Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::frag_picker::scores::RamaScore Class Reference

RamaScore score counts identical residues. More...

#include <RamaScore.hh>

Public Member Functions

 RamaScore (Size, Real, bool, std::string &, std::string)
 
 RamaScore (Size, Real, bool, std::string &, core::fragment::SecondaryStructureOP, std::string)
 
void SetupRamaTables ()
 
void do_caching (VallChunkOP)
 
void clean_up ()
 
bool score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
 
bool cached_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map)
 
bool describe_score (FragmentCandidateOP f, FragmentScoreMapOP empty_map, std::ostream &out)
 prints a detailed explanation how a fragment score has been computed More...
 
std::stringget_prediction_name ()
 
- 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::stringget_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

Real minScoreAllowed_
 
std::stringquery_
 
core::fragment::SecondaryStructureOP query_ss_
 
std::string prediction_name_
 
std::string cached_scores_id_
 
utility::vector1
< utility::vector1< Real > > 
scores_
 

Static Private Attributes

static utility::vector1
< utility::vector1
< utility::vector1< Real > > > 
sequence_rama_tables_
 

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

RamaScore score counts identical residues.

Detailed: Resulting score is the number of identical residues
on corresponding positions in a vall fragment and a query sequence

Constructor & Destructor Documentation

protocols::frag_picker::scores::RamaScore::RamaScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string fastaQuery,
std::string  prediction_name 
)
protocols::frag_picker::scores::RamaScore::RamaScore ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string fastaQuery,
core::fragment::SecondaryStructureOP  query_prediction,
std::string  prediction_name 
)

References SetupRamaTables().

Member Function Documentation

bool protocols::frag_picker::scores::RamaScore::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual
void protocols::frag_picker::scores::RamaScore::clean_up ( )
virtual
bool protocols::frag_picker::scores::RamaScore::describe_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map,
std::ostream &  out 
)

prints a detailed explanation how a fragment score has been computed

Detailed: besides extensive output, the method should return the same result as score()
void protocols::frag_picker::scores::RamaScore::do_caching ( VallChunkOP  current_chunk)
virtual
std::string& protocols::frag_picker::scores::RamaScore::get_prediction_name ( )
inline

References prediction_name_.

bool protocols::frag_picker::scores::RamaScore::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual
void protocols::frag_picker::scores::RamaScore::SetupRamaTables ( )

Member Data Documentation

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

Referenced by cached_score(), and do_caching().

Real protocols::frag_picker::scores::RamaScore::minScoreAllowed_
private
std::string protocols::frag_picker::scores::RamaScore::prediction_name_
private

Referenced by get_prediction_name().

std::string& protocols::frag_picker::scores::RamaScore::query_
private
core::fragment::SecondaryStructureOP protocols::frag_picker::scores::RamaScore::query_ss_
private

Referenced by RamaScore(), and SetupRamaTables().

utility::vector1< utility::vector1< Real > > protocols::frag_picker::scores::RamaScore::scores_
private

Referenced by cached_score(), and do_caching().

utility::vector1< utility::vector1< utility::vector1< Real > > > protocols::frag_picker::scores::RamaScore::sequence_rama_tables_
staticprivate

Referenced by do_caching(), and SetupRamaTables().


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