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

SequenceIdentity score counts identical residues. More...

#include <SequenceIdentity.hh>

Public Member Functions

 SequenceIdentity (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string &fastaQuerySequence)
 
bool 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...
 
- 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...
 

Static Public Attributes

static const int REWARD = 0
 will be added if the two residues are identical More...
 
static const int PENALTY = 1
 will be added if the two residues are NOT identical More...
 

Private Attributes

Real minScoreAllowed_
 
std::stringquery_
 

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

SequenceIdentity 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::SequenceIdentity::SequenceIdentity ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string fastaQuerySequence 
)
inline

Member Function Documentation

bool protocols::frag_picker::scores::SequenceIdentity::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()

References F, I, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, PENALTY, query_, REWARD, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

bool protocols::frag_picker::scores::SequenceIdentity::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual

Member Data Documentation

Real protocols::frag_picker::scores::SequenceIdentity::minScoreAllowed_
private
const int protocols::frag_picker::scores::SequenceIdentity::PENALTY = 1
static

will be added if the two residues are NOT identical

Referenced by describe_score(), and score().

std::string& protocols::frag_picker::scores::SequenceIdentity::query_
private

Referenced by describe_score(), and score().

const int protocols::frag_picker::scores::SequenceIdentity::REWARD = 0
static

will be added if the two residues are identical

Referenced by describe_score(), and score().


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