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

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

#include <FragmentChunkCrms.hh>

Public Member Functions

 FragmentChunkCrms (Size, Real, bool, std::string, core::pose::PoseOP, FArray1D_int &)
 creates a tmscore-based scoring function. More...
 
 ~FragmentChunkCrms ()
 
bool score (FragmentCandidateOP, FragmentScoreMapOP)
 
- 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 Member Functions

void fill_bb_coords (core::pose::Pose const &, FArray2_double &, Size)
 
void fill_bb_coords (core::pose::Pose const &, FArray2_double &, FArray1D_int &)
 

Private Attributes

std::string cached_scores_id_
 
Size n_atoms_
 
pose::PoseOP reference_pose_
 
pose::PoseOP fragment_pose_
 
FArray2D_double reference_coordinates_
 
FArray2D_double chunk_coordinates_
 
FArray2D_double fragment_coordinates_
 
FArray1D_double weights_
 
FArray1D_int seqmapping_
 

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 tmscore to the given reference structure

Constructor & Destructor Documentation

protocols::frag_picker::scores::FragmentChunkCrms::FragmentChunkCrms ( Size  priority,
Real  lowest_acceptable_value,
bool  use_lowest,
std::string  query_sequence,
core::pose::PoseOP  reference_pose,
FArray1D_int &  seqmapping 
)

creates a tmscore-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 fill_bb_coords(), fragment_pose_, core::pose::make_pose_from_sequence(), n_atoms_, reference_coordinates_, reference_pose_, residue_type_set, seqmapping_, core::pose::Pose::total_residue(), and weights_.

protocols::frag_picker::scores::FragmentChunkCrms::~FragmentChunkCrms ( )

Member Function Documentation

void protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords ( core::pose::Pose const &  pose,
FArray2_double &  coords,
Size  n_atoms 
)
private
void protocols::frag_picker::scores::FragmentChunkCrms::fill_bb_coords ( core::pose::Pose const &  pose,
FArray2_double &  coords,
FArray1D_int &  seqmapping 
)
private
bool protocols::frag_picker::scores::FragmentChunkCrms::score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map 
)
virtual

Member Data Documentation

std::string protocols::frag_picker::scores::FragmentChunkCrms::cached_scores_id_
private
FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::chunk_coordinates_
private
FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::fragment_coordinates_
private

Referenced by score().

pose::PoseOP protocols::frag_picker::scores::FragmentChunkCrms::fragment_pose_
private

Referenced by FragmentChunkCrms(), and score().

Size protocols::frag_picker::scores::FragmentChunkCrms::n_atoms_
private

Referenced by FragmentChunkCrms(), and score().

FArray2D_double protocols::frag_picker::scores::FragmentChunkCrms::reference_coordinates_
private

Referenced by FragmentChunkCrms(), and score().

pose::PoseOP protocols::frag_picker::scores::FragmentChunkCrms::reference_pose_
private

Referenced by FragmentChunkCrms().

FArray1D_int protocols::frag_picker::scores::FragmentChunkCrms::seqmapping_
private

Referenced by FragmentChunkCrms(), and score().

FArray1D_double protocols::frag_picker::scores::FragmentChunkCrms::weights_
private

Referenced by FragmentChunkCrms().


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