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protocols::match::downstream::ScoringSecMatchRPE Class Reference

#include <ScoringSecMatchRPE.hh>

Inheritance diagram for protocols::match::downstream::ScoringSecMatchRPE:
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Public Member Functions

 ScoringSecMatchRPE (std::string const &s_in, core::pose::Pose const &ref_pose)
 
 ~ScoringSecMatchRPE () override
 
virtual core::Real getCutoff () const
 
core::scoring::ScoreFunctionCOP get_score_function () const
 
core::scoring::ScoreFunctionOP get_score_function ()
 
virtual void setPose (core::pose::Pose const &ref_pose)
 
bool evaluate_residues (core::conformation::Residue const &match_res, core::conformation::Residue const &target_res) const override
 Returns true if the interaction between the two residues satisifies the secondary match requirement. candidate_res: the rotamer of the residue trying to be placed target_res: the previously placed residue. More...
 
virtual bool eval_cd_2b_residues (core::conformation::Residue const &match_res, core::conformation::Residue const &target_res) const
 
virtual bool eval_longRange_2b_residue (core::conformation::Residue const &match_res, core::conformation::Residue const &target_res) const
 
bool require_all_target_residue_atom_coordinates () const override
 Returns true if all coordinates of the target residue are required in order to evaluate the interaction between the candidate and the target residues. More...
 
bool require_target_atom_coordinate (core::Size target_atom_id) const override
 If require_all_target_residue_atom_coordinates() returns false, then this method should return true for the atoms on the target residue that the evaluator requires. More...
 
virtual bool check2bsc (core::scoring::ScoreType sType, core::Real wts)
 
- Public Member Functions inherited from protocols::match::downstream::SecMatchResiduePairEvaluator
 SecMatchResiduePairEvaluator ()
 
 ~SecMatchResiduePairEvaluator () override
 
virtual bool require_candidate_residue_atoms_to_lie_near_target_atom (core::Size target_atom_id) const
 Are there atoms of the candidate residue that must be within some cutoff distance of a given atom on the target residue? Base class implementation returns false. More...
 
virtual utility::vector1< core::Sizecandidate_res_atoms_reqd_near_target_atom (core::Size target_atom_id) const
 Return a list of atom indices on the candidate residue; if all atoms in this list are further than max_separation_dist_to_target_atom() away from the target_atom_id atom for a given pair of conformations of the target_residue and the candidate_residue, then this evaluator will return false in the call to evaluate( candidate_residue, target_residue ). This list will allow the SecondaryMatcher to (conservatively!) prune conformations of the candidate_residue from consideration. The base class implements a noop – it returns an empty list. More...
 
virtual Real max_separation_dist_to_target_atom (core::Size target_atom_id) const
 Return the maximum separation distance that any of the match-residue atoms identified by the function match_atoms_reqd_near_target_atom may be from a particular atom on the target residue. Returns a negative value if there is no requirement that any atom be within a certain radius of the target atom. The base class implementation returns -1.0. More...
 

Public Attributes

core::Size scoringEval_counter
 

Private Attributes

utility::vector1< core::scoring::ScoreTypesecmatch_scotypes_cutoff_
 
utility::vector1< core::Realsecmatch_value_cutoff_
 
core::Real total_score_cutoff_
 
bool cutoff_flag_
 
bool cutoff_scoreType_flag_
 
core::pose::PoseOP ref_pose_
 
core::scoring::ScoreFunctionOP sfxn_
 
bool shortRange_
 
bool longRange_
 
core::pose::PoseOP cd_2b_pose_
 

Additional Inherited Members

- Public Types inherited from protocols::match::downstream::SecMatchResiduePairEvaluator
typedef core::Size Size
 
typedef core::Real Real
 

Constructor & Destructor Documentation

◆ ScoringSecMatchRPE()

protocols::match::downstream::ScoringSecMatchRPE::ScoringSecMatchRPE ( std::string const &  s_in,
core::pose::Pose const &  ref_pose 
)

1) I have not implement long range two bodies constraint. 2) I will not check "weight" parameter for two bodies constraint. 3) I check two bodies constraint for cutoff parameter. 4) All inputs constraints are handled in the constructor.

References cd_2b_pose_, check2bsc(), cutoff_flag_, cutoff_scoreType_flag_, core::sequence::end, core::scoring::ScoreTypeManager::is_score_type(), longRange_, ref_pose_, core::scoring::ScoreTypeManager::score_type_from_name(), secmatch_scotypes_cutoff_, secmatch_value_cutoff_, sfxn_, shortRange_, total_score_cutoff_, and protocols::match::downstream::TR().

◆ ~ScoringSecMatchRPE()

protocols::match::downstream::ScoringSecMatchRPE::~ScoringSecMatchRPE ( )
overridedefault

Member Function Documentation

◆ check2bsc()

bool protocols::match::downstream::ScoringSecMatchRPE::check2bsc ( core::scoring::ScoreType  sType,
core::Real  wts 
)
virtual

◆ eval_cd_2b_residues()

bool protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues ( core::conformation::Residue const &  match_res,
core::conformation::Residue const &  target_res 
) const
virtual

◆ eval_longRange_2b_residue()

bool protocols::match::downstream::ScoringSecMatchRPE::eval_longRange_2b_residue ( core::conformation::Residue const &  match_res,
core::conformation::Residue const &  target_res 
) const
virtual

◆ evaluate_residues()

bool protocols::match::downstream::ScoringSecMatchRPE::evaluate_residues ( core::conformation::Residue const &  candidate_res,
core::conformation::Residue const &  target_res 
) const
overridevirtual

Returns true if the interaction between the two residues satisifies the secondary match requirement. candidate_res: the rotamer of the residue trying to be placed target_res: the previously placed residue.

Implements protocols::match::downstream::SecMatchResiduePairEvaluator.

References core::io::pdb::dump_pdb_residue(), eval_cd_2b_residues(), eval_longRange_2b_residue(), longRange_, core::conformation::membrane::out, shortRange_, and protocols::stepwise::modeler::rna::sleep().

◆ get_score_function() [1/2]

core::scoring::ScoreFunctionOP protocols::match::downstream::ScoringSecMatchRPE::get_score_function ( )

References sfxn_.

◆ get_score_function() [2/2]

core::scoring::ScoreFunctionCOP protocols::match::downstream::ScoringSecMatchRPE::get_score_function ( ) const

References sfxn_.

◆ getCutoff()

core::Real protocols::match::downstream::ScoringSecMatchRPE::getCutoff ( ) const
virtual

References total_score_cutoff_.

◆ require_all_target_residue_atom_coordinates()

bool protocols::match::downstream::ScoringSecMatchRPE::require_all_target_residue_atom_coordinates ( ) const
overridevirtual

Returns true if all coordinates of the target residue are required in order to evaluate the interaction between the candidate and the target residues.

Implements protocols::match::downstream::SecMatchResiduePairEvaluator.

◆ require_target_atom_coordinate()

bool protocols::match::downstream::ScoringSecMatchRPE::require_target_atom_coordinate ( core::Size  target_atom_id) const
overridevirtual

If require_all_target_residue_atom_coordinates() returns false, then this method should return true for the atoms on the target residue that the evaluator requires.

Implements protocols::match::downstream::SecMatchResiduePairEvaluator.

◆ setPose()

void protocols::match::downstream::ScoringSecMatchRPE::setPose ( core::pose::Pose const &  ref_pose)
virtual

References ref_pose_.

Member Data Documentation

◆ cd_2b_pose_

core::pose::PoseOP protocols::match::downstream::ScoringSecMatchRPE::cd_2b_pose_
private

Referenced by ScoringSecMatchRPE().

◆ cutoff_flag_

bool protocols::match::downstream::ScoringSecMatchRPE::cutoff_flag_
private

◆ cutoff_scoreType_flag_

bool protocols::match::downstream::ScoringSecMatchRPE::cutoff_scoreType_flag_
private

◆ longRange_

bool protocols::match::downstream::ScoringSecMatchRPE::longRange_
private

◆ ref_pose_

core::pose::PoseOP protocols::match::downstream::ScoringSecMatchRPE::ref_pose_
private

◆ scoringEval_counter

core::Size protocols::match::downstream::ScoringSecMatchRPE::scoringEval_counter

◆ secmatch_scotypes_cutoff_

utility::vector1< core::scoring::ScoreType > protocols::match::downstream::ScoringSecMatchRPE::secmatch_scotypes_cutoff_
private

◆ secmatch_value_cutoff_

utility::vector1< core::Real > protocols::match::downstream::ScoringSecMatchRPE::secmatch_value_cutoff_
private

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::match::downstream::ScoringSecMatchRPE::sfxn_
private

◆ shortRange_

bool protocols::match::downstream::ScoringSecMatchRPE::shortRange_
private

◆ total_score_cutoff_

core::Real protocols::match::downstream::ScoringSecMatchRPE::total_score_cutoff_
private

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