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protocols::frag_picker::scores::PCS_FragDistance Class Reference

scores a fragment by the root mean square deviation of Phi and Psi angles. More...

#include <PCS_FragDistance.hh>

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

 PCS_FragDistance (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, ObjexxFCL::FArray2D_double target_ca_dev, ObjexxFCL::FArray2D_double target_ca_dist, core::Size largest_fragment, core::Size max_length)
 creates a Calpha distance based scoring function. More...
 
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 Attributes

core::Size n_res_
 
std::string cached_scores_id_
 
ObjexxFCL::FArray2D_double chunk_ca_distances_
 
ObjexxFCL::FArray2D_double target_ca_dev_
 
ObjexxFCL::FArray2D_double target_ca_dist_
 
core::Size largest_fragment_
 
core::Size max_length_
 

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 the root mean square deviation of Phi and Psi angles.

Constructor & Destructor Documentation

protocols::frag_picker::scores::PCS_FragDistance::PCS_FragDistance ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
ObjexxFCL::FArray2D_double  target_ca_dev,
ObjexxFCL::FArray2D_double  target_ca_dist,
core::Size  largest_fragment,
core::Size  max_length 
)

creates a Calpha distance based scoring function.

Scores distance matches for short range disulfides (ie: within fragment)

Member Function Documentation

bool protocols::frag_picker::scores::PCS_FragDistance::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual
void protocols::frag_picker::scores::PCS_FragDistance::clean_up ( )
overridevirtual
void protocols::frag_picker::scores::PCS_FragDistance::do_caching ( VallChunkOP  current_chunk)
overridevirtual
bool protocols::frag_picker::scores::PCS_FragDistance::score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual

Member Data Documentation

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

Referenced by cached_score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::PCS_FragDistance::chunk_ca_distances_
private

Referenced by cached_score(), and do_caching().

core::Size protocols::frag_picker::scores::PCS_FragDistance::largest_fragment_
private

Referenced by do_caching().

core::Size protocols::frag_picker::scores::PCS_FragDistance::max_length_
private

Referenced by cached_score().

core::Size protocols::frag_picker::scores::PCS_FragDistance::n_res_
private

Referenced by cached_score(), and do_caching().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::PCS_FragDistance::target_ca_dev_
private

Referenced by cached_score().

ObjexxFCL::FArray2D_double protocols::frag_picker::scores::PCS_FragDistance::target_ca_dist_
private

Referenced by cached_score().


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