Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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>

Inheritance diagram for protocols::frag_picker::scores::RamaScore:
Inheritance graph
[legend]

Public Member Functions

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

std::string & query_
 
core::fragment::SecondaryStructureOP query_ss_
 
std::string prediction_name_
 
std::string cached_scores_id_
 
utility::vector1
< utility::vector1< core::Real > > 
scores_
 

Static Private Attributes

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

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

RamaScore score counts identical residues.

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 ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
std::string &  fastaQuery,
std::string const &  prediction_name 
)

References query_, query_ss_, and SetupRamaTables().

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

References SetupRamaTables().

Member Function Documentation

bool protocols::frag_picker::scores::RamaScore::cached_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
overridevirtual
void protocols::frag_picker::scores::RamaScore::clean_up ( )
overridevirtual
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

besides extensive output, the method should return the same result as score()

void protocols::frag_picker::scores::RamaScore::do_caching ( VallChunkOP  current_chunk)
overridevirtual
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 
)
overridevirtual
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().

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< core::Real > > protocols::frag_picker::scores::RamaScore::scores_
private

Referenced by cached_score(), and do_caching().

utility::vector1< utility::vector1< utility::vector1< core::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: