFCL::FArray2D_double	chunk_coordinates_
ObjexxFCL::FArray2D_double	fragment_coordinates_
ObjexxFCL::FArray1D_double	weights_
ObjexxFCL::FArray1D_int	seqmapping_

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 tmscore to the given reference structure

Constructor & Destructor Documentation

FragmentChunkCrms()

protocols::frag_picker::scores::FragmentChunkCrms::FragmentChunkCrms	(	core::Size	,
		core::Real	,
		bool	,
		std::string	,
		core::pose::PoseOP	,
		ObjexxFCL::FArray1D_int &
	)

creates a tmscore-based scoring function.

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

References fill_bb_coords(), fragment_pose_, core::pose::make_pose_from_sequence(), n_atoms_, reference_coordinates_, reference_pose_, seqmapping_, and weights_.

~FragmentChunkCrms()

protocols::frag_picker::scores::FragmentChunkCrms::~FragmentChunkCrms ( )

overridedefault

Member Function Documentation

fill_bb_coords() [1/2]

void protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords ( core::pose::Pose const &  , ObjexxFCL::FArray2_double &  , core::Size    )

private

Referenced by FragmentChunkCrms(), and score().

fill_bb_coords() [2/2]

void protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords ( core::pose::Pose const &  , ObjexxFCL::FArray2_double &  , ObjexxFCL::FArray1D_int &    )

private

score()

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

overridevirtual

Implements protocols::frag_picker::scores::FragmentScoringMethod.

References fill_bb_coords(), fragment_coordinates_, fragment_pose_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, n_atoms_, reference_coordinates_, seqmapping_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Member Data Documentation

cached_scores_id_

std::string protocols::frag_picker::scores::FragmentChunkCrms::cached_scores_id_

private

chunk_coordinates_

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::chunk_coordinates_

private

fragment_coordinates_

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::fragment_coordinates_

private

Referenced by score().

fragment_pose_

core::pose::PoseOP protocols::frag_picker::scores::FragmentChunkCrms::fragment_pose_

private

Referenced by FragmentChunkCrms(), and score().

n_atoms_

core::Size protocols::frag_picker::scores::FragmentChunkCrms::n_atoms_

private

Referenced by FragmentChunkCrms(), and score().

reference_coordinates_

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::reference_coordinates_

private

Referenced by FragmentChunkCrms(), and score().

reference_pose_

core::pose::PoseOP protocols::frag_picker::scores::FragmentChunkCrms::reference_pose_

private

Referenced by FragmentChunkCrms().

seqmapping_

ObjexxFCL::FArray1D_int protocols::frag_picker::scores::FragmentChunkCrms::seqmapping_

private

Referenced by FragmentChunkCrms(), and score().

weights_

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::FragmentChunkCrms::weights_

private

Referenced by FragmentChunkCrms().

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

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