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

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

#include <FragmentChunkCrms.hh>

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

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

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 tmscore to the given reference structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentChunkCrms::FragmentChunkCrms	(	Size	priority,
		Real	lowest_acceptable_value,
		bool	use_lowest,
		std::string	query_sequence,
		core::pose::PoseOP	reference_pose,
		FArray1D_int &	seqmapping
	)

creates a tmscore-based scoring function.

Detailed: 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_, residue_type_set, seqmapping_, core::pose::Pose::total_residue(), and weights_.

protocols::frag_picker::scores::FragmentChunkCrms::~FragmentChunkCrms

(

)

Member Function Documentation

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

private

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

Referenced by FragmentChunkCrms(), and score().

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

private

References core::pose::Pose::total_residue(), protocols::frag_picker::scores::trTmScore, and core::pose::Pose::xyz().

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

virtual

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_, numeric::model_quality::rms_wrapper(), seqmapping_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Member Data Documentation

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

private

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

private

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

private

Referenced by score().

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

private

Referenced by FragmentChunkCrms(), and score().

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

private

Referenced by FragmentChunkCrms(), and score().

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

private

Referenced by FragmentChunkCrms(), and score().

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

private

Referenced by FragmentChunkCrms().

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

private

Referenced by FragmentChunkCrms(), and score().

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:

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