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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:
Inheritance graph
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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

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_.

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

Member Function Documentation

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

Referenced by FragmentChunkCrms(), and score().

void protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords ( core::pose::Pose const &  ,
ObjexxFCL::FArray2_double &  ,
ObjexxFCL::FArray1D_int &   
)
private
bool protocols::frag_picker::scores::FragmentChunkCrms::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual

Member Data Documentation

std::string protocols::frag_picker::scores::FragmentChunkCrms::cached_scores_id_
private
ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::chunk_coordinates_
private
ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::fragment_coordinates_
private

Referenced by score().

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

Referenced by FragmentChunkCrms(), and score().

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

Referenced by FragmentChunkCrms(), and score().

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

Referenced by FragmentChunkCrms(), and score().

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

Referenced by FragmentChunkCrms().

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

Referenced by FragmentChunkCrms(), and score().

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

Referenced by FragmentChunkCrms().


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