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protocols::frag_picker::scores::PhiPsiRmsd Class Reference

scores a fragment by the root mean square deviation of Phi and Psi angles. More...

#include <PhiPsiRmsd.hh>

Inheritance diagram for protocols::frag_picker::scores::PhiPsiRmsd:
Inheritance graph
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Public Member Functions

 PhiPsiRmsd (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, core::pose::PoseOP reference_pose)
 creates a Phi-Psi-based scoring function. More...
 
 PhiPsiRmsd (core::Size, core::Real, bool, PhiPsiTalosIO &)
 
void do_caching (VallChunkOP) override
 
void clean_up () override
 
bool score (FragmentCandidateOP, FragmentScoreMapOP) override
 
bool cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
 
bool describe_score (FragmentCandidateOP, FragmentScoreMapOP, std::ostream &)
 Print debugging informations about a score for a given fragment. More...
 
- 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 Member Functions

void read_talos_phi_psi (std::string const &)
 

Private Attributes

std::string cached_scores_id_
 
core::Size n_atoms_
 
ObjexxFCL::FArray1D_double chunk_phi_
 
ObjexxFCL::FArray1D_double chunk_psi_
 
ObjexxFCL::FArray1D_double query_phi_
 
ObjexxFCL::FArray1D_double query_psi_
 
utility::vector1< boolexisting_data_
 

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

scores a fragment by the root mean square deviation of Phi and Psi angles.

Constructor & Destructor Documentation

protocols::frag_picker::scores::PhiPsiRmsd::PhiPsiRmsd ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
core::pose::PoseOP  reference_pose 
)

creates a Phi-Psi-based scoring function.

Phi-Psi angles from a fragment will be compared to relevant angles in a given pose, which should have the same number of residues a the query sequence

References existing_data_, n_atoms_, query_phi_, and query_psi_.

protocols::frag_picker::scores::PhiPsiRmsd::PhiPsiRmsd ( core::Size  priority,
core::Real  lowest_acceptable_value,
bool  use_lowest,
PhiPsiTalosIO reader 
)

Member Function Documentation

bool protocols::frag_picker::scores::PhiPsiRmsd::cached_score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual
void protocols::frag_picker::scores::PhiPsiRmsd::clean_up ( )
overridevirtual
bool protocols::frag_picker::scores::PhiPsiRmsd::describe_score ( FragmentCandidateOP  f,
FragmentScoreMapOP  empty_map,
std::ostream &  out 
)
void protocols::frag_picker::scores::PhiPsiRmsd::do_caching ( VallChunkOP  current_chunk)
overridevirtual
void protocols::frag_picker::scores::PhiPsiRmsd::read_talos_phi_psi ( std::string const &  )
private
bool protocols::frag_picker::scores::PhiPsiRmsd::score ( FragmentCandidateOP  fragment,
FragmentScoreMapOP  scores 
)
overridevirtual

Member Data Documentation

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

Referenced by cached_score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::chunk_phi_
private
ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::chunk_psi_
private
utility::vector1<bool> protocols::frag_picker::scores::PhiPsiRmsd::existing_data_
private

Referenced by cached_score(), and PhiPsiRmsd().

core::Size protocols::frag_picker::scores::PhiPsiRmsd::n_atoms_
private

Referenced by PhiPsiRmsd().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::query_phi_
private
ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiRmsd::query_psi_
private

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