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protocols::frag_picker::scores::FragmentCrmsdResDepth Class Reference

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

#include <FragmentCrmsdResDepth.hh>

Inheritance diagram for protocols::frag_picker::scores::FragmentCrmsdResDepth:
Inheritance graph
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Public Member Functions

 FragmentCrmsdResDepth (core::Size, core::Real, bool, core::pose::PoseOP, utility::vector1< core::Real > &query_residue_depth)
 creates a crmsd-based scoring function. More...
 
 FragmentCrmsdResDepth (core::Size, core::Real, bool, utility::vector1< utility::vector1< core::Real > >, utility::vector1< core::Real > &query_residue_depth)
 creates a crmsd-based scoring function. More...
 
 ~FragmentCrmsdResDepth () override
 
void do_caching (VallChunkOP) override
 
void clean_up () override
 
bool score (FragmentCandidateOP, FragmentScoreMapOP) override
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
 
- Public Member Functions inherited from protocols::frag_picker::scores::CachingScoringMethod
 CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name)
 
- 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_CA_coords (core::pose::Pose const &, ObjexxFCL::FArray2_double &, core::Size)
 

Private Attributes

std::string cached_scores_id_
 
core::Size n_atoms_
 
core::pose::PoseOP reference_pose_
 
ObjexxFCL::FArray2D_double reference_coordinates_
 
ObjexxFCL::FArray2D_double chunk_coordinates_
 
ObjexxFCL::FArray2D_double fragment_coordinates_
 
ObjexxFCL::FArray2D_double frag_pos_coordinates_
 
ObjexxFCL::FArray1D_double weights_
 
utility::vector1< core::Realquery_residue_depth_
 

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 crmsd to the given reference structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentCrmsdResDepth::FragmentCrmsdResDepth ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
core::pose::PoseOP  reference_pose,
utility::vector1< core::Real > &  query_residue_depth 
)

creates a crmsd-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_CA_coords(), n_atoms_, query_residue_depth_, reference_coordinates_, reference_pose_, and weights_.

protocols::frag_picker::scores::FragmentCrmsdResDepth::FragmentCrmsdResDepth ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
utility::vector1< utility::vector1< core::Real > >  xyz,
utility::vector1< core::Real > &  query_residue_depth 
)

creates a crmsd-based scoring function.

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

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

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

Member Function Documentation

bool protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual
void protocols::frag_picker::scores::FragmentCrmsdResDepth::clean_up ( )
overridevirtual
void protocols::frag_picker::scores::FragmentCrmsdResDepth::do_caching ( VallChunkOP  current_chunk)
overridevirtual
void protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords ( core::pose::Pose const &  ,
ObjexxFCL::FArray2_double &  ,
core::Size   
)
private
bool protocols::frag_picker::scores::FragmentCrmsdResDepth::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual

Member Data Documentation

std::string protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_scores_id_
private

Referenced by cached_score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsdResDepth::chunk_coordinates_
private

Referenced by cached_score(), and do_caching().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsdResDepth::frag_pos_coordinates_
private

Referenced by cached_score(), and score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsdResDepth::fragment_coordinates_
private

Referenced by cached_score(), and score().

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

Referenced by FragmentCrmsdResDepth().

utility::vector1<core::Real> protocols::frag_picker::scores::FragmentCrmsdResDepth::query_residue_depth_
private
ObjexxFCL::FArray2D_double protocols::frag_picker::scores::FragmentCrmsdResDepth::reference_coordinates_
private
core::pose::PoseOP protocols::frag_picker::scores::FragmentCrmsdResDepth::reference_pose_
private

Referenced by FragmentCrmsdResDepth().

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

Referenced by FragmentCrmsdResDepth().


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