protocols::frag_picker::scores::PhiPsiSquareWell Class Reference

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

#include <PhiPsiSquareWell.hh>

Inheritance diagram for protocols::frag_picker::scores::PhiPsiSquareWell:

Public Member Functions
	PhiPsiSquareWell (core::Size, core::Real, bool, PhiPsiTalosIO &)
	creates a Phi-Psi-based scoring function. More...
	PhiPsiSquareWell (core::Size, core::Real, bool, core::pose::PoseOP)
void	do_caching (VallChunkOP) override
void	clean_up () override
bool	cached_score (FragmentCandidateOP, FragmentScoreMapOP) override
bool	score (FragmentCandidateOP, FragmentScoreMapOP) override
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 Attributes
std::string	cached_scores_id_
ObjexxFCL::FArray1D_double	chunk_phi_
ObjexxFCL::FArray1D_double	chunk_psi_
ObjexxFCL::FArray1D_double	query_phi_
ObjexxFCL::FArray1D_double	query_psi_
ObjexxFCL::FArray1D_double	query_d_phi_
ObjexxFCL::FArray1D_double	query_d_psi_
ObjexxFCL::FArray1D_double	query_dist_
ObjexxFCL::FArray1D_double	query_s2_
utility::vector1< core::Size >	query_cnt_
utility::vector1< std::string >	query_class_
utility::vector1< bool >	existing_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::PhiPsiSquareWell::PhiPsiSquareWell	(	core::Size	priority,
		core::Real	lowest_acceptable_value,
		bool	use_lowest,
		PhiPsiTalosIO &	reader
	)

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 protocols::frag_picker::PhiPsiTalosIO::d_phi(), protocols::frag_picker::PhiPsiTalosIO::d_psi(), existing_data_, protocols::frag_picker::PhiPsiTalosIO::get_sequence(), protocols::frag_picker::PhiPsiTalosIO::has_entry(), protocols::frag_picker::PhiPsiTalosIO::phi(), protocols::frag_picker::PhiPsiTalosIO::psi(), protocols::frag_picker::PhiPsiTalosIO::quality(), query_class_, query_cnt_, query_d_phi_, query_d_psi_, query_dist_, query_phi_, query_psi_, query_s2_, and protocols::frag_picker::scores::tr().

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

References existing_data_, query_d_phi_, query_d_psi_, query_phi_, and query_psi_.

Member Function Documentation

bool protocols::frag_picker::scores::PhiPsiSquareWell::cached_score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

overridevirtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References score().

void protocols::frag_picker::scores::PhiPsiSquareWell::clean_up ( )

overridevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

void protocols::frag_picker::scores::PhiPsiSquareWell::do_caching ( VallChunkOP  current_chunk )

overridevirtual

Implements protocols::frag_picker::scores::CachingScoringMethod.

References chunk_phi_, and chunk_psi_.

bool protocols::frag_picker::scores::PhiPsiSquareWell::score ( FragmentCandidateOP  fragment, FragmentScoreMapOP  scores  )

overridevirtual

Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.

References existing_data_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, query_d_phi_, query_d_psi_, query_phi_, query_psi_, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.

Referenced by cached_score().

Member Data Documentation

std::string protocols::frag_picker::scores::PhiPsiSquareWell::cached_scores_id_

private

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::chunk_phi_

private

Referenced by do_caching().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::chunk_psi_

private

Referenced by do_caching().

utility::vector1<bool> protocols::frag_picker::scores::PhiPsiSquareWell::existing_data_

private

Referenced by PhiPsiSquareWell(), and score().

utility::vector1<std::string> protocols::frag_picker::scores::PhiPsiSquareWell::query_class_

private

Referenced by PhiPsiSquareWell().

utility::vector1<core::Size> protocols::frag_picker::scores::PhiPsiSquareWell::query_cnt_

private

Referenced by PhiPsiSquareWell().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_d_phi_

private

Referenced by PhiPsiSquareWell(), and score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_d_psi_

private

Referenced by PhiPsiSquareWell(), and score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_dist_

private

Referenced by PhiPsiSquareWell().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_phi_

private

Referenced by PhiPsiSquareWell(), and score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_psi_

private

Referenced by PhiPsiSquareWell(), and score().

ObjexxFCL::FArray1D_double protocols::frag_picker::scores::PhiPsiSquareWell::query_s2_

private

Referenced by PhiPsiSquareWell().

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

• src/protocols/frag_picker/scores/PhiPsiSquareWell.hh
• src/protocols/frag_picker/scores/PhiPsiSquareWell.cc