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

#include <ScoringSecMatchRPE.hh>

Public Member Functions
	ScoringSecMatchRPE (std::string const &s_in, core::pose::Pose const &ref_pose)
virtual	~ScoringSecMatchRPE ()
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)
virtual bool	evaluate_residues (core::conformation::Residue const &match_res, core::conformation::Residue const &target_res) const
	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
virtual bool	require_all_target_residue_atom_coordinates () const
	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...
virtual bool	require_target_atom_coordinate (Size target_atom_id) const
	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 ()
virtual	~SecMatchResiduePairEvaluator ()
virtual bool	require_candidate_residue_atoms_to_lie_near_target_atom (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< Size >	candidate_res_atoms_reqd_near_target_atom (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 (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::ScoreType >	secmatch_scotypes_cutoff_
utility::vector1< core::Real >	secmatch_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

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_, end, exit, core::scoring::ScoreTypeManager::is_score_type(), longRange_, ref_pose_, core::scoring::ScoreTypeManager::score_type_from_name(), secmatch_scotypes_cutoff_, secmatch_value_cutoff_, sfxn_, shortRange_, utility::string_split(), total_score_cutoff_, protocols::match::downstream::TR, utility_exit_with_message, and weight.

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

virtual

Member Function Documentation

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

virtual

Check incoming scoreType is two bodies scoreType. We also setup the long range and short range scoreType flag.

References cd_1b, cd_2b, cd_lr_2b, ci_1b, ci_2b, ci_lr_2b, core::scoring::ScoringManager::get_instance(), longRange_, method, core::scoring::ScoreTypeManager::name_from_score_type(), shortRange_, protocols::match::downstream::TR, utility_exit_with_message, and ws.

Referenced by ScoringSecMatchRPE().

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

virtual

References cutoff_flag_, cutoff_scoreType_flag_, core::scoring::EMapVector::dot(), core::scoring::n_ci_2b_score_types, core::scoring::n_shortranged_2b_score_types, ref_pose_, core::pose::Pose::replace_residue(), secmatch_scotypes_cutoff_, secmatch_value_cutoff_, core::conformation::Residue::seqpos(), sfxn_, total_score_cutoff_, and protocols::match::downstream::TR.

Referenced by evaluate_residues().

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

virtual

References protocols::match::downstream::TR, and utility_exit_with_message.

Referenced by evaluate_residues().

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

virtual

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 utility::io::ozstream::close(), core::io::pdb::dump_pdb_residue(), eval_cd_2b_residues(), eval_longRange_2b_residue(), longRange_, utility::io::ozstream::open(), out, numeric::random::random_range(), shortRange_, and protocols::stepwise::modeler::rna::sleep().

core::scoring::ScoreFunctionCOP protocols::match::downstream::ScoringSecMatchRPE::get_score_function

(

)

const

References sfxn_.

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

(

)

References sfxn_.

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

virtual

References total_score_cutoff_.

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

virtual

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.

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

virtual

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.

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

virtual

References ref_pose_.

Member Data Documentation

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

private

Referenced by ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), and ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), and ScoringSecMatchRPE().

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

private

Referenced by check2bsc(), evaluate_residues(), and ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), ScoringSecMatchRPE(), and setPose().

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

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

private

Referenced by eval_cd_2b_residues(), and ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), and ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), get_score_function(), and ScoringSecMatchRPE().

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

private

Referenced by check2bsc(), evaluate_residues(), and ScoringSecMatchRPE().

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

private

Referenced by eval_cd_2b_residues(), getCutoff(), and ScoringSecMatchRPE().

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

• src/protocols/match/downstream/ScoringSecMatchRPE.hh
• src/protocols/match/downstream/ScoringSecMatchRPE.cc