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protocols::frag_picker::scores::GunnCostScore Class Reference

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

#include <GunnCostScore.hh>

Inheritance diagram for protocols::frag_picker::scores::GunnCostScore:
Inheritance graph
Collaboration diagram for protocols::frag_picker::scores::GunnCostScore:
Collaboration graph

Public Member Functions

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

Size n_atoms_
pose::PoseOP reference_pose_
utility::vector1< Sizefrag_sizes_
Size max_chunk_size_
< utility::vector1< GunnTuple > > 
< utility::vector1< GunnTuple > > 
GunnCost gunn_cost_

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 crmsd to the given reference structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::GunnCostScore::GunnCostScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
core::pose::PoseOP  reference_pose,
utility::vector1< Size frag_sizes,
Size  max_chunk_size 

creates a crmsd-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 chunk_gunn_data_, computeGunnTuples(), frag_sizes_, max_chunk_size_, n_atoms_, ref_gunn_data_, reference_pose_, and protocols::frag_picker::scores::trGunnScore().

protocols::frag_picker::scores::GunnCostScore::~GunnCostScore ( )

Member Function Documentation

bool protocols::frag_picker::scores::GunnCostScore::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
void protocols::frag_picker::scores::GunnCostScore::clean_up ( )
void protocols::frag_picker::scores::GunnCostScore::computeGunnTuples ( core::pose::Pose pose,
Size  frag_size,
utility::vector1< GunnTuple > &  result 
void protocols::frag_picker::scores::GunnCostScore::do_caching ( VallChunkOP  current_chunk)
bool protocols::frag_picker::scores::GunnCostScore::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 

Member Data Documentation

utility::vector1<utility::vector1<GunnTuple> > protocols::frag_picker::scores::GunnCostScore::chunk_gunn_data_
utility::vector1<Size> protocols::frag_picker::scores::GunnCostScore::frag_sizes_
GunnCost protocols::frag_picker::scores::GunnCostScore::gunn_cost_
Size protocols::frag_picker::scores::GunnCostScore::max_chunk_size_

Referenced by GunnCostScore().

Size protocols::frag_picker::scores::GunnCostScore::n_atoms_

Referenced by GunnCostScore().

utility::vector1<utility::vector1<GunnTuple> > protocols::frag_picker::scores::GunnCostScore::ref_gunn_data_

Referenced by cached_score(), and GunnCostScore().

pose::PoseOP protocols::frag_picker::scores::GunnCostScore::reference_pose_

Referenced by GunnCostScore(), and score().

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